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Sample records for comparing tiling array

  1. TileMap: create chromosomal map of tiling array hybridizations.

    PubMed

    Ji, Hongkai; Wong, Wing Hung

    2005-09-15

    Tiling array is a new type of microarray that can be used to survey genomic transcriptional activities and transcription factor binding sites at high resolution. The goal of this paper is to develop effective statistical tools to identify genomic loci that show transcriptional or protein binding patterns of interest. A two-step approach is proposed and is implemented in TileMap. In the first step, a test-statistic is computed for each probe based on a hierarchical empirical Bayes model. In the second step, the test-statistics of probes within a genomic region are used to infer whether the region is of interest or not. Hierarchical empirical Bayes model shrinks variance estimates and increases sensitivity of the analysis. It allows complex multiple sample comparisons that are essential for the study of temporal and spatial patterns of hybridization across different experimental conditions. Neighboring probes are combined through a moving average method (MA) or a hidden Markov model (HMM). Unbalanced mixture subtraction is proposed to provide approximate estimates of false discovery rate for MA and model parameters for HMM. TileMap is freely available at http://biogibbs.stanford.edu/~jihk/TileMap/index.htm. http://biogibbs.stanford.edu/~jihk/TileMap/index.htm (includes coloured versions of all figures).

  2. Detecting transcriptionally active regions using genomic tiling arrays

    PubMed Central

    Halasz, Gabor; van Batenburg, Marinus F; Perusse, Joelle; Hua, Sujun; Lu, Xiang-Jun; White, Kevin P; Bussemaker, Harmen J

    2006-01-01

    We have developed a method for interpreting genomic tiling array data, implemented as the program TranscriptionDetector. Probed loci expressed above background are identified by combining replicates in a way that makes minimal assumptions about the data. We performed medium-resolution Anopheles gambiae tiling array experiments and found extensive transcription of both coding and non-coding regions. Our method also showed improved detection of transcriptional units when applied to high-density tiling array data for ten human chromosomes. PMID:16859498

  3. Design optimization methods for genomic DNA tiling arrays

    PubMed Central

    Bertone, Paul; Trifonov, Valery; Rozowsky, Joel S.; Schubert, Falk; Emanuelsson, Olof; Karro, John; Kao, Ming-Yang; Snyder, Michael; Gerstein, Mark

    2006-01-01

    A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central issue in designing tiling arrays is that of arriving at a single-copy tile path, as significant sequence cross-hybridization can result from the presence of non-unique probes on the array. Due to the fragmentation of genomic DNA caused by the widespread distribution of repetitive elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequence tiles that are to be included in the design. This becomes increasingly problematic when considering complex eukaryotic genomes that contain many thousands of interspersed repeats. The general problem of sequence tiling can be framed as finding an optimal partitioning of non-repetitive subsequences over a prescribed range of tile sizes, on a DNA sequence comprising repetitive and non-repetitive regions. Exact solutions to the tiling problem become computationally infeasible when applied to large genomes, but successive optimizations are developed that allow their practical implementation. These include an efficient method for determining the degree of similarity of many oligonucleotide sequences over large genomes, and two algorithms for finding an optimal tile path composed of longer sequence tiles. The first algorithm, a dynamic programming approach, finds an optimal tiling in linear time and space; the second applies a heuristic search to reduce the space complexity to a constant requirement. A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences. PMID:16365382

  4. Methylation profiling using methylated DNA immunoprecipitation and tiling array hybridization.

    PubMed

    Cheung, Hoi-Hung; Lee, Tin-Lap; Rennert, Owen M; Chan, Wai-Yee

    2012-01-01

    DNA methylation is an important epigenetic modification that regulates development and plays a role in the pathophysiology of many diseases. It is dynamically changed during germline development. Methylated DNA immunoprecipitation (MeDIP) is an efficient, cost-effective method for locus-specific and genome-wide analysis. Methylated DNA fragments are enriched by a 5-methylcytidine-recognizing antibody, therefore allowing the analysis of both CpG and non-CpG methylation. The enriched DNA fragments can be amplified and hybridized to tiling arrays covering CpG islands, promoters, or the entire genome. Comparison of different methylomes permits the discovery of differentially methylated regions that might be important in disease- or tissue-specific expression. Here, we describe an established MeDIP protocol and tiling array hybridization method for profiling methylation of testicular germ cells.

  5. Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics

    PubMed Central

    2015-01-01

    Controlled nucleation of nanoscale building blocks by geometrically defined seeds implanted in DNA nanoscaffolds represents a unique strategy to study and understand the dynamic processes of molecular self-assembly. Here we utilize a two-dimensional DNA origami frame with a hollow interior and selectively positioned DNA hybridization seeds to control the self-assembly of DNA tile building blocks, where the small DNA tiles are directed to fill the interior of the frame through prescribed sticky end interactions. This design facilitates the construction of DNA origami/array hybrids that adopt the overall shape and dimensions of the origami frame, forming a 2D array in the core consisting of a large number of simple repeating DNA tiles. The formation of the origami/array hybrid was characterized with atomic force microscopy, and the nucleation dynamics were monitored by serial AFM scanning and fluorescence spectroscopy, which revealed faster kinetics of growth within the frame as compared to growth without the presence of a frame. Our study provides insight into the fundamental behavior of DNA-based self-assembling systems. PMID:24575893

  6. Switched Antenna Array Tile for Real-Time Microwave Imaging Aperture

    DTIC Science & Technology

    2016-06-26

    formed with a tile prototype . I. INTRODUCTION In recent years, microwave imaging has emerged as a valuable tool for concealed weapons detection [1]. While...Laboratory. One critical aspect of this system is the switched array used to sample the scene. This paper discusses realization of a sub- aperture or “tile

  7. Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays

    PubMed Central

    Clement, Lieven; De Beuf, Kristof; Thas, Olivier; Vuylsteke, Marnik; Irizarry, Rafael A.; Crainiceanu, Ciprian M.

    2013-01-01

    For a better understanding of the biology of an organism, a complete description is needed of all regions of the genome that are actively transcribed. Tiling arrays are used for this purpose. They allow for the discovery of novel transcripts and the assessment of differential expression between two or more experimental conditions such as genotype, treatment, tissue, etc. In tiling array literature, many efforts are devoted to transcript discovery, whereas more recent developments also focus on differential expression. To our knowledge, however, no methods for tiling arrays have been described that can simultaneously assess transcript discovery and identify differentially expressed transcripts. In this paper, we adopt wavelet based functional models to the context of tiling arrays. The high dimensionality of the data triggered us to avoid inference based on Bayesian MCMC methods. Instead, we introduce a fast empirical Bayes method that provides adaptive regularization of the functional effects. A simulation study and a case study illustrate that our approach is well suited for the simultaneous assessment of transcript discovery and differential expression in tiling array studies, and that it outperforms methods that accomplish only one of these tasks. PMID:22499683

  8. Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays.

    PubMed

    Boccara, Martine; Sarazin, Alexis; Billoud, Bernard; Bulski, Agnes; Chapell, Louise; Baulcombe, David; Colot, Vincent

    2017-01-01

    Epigenetic response to stress in plants involves changes in DNA methylation, histone modifications, and expression of small noncoding RNAs (sRNA). Here we present the method of analysis of differential expression of sRNA populations using DNA tiling arrays. sRNA extracted from Arabidopsis thaliana plants exposed to pathogen elicitor or control plants were reverse-transcribed into cDNAs, and subsequently hybridized after labeling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals. Furthermore, hybridization signals along chromosome 4 were in good agreement with sRNA abundance as previously determined by massive parallel sequence signature (MPSS) in the case of untreated plants, but differed substantially after stress treatment. These results demonstrate the utility of hybridization to DNA tiling arrays to detect major changes in sRNA abundance.

  9. Aerodynamic heating in gaps of thermal protection system tile arrays in laminar and turbulent boundary layers

    NASA Technical Reports Server (NTRS)

    Avery, D. E.

    1978-01-01

    An experimental heat-transfer investigation was conducted on two staggered arrays of metallic tiles in laminar and turbulent boundary layers. This investigation was conducted for two purposes. The impingement heating distribution where flow in a longitudinal gap intersects a transverse gap and impinges on a downstream blocking tile was defined. The influence of tile and gap geometries was analyzed to develop empirical relationships for impingement heating in laminar and turbulent boundary layers. Tests were conducted in a high temperature structures tunnel at a nominal Mach number of 7, a nominal total temperature of 1800 K, and free-stream unit Reynolds numbers from 1.0 x 10 million to 4.8 x 10 million per meter. The test results were used to assess the impingement heating effects produced by parameters that include gap width, longitudinal gap length, slope of the tile forward-facing wall, boundary-layer displacement thickness, Reynolds number, and local surface pressure.

  10. Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics*

    PubMed Central

    Kechris, Katerina J; Biehs, Brian; Kornberg, Thomas B

    2010-01-01

    High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments. PMID:20812907

  11. Generalizing moving averages for tiling arrays using combined p-value statistics.

    PubMed

    Kechris, Katerina J; Biehs, Brian; Kornberg, Thomas B

    2010-01-01

    High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.

  12. chipD: a web tool to design oligonucleotide probes for high-density tiling arrays

    PubMed Central

    Dufour, Yann S.; Wesenberg, Gary E.; Tritt, Andrew J.; Glasner, Jeremy D.; Perna, Nicole T.; Mitchell, Julie C.; Donohue, Timothy J.

    2010-01-01

    chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences, a set of parameters that allow probe design to be tailored to specific applications, protocols or the array manufacturer’s requirements. The algorithm optimizes probes to meet three objectives: (i) probes should be specific; (ii) probes should have similar thermodynamic properties; and (iii) the target sequence coverage should be homogeneous and avoid significant gaps. The output provides in a text format, the list of probe sequences with their genomic locations, targeted strands and hybridization characteristics. chipD has been used successfully to design tiling arrays for bacteria and yeast. chipD is available at http://chipd.uwbacter.org/. PMID:20529880

  13. Pressure gradient effects on heat transfer to reusable surface insulation tile-array gaps

    NASA Technical Reports Server (NTRS)

    Throckmorton, D. A.

    1975-01-01

    An experimental investigation was performed to determine the effect of pressure gradient on the heat transfer within space shuttle reusable surface insulation (RSI) tile-array gaps under thick, turbulent boundary-layer conditions. Heat-transfer and pressure measurements were obtained on a curved array of full-scale simulated RSI tiles in a tunnel-wall boundary layer at a nominal free-stream Mach number and free-stream Reynolds numbers. Transverse pressure gradients of varying degree were induced over the model surface by rotating the curved array with respect to the flow. Definition of the tunnel-wall boundary-layer flow was obtained by measurement of boundary-layer pitot pressure profiles, wall pressure, and heat transfer. Flat-plate heat-transfer data were correlated and a method was derived for prediction of heat transfer to a smooth curved surface in the highly three-dimensional tunnel-wall boundary-layer flow. Pressure on the floor of the RSI tile-array gap followed the trends of the external surface pressure. Heat transfer to the surface immediately downstream of a transverse gap is higher than that for a smooth surface at the same location. Heating to the wall of a transverse gap, and immediately downstream of it, at its intersection with a longitudinal gap is significantly greater than that for the simple transverse gap.

  14. From nonfinite to finite 1D arrays of origami tiles.

    PubMed

    Wu, Tsai Chin; Rahman, Masudur; Norton, Michael L

    2014-06-17

    CONSPECTUS: DNA based nanotechnology provides a basis for high-resolution fabrication of objects almost without physical size limitations. However, the pathway to large-scale production of large objects is currently unclear. Operationally, one method forward is to use high information content, large building blocks, which can be generated with high yield and reproducibility. Although flat DNA origami naturally invites comparison to pixels in zero, one, and two dimensions and voxels in three dimensions and has provided an excellent mechanism for generating blocks of significant size and complexity and a multitude of shapes, the field is young enough that a single "brick" has not become the standard platform used by the majority of researchers in the field. In this Account, we highlight factors we considered that led to our adoption of a cross-shaped, non-space-filling origami species, designed by Dr. Liu of the Seeman laboratory, as the building block ideal for use in the fabrication of finite one-dimensional arrays. Three approaches that can be employed for uniquely coding origami-origami linkages are presented. Such coding not only provides the energetics for tethering the species but also uniquely designates the relative orientation of the origami building blocks. The strength of the coding approach implemented in our laboratory is demonstrated using examples of oligomers ranging from finite multimers composed of four, six, and eight origami structures to semi-infinite polymers (100mers). Two approaches to finite array design and the series of assembly steps that each requires are discussed. The process of AFM observation for array characterization is presented as a critical case study. For these soft species, the array images do not simply present the solution phase geometry projected onto a two-dimensional surface. There are additional perturbations associated with fluidic forces associated with sample preparation. At this time, reconstruction of the "true" or

  15. X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation

    PubMed Central

    Madrigal, I; Rodríguez-Revenga, L; Armengol, L; González, E; Rodriguez, B; Badenas, C; Sánchez, A; Martínez, F; Guitart, M; Fernández, I; Arranz, JA; Tejada, MI; Pérez-Jurado, LA; Estivill, X; Milà, M

    2007-01-01

    Background Aproximately 5–10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to uncover cryptic rearrangements in X-linked mental retardation (XLMR) patients. We have constructed an X-chromosome tiling path array using bacterial artificial chromosomes (BACs) and validated it using samples with cytogenetically defined copy number changes. We have studied 54 patients with idiopathic mental retardation and 20 controls subjects. Results Known genomic aberrations were reliably detected on the array and eight novel submicroscopic imbalances, likely causative for the mental retardation (MR) phenotype, were detected. Putatively pathogenic rearrangements included three deletions and five duplications (ranging between 82 kb to one Mb), all but two affecting genes previously known to be responsible for XLMR. Additionally, we describe different CNV regions with significant different frequencies in XLMR and control subjects (44% vs. 20%). Conclusion This tiling path array of the human X chromosome has proven successful for the detection and characterization of known rearrangements and novel CNVs in XLMR patients. PMID:18047645

  16. Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models.

    PubMed

    Toyoda, Tetsuro; Shinozaki, Kazuo

    2005-08-01

    Tiling arrays of high-density oligonucleotide probes spanning the entire genome are powerful tools for the discovery of new genes. However, it is difficult to determine the structure of the spliced product of a structurally unknown gene from noisy array signals only. Here we introduce a statistical method that estimates the precise splicing points and the exon/intron structure of a structurally unknown gene by maximizing the odds or the ratio of posterior probabilities of the structure under the observation of array signal intensities and nucleic acid sequences. Our method more accurately predicted the gene structures than the simple threshold-based method, and more correctly estimated the expression values of structurally unknown genes than the window-based method. It was observed that the Markov model contributed to the precision of splice points, and that the statistical significance of expression (P-value) represented the reliability of the estimated gene structure and expression value well. We have implemented the method as a program ARTADE (ARabidopsis Tiling Array-based Detection of Exons) and applied it to the Arabidopsis thaliana whole-genome array data analysis. The database of the predicted results and the ARTADE program are available at http://omicspace.riken.jp/ARTADE/.

  17. ENCODE Tiling Array Analysis Identifies Differentially Expressed Annotated and Novel 5′ Capped RNAs in Hepatitis C Infected Liver

    PubMed Central

    Maxwell, Christopher I.; Nelson, Cassie A.; Schwartz, Jason J.; Nix, David A.; Hagedorn, Curt H.

    2011-01-01

    Microarray studies of chronic hepatitis C infection have provided valuable information regarding the host response to viral infection. However, recent studies of the human transcriptome indicate pervasive transcription in previously unannotated regions of the genome and that many RNA transcripts have short or lack 3′ poly(A) ends. We hypothesized that using ENCODE tiling arrays (1% of the genome) in combination with affinity purifying Pol II RNAs by their unique 5′ m7GpppN cap would identify previously undescribed annotated and unannotated genes that are differentially expressed in liver during hepatitis C virus (HCV) infection. Both 5′-capped and poly(A)+ populations of RNA were analyzed using ENCODE tiling arrays. Sixty-four annotated genes were significantly increased in HCV cirrhotic as compared to control liver; twenty-seven (42%) of these genes were identified only by analyzing 5′ capped RNA. Thirty-one annotated genes were significantly decreased; sixteen (50%) of these were identified only by analyzing 5′ capped RNA. Bioinformatic analysis showed that capped RNA produced more consistent results, provided a more extensive expression profile of intronic regions and identified upregulated Pol II transcriptionally active regions in unannotated areas of the genome in HCV cirrhotic liver. Two of these regions were verified by PCR and RACE analysis. qPCR analysis of liver biopsy specimens demonstrated that these unannotated transcripts, as well as IRF1, TRIM22 and MET, were also upregulated in hepatitis C with mild inflammation and no fibrosis. The analysis of 5′ capped RNA in combination with ENCODE tiling arrays provides additional gene expression information and identifies novel upregulated Pol II transcripts not previously described in HCV infected liver. This approach, particularly when combined with new RNA sequencing technologies, should also be useful in further defining Pol II transcripts differentially regulated in specific disease states and

  18. ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver.

    PubMed

    Folkers, Milan E; Delker, Don A; Maxwell, Christopher I; Nelson, Cassie A; Schwartz, Jason J; Nix, David A; Hagedorn, Curt H

    2011-02-16

    Microarray studies of chronic hepatitis C infection have provided valuable information regarding the host response to viral infection. However, recent studies of the human transcriptome indicate pervasive transcription in previously unannotated regions of the genome and that many RNA transcripts have short or lack 3' poly(A) ends. We hypothesized that using ENCODE tiling arrays (1% of the genome) in combination with affinity purifying Pol II RNAs by their unique 5' m⁷GpppN cap would identify previously undescribed annotated and unannotated genes that are differentially expressed in liver during hepatitis C virus (HCV) infection. Both 5'-capped and poly(A)+ populations of RNA were analyzed using ENCODE tiling arrays. Sixty-four annotated genes were significantly increased in HCV cirrhotic as compared to control liver; twenty-seven (42%) of these genes were identified only by analyzing 5' capped RNA. Thirty-one annotated genes were significantly decreased; sixteen (50%) of these were identified only by analyzing 5' capped RNA. Bioinformatic analysis showed that capped RNA produced more consistent results, provided a more extensive expression profile of intronic regions and identified upregulated Pol II transcriptionally active regions in unannotated areas of the genome in HCV cirrhotic liver. Two of these regions were verified by PCR and RACE analysis. qPCR analysis of liver biopsy specimens demonstrated that these unannotated transcripts, as well as IRF1, TRIM22 and MET, were also upregulated in hepatitis C with mild inflammation and no fibrosis. The analysis of 5' capped RNA in combination with ENCODE tiling arrays provides additional gene expression information and identifies novel upregulated Pol II transcripts not previously described in HCV infected liver. This approach, particularly when combined with new RNA sequencing technologies, should also be useful in further defining Pol II transcripts differentially regulated in specific disease states and in

  19. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor; Samanta, Manoj Pratim; Tongprasit, Waraporn; Sethi, Himanshu; Liang, Shoudan; Nelson, David C.; Hegeman, Adrian; Nelson, Clark; Rancour, David; Bednarek, Sebastian; Ulrich, Eldon L.; Zhao, Qin; Wrobel, Russell L.; Newman, Craig S.; Fox, Brian G.; Phillips, George N Jr; Markley, John L.; Sussman, Michael R.

    2005-01-01

    Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana. RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intron-exon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions "antisense" to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage.

  20. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor; Samanta, Manoj Pratim; Tongprasit, Waraporn; Sethi, Himanshu; Liang, Shoudan; Nelson, David C.; Hegeman, Adrian; Nelson, Clark; Rancour, David; Bednarek, Sebastian; hide

    2005-01-01

    Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of the plant Arabidopsis thaliana. RNA expression was determined for the complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated Arabidopsis cell culture line. Transcripts were detected from at least 60% of the nearly 26,330 annotated genes, which included 151 predicted genes that were not identified previously by a similar genome-wide hybridization study on four different cell lines. In comparison with previously published results with 25-mer tiling arrays produced by chromium masking-based photolithography technique, 36-mer oligonucleotide probes were found to be more useful in identifying intron-exon boundaries. Using two-dimensional HPLC tandem mass spectrometry, a small-scale proteomic analysis was performed with the same cells. A large amount of strongly hybridizing RNA was found in regions "antisense" to known genes. Similarity of antisense activities between the 25-mer and 36-mer data sets suggests that it is a reproducible and inherent property of the experiments. Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage.

  1. Nutrient export in tile drainage: Comparing manure injection to fertigation

    USDA-ARS?s Scientific Manuscript database

    Subsurface tile drainage of agricultural land is implicated as a major source of nutrients to the Mississippi River. To protect water quality, land application of manure should maximize crop nutrient use and minimize nutrient loss. Weather constraints and regulations restrict the period during which...

  2. An experimental summary of plasma arc exposures of space shuttle high-temperature reusable surface insulation tile array with a single missing tile (conducted at the Ames Research Center)

    NASA Technical Reports Server (NTRS)

    Galanter, S. A.

    1975-01-01

    A space shuttle high temperature reusable surface insulation (HRSI) tile array with a single missing or lost tile was exposed to a hot gas simulated reentry environment to investigate the heating conditions in and around the vicinity of the missing HRSI tile. Heat flux and pressure data for the lost tile condition were obtained by the use of a water cooled lost tile calibration model. The maximum aluminum substrate temperature obtained during the simulated reentry was 128 C (263 F). The lost tile calibration data indicated a maximum heat flux in the lost tile cavity region of 63 percent of the upstream reference value. This test was conducted at the Ames Research Center in the 20 MW semielliptical thermal protection system (TPS) pilot plasma arc test facility.

  3. Technical note: comparing von Luschan skin color tiles and modern spectrophotometry for measuring human skin pigmentation.

    PubMed

    Swiatoniowski, Anna K; Quillen, Ellen E; Shriver, Mark D; Jablonski, Nina G

    2013-06-01

    Prior to the introduction of reflectance spectrophotometry into anthropological field research during the 1950s, human skin color was most commonly classified by visual skin color matching using the von Luschan tiles, a set of 36 standardized, opaque glass tiles arranged in a chromatic scale. Our goal was to establish a conversion formula between the tile-based color matching method and modern reflectance spectrophotometry to make historical and contemporary data comparable. Skin pigmentation measurements were taken on the forehead, inner upper arms, and backs of the hands using both the tiles and a spectrophotometer on 246 participants showing a broad range of skin pigmentation. From these data, a second-order polynomial conversion formula was derived by jackknife analysis to estimate melanin index (M-index) based on tile values. This conversion formula provides a means for comparing modern data to von Luschan tile measurements recorded in historical reports. This is particularly important for populations now extinct, extirpated, or admixed for which tile-based measures of skin pigmentation are the only data available.

  4. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

    PubMed Central

    Hazen, Samuel P; Naef, Felix; Quisel, Tom; Gendron, Joshua M; Chen, Huaming; Ecker, Joseph R; Borevitz, Justin O; Kay, Steve A

    2009-01-01

    Background Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome. Results As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons, creating a transcript that, if translated, would be expected to produce a truncated protein. In some cases, such as the MYB transcription factor AT2G20400, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic. In addition to several known noncoding transcripts, including microRNA, trans-acting short interfering RNA, and small nucleolar RNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or noncoding. Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic. Conclusions This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known. PMID:19210792

  5. Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array

    PubMed Central

    Biemar, Frédéric; Nix, David A.; Piel, Jessica; Peterson, Brant; Ronshaugen, Matthew; Sementchenko, Victor; Bell, Ian; Manak, J. Robert; Levine, Michael S.

    2006-01-01

    Dorsal–ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence-specific transcription factor distributed in a broad nuclear gradient in the precellular embryo. Previous studies have identified as many as 70 protein-coding genes and one microRNA (miRNA) gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30 protein-coding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5′ exons were identified for at least 10 of the ≈100 protein-coding genes that were missed in earlier annotations. As many as nine intergenic uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and -9a. We discuss the potential functions of these recently identified genes and suggest that intronic enhancers are a common feature of the DV gene network. PMID:16908844

  6. Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics.

    PubMed

    Veneman, Wouter J; de Sonneville, Jan; van der Kolk, Kees-Jan; Ordas, Anita; Al-Ars, Zaid; Meijer, Annemarie H; Spaink, Herman P

    2015-03-01

    We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTiles software to the analysis of previously published and newly obtained RNAseq datasets of our zebrafish infection model, and we have shown the applicability of this approach also to published RNAseq datasets of other organisms by comparing our data with a published mammalian infection study. In addition, we have implemented the DEXSeq module in the GeneTiles software to identify genes, such as glucagon A, that are differentially spliced under infection conditions. In the analysis of our RNAseq data, this has led to the possibility to improve the size of data sets that could be efficiently compared without using problem-dedicated programs, leading to a quick identification of marker sets. Therefore, this approach will also be highly useful for transcriptome analyses of other organisms for which well-characterised genomes are available.

  7. Deciphering Transcription Factor Binding Patterns from Genome-Wide High Density ChIP-chip Tiling Array Data

    NASA Astrophysics Data System (ADS)

    Li, Juntao; Zhu, Lei; Eshaghi, Majid; Liu, Jianhua; Karuturi, Radha Krishna Murthy

    The binding events of DNA-binding proteins can be extensively characterized by high density ChIP-chip tiling array data. The binding sites and binding occupancy patterns are all very useful to understand the DNA-protein interaction. We propose a statistical procedure which focuses on identifying the interaction signal regions and the patterns of interaction using peakedness and skewness tests. Its utility to annotate the binding signals by analyzing the Tbp1 and Rpb1 ChIP-chip datasets in fission yeast is demonstrated.

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

    PubMed

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

    2013-03-01

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

  9. Aerodynamic heating to the gaps and surfaces of simulated reusable-surface-insulation tile arrays in turbulent flow at Mach 6.6

    NASA Technical Reports Server (NTRS)

    Weinstein, I.; Avery, D. E.; Chapman, A. J.

    1975-01-01

    An experimental investigation was made on a simulated reusable-surface-insulation tile array in a turbulent boundary layer to determine aerodynamic-heating distributions representative of those expected on the surface of the shuttle orbiter during earth entry due to the presence of longitudinal and transverse surface gaps. The tests were conducted in an 8-foot high-temperature structures tunnel in a test medium of methane-air combustion products at a nominal Mach number of 6.6 and over a free-stream Reynolds number range from 2,000,000 to 4,900,000 per meter (600,000 to 1,500,000 per foot). The results were used to assess the aerodynamic heating effects produced by parameters that include gap width, boundary-layer displacement thickness, in-line and staggered tile arrangement, and tile protrusion.

  10. Massively Parallel Implementation of Explicitly Correlated Coupled-Cluster Singles and Doubles Using TiledArray Framework.

    PubMed

    Peng, Chong; Calvin, Justus A; Pavošević, Fabijan; Zhang, Jinmei; Valeev, Edward F

    2016-12-29

    A new distributed-memory massively parallel implementation of standard and explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) with canonical O(N(6)) computational complexity is described. The implementation is based on the TiledArray tensor framework. Novel features of the implementation include (a) all data greater than O(N) is distributed in memory and (b) the mixed use of density fitting and integral-driven formulations that optionally allows to avoid storage of tensors with three and four unoccupied indices. Excellent strong scaling is demonstrated on a multicore shared-memory computer, a commodity distributed-memory computer, and a national-scale supercomputer. The performance on a shared-memory computer is competitive with the popular CCSD implementations in ORCA and Psi4. Moreover, the CCSD performance on a commodity-size cluster significantly improves on the state-of-the-art package NWChem. The large-scale parallel explicitly correlated coupled-cluster implementation makes routine accurate estimation of the coupled-cluster basis set limit for molecules with 20 or more atoms. Thus, it can provide valuable benchmarks for the merging reduced-scaling coupled-cluster approaches. The new implementation allowed us to revisit the basis set limit for the CCSD contribution to the binding energy of π-stacked uracil dimer, a challenging paradigm of π-stacking interactions from the S66 benchmark database. The revised value for the CCSD correlation binding energy obtained with the help of quadruple-ζ CCSD computations, -8.30 ± 0.02 kcal/mol, is significantly different from the S66 reference value, -8.50 kcal/mol, as well as other CBS limit estimates in the recent literature.

  11. Interference Lattice-based Loop Nest Tilings for Stencil Computations

    NASA Technical Reports Server (NTRS)

    VanderWijngaart, Rob F.; Frumkin, Michael

    2000-01-01

    A common method for improving performance of stencil operations on structured multi-dimensional discretization grids is loop tiling. Tile shapes and sizes are usually determined heuristically, based on the size of the primary data cache. We provide a lower bound on the numbers of cache misses that must be incurred by any tiling, and a close achievable bound using a particular tiling based on the grid interference lattice. The latter tiling is used to derive highly efficient loop orderings. The total number of cache misses of a code is the sum of (necessary) cold misses and misses caused by elements being dropped from the cache between successive loads (replacement misses). Maximizing temporal locality is equivalent to minimizing replacement misses. Temporal locality of loop nests implementing stencil operations is optimized by tilings that avoid data conflicts. We divide the loop nest iteration space into conflict-free tiles, derived from the cache miss equation. The tiling involves the definition of the grid interference lattice an equivalence class of grid points whose images in main memory map to the same location in the cache-and the construction of a special basis for the lattice. Conflicts only occur on the boundaries of the tiles, unless the tiles are too thin. We show that the surface area of the tiles is bounded for grids of any dimensionality, and for caches of any associativity, provided the eccentricity of the fundamental parallelepiped (the tile spanned by the basis) of the lattice is bounded. Eccentricity is determined by two factors, aspect ratio and skewness. The aspect ratio of the parallelepiped can be bounded by appropriate array padding. The skewness can be bounded by the choice of a proper basis. Combining these two strategies ensures that pathologically thin tiles are avoided. They do not, however, minimize replacement misses per se. The reason is that tile visitation order influences the number of data conflicts on the tile boundaries. If two

  12. An experimental investigation of heat transfer to reusable surface insulation tile array gaps in a turbulent boundary layer with pressure gradient. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Throckmorton, D. A.

    1975-01-01

    An experimental investigation was performed to determine the effect of pressure gradient on the heat transfer to space shuttle reusable surface insulation (RSI) tile array gaps under thick, turbulent boundary layer conditions. Heat transfer and pressure measurements were obtained on a curved array of full-scale simulated RSI tiles in a tunnel wall boundary layer at a nominal freestream Mach number of 10.3 and freestream unit Reynolds numbers of 1.6, 3.3, and and 6.1 million per meter. Transverse pressure gradients were induced over the model surface by rotating the curved array with respect to the flow. Definition of the tunnel wall boundary layer flow was obtained by measurement of boundary layer pitot pressure profiles, and flat plate wall pressure and heat transfer. Flat plate wall heat transfer data were correlated and a method was derived for prediction of smooth, curved array heat transfer in the highly three-dimensional tunnel wall boundary layer flow and simulation of full-scale space shuttle vehicle pressure gradient levels was assessed.

  13. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

    PubMed Central

    2010-01-01

    High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197

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

    PubMed

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

    2014-12-01

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

  15. Filter arrays

    DOEpatents

    Page, Ralph H.; Doty, Patrick F.

    2017-08-01

    The various technologies presented herein relate to a tiled filter array that can be used in connection with performance of spatial sampling of optical signals. The filter array comprises filter tiles, wherein a first plurality of filter tiles are formed from a first material, the first material being configured such that only photons having wavelengths in a first wavelength band pass therethrough. A second plurality of filter tiles is formed from a second material, the second material being configured such that only photons having wavelengths in a second wavelength band pass therethrough. The first plurality of filter tiles and the second plurality of filter tiles can be interspersed to form the filter array comprising an alternating arrangement of first filter tiles and second filter tiles.

  16. Computational Methods for the Analysis of Array Comparative Genomic Hybridization

    PubMed Central

    Chari, Raj; Lockwood, William W.; Lam, Wan L.

    2006-01-01

    Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development. PMID:17992253

  17. Tiled Multicore Processors

    NASA Astrophysics Data System (ADS)

    Taylor, Michael B.; Lee, Walter; Miller, Jason E.; Wentzlaff, David; Bratt, Ian; Greenwald, Ben; Hoffmann, Henry; Johnson, Paul R.; Kim, Jason S.; Psota, James; Saraf, Arvind; Shnidman, Nathan; Strumpen, Volker; Frank, Matthew I.; Amarasinghe, Saman; Agarwal, Anant

    For the last few decades Moore’s Law has continually provided exponential growth in the number of transistors on a single chip. This chapter describes a class of architectures, called tiled multicore architectures, that are designed to exploit massive quantities of on-chip resources in an efficient, scalable manner. Tiled multicore architectures combine each processor core with a switch to create a modular element called a tile. Tiles are replicated on a chip as needed to create multicores with any number of tiles. The Raw processor, a pioneering example of a tiled multicore processor, is examined in detail to explain the philosophy, design, and strengths of such architectures. Raw addresses the challenge of building a general-purpose architecture that performs well on a larger class of stream and embedded computing applications than existing microprocessors, while still running existing ILP-based sequential programs with reasonable performance. Central to achieving this goal is Raw’s ability to exploit all forms of parallelism, including ILP, DLP, TLP, and Stream parallelism. Raw approaches this challenge by implementing plenty of on-chip resources - including logic, wires, and pins - in a tiled arrangement, and exposing them through a new ISA, so that the software can take advantage of these resources for parallel applications. Compared to a traditional superscalar processor, Raw performs within a factor of 2x for sequential applications with a very low degree of ILP, about 2x-9x better for higher levels of ILP, and 10x-100x better when highly parallel applications are coded in a stream language or optimized by hand.

  18. Impacts of Space Shuttle thermal protection system tile on F-15 aircraft vertical tile

    NASA Technical Reports Server (NTRS)

    Ko, W. L.

    1985-01-01

    Impacts of the space shuttle thermal protection system (TPS) tile on the leading edge and the side of the vertical tail of the F-15 aircraft were analyzed under different TPS tile orientations. The TPS tile-breaking tests were conducted to simulate the TPS tile impacts. It was found that the predicted tile impact forces compare fairly well with the tile-breaking forces, and the impact forces exerted on the F-15 aircraft vertical tail were relatively low because a very small fraction of the tile kinetic energy was dissipated in the impact, penetration, and fracture of the tile. It was also found that the oblique impact of the tile on the side of the F-15 aircraft vertical tail was unlikely to dent the tail surface.

  19. Empirical covariance modeling for 21 cm power spectrum estimation: A method demonstration and new limits from early Murchison Widefield Array 128-tile data

    NASA Astrophysics Data System (ADS)

    Dillon, Joshua S.; Neben, Abraham R.; Hewitt, Jacqueline N.; Tegmark, Max; Barry, N.; Beardsley, A. P.; Bowman, J. D.; Briggs, F.; Carroll, P.; de Oliveira-Costa, A.; Ewall-Wice, A.; Feng, L.; Greenhill, L. J.; Hazelton, B. J.; Hernquist, L.; Hurley-Walker, N.; Jacobs, D. C.; Kim, H. S.; Kittiwisit, P.; Lenc, E.; Line, J.; Loeb, A.; McKinley, B.; Mitchell, D. A.; Morales, M. F.; Offringa, A. R.; Paul, S.; Pindor, B.; Pober, J. C.; Procopio, P.; Riding, J.; Sethi, S.; Shankar, N. Udaya; Subrahmanyan, R.; Sullivan, I.; Thyagarajan, Nithyanandan; Tingay, S. J.; Trott, C.; Wayth, R. B.; Webster, R. L.; Wyithe, S.; Bernardi, G.; Cappallo, R. J.; Deshpande, A. A.; Johnston-Hollitt, M.; Kaplan, D. L.; Lonsdale, C. J.; McWhirter, S. R.; Morgan, E.; Oberoi, D.; Ord, S. M.; Prabu, T.; Srivani, K. S.; Williams, A.; Williams, C. L.

    2015-06-01

    The separation of the faint cosmological background signal from bright astrophysical foregrounds remains one of the most daunting challenges of mapping the high-redshift intergalactic medium with the redshifted 21 cm line of neutral hydrogen. Advances in mapping and modeling of diffuse and point source foregrounds have improved subtraction accuracy, but no subtraction scheme is perfect. Precisely quantifying the errors and error correlations due to missubtracted foregrounds allows for both the rigorous analysis of the 21 cm power spectrum and for the maximal isolation of the "EoR window" from foreground contamination. We present a method to infer the covariance of foreground residuals from the data itself in contrast to previous attempts at a priori modeling. We demonstrate our method by setting limits on the power spectrum using a 3 h integration from the 128-tile Murchison Widefield Array. Observing between 167 and 198 MHz, we find at 95% confidence a best limit of Δ2(k )<3.7 ×104 mK2 at comoving scale k =0.18 h Mpc-1 and at z =6.8 , consistent with existing limits.

  20. An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma.

    PubMed

    Lim, Gloria; Karaskova, Jana; Beheshti, Ben; Vukovic, Bisera; Bayani, Jane; Selvarajah, Shamini; Watson, Spencer K; Lam, Wan L; Zielenska, Maria; Squire, Jeremy A

    2005-04-01

    Osteosarcoma (OS) is characterized by chromosomal instability and high-copy-number gene amplification. The breakage-fusion-bridge (BFB) cycle is a well-established mechanism of genomic instability in tumors and in vitro models used to study the origins of complex chromosomal rearrangements and cancer genome amplification. However, until now, there have been no high-resolution cytogenetic or genomic array studies of BFB events in OS. In the present study, multicolor banding (mBAND) FISH and submegabase resolution tiling set (SMRT) array comparative genomic hybridization (CGH) were used to identify and map genomic signatures of BFB events in four OS cell lines and one patient tumor. The expected intermediates associated with BFB-dicentric chromosomes, inverted duplications, and intra- and interchromosomal amplifications-were identified. mBAND analysis provided detailed mapping of rearrangements in 1p, 6p, and 8q and showed that translocation junctions were often in close proximity to fragile sites. More detailed mBAND studies of OS cell line MG-63 revealed ladderlike FISH signals of equally spaced interchromosomal coamplifications of 6p21, 8q24, and 9p21-p22 in a homogeneously staining region (hsr). Focal amplifications that concordantly mapped to the hsr were localized to discrete genomic intervals by SMRT array CGH. The complex amplicon structure in this hsr suggests focal amplifications immediately adjacent to microdeletions. Moreover, the genomic regions in which there was deletion/amplification had a preponderance of fragile sites. In summary, this study has provided further support for the role of the BFB mechanism and fragile sites in facilitating gene amplification and chromosomal rearrangement in OS.

  1. Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array

    PubMed Central

    2010-01-01

    Background Non-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In the past few years, a growing number of regulatory RNA elements have been predicted by computational methods, mostly in well-studied γ-proteobacteria but lately in several α-proteobacteria as well. Here, we have compared an extensive compilation of these non-coding RNA predictions to intergenic expression data of a whole-genome high-resolution tiling array in the soil-dwelling α-proteobacterium Rhizobium etli. Results Expression of 89 candidate ncRNAs was detected, both on the chromosome and on the six megaplasmids encompassing the R. etli genome. Of these, 11 correspond to functionally well characterized ncRNAs, 12 were previously identified in other α-proteobacteria but are as yet uncharacterized and 66 were computationally predicted earlier but had not been experimentally identified and were therefore classified as novel ncRNAs. The latter comprise 17 putative sRNAs and 49 putative cis-regulatory ncRNAs. A selection of these candidate ncRNAs was validated by RT-qPCR, Northern blotting and 5' RACE, confirming the existence of 4 ncRNAs. Interestingly, individual transcript levels of numerous ncRNAs varied during free-living growth and during interaction with the eukaryotic host plant, pointing to possible ncRNA-dependent regulation of these specialized processes. Conclusions Our data support the practical value of previous ncRNA prediction algorithms and significantly expand the list of candidate ncRNAs encoded in the intergenic regions of R. etli and, by extension, of α-proteobacteria. Moreover, we show high-resolution tiling arrays to be suitable tools for studying intergenic ncRNA transcription profiles across the genome. The differential expression levels of some of these ncRNAs may indicate a role in adaptation to changing environmental conditions. PMID:20089193

  2. Aerodynamic heat transfer to RSI tile surfaces and gap intersections. [Reusable Surface Insulation

    NASA Technical Reports Server (NTRS)

    Dunavant, J. C.; Throckmorton, D. A.

    1974-01-01

    Review of the results of aerothermal heating tests of a simulated reusable surface insulation (RSI) tile array, performed on the sidewall of a Mach-10 hypersonic tunnel. In particular, the heating characteristics of the tile array, such as they result from heating inside the tile-expansion-space providing gaps between individual tiles, are investigated. The results include the finding that heating on the upstream face of a tile is strongly affected by the interacting longitudinal gap flow.

  3. Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae.

    PubMed

    Xu, Weihong; Aparicio, Jennifer G; Aparicio, Oscar M; Tavaré, Simon

    2006-10-26

    Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms remain poorly understood. A key to understanding the exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences that control origin function. In S. cerevisiae, Autonomously Replicating Sequences (ARSs) contain a consensus sequence (ACS) that binds the Origin Recognition Complex (ORC) and is essential for origin function. However, an ACS is not sufficient for origin function and the majority of ACS matches do not function as ORC binding sites, complicating the specific identification of these sites. To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and Mcm2p binding sites at high resolution. These binding sites define a set of potential Autonomously Replicating Sequences (ARSs), which we term nimARSs. The nimARS set comprises 529 ORC and/or Mcm2p binding sites, which includes 95% of known ARSs, and experimental verification demonstrates that 94% are functional. The resolution of the analysis facilitated identification of potential ACSs (nimACSs) within 370 nimARSs. Cross-validation shows that the nimACS predictions include 58% of known ACSs, and experimental verification indicates that 82% are essential for ARS activity. These findings provide the most comprehensive, accurate, and detailed mapping of ORC binding sites to date, adding to the emerging picture of the chromatin organization of the budding yeast genome.

  4. Interlocking wettable ceramic tiles

    SciTech Connect

    Tabereaux, Jr., Alton T.; Fredrickson, Guy L.; Groat, Eric; Mroz, Thomas; Ulicny, Alan; Walker, Mark F.

    2005-03-08

    An electrolytic cell for the reduction of aluminum having a layer of interlocking cathode tiles positioned on a cathode block. Each tile includes a main body and a vertical restraining member to prevent movement of the tiles away from the cathode block during operation of the cell. The anode of the electrolytic cell may be positioned about 1 inch from the interlocking cathode tiles.

  5. Preassembly Of Insulating Tiles

    NASA Technical Reports Server (NTRS)

    Izu, Y. D.; Yoshioka, E. N.; Rosario, T.

    1988-01-01

    Concept for preassembling high-temperature insulating tiles speeds and simplifies installation and repair and reduces damage from handling. Preassembly concept facilitates placement of tiles on gently contoured surfaces as well as on flat ones. Tiles bonded to nylon mesh with room-temperature-vulcanizing silicon rubber. Spacing between tiles is 0.03 in. Applications include boilers, kilns, and furnaces.

  6. Identification of alternative splicing events regulated by an Arabidopsis serine/arginine-like protein, atSR45a, in response to high-light stress using a tiling array.

    PubMed

    Yoshimura, Kazuya; Mori, Tatsuya; Yokoyama, Kunihiro; Koike, Yoshiyuki; Tanabe, Noriaki; Sato, Nobuo; Takahashi, Hiro; Maruta, Takanori; Shigeoka, Shigeru

    2011-10-01

    We have demonstrated that an Arabidopsis serine/arginine rich-like protein, atSR45a, interacts with other splicing factors and its expression is markedly induced by high-light stress, suggesting the involvement of atSR45a in the regulation of stress-responsive alternative splicing. A whole-genome tiling array identified the alternative splicing of genes regulated by atSR45a by comparing gene expression profiles in wild-type and knockout atSR45a (KO-sr45a) plants under high-light stress. The expression levels of genomic regions within 217 genes were significantly altered in the KO-sr45a plants compared with the wild-type plants. Many genes encoded factors involved in signal transduction, cell cycle and DNA processing, protein fate and transcription. A semi-quantitative reverse transcription-PCR (RT-PCR) analysis confirmed changes in the transcript levels and/or alternative splicing efficiency under high-light stress in 18 genes, suggesting that atSR45a affects directly or indirectly not only alternative splicing efficiency but also the transcription of these target genes. Changes in the expression of atSR45a in response to high-light stress temporally correlated with changes in the alternative splicing efficiency and transcript levels of three and one target genes, respectively. Sequencing of the alternatively spliced variants of three target genes showed that atSR45a suppresses the splicing efficiency of intron retention-type alternative splicing events. These findings indicated the importance of atSR45a to the diversification of the transcriptome under high-light stress.

  7. Repairing ceramic insulating tiles

    NASA Technical Reports Server (NTRS)

    Dunn, B. R.; Laymance, E. L.

    1980-01-01

    Fused-silica tiles containing large voids or gauges are repaired without adhesives by plug insertion method. Tiles are useful in conduits for high-temperature gases, in furnaces, and in other applications involving heat insulation.

  8. A comparative study of the radiation hardness of plastic scintillators for the upgrade of the Tile Calorimeter of the ATLAS detector

    NASA Astrophysics Data System (ADS)

    Liao, S.; Erasmus, R.; Jivan, H.; Pelwan, C.; Peters, G.; Sideras-Haddad, E.

    2015-10-01

    The influence of radiation on the light transmittance of plastic scintillators was studied experimentally. The high optical transmittance property of plastic scintillators makes them essential in the effective functioning of the Tile calorimeter of the ATLAS detector at CERN. This significant role played by the scintillators makes this research imperative in the movement towards the upgrade of the tile calorimeter. The radiation damage of polyvinyl toluene (PVT) based plastic scintillators was studied, namely, EJ-200, EJ-208 and EJ-260, all manufactured and provided to us by ELJEN technology. In addition, in order to compare to scintillator brands actually in use at the ATLAS detector currently, two polystyrene (PS) based scintillators and an additional PVT based scintillator were also scrutinized in this study, namely, Dubna, Protvino and Bicron, respectively. All the samples were irradiated using a 6 MeV proton beam at different doses at iThemba LABS Gauteng. The radiation process was planned and mimicked by doing simulations using a SRIM program. In addition, transmission spectra for the irradiated and unirradiated samples of each grade were obtained, observed and analyzed.

  9. Handmade Tile Mosaics

    ERIC Educational Resources Information Center

    Keeler, Rusty

    2007-01-01

    Just like the classroom, children's outdoor environments should be filled with artistic creations that add sparkle and imagination to the space. One of the author's favorite ways to add art to the outdoors is by installing a mosaic mural of child-made tiles. The process of making the tiles is fun for all; each tile is a charming work of art in…

  10. Hemispheric Imaging of Galactic Neutral Hydrogen with a Phased Array Antenna System

    NASA Astrophysics Data System (ADS)

    Wijnholds, Stefan J.; De Bruyn, A. Ger; Bregman, Jaap D.; Bij De Vaate, Jan Geralt

    2004-06-01

    The thousand element array (THEA) system is a phased array system consisting of 1 m2 tiles having 64 Vivaldi elements each, arranged on a regular 8-by-8 grid, which has been developed as a demonstrator of technology and applicability for SKA. In this paper we present imaging results of Galactic neutral hydrogen with THEA. Measurements have been taken using a dense 2-by-2 array of four tiles as a four tile adder. The results are compared with results from the Leiden-Dwingeloo Survey, showing qualitative agreement, but also indicating that further studies are needed on the instrumental characteristics.

  11. Fibonacci words, hyperbolic tilings and grossone

    NASA Astrophysics Data System (ADS)

    Margenstern, Maurice

    2015-04-01

    In this paper, we study the contribution of the theory of grossone to the study of infinite Fibonacci words, combining this tool with the help of a particular tiling of the hyperbolic plane: the tiling { 7, 3 } , called the heptagrid. With the help of the numeral system based on grossone, we obtain a richer family of infinite Fibonacci words compared with the traditional approach.

  12. Fast linear transformation for tiled images.

    PubMed

    Rao, A; Perens, B

    1996-01-01

    This work describes an efficient algorithm for linear coordinate transformation developed specifically for a tiled image processing system. A detailed description of the algorithm is presented, and its performance is compared with that of other techniques. The effect of image size on relative performance is analyzed and correlated with the tile-based storage technique.

  13. Comparative use of the computer-aided angiography and rapid prototyping technology versus conventional imaging in the management of the Tile C pelvic fractures.

    PubMed

    Li, Baofeng; Chen, Bei; Zhang, Ying; Wang, Xinyu; Wang, Fei; Xia, Hong; Yin, Qingshui

    2016-01-01

    Computed tomography (CT) scan with three-dimensional (3D) reconstruction has been used to evaluate complex fractures in pre-operative planning. In this study, rapid prototyping of a life-size model based on 3D reconstructions including bone and vessel was applied to evaluate the feasibility and prospect of these new technologies in surgical therapy of Tile C pelvic fractures by observing intra- and perioperative outcomes. The authors conducted a retrospective study on a group of 157 consecutive patients with Tile C pelvic fractures. Seventy-six patients were treated with conventional pre-operative preparation (A group) and 81 patients were treated with the help of computer-aided angiography and rapid prototyping technology (B group). Assessment of the two groups considered the following perioperative parameters: length of surgical procedure, intra-operative complications, intra- and postoperative blood loss, postoperative pain, postoperative nausea and vomiting (PONV), length of stay, and type of discharge. The two groups were homogeneous when compared in relation to mean age, sex, body weight, injury severity score, associated injuries and pelvic fracture severity score. Group B was performed in less time (105 ± 19 minutes vs. 122 ± 23 minutes) and blood loss (31.0 ± 8.2 g/L vs. 36.2 ± 7.4 g/L) compared with group A. Patients in group B experienced less pain (2.5 ± 2.3 NRS score vs. 2.8 ± 2.0 NRS score), and PONV affected only 8 % versus 10 % of cases. Times to discharge were shorter (7.8 ± 2.0 days vs. 10.2 ± 3.1 days) in group B, and most of patients were discharged to home. In our study, patients of Tile C pelvic fractures treated with computer-aided angiography and rapid prototyping technology had a better perioperative outcome than patients treated with conventional pre-operative preparation. Further studies are necessary to investigate the advantages in terms of clinical results in the short and long run.

  14. Boeing's High Voltage Solar Tile Test Results

    NASA Technical Reports Server (NTRS)

    Reed, Brian J.; Harden, David E.; Ferguson, Dale C.; Snyder, David B.

    2002-01-01

    Real concerns of spacecraft charging and experience with solar array augmented electrostatic discharge arcs on spacecraft have minimized the use of high voltages on large solar arrays despite numerous vehicle system mass and efficiency advantages. Boeing's solar tile (patent pending) allows high voltage to be generated at the array without the mass and efficiency losses of electronic conversion. Direct drive electric propulsion and higher power payloads (lower spacecraft weight) will benefit from this design. As future power demand grows, spacecraft designers must use higher voltage to minimize transmission loss and power cable mass for very large area arrays. This paper will describe the design and discuss the successful test of Boeing's 500-Volt Solar Tile in NASA Glenn's Tenney chamber in the Space Plasma Interaction Facility. The work was sponsored by NASA's Space Solar Power Exploratory Research and Technology (SERT) Program and will result in updated high voltage solar array design guidelines being published.

  15. Generalized quasiperiodic Rauzy tilings

    NASA Astrophysics Data System (ADS)

    Vidal, Julien; Mosseri, Rémy

    2001-05-01

    We present a geometrical description of new canonical d-dimensional codimension one quasiperiodic tilings based on generalized Fibonacci sequences. These tilings are made up of rhombi in 2d and rhombohedra in 3d as the usual Penrose and icosahedral tilings. Thanks to a natural indexing of the sites according to their local environment, we easily write down, for any approximant, the sites coordinates, the connectivity matrix and we compute the structure factor.

  16. Solar-energy treatment of ceramic tile. Final report

    SciTech Connect

    Harris, J.N.; Clayton, M.E.

    1981-12-01

    The 400 kW Advanced Components Test Facility was used to provide a concentrated source of solar energy for firing ceramic wall tile. A domed top cylindrical cavity with a white refractory fiber lining provided diffuse reflection of the concentrated solar beam directly onto the upper surface of the unfired wall tile. The tile were placed directly on the cavity floor in a circular pattern, centered at 45/sup 0/ intervals so that eight tile could be fired at one time. The tile and cavity walls were instrumented with thermocouples, and pyrometric cones were used to determine temperature distribution within the cavity. The glazed and unglazed solar fired tiles were subjected to standard ceramic testing procedures to determine: flatness, modulus of rupture, water absorption, porosity, bulk density, apparent specific gravity, percent linear thermal expansion and crystalline phases present in the fired bodies. These data were compared with the same data for commercial fired tiles from the same batch of raw materials. The glazed tile surfaces were compared with commercially fired tile for reflectance and color match. The major problems encountered were: cracking by thermal shock, and uneven shrinkage and glaze maturity across individual tile. The cavity also failed to provide even heating at all eight tile positions. An alternate air heat exchanger system is recommended to fire the tile by convection rather than direct radiation.

  17. 39. West tile gauge on south pier. Each square tile ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    39. West tile gauge on south pier. Each square tile is 4' in size. Bottom left hand corner of west tile - Duluth Ship Canal, South Pier, North end of Minnesota Point & Canal Park, Duluth, St. Louis County, MN

  18. 40. West tile gauge on south pier. Each square tile ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    40. West tile gauge on south pier. Each square tile is 4' in size. Bottom right hand corner of west tile - Duluth Ship Canal, South Pier, North end of Minnesota Point & Canal Park, Duluth, St. Louis County, MN

  19. Structural clay tile component behavior

    SciTech Connect

    Columber, Christopher Eugene

    1994-12-18

    The basic properties of structural clay tile walls were determined through component and composite testing of structural clay tile and mortar. The fundamental material parameters and strengths of clay tile coupons were determined through compression, tension, modulus of rupture and absorption tests. Mortar cylinders were tested in both compression and split cylinder fashion. Stress-strain curves for mortar under compression were determined. Four miniature prisms were tested in compression. These prisms were made from two 8 inches x 12 inches x 12 inches structural clay tiles, using a stack bond with a 3/4 inches mortar joint. Stress strain curves as well as material property values were obtained. These results were compared with previous tests on larger (2 feet x 4 feet) prisms. Twenty five bond wrench samples were tested. Two series of bond wrench samples were run. The first series (six tests) were fitted with LVDTs so that load deflection curves as well as flexural strengths could be obtained. A shifting of the neutral axis towards the compression face was observed. The second series were made with different mortar types: type N masonry cement mortar, type S masonry cement mortar, type N portland cement lime (PCL) mortar, and type S PCL mortar. Type S mortar and portland cement lime mortar were found to improve the bond strength.

  20. Rewaterproofing Silica Tiles

    NASA Technical Reports Server (NTRS)

    Lleger, L. J.; Wade, D. C.

    1983-01-01

    Waterproofing agent, vaporized in bubbler transported by gas flowing in system and deposits in pores of tiles. Vapor carried through hole of approximately 1/16 inch (1.6.mm) diameter made in tile coating. Technique used to waterproof buildups (concrete and brick) and possibly fabrics.

  1. Rewaterproofing Silica Tiles

    NASA Technical Reports Server (NTRS)

    Lleger, L. J.; Wade, D. C.

    1983-01-01

    Waterproofing agent, vaporized in bubbler transported by gas flowing in system and deposits in pores of tiles. Vapor carried through hole of approximately 1/16 inch (1.6.mm) diameter made in tile coating. Technique used to waterproof buildups (concrete and brick) and possibly fabrics.

  2. Distributed graph visualization on tiled displays

    NASA Astrophysics Data System (ADS)

    Chae, Sangwon

    2013-03-01

    In this paper, we propose a distributed force-directed layout algorithm in order to handle large graph data on tiled display that consists of multiple computing machines and multiple displays connected to each computing machine through Ethernet. The distributed tiled display makes one big screen using multiple displays in order to discern data obviously. Besides, multiple computing devices on tiled displays share the parts of an entire dataset. Therefore, it can dramatically reduce the processing time to visualize data on screen compared with the processing time on a single machine.

  3. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

    PubMed Central

    Jaing, Crystal J.; McLoughlin, Kevin S.; Thissen, James B.; Zemla, Adam; Vergez, Lisa M.; Bourguet, Feliza; Mabery, Shalini; Fofanov, Viacheslav Y.; Koshinsky, Heather; Jackson, Paul J.

    2016-01-01

    Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms. PMID:27668749

  4. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

    SciTech Connect

    Jaing, Crystal J.; McLoughlin, Kevin S.; Thissen, James B.; Zemla, Adam; Gardner, Shea N.; Vergez, Lisa M.; Bourguet, Feliza; Mabery, Shalini; Fofanov, Viacheslav Y.; Koshinsky, Heather; Jackson, Paul J.; Wang, Junwen

    2016-09-26

    Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we then selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. For genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Finally, structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.

  5. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing

    DOE PAGES

    Jaing, Crystal J.; McLoughlin, Kevin S.; Thissen, James B.; ...

    2016-09-26

    Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, providemore » better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we then selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. For genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Finally, structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.« less

  6. Comparing viewer and array mental rotations in different planes

    NASA Technical Reports Server (NTRS)

    Carpenter, M.; Proffitt, D. R.; Kaiser, M. K. (Principal Investigator)

    2001-01-01

    Participants imagined rotating either themselves or an array of objects that surrounded them. Their task was to report on the egocentric position of an item in the array following the imagined rotation. The dependent measures were response latency and number of errors committed. Past research has shown that self-rotation is easier than array rotation. However, we found that imagined egocentric rotations were as difficult to imagine as rotations of the environment when people performed imagined rotations in the midsagittal or coronal plane. The advantages of imagined self-rotations are specific to mental rotations performed in the transverse plane.

  7. Array comparative genomic hybridization in retinoma and retinoblastoma tissues.

    PubMed

    Sampieri, Katia; Amenduni, Mariangela; Papa, Filomena Tiziana; Katzaki, Eleni; Mencarelli, Maria Antonietta; Marozza, Annabella; Epistolato, Maria Carmela; Toti, Paolo; Lazzi, Stefano; Bruttini, Mirella; De Filippis, Roberta; De Francesco, Sonia; Longo, Ilaria; Meloni, Ilaria; Mari, Francesca; Acquaviva, Antonio; Hadjistilianou, Theodora; Renieri, Alessandra; Ariani, Francesca

    2009-03-01

    In retinoblastoma, two RB1 mutations are necessary for tumor development. Recurrent genomic rearrangements may represent subsequent events required for retinoblastoma progression. Array-comparative genomic hybridization was carried out in 18 eye samples, 10 from bilateral and eight from unilateral retinoblastoma patients. Two unilateral cases also showed areas of retinoma. The most frequent imbalance in retinoblastomas was 6p gain (40%), followed by gains at 1q12-q25.3, 2p24.3-p24.2, 9q22.2, and 9q33.1 and losses at 11q24.3, 13q13.2-q22.3, and 16q12.1-q21. Bilateral cases showed a lower number of imbalances than unilateral cases (P = 0.002). Unilateral cases were divided into low-level (< or = 4) and high-level (> or = 7) chromosomal instability groups. The first group presented with younger age at diagnosis (mean 511 days) compared with the second group (mean 1606 days). In one retinoma case ophthalmoscopically diagnosed as a benign lesion no rearrangements were detected, whereas the adjacent retinoblastoma displayed seven aberrations. The other retinoma case identified by retrospective histopathological examination shared three rearrangements with the adjacent retinoblastoma. Two other gene-free rearrangements were retinoma specific. One rearrangement, dup5p, was retinoblastoma specific and included the SKP2 gene. Genomic profiling indicated that the first retinoma was a pretumoral lesion, whereas the other represents a subclone of cells bearing 'benign' rearrangements overwhelmed by another subclone presenting aberrations with higher 'oncogenic' potential. In summary, the present study shows that bilateral and unilateral retinoblastoma have different chromosomal instability that correlates with the age of tumor onset in unilateral cases. This is the first report of genomic profiling in retinoma tissue, shedding light on the different nature of lesions named 'retinoma'.

  8. A Comparative Study of Inspection Techniques for Array Packages

    NASA Technical Reports Server (NTRS)

    Mohammed, Jelila; Green, Christopher

    2008-01-01

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

  9. Array comparative genomic hybridization analysis of olfactory neuroblastoma.

    PubMed

    Guled, Mohamed; Myllykangas, Samuel; Frierson, Henry F; Mills, Stacey E; Knuutila, Sakari; Stelow, Edward B

    2008-06-01

    Olfactory neuroblastoma is an unusual neuroectodermal malignancy, which is thought to arise at the olfactory membrane of the sinonasal tract. Due to its rarity, little is understood regarding its molecular and cytogenetic abnormalities. The aim of the current study is to identify specific DNA copy number changes in olfactory neuroblastoma. Thirteen dissected tissue samples were analyzed using array comparative genomic hybridization. Our results show that gene copy number profiles of olfactory neuroblastoma samples are complex. The most frequent changes included gains at 7q11.22-q21.11, 9p13.3, 13q, 20p/q, and Xp/q, and losses at 2q31.1, 2q33.3, 2q37.1, 6q16.3, 6q21.33, 6q22.1, 22q11.23, 22q12.1, and Xp/q. Gains were more frequent than losses, and high-stage tumors showed more alterations than low-stage olfactory neuroblastoma. Frequent changes in high-stage tumors were gains at 13q14.2-q14.3, 13q31.1, and 20q11.21-q11.23, and loss of Xp21.1 (in 66% of cases). Gains at 5q35, 13q, and 20q, and losses at 2q31.1, 2q33.3, and 6q16-q22, were present in 50% of cases. The identified regions of gene copy number change have been implicated in a variety of tumors, especially carcinomas. In addition, our results indicate that gains in 20q and 13q may be important in the progression of this cancer, and that these regions possibly harbor genes with functional relevance in olfactory neuroblastoma.

  10. Tiling motion patches.

    PubMed

    Hyun, Kyunglyul; Kim, Manmyung; Hwang, Youngseok; Lee, Jehee

    2013-11-01

    Simulating multiple character interaction is challenging because character actions must be carefully coordinated to align their spatial locations and synchronized with each other. We present an algorithm to create a dense crowd of virtual characters interacting with each other. The interaction may involve physical contacts, such as hand shaking, hugging, and carrying a heavy object collaboratively. We address the problem by collecting deformable motion patches, each of which describes an episode of multiple interacting characters, and tiling them spatially and temporally. The tiling of motion patches generates a seamless simulation of virtual characters interacting with each other in a nontrivial manner. Our tiling algorithm uses a combination of stochastic sampling and deterministic search to address the discrete and continuous aspects of the tiling problem. Our tiling algorithm made it possible to automatically generate highly complex animation of multiple interacting characters. We achieve the level of interaction complexity far beyond the current state of the art that animation techniques could generate, in terms of the diversity of human behaviors and the spatial/temporal density of interpersonal interactions.

  11. Tiling Motion Patches.

    PubMed

    Hyun, Kyunglyul; Kim, Manmyung; Hwang, Youngseok; Lee, Jehee

    2013-05-08

    Simulating multiple character interaction is challenging because character actions must be carefully coordinated to align their spatial locations and synchronized with each other. We present an algorithm to create a dense crowd of virtual characters interacting with each other. The interaction may involve physical contacts, such as hand shaking, hugging, and carrying a heavy object collaboratively. We address the problem by collecting deformable motion patches, each of which describes an episode of multiple interacting characters, and tiling them spatially and temporally. The tiling of motion patches generates a seamless simulation of virtual characters interacting with each other in a non-trivial manner. Our tiling algorithm uses a combination of stochastic sampling and deterministic search to address the discrete and continuous aspects of the tiling problem. Our tiling algorithm made it possible to automatically generate highly-complex animation of multiple interacting characters. We achieved the level of complexity far beyond the current state-of-the-art animation techniques could generate, in terms of the diversity of human behaviors and the spatial/temporal density of interpersonal interactions.

  12. Seamless tiled display system

    NASA Technical Reports Server (NTRS)

    Dubin, Matthew B. (Inventor); Larson, Brent D. (Inventor); Kolosowsky, Aleksandra (Inventor)

    2006-01-01

    A modular and scalable seamless tiled display apparatus includes multiple display devices, a screen, and multiple lens assemblies. Each display device is subdivided into multiple sections, and each section is configured to display a sectional image. One of the lens assemblies is optically coupled to each of the sections of each of the display devices to project the sectional image displayed on that section onto the screen. The multiple lens assemblies are configured to merge the projected sectional images to form a single tiled image. The projected sectional images may be merged on the screen by magnifying and shifting the images in an appropriate manner. The magnification and shifting of these images eliminates any visual effect on the tiled display that may result from dead-band regions defined between each pair of adjacent sections on each display device, and due to gaps between multiple display devices.

  13. The ATLAS Tile Calorimeter

    SciTech Connect

    Henriques, A.

    2015-07-01

    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)

  14. Array-based comparative genomic hybridization (array CGH) for rapid prenatal diagnosis of cytogenetic abnormalities

    USDA-ARS?s Scientific Manuscript database

    We have shown in a prospective validation study that an array CGH test was highly accurate for rapid detection of chromosomal aneuploidies and deletions or duplications on fetal DNA samples in a clinical prenatal diagnostic setting. Here we present our updated "post-validation phase" experience with...

  15. Photovoltaic roofing tile systems

    NASA Astrophysics Data System (ADS)

    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.

  16. Geopolymers as potential repair material in tiles conservation

    NASA Astrophysics Data System (ADS)

    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.

  17. METHOD FOR EVALUATING MOLD GROWTH ON CEILING TILE

    EPA Science Inventory

    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...

  18. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

    PubMed Central

    Menten, Björn; Pattyn, Filip; De Preter, Katleen; Robbrecht, Piet; Michels, Evi; Buysse, Karen; Mortier, Geert; De Paepe, Anne; van Vooren, Steven; Vermeesch, Joris; Moreau, Yves; De Moor, Bart; Vermeulen, Stefan; Speleman, Frank; Vandesompele, Jo

    2005-01-01

    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 . PMID:15910681

  19. Planar tilings by polyominoes, polyhexes, and polyiamonds

    NASA Astrophysics Data System (ADS)

    Rhoads, Glenn C.

    2005-02-01

    Using computer programs, we enumerate and classify the tiling behavior of small polyominoes (n[less-than-or-equals, slant]9), polyhexes (n[less-than-or-equals, slant]7), and polyiamonds (n[less-than-or-equals, slant]10). For tiles that tile the Euclidean plane, we give diagrams illustrating how they tile. We also show several larger tiles whose minimal fundamental domain in any admitted (periodic) tiling is significantly larger than for any previously known tile.

  20. Tiling strategies for optical follow-up of gravitational-wave triggers by telescopes with a wide field of view

    NASA Astrophysics Data System (ADS)

    Ghosh, Shaon; Bloemen, Steven; Nelemans, Gijs; Groot, Paul J.; Price, Larry R.

    2016-08-01

    Aims: Binary neutron stars are among the most promising candidates for joint gravitational-wave and electromagnetic astronomy. The goal of this work is to investigate various observing strategies that telescopes with wide field of view might incorporate while searching for electromagnetic counterparts of gravitational-wave triggers. Methods: We examined various strategies of scanning the gravitational-wave sky localizations on the mock 2015-16 gravitational-wave events. First, we studied the performance of the sky coverage using a naive tiling system that completely covers a given confidence interval contour using a fixed grid. Then we propose the ranked-tiling strategy where we sample the localization in discrete two-dimensional intervals that are equivalent to the telescope's field of view and rank them based on their sample localizations. We then introduce an optimization of the grid by iterative sliding of the tiles. Next, we conducted tests for all the methods on a large sample of sky localizations that are expected in the first two years of operation of the Laser interferometer Gravitational-wave Observatory (LIGO) and Virgo detectors. We investigated the performance of the ranked-tiling strategy for telescope arrays and compared their performance against monolithic telescopes with a giant field of view. Finally, we studied the ability of optical counterpart detection by various types of telescopes. Results: Our analysis reveals that the ranked-tiling strategy improves the localization coverage over the contour-covering method. The improvement is more significant for telescopes with larger fields of view. We also find that while optimizing the position of the tiles significantly improves the coverage compared to contour-covering tiles. For ranked-tiles the same procedure leads to negligible improvement in the coverage of the sky localizations. We observed that distributing the field of view of the telescopes into arrays of multiple telescopes significantly

  1. An efficient pseudomedian filter for tiling microrrays

    PubMed Central

    Royce, Thomas E; Carriero, Nicholas J; Gerstein, Mark B

    2007-01-01

    Background Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding sites, detection of methylated DNA and several other applications in several model organisms. These experiments are being conducted at increasingly finer resolutions as the microarray technology enjoys increasingly greater feature densities. The increased densities naturally lead to increased data analysis requirements. Specifically, the most widely employed algorithm for tiling array analysis involves smoothing observed signals by computing pseudomedians within sliding windows, a O(n2logn) calculation in each window. This poor time complexity is an issue for tiling array analysis and could prove to be a real bottleneck as tiling microarray experiments become grander in scope and finer in resolution. Results We therefore implemented Monahan's HLQEST algorithm that reduces the runtime complexity for computing the pseudomedian of n numbers to O(nlogn) from O(n2logn). For a representative tiling microarray dataset, this modification reduced the smoothing procedure's runtime by nearly 90%. We then leveraged the fact that elements within sliding windows remain largely unchanged in overlapping windows (as one slides across genomic space) to further reduce computation by an additional 43%. This was achieved by the application of skip lists to maintaining a sorted list of values from window to window. This sorted list could be maintained with simple O(log n) inserts and deletes. We illustrate the favorable scaling properties of our algorithms with both time complexity analysis and benchmarking on synthetic datasets. Conclusion Tiling microarray analyses that rely upon a sliding window pseudomedian calculation can require many hours of computation. We have eased this requirement significantly by implementing efficient algorithms that scale well with genomic

  2. Producing superhydrophobic roof tiles.

    PubMed

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

    2016-03-04

    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.

  3. Producing superhydrophobic roof tiles

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  4. Comparative study of absorption in tilted silicon nanowire arrays for photovoltaics.

    PubMed

    Kayes, Md Imrul; Leu, Paul W

    2014-01-01

    Silicon nanowire arrays have been shown to demonstrate light trapping properties and promising potential for next-generation photovoltaics. In this paper, we show that the absorption enhancement in vertical nanowire arrays on a perfectly electric conductor can be further improved through tilting. Vertical nanowire arrays have a 66.2% improvement in ultimate efficiency over an ideal double-pass thin film of the equivalent amount of material. Tilted nanowire arrays, with the same amount of material, exhibit improved performance over vertical nanowire arrays across a broad range of tilt angles (from 38° to 72°). The optimum tilt of 53° has an improvement of 8.6% over that of vertical nanowire arrays and 80.4% over that of the ideal double-pass thin film. Tilted nanowire arrays exhibit improved absorption over the solar spectrum compared with vertical nanowires since the tilt allows for the excitation of additional modes besides the HE 1m modes that are excited at normal incidence. We also observed that tilted nanowire arrays have improved performance over vertical nanowire arrays for a large range of incidence angles (under about 60°).

  5. Improve load balancing and coding efficiency of tiles in high efficiency video coding by adaptive tile boundary

    NASA Astrophysics Data System (ADS)

    Chan, Chia-Hsin; Tu, Chun-Chuan; Tsai, Wen-Jiin

    2017-01-01

    High efficiency video coding (HEVC) not only improves the coding efficiency drastically compared to the well-known H.264/AVC but also introduces coding tools for parallel processing, one of which is tiles. Tile partitioning is allowed to be arbitrary in HEVC, but how to decide tile boundaries remains an open issue. An adaptive tile boundary (ATB) method is proposed to select a better tile partitioning to improve load balancing (ATB-LoadB) and coding efficiency (ATB-Gain) with a unified scheme. Experimental results show that, compared to ordinary uniform-space partitioning, the proposed ATB can save up to 17.65% of encoding times in parallel encoding scenarios and can reduce up to 0.8% of total bit rates for coding efficiency.

  6. Arithmetic theory of brick tilings

    SciTech Connect

    Egorov, A V; Prikhod'ko, A A

    1998-12-31

    A new, 'arithmetic', approach to the algebraic theory of brick tilings is developed. This approach enables one to construct a simple classification of brick tilings in Z{sup d} and to find new proofs of several classical results on brick packing and tilings in Z{sup d}. In addition, possible generalizations of results on integer brick packing to the Euclidean plane R{sup 2} are investigated.

  7. Steep-Slope Assembly Testing of Clay and Concrete Tile With and Without Cool Pigmented Colors

    SciTech Connect

    Miller, William A

    2005-11-01

    Cool color pigments and sub-tile venting of clay and concrete tile roofs significantly impact the heat flow crossing the roof deck of a steep-slope roof. Field measures for the tile roofs revealed a 70% drop in the peak heat flow crossing the deck as compared to a direct-nailed asphalt shingle roof. The Tile Roofing Institute (TRI) and its affiliate members are keenly interested in documenting the magnitude of the drop for obtaining solar reflectance credits with state and federal "cool roof" building efficiency standards. Tile roofs are direct-nailed or are attached to a deck with batten or batten and counter-batten construction. S-Misson clay and concrete tile roofs, a medium-profile concrete tile roof, and a flat slate tile roof were installed on fully nstrumented attic test assemblies. Temperature measures of the roof, deck, attic, and ceiling, heat flows, solar reflectance, thermal emittance, and the ambient weather were recorded for each of the tile roofs and also on an adjacent attic cavity covered with a conventional pigmented and directnailed asphalt shingle roof. ORNL measured the tile's underside temperature and the bulk air temperature and heat flows just underneath the tile for batten and counter-batten tile systems and compared the results to the conventional asphalt shingle.

  8. Ceramic tile expansion engine housing

    DOEpatents

    Myers, B.

    1995-04-11

    An expandable ceramic tile housing for a high temperature engine is disclosed wherein each tile is independently supported in place in an interlocking matrix by retention mechanisms which mechanically couple the individual ceramic tiles to an outer metal support housing while maintaining thermal isolation of the metal housing from the ceramic tiles. The ceramic tiles are formed with either an octagonal front face portion and a square shank portion or a square front face portion with an octagonal shank portion. The length of the sides of the octagonal front face portion on one tile is equal to the length of the sides of the square front face portion of adjoining tiles to permit formation of an interlocking matrix. Fibrous ceramic sealing material may be placed between radial and tangential facing surfaces of adjacent tiles to limit radial gas flow there between. Labyrinth-sealed pressure-controlled compartments may be established between the tile housing and the outer metal support housing to control radial gas flow. 8 figures.

  9. Ceramic tile expansion engine housing

    SciTech Connect

    Myers, Blake

    1995-01-01

    An expandable ceramic tile housing for a high temperature engine is disclosed wherein each tile is independently supported in place in an interlocking matrix by retention mechanisms which mechanically couple the individual ceramic tiles to an outer metal support housing while maintaining thermal isolation of the metal housing from the ceramic tiles. The ceramic tiles are formed with either an octagonal front face portion and a square shank portion or a square front face portion with an octagonal shank portion. The length of the sides of the octagonal front face portion on one tile is equal to the length of the sides of the square front face portion of adjoining tiles to permit formation of an interlocking matrix. Fibrous ceramic sealing material may be placed between radial and tangential facing surfaces of adjacent tiles to limit radial gas flow therebetween. Labyrinth-sealed pressure-controlled compartments may be established between the tile housing and the outer metal support housing to control radial gas flow.

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

    NASA Astrophysics Data System (ADS)

    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.

  11. Covering the Plane with Rep-Tiles.

    ERIC Educational Resources Information Center

    Fosnaugh, Linda S.; Harrell, Marvin E.

    1996-01-01

    Presents an activity in which students use geometric figures, rep-tiles, to design a tile floor. Rep-tiles are geometric figures of which copies can fit together to form a larger similar figure. Includes reproducible student worksheet. (MKR)

  12. Radioactivity level in Chinese building ceramic tile.

    PubMed

    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 H(ex) 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).

  13. Detecting Filler Spaces Under Tiles

    NASA Technical Reports Server (NTRS)

    Mende, Paul; Shinkevich, David; Scheuer, John

    1991-01-01

    Eddy-current probe nondestructively and indirectly indicates whether screed present under ceramic tile on aluminum substrate. Transducer coil excites eddy currents in aluminum substrate material. Response appears on oscilloscope or meter. Changes in response indicate spatially abrupt changes in substrate. Intended for use on insulating tiles on Space Shuttle, potential terrestrial applications in nondestructive testing.

  14. Kinetics of DNA tile dimerization.

    PubMed

    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.

  15. Comparing a new laser strainmeter array with an adjacent, parallel running quartz tube strainmeter array.

    PubMed

    Kobe, Martin; Jahr, Thomas; Pöschel, Wolfgang; Kukowski, Nina

    2016-03-01

    In summer 2011, two new laser strainmeters about 26.6 m long were installed in N-S and E-W directions parallel to an existing quartz tube strainmeter system at the Geodynamic Observatory Moxa, Thuringia/Germany. This kind of installation is unique in the world and allows the direct comparison of measurements of horizontal length changes with different types of strainmeters for the first time. For the comparison of both data sets, we used the tidal analysis over three years, the strain signals resulting from drilling a shallow 100 m deep borehole on the ground of the observatory and long-period signals. The tidal strain amplitude factors of the laser strainmeters are found to be much closer to theoretical values (85%-105% N-S and 56%-92% E-W) than those of the quartz tube strainmeters. A first data analysis shows that the new laser strainmeters are more sensitive in the short-periodic range with an improved signal-to-noise ratio and distinctly more stable during long-term drifts of environmental parameters such as air pressure or groundwater level. We compared the signal amplitudes of both strainmeter systems at variable signal periods and found frequency-dependent amplitude differences. Confirmed by the tidal parameters, we have now a stable and high resolution laser strainmeter system that serves as calibration reference for quartz tube strainmeters.

  16. Comparing a new laser strainmeter array with an adjacent, parallel running quartz tube strainmeter array

    NASA Astrophysics Data System (ADS)

    Kobe, Martin; Jahr, Thomas; Pöschel, Wolfgang; Kukowski, Nina

    2016-03-01

    In summer 2011, two new laser strainmeters about 26.6 m long were installed in N-S and E-W directions parallel to an existing quartz tube strainmeter system at the Geodynamic Observatory Moxa, Thuringia/Germany. This kind of installation is unique in the world and allows the direct comparison of measurements of horizontal length changes with different types of strainmeters for the first time. For the comparison of both data sets, we used the tidal analysis over three years, the strain signals resulting from drilling a shallow 100 m deep borehole on the ground of the observatory and long-period signals. The tidal strain amplitude factors of the laser strainmeters are found to be much closer to theoretical values (85%-105% N-S and 56%-92% E-W) than those of the quartz tube strainmeters. A first data analysis shows that the new laser strainmeters are more sensitive in the short-periodic range with an improved signal-to-noise ratio and distinctly more stable during long-term drifts of environmental parameters such as air pressure or groundwater level. We compared the signal amplitudes of both strainmeter systems at variable signal periods and found frequency-dependent amplitude differences. Confirmed by the tidal parameters, we have now a stable and high resolution laser strainmeter system that serves as calibration reference for quartz tube strainmeters.

  17. Substructure procedure for including tile flexibility in stress analysis of shuttle thermal protection system

    NASA Technical Reports Server (NTRS)

    Giles, G. L.

    1980-01-01

    A substructure procedure to include the flexibility of the tile in the stress analysis of the shuttle thermal protection system (TPS) is described. In this procedure, the TPS is divided into substructures of (1) the tile which is modeled by linear finite elements and (2) the SIP which is modeled as a nonlinear continuum. This procedure was applied for loading cases of uniform pressure, uniform moment, and an aerodynamic shock on various tile thicknesses. The ratios of through-the-thickness stresses in the SIP which were calculated using a flexible tile compared to using a rigid tile were found to be less than 1.05 for the cases considered.

  18. Application of array-based comparative genomic hybridization to pediatric neurologic diseases.

    PubMed

    Byeon, Jung Hye; Shin, Eunsim; Kim, Gun-Ha; Lee, Kyungok; Hong, Young Sook; Lee, Joo Won; Eun, Baik-Lin

    2014-01-01

    Array comparative genomic hybridization (array-CGH) is a technique used to analyze quantitative increase or decrease of chromosomes by competitive DNA hybridization of patients and controls. This study aimed to evaluate the benefits and yield of array-CGH in comparison with conventional karyotyping in pediatric neurology patients. We included 87 patients from the pediatric neurology clinic with at least one of the following features: developmental delay, mental retardation, dysmorphic face, or epilepsy. DNA extracted from patients and controls was hybridized on the Roche NimbleGen 135K oligonucleotide array and compared with G-band karyotyping. The results were analyzed with findings reported in recent publications and internet databases. Chromosome imbalances, including 9 cases detected also by G-band karyotyping, were found in 28 patients (32.2%), and at least 19 of them seemed to be causally related to the abnormal phenotypes. Regarding each clinical symptom, 26.2% of 42 developmental delay patients, 44.4% of 18 mental retardation patients, 42.9% of 28 dysmorphic face patients, and 34.6% of 26 epilepsy patients showed abnormal array results. Although there were relatively small number of tests in patients with pediatric neurologic disease, this study demonstrated that array-CGH is a very useful tool for clinical diagnosis of unknown genome abnormalities performed in pediatric neurology clinics.

  19. Application of Array-Based Comparative Genomic Hybridization to Pediatric Neurologic Diseases

    PubMed Central

    Byeon, Jung Hye; Shin, Eunsim; Kim, Gun-Ha; Lee, Kyungok; Hong, Young Sook; Lee, Joo Won

    2014-01-01

    Purpose Array comparative genomic hybridization (array-CGH) is a technique used to analyze quantitative increase or decrease of chromosomes by competitive DNA hybridization of patients and controls. This study aimed to evaluate the benefits and yield of array-CGH in comparison with conventional karyotyping in pediatric neurology patients. Materials and Methods We included 87 patients from the pediatric neurology clinic with at least one of the following features: developmental delay, mental retardation, dysmorphic face, or epilepsy. DNA extracted from patients and controls was hybridized on the Roche NimbleGen 135K oligonucleotide array and compared with G-band karyotyping. The results were analyzed with findings reported in recent publications and internet databases. Results Chromosome imbalances, including 9 cases detected also by G-band karyotyping, were found in 28 patients (32.2%), and at least 19 of them seemed to be causally related to the abnormal phenotypes. Regarding each clinical symptom, 26.2% of 42 developmental delay patients, 44.4% of 18 mental retardation patients, 42.9% of 28 dysmorphic face patients, and 34.6% of 26 epilepsy patients showed abnormal array results. Conclusion Although there were relatively small number of tests in patients with pediatric neurologic disease, this study demonstrated that array-CGH is a very useful tool for clinical diagnosis of unknown genome abnormalities performed in pediatric neurology clinics. PMID:24339284

  20. Spectral response data for development of cool coloured tile coverings

    NASA Astrophysics Data System (ADS)

    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.

  1. Stochastic segmentation models for array-based comparative genomic hybridization data analysis.

    PubMed

    Lai, Tze Leung; Xing, Haipeng; Zhang, Nancy

    2008-04-01

    Array-based comparative genomic hybridization (array-CGH) is a high throughput, high resolution technique for studying the genetics of cancer. Analysis of array-CGH data typically involves estimation of the underlying chromosome copy numbers from the log fluorescence ratios and segmenting the chromosome into regions with the same copy number at each location. We propose for the analysis of array-CGH data, a new stochastic segmentation model and an associated estimation procedure that has attractive statistical and computational properties. An important benefit of this Bayesian segmentation model is that it yields explicit formulas for posterior means, which can be used to estimate the signal directly without performing segmentation. Other quantities relating to the posterior distribution that are useful for providing confidence assessments of any given segmentation can also be estimated by using our method. We propose an approximation method whose computation time is linear in sequence length which makes our method practically applicable to the new higher density arrays. Simulation studies and applications to real array-CGH data illustrate the advantages of the proposed approach.

  2. Genomic Array as Compared to Karyotyping in Myelodysplastic Syndromes in a Prospective Clinical trial.

    PubMed

    Stevens-Kroef, Marian J; Olde Weghuis, Daniel; ElIdrissi-Zaynoun, Najat; van der Reijden, Bert; Cremers, Eline M P; Alhan, Canan; Westers, Theresia M; Visser-Wisselaar, Heleen A; Chitu, Dana A; Cunha, Sonia M; Vellenga, Edo; Klein, Saskia K; Wijermans, Pierre; de Greef, Georgine E; Schaafsma, M R; Muus, Petra; Ossenkoppele, Gert J; van de Loosdrecht, Arjan A; Jansen, Joop H

    2017-02-25

    Karyotyping is considered as the gold standard in the genetic subclassification of myelodysplastic syndrome (MDS). Oligo/SNP-based genomic array profiling is a high-resolution tool that also enables genome wide analysis. We compared karyotyping with oligo/SNP-based array profiling in 104 MDS patients from the HOVON-89 study. Oligo/SNP-array identified all cytogenetically defined genomic lesions, except for subclones in two cases and balanced translocations in three cases. On the other hand oligo/SNP-based genomic array profiling had a higher success rate, showing 55 abnormal cases, while an abnormal karyotype was found in only 35 patients. In 9 patients whose karyotyping was unsuccessful because of insufficient metaphases or failure, oligo/SNP-based array analysis was successful. Based on cytogenetic visible abnormalities as identified by oligo/SNP-based genomic array prognostic scores based on IPSS/-R were assigned. These prognostic scores were identical to the IPSS/-R scores as obtained with karyotyping in 95-96% of the patients. In addition to the detection of cytogenetically defined lesions, oligo/SNP-based genomic profiling identified focal copy number abnormalities or regions of copy neutral loss of heterozygosity that were out of the scope of karyotyping and fluorescence in situ hybridization. Of interest, in 26 patients we demonstrated such cytogenetic invisible abnormalities. These abnormalities often involved regions that are recurrently affected in hematological malignancies, and may therefore be of clinical relevance. Our findings indicate that oligo/SNP-based genomic array can be used to identify the vast majority of recurrent cytogenetic abnormalities in MDS. Furthermore, oligo/SNP-based array profiling yields additional genetic abnormalities that may be of clinical importance. This article is protected by copyright. All rights reserved.

  3. Kinetics of DNA Tile Dimerization

    PubMed Central

    2015-01-01

    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. PMID:24794259

  4. Complex Archimedean tiling self-assembled from DNA nanostructures.

    PubMed

    Zhang, Fei; Liu, Yan; Yan, Hao

    2013-05-22

    Archimedean tilings are periodic polygonal tessellations that are created by placing regular polygons edge-to-edge around a vertex to fill the plane. Here we show that three- and four-arm DNA junction tiles with specifically designed arm lengths and intertile sticky-end interactions can be used to form sophisticated two-dimensional (2D) and three-dimensional (3D) tessellation patterns. We demonstrate two different complex Archimedean patterns, (3(3).4(2)) and (3(2).4.3.4), and the formation of 2D lattices, 3D tubes, and sealed polygon-shaped pockets from the tessellations. The successful growth of hybrid DNA tile motif arrays suggests that it maybe possible to generate 2D quasi-crystals from DNA building blocks.

  5. Foam on Tile Impact Modeling for the STS-107 Investigation

    NASA Technical Reports Server (NTRS)

    Stellingwerf, R. F.; Robinson, J. H.; Richardson, S.; Evans, S. W.; Stallworth, R.; Hovater, M.

    2004-01-01

    Following the breakup of the Space Shuttle Columbia during reentry a NASA/Contractor investigation team was formed to examine the probable damage inflicted on Orbiter Thermal Protection System elements by impact of External Tank insulating foam projectiles. The authors formed a working subgroup within the larger team to apply the Smooth Particle Hydrodynamics code SPHC to the damage estimation problem. Numerical models of the Orbiter's tiles and of the Tank's foam were constructed and used as inputs into the code. Material properties needed to properly model the tiles and foam were obtained from other working subgroups who performed tests on these items for this purpose. Two- and three-dimensional models of the tiles were constructed, including the glass outer layer, the main body of LI-900 insulation, the densified lower layer of LI-900, the Nomex felt mounting layer, and the Aluminum 2024 vehicle skin. A model for the BX-250 foam including porous compression, elastic rebound, and surface erosion was developed. Code results for the tile damage and foam behavior were extensively validated through comparison with Southwest Research Institute foam-on-tile impact experiments carried out in 1999. These tests involved small projectiles striking individual tiles and small tile arrays. Following code and model validation we simulated impacts of larger foam projectiles on the examples of tile systems used on the Orbiter. Results for impacts on the main landing gear door are presented in this paper, including effects of impacts at several angles, and of rapidly rotating projectiles. General results suggest that foam impacts on tiles at about 500 mph could cause appreciable damage if the impact angle is greater than about 20 degrees. Some variations of the foam properties, such as increased brittleness or increased density could increase damage in some cases. Rotation up to 17 rps failed to increase the damage for the two cases considered. This does not rule out other cases

  6. A hadronic tile calorimeter report

    NASA Astrophysics Data System (ADS)

    Boca, Gianluigi; Gourlay, S.; Chung, Yeon Sei; Lee, Kyoung-Beom; Malvezzi, S.; Sala, A.; Arena, V.; Bonomi, G.; Gianini, G.; Merlo, M.; Ratti, S.; Riccardi, C.; Viola, L.; Vitulo, P.

    1998-02-01

    The design and first performances of a new hadronic calorimeter for the experiment Focus (E831) at Fermilab are presented. It is a sampling calorimeter, with 28 iron (passive) and scintillator (active) planes. The active planes are composed of tiles read out by WaveLength Shifter fibers spliced to clear fibers. This is the first tile calorimeter actually used (1997)in a running experiment.

  7. Comparative genomic hybridization array study and its utility in detection of constitutional and acquired anomalies.

    PubMed

    Andrieux, Joris; Sheth, Frenny

    2009-10-01

    The last decade has witnessed an upsurge in the knowledge of cytogenetic disorders and putting the old technology in a new basket with molecular genetics. As conventional cytogenetic can detect the genetic alteration of 10-15 Mb, many of the micro-deletions and micro-duplications are missed. However, with the advent of technology of fluorescence in situ hybridization (FISH), the resolution of genetic aberrations can reach to 3-5 Mb, nonetheless the anomalies smaller than the above, need further precision which has been achieved using comparative genomic hybridization array (CGH-array). Introduction of array-CGH has brought higher sensitivity with automated DNA fragment analyzer and DNA chip for submicroscopic chromosomal anomalies that are missed till date in many of the acquired and constitutional genetic disorders. The resolution of the technology varies from several Kb to 1 Mb depending upon the type of array selected. With the recent improvement in the array-CGH technology, a link between cytogenetic and molecular biology has been established without replacing conventional cytogenetic technique. The wider accessibility of the technology shall certainly provide a clue to the many unidentified/unexplained genetic disorders which shall prove to be a boon to the clinicians.

  8. Orion Tile Fitting

    NASA Image and Video Library

    2016-10-24

    Tile blocks have been prefitted around the heat shield for the Orion crew module inside the Neil Armstrong Operations and Checkout Building high bay at NASA’s Kennedy Space Center in Florida. The heat shield is one of the most critical elements of Orion and protects it and the future astronauts inside from searing temperatures experienced during reentry through Earth’s atmosphere when they return home. For Exploration Mission-1, the top layer of Orion’s heat shield that is primarily responsible for helping the crew module endure reentry heat will be composed of approximately 180 blocks, which are made of an ablative material called Avcoat designed to wear away as it heats up. Orion is being prepared for its flight on the agency’s Space Launch System for Exploration Mission-1 in late 2018. Orion is the exploration spacecraft designed to carry astronauts to destinations not yet explored by humans, including an asteroid and NASA’s Journey to Mars. It will have emergency abort capability, sustain the crew during space travel and provide safe re-entry from deep space return velocities. For more information, visit http://www.nasa.gov/orion.

  9. Using Array-Based Comparative Genomic Hybridization to Diagnose Pallister-Killian Syndrome

    PubMed Central

    Lee, Mi-Na; Lee, Jiwon; Yu, Hee Joon; Lee, Jeehun

    2017-01-01

    Pallister-Killian syndrome (PKS) is a rare multisystem disorder characterized by isochromosome 12p and tissue-limited mosaic tetrasomy 12p. In this study, we diagnosed three pediatric patients who were suspicious of having PKS using array-based comparative genomic hybridization (array CGH) and FISH analyses performed on peripheral lymphocytes. Patients 1 and 2 presented with craniofacial dysmorphic features, hypotonia, and a developmental delay. Array CGH revealed two to three copies of 12p in patient 1 and three copies in patient 2. FISH analysis showed trisomy or tetrasomy 12p. Patient 3, who had clinical features comparable to those of patients 1 and 2, was diagnosed by using FISH analysis alone. Here, we report three patients with mosaic tetrasomy 12p. There have been only reported cases diagnosed by chromosome analysis and FISH analysis on skin fibroblast or amniotic fluid. To our knowledge, patient 1 was the first case diagnosed by using array CGH performed on peripheral lymphocytes in Korea. PMID:27834069

  10. Using Array-Based Comparative Genomic Hybridization to Diagnose Pallister-Killian Syndrome.

    PubMed

    Lee, Mi Na; Lee, Jiwon; Yu, Hee Joon; Lee, Jeehun; Kim, Sun Hee

    2017-01-01

    Pallister-Killian syndrome (PKS) is a rare multisystem disorder characterized by isochromosome 12p and tissue-limited mosaic tetrasomy 12p. In this study, we diagnosed three pediatric patients who were suspicious of having PKS using array-based comparative genomic hybridization (array CGH) and FISH analyses performed on peripheral lymphocytes. Patients 1 and 2 presented with craniofacial dysmorphic features, hypotonia, and a developmental delay. Array CGH revealed two to three copies of 12p in patient 1 and three copies in patient 2. FISH analysis showed trisomy or tetrasomy 12p. Patient 3, who had clinical features comparable to those of patients 1 and 2, was diagnosed by using FISH analysis alone. Here, we report three patients with mosaic tetrasomy 12p. There have been only reported cases diagnosed by chromosome analysis and FISH analysis on skin fibroblast or amniotic fluid. To our knowledge, patient 1 was the first case diagnosed by using array CGH performed on peripheral lymphocytes in Korea.

  11. Zoom‐in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes

    PubMed Central

    Johnston, Jennifer J; Walker, Robert L; Davis, Sean; Facio, Flavia; Turner, Joyce T; Bick, David P; Daentl, Donna L; Ellison, Jay W; Meltzer, Paul S; Biesecker, Leslie G

    2007-01-01

    Contiguous gene syndromes cause disorders via haploinsufficiency for adjacent genes. Some contiguous gene syndromes (CGS) have stereotypical breakpoints, but others have variable breakpoints. In CGS that have variable breakpoints, the extent of the deletions may be correlated with severity. The Greig cephalopolysyndactyly contiguous gene syndrome (GCPS‐CGS) is a multiple malformation syndrome caused by haploinsufficiency of GLI3 and adjacent genes. In addition, non‐CGS GCPS can be caused by deletions or duplications in GLI3. Although fluorescence in situ hybridisation (FISH) can identify large deletion mutations in patients with GCPS or GCPS‐CGS, it is not practical for identification of small intragenic deletions or insertions, and it is difficult to accurately characterise the extent of the large deletions using this technique. We have designed a custom comparative genomic hybridisation (CGH) array that allows identification of deletions and duplications at kilobase resolution in the vicinity of GLI3. The array averages one probe every 730 bp for a total of about 14 000 probes over 10 Mb. We have analysed 16 individuals with known or suspected deletions or duplications. In 15 of 16 individuals (14 deletions and 1 duplication), the array confirmed the prior results. In the remaining patient, the normal CGH array result was correct, and the prior assessment was a false positive quantitative polymerase chain reaction result. We conclude that high‐density CGH array analysis is more sensitive than FISH analysis for detecting deletions and provides clinically useful results on the extent of the deletion. We suggest that high‐density CGH array analysis should replace FISH analysis for assessment of deletions and duplications in patients with contiguous gene syndromes caused by variable deletions. PMID:17098889

  12. Upgrade of the ATLAS Tile Calorimeter Electronics

    NASA Astrophysics Data System (ADS)

    Carrió, F.; Tile Calorimeter System, ATLAS

    2015-02-01

    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 (1034 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 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.

  13. Chemical Composition of Ceramic Tile Glazes

    NASA Astrophysics Data System (ADS)

    Anufrik, S. S.; Kurian, N. N.; Zhukova, I. I.; Znosko, K. F.; Belkov, M. V.

    2016-11-01

    We have carried out laser emission and x-ray fluorescence spectral analysis of glaze before and after its application to ceramic tile produced by Keramin JSC (Belarus). We have studied the internal microstructure of the ceramic samples. It was established that on the surface and within the bulk interior of all the samples, there are micropores of sizes ranging from a few micrometers to tens of micrometers and microcracks as long as several hundred micrometers. The presence of micropores on the surface of the ceramic tile leads to an increase in the water absorption level and a decrease in frost resistance. It was found that a decrease in the surface tension of ceramic tile coatings is promoted by substitution of sodium by potassium, silica by boric anhydride, magnesium and barium by calcium, CaO by sodium oxide, and SiO2 by chromium oxide. We carried out a comparative analysis of the chemical composition of glaze samples using S4 Pioneer and ElvaX x-ray fluorescence spectrometers and also an LIBS laser emission analyzer.

  14. Oligonucleotide Arrays vs. Metaphase-Comparative Genomic Hybridisation and BAC Arrays for Single-Cell Analysis: First Applications to Preimplantation Genetic Diagnosis for Robertsonian Translocation Carriers

    PubMed Central

    Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

    2014-01-01

    Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers. PMID:25415307

  15. Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers.

    PubMed

    Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima

    2014-01-01

    Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

  16. Copy-number variations on the X chromosome in Japanese patients with mental retardation detected by array-based comparative genomic hybridization analysis.

    PubMed

    Honda, Shozo; Hayashi, Shin; Imoto, Issei; Toyama, Jun; Okazawa, Hitoshi; Nakagawa, Eiji; Goto, Yu-Ichi; Inazawa, Johji

    2010-09-01

    X-linked mental retardation (XLMR) is a common, clinically complex and genetically heterogeneous disease arising from many mutations along the X chromosome. Although research during the past decade has identified >90 XLMR genes, many more remain uncharacterized. In this study, copy-number variations (CNVs) were screened in individuals with MR from 144 families by array-based comparative genomic hybridization (aCGH) using a bacterial artificial chromosome-based X-tiling array. Candidate pathogenic CNVs (pCNVs) were detected in 10 families (6.9%). Five of the families had pCNVs involving known XLMR genes, duplication of Xq28 containing MECP2 in three families, duplication of Xp11.22-p11.23 containing FTSJ1 and PQBP1 in one family, and deletion of Xp11.22 bearing SHROOM4 in one family. New candidate pCNVs were detected in five families as follows: identical complex pCNVs involved in dup(X)(p22.2) and dup(X)(p21.3) containing part of REPS2, NHS and IL1RAPL1 in two unrelated families, duplication of Xp22.2 including part of FRMPD4, duplication of Xq21.1 including HDX and deletion of Xq24 noncoding region in one family, respectively. Both parents and only mother samples were available in six and three families, respectively, and pCNVs were inherited from each of their mothers in those families other than a family of the proband with deletion of SHROOM4. This study should help to identify the novel XLMR genes and mechanisms leading to MR and reveal the clinical conditions and genomic background of XLMR.

  17. Clinical utility of an array comparative genomic hybridization analysis for Williams syndrome.

    PubMed

    Yagihashi, Tatsuhiko; Torii, Chiharu; Takahashi, Reiko; Omori, Mikimasa; Kosaki, Rika; Yoshihashi, Hiroshi; Ihara, Masahiro; Minagawa-Kawai, Yasuyo; Yamamoto, Junichi; Takahashi, Takao; Kosaki, Kenjiro

    2014-11-01

    To reveal the relation between intellectual disability and the deleted intervals in Williams syndrome, we performed an array comparative genomic hybridization analysis and standardized developmental testing for 11 patients diagnosed as having Williams syndrome based on fluorescent in situ hybridization testing. One patient had a large 4.2-Mb deletion spanning distally beyond the common 1.5-Mb intervals observed in 10/11 patients. We formulated a linear equation describing the developmental age of the 10 patients with the common deletion; the developmental age of the patient with the 4.2-Mb deletion was significantly below the expectation (developmental age = 0.51 × chronological age). The large deletion may account for the severe intellectual disability; therefore, the use of array comparative genomic hybridization may provide practical information regarding individuals with Williams syndrome. © 2014 Japanese Teratology Society.

  18. Detection of DNA copy number alterations in cancer by array comparative genomic hybridization.

    PubMed

    Michels, Evi; De Preter, Katleen; Van Roy, Nadine; Speleman, Frank

    2007-09-01

    Over the past few years, various reliable platforms for high-resolution detection of DNA copy number changes have become widely available. Together with optimized protocols for labeling and hybridization and algorithms for data analysis and representation, this has lead to a rapid increase in the application of this technology in the study of copy number variation in the human genome in normal cells and copy number imbalances in genetic diseases, including cancer. In this review, we briefly discuss specific technical issues relevant for array comparative genomic hybridization analysis in cancer tissues. We specifically focus on recent successes of array comparative genomic hybridization technology in the progress of our understanding of oncogenesis in a variety of cancer types. A third section highlights the potential of sensitive genome-wide detection of patterns of DNA imbalances or molecular portraits for class discovery and therapeutic stratification.

  19. Radiation hardness of 3HF-tile/O2-WLS-fiber calorimeter

    SciTech Connect

    Han, S.W.; Hu, L.D.; Liu, N.Z.

    1993-11-01

    The radiation hardness of a 3HF-tile/O2-WLS-fiber calorimeter with two different tile/fiber patterns has been studied. Two calorimeter modules were irradiated up to 10 Mrad with the BEPC 1.3 GeV electron beam. The radiation damage of these modules is compared with our previous measurements from SCSN81-tile/BCF91A-WLS-fiber modules. The longitudinal damage profiles are fitted as a function of depth.

  20. Optically Tiled Flat Panel Displays. A Feasibility Study

    DTIC Science & Technology

    1992-11-01

    distortion. The fabrication of a traditional rotational symmetric Fresnel lens could be possible using diamond turning methods. However the rotational...and allow the microlens array to be located next to the LCD module output polarizer and immediately followed by the negative Fresnel lens and then the...microlenses remapping the pixels onto a diffuser through a 4 negative Fresnel lens (Figure 11). This method could tile together LCD modules separated by a

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

    PubMed

    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.

  2. Ultrasound therapy transducers with space-filling non-periodic arrays.

    PubMed

    Raju, Balasundar I; Hall, Christopher S; Seip, Ralf

    2011-05-01

    Ultrasound transducers designed for therapeutic purposes such as tissue ablation, histotripsy, or drug delivery require large apertures for adequate spatial localization while providing sufficient power and steerability without the presence of secondary grating lobes. In addition, it is highly preferred to minimize the total number of channels and to maintain simplicity in electrical matching network design. To this end, we propose array designs that are both space-filling and non-periodic in the placement of the elements. Such array designs can be generated using the mathematical concept of non-periodic or aperiodic tiling (tessellation) and can lead to reduced grating lobes while maintaining full surface area coverage to deliver maximum power. For illustration, we designed two 2-D space-filling therapeutic arrays with 128 elements arranged on a spherical shell. One was based on the two-shape Penrose rhombus tiling, and the other was based on a single rectangular shape arranged non-periodically. The steerability performance of these arrays was studied using acoustic field simulations. For comparison, we also studied two other arrays, one with circular elements distributed randomly, and the other a periodic array with square elements. Results showed that the two space-filling non-periodic arrays were able to steer to treat a volume of 16 x 16 x 20 mm while ensuring that the grating lobes were under -10 dB compared with the main lobe. The rectangular non-periodic array was able to generate two and half times higher power than the random circles array. The rectangular array was then fabricated by patterning the array using laser scribing methods and its steerability performance was validated using hydrophone measurements. This work demonstrates that the concept of space-filling aperiodic/non-periodic tiling can be used to generate therapy arrays that are able to provide higher power for the same total transducer area compared with random arrays while maintaining

  3. Tiling spaces are inverse limits

    NASA Astrophysics Data System (ADS)

    Sadun, Lorenzo

    2003-11-01

    Let M be an arbitrary Riemannian homogeneous space, and let Ω be a space of tilings of M, with finite local complexity (relative to some symmetry group Γ) and closed in the natural topology. Then Ω is the inverse limit of a sequence of compact finite-dimensional branched manifolds. The branched manifolds are (finite) unions of cells, constructed from the tiles themselves and the group Γ. This result extends previous results of Anderson and Putnam, of Ormes, Radin, and Sadun, of Bellissard, Benedetti, and Gambaudo, and of Gähler. In particular, the construction in this paper is a natural generalization of Gähler's.

  4. Active aperture phased arrays

    NASA Astrophysics Data System (ADS)

    Shenoy, R. P.

    1989-04-01

    Developments towards the realization of active aperture phased arrays are reviewed. The technology and cost aspects of the power amplifier and phase shifter subsystems are discussed. Consideration is given to research concerning T/R modules, MESFETs, side lobe control, beam steering, optical control techniques, and printed circuit antennas. Methods for configuring the array are examined, focusing on the tile and brick configurations. It is found that there is no technological impediment for introducing active aperture phased arrays.

  5. Development of SiPM-based scintillator tile detectors for a multi-layer fast neutron tracker

    NASA Astrophysics Data System (ADS)

    Preston, R.; Jakubek, J.; Prokopovich, D.; Uher, J.

    2012-10-01

    We are developing thin tile scintillator detectors with silicon photomultiplier (SiPM) readout for use in a multi-layer fast-neutron tracker. The tracker is based on interleaved Timepix and plastic scintillator layers. The thin 15 × 15 × 2 mm plastic scintillators require suitable optical readout in order to detect and measure the energy lost by energetic protons that have been recoiled by fast neutrons. Our first prototype used dual SiPMs, coupled to opposite edges of the scintillator tile using light-guides. An alternative readout geometry was designed in an effort to increase the fraction of scintillation light detected by the SiPMs. The new prototype uses a larger SiPM array to cover the entire top face of the tile. This paper details the comparative performance of the two prototype designs. A deuterium-tritium (DT) fast-neutron source was used to compare the relative light collection efficiency of the two designs. A collimated UV light source was scanned across the detector face to map the uniformity. The new prototype was found to have 9.5 times better light collection efficiency over the original design. Both prototypes exhibit spatial non-uniformity in their response. Methods of correcting this non-uniformity are discussed.

  6. Composite treatment of ceramic tile armor

    DOEpatents

    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.

  7. Composite treatment of ceramic tile armor

    DOEpatents

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

    2012-01-02

    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.

  8. Production Process for Strong, Light Ceramic Tiles

    NASA Technical Reports Server (NTRS)

    Holmquist, G. R.; Cordia, E. R.; Tomer, R. S.

    1985-01-01

    Proportions of ingredients and sintering time/temperature schedule changed. Production process for lightweight, high-strength ceramic insulating tiles for Space Shuttle more than just scaled-up version of laboratory process for making small tiles. Boron in aluminum borosilicate fibers allows fusion at points where fibers contact each other during sintering, thereby greatly strengthening tiles structure.

  9. Production Process for Strong, Light Ceramic Tiles

    NASA Technical Reports Server (NTRS)

    Holmquist, G. R.; Cordia, E. R.; Tomer, R. S.

    1985-01-01

    Proportions of ingredients and sintering time/temperature schedule changed. Production process for lightweight, high-strength ceramic insulating tiles for Space Shuttle more than just scaled-up version of laboratory process for making small tiles. Boron in aluminum borosilicate fibers allows fusion at points where fibers contact each other during sintering, thereby greatly strengthening tiles structure.

  10. Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.

    PubMed

    Schwenk, Jochen M; Igel, Ulrika; Kato, Bernet S; Nicholson, George; Karpe, Fredrik; Uhlén, Mathias; Nilsson, Peter

    2010-02-01

    In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead array. The intensity levels were used to define protein profiles and no significant differences between serum and plasma were observed for 79% of the 174 antibodies (targeting 156 proteins). By excluding 36 antibodies giving rise to differential intensity levels, cluster analysis revealed donor-specific rather than preparation-dependent grouping. With a cohort from a clinically relevant medical condition, the metabolic syndrome, the influence of the sample type on a multiplexed biomarker discovery approach was further investigated. Independent comparisons of protein profiles in serum and plasma revealed an antibody targeting ADAMTSL-4, a protein that would qualify to be studied further in association with the condition. In general, the preparation type had an impact on the results of the applied antibody suspension bead array, and while the technical variability was equal, plasma offered a greater biological variability and allowed to give rise to more discoveries than serum.

  11. Theoretical and experimental comparative analysis of beamforming methods for loudspeaker arrays under given performance constraints

    NASA Astrophysics Data System (ADS)

    Olivieri, Ferdinando; Fazi, Filippo Maria; Nelson, Philip A.; Shin, Mincheol; Fontana, Simone; Yue, Lang

    2016-07-01

    Methods for beamforming are available that provide the signals used to drive an array of sources for the implementation of systems for the so-called personal audio. In this work, performance of the delay-and-sum (DAS) method and of three widely used methods for optimal beamforming are compared by means of computer simulations and experiments in an anechoic environment using a linear array of sources with given constraints on quality of the reproduced field at the listener's position and limit to input energy to the array. Using the DAS method as a benchmark for performance, the frequency domain responses of the loudspeaker filters can be characterized in three regions. In the first region, at low frequencies, input signals designed with the optimal methods are identical and provide higher directivity performance than that of the DAS. In the second region, performance of the optimal methods are similar to the DAS method. The third region starts above the limit due to spatial aliasing. A method is presented to estimate the boundaries of these regions.

  12. Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays.

    PubMed

    Huang, Xiaohong; Pan, Wei

    2002-08-01

    Microarray experiments are being increasingly used in molecular biology. A common task is to detect genes with differential expression across two experimental conditions, such as two different tissues or the same tissue at two time points of biological development. To take proper account of statistical variability, some statistical approaches based on the t-statistic have been proposed. In constructing the t-statistic, one needs to estimate the variance of gene expression levels. With a small number of replicated array experiments, the variance estimation can be challenging. For instance, although the sample variance is unbiased, it may have large variability, leading to a large mean squared error. For duplicated array experiments, a new approach based on simple averaging has recently been proposed in the literature. Here we consider two more general approaches based on nonparametric smoothing. Our goal is to assess the performance of each method empirically. The three methods are applied to a colon cancer data set containing 2,000 genes. Using two arrays, we compare the variance estimates obtained from the three methods. We also consider their impact on the t-statistics. Our results indicate that the three methods give variance estimates close to each other. Due to its simplicity and generality, we recommend the use of the smoothed sample variance for data with a small number of replicates.

  13. Thermodynamics and Kinetics of DNA Tile-Based Self-Assembly

    NASA Astrophysics Data System (ADS)

    Jiang, Shuoxing

    Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states with unique assembly pathways. First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed "multitile" arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step. The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, The works presented here could also be

  14. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations

    PubMed Central

    Le Caignec, C; Boceno, M; Saugier-Veber, P; Jacquemont, S; Joubert, M; David, A; Frebourg, T; Rival, J

    2005-01-01

    Background: Malformations are a major cause of morbidity and mortality in full term infants and genomic imbalances are a significant component of their aetiology. However, the causes of defects in many patients with multiple congenital malformations remain unexplained despite thorough clinical examination and laboratory investigations. Methods: We used a commercially available array based comparative genomic hybridisation method (array CGH), able to screen all subtelomeric regions, main microdeletion syndromes, and 201 other regions covering the genome, to detect submicroscopic chromosomal imbalances in 49 fetuses with three or more significant anomalies and normal karyotype. Results: Array CGH identified eight genomic rearrangements (16.3%), all confirmed by quantitative multiplex PCR of short fluorescent fragments. Subtelomeric and interstitial deletions, submicroscopic duplications, and a complex genomic imbalance were identified. In four de novo cases (15qtel deletion, 16q23.1–q23.3 deletion, 22q11.2 deletion, and mosaicism for a rearranged chromosome 18), the genomic imbalance identified clearly underlay the pathological phenotype. In one case, the relationship between the genotype and phenotype was unclear, since a subtelomeric 6q deletion was detected in a mother and her two fetuses bearing multiple malformations. In three cases, a subtelomeric 10q duplication, probably a genomic polymorphism, was identified. Conclusions: The detection of 5/49 causative chromosomal imbalances (or 4/49 if the 6qtel deletion is not considered as causative) suggests wide genome screening when standard chromosome analysis is normal and confirms that array CGH will have a major impact on pre and postnatal diagnosis as well as providing information for more accurate genetic counselling. PMID:15689449

  15. A Custom Rat and Baboon Hypertension Gene Array to Compare Experimental Models

    PubMed Central

    Northcott, Carrie A.; Glenn, Jeremy P.; Shade, Robert E.; Kammerer, Candace M.; Hinojosa-Laborde, Carmen; Fink, Gregory D.; Haywood, Joseph R.; Cox, Laura A.

    2013-01-01

    One challenge in understanding the polygenic disease of hypertension is elucidating the genes involved and defining responses to environmental factors. Many studies focus on animal models of hypertension; however, this does not necessarily extrapolate to humans. Current technology and cost limitations are prohibitive in fully evaluating hypertension within humans. Thus, we have designed a single array platform that allows direct comparison of genes relevant to hypertension in animal models and non-human primates/human hypertension. The custom array is targeted to 328 genes known to be potentially related to blood pressure control. Studies compared gene expression in the kidney from normotensive rats and baboons. We found 74 genes expressed in both the rat and baboon kidney, 41 genes expressed in the rat kidney that were not detected in the baboon kidney and 34 genes expression in the baboon kidney that were not detected in the rat kidney. To begin the evaluation of the array in a pathological condition, kidney gene expression was compared between the salt sensitive DOCA rat model of hypertension and sham animals. Gene expression in renal cortex and medulla from hypertensive DOCA compared with sham rats revealed 3 genes differentially expressed in the renal cortex: Annexin A1 (up-regulated; relative intensity: 1.316 ± 0.321 vs. 2.312 ± 0.283), Glutamate-cysteine ligase (down-regulated; relative intensity: 3.738 ± 0.174 vs. 2.645 ± 0.364) and Glutathione-S transferase (down-regulated; relative intensity: 5.572 ± 0.246 vs. 4.215 ± 0.411) and 21 genes differentially expressed in renal medulla. Interestingly, few genes were differentially expressed in the kidney in the DOCA-salt model of hypertension; this may suggest that the complexity of hypertension may be the result of only a few gene-by-environment responsive events. PMID:22228705

  16. Array comparative genomic hybridization analysis of small supernumerary marker chromosomes in human infertility.

    PubMed

    Guediche, N; Tosca, L; Kara Terki, A; Bas, C; Lecerf, L; Young, J; Briand-Suleau, A; Tou, B; Bouligand, J; Brisset, S; Misrahi, M; Guiochon-Mantel, A; Goossens, M; Tachdjian, G

    2012-01-01

    Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by conventional banding cytogenetics. This study describes four patients with sSMC in relation with infertility. Patient 1 had primary infertility. His brother, fertile, carried the same sSMC (patient 2). Patient 3 presented polycystic ovary syndrome and patient 4 primary ovarian insufficiency. Cytogenetic studies, array comparative genomic hybridization (CGH) and sperm analyses were compared with cases previously reported. sSMC corresponded to the 15q11.2 region (patients 1 and 2), the centromeric chromosome 15 region (patient 3) and the 21p11.2 region (patient 4). Array CGH showed 3.6-Mb gain for patients 1 and 2 and 0.266-Mb gain for patient 4. Sperm fluorescent in-situ hybridization analyses found ratios of 0.37 and 0.30 of sperm nuclei with sSMC(15) for patients 1 and 2, respectively (P < 0.001). An increase of sperm nuclei with disomy X, Y and 18 was noted for patient 1 compared with control and patient 2 (P < 0.001). Among the genes mapped in the unbalanced chromosomal regions, POTE B and BAGE are related to the testis and ovary, respectively. The implication of sSMC in infertility could be due to duplication, but also to mechanical effects perturbing meiosis. Copyright © 2011 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  17. New class tiling design for dot-diffused halftoning.

    PubMed

    Liu, Yun-Fu; Guo, Jing-Ming

    2013-03-01

    In this paper, a new class tiling designed dot diffusion along with the optimized class matrix and diffused matrix are proposed. The result of this method presents a nearly periodic-free halftone when compared to the former schemes. Formerly, the class matrix of the dot diffusion is duplicated and orthogonally tiled to fulfill the entire image for further thresholding and quantized-error diffusion, which accompanies subsequent periodic artifacts. In our observation, this artifact can be solved by manipulating the class tiling with comprising rotation, transpose, and alternatively shifting of the class matrices. As documented in the experimental results, the proposed dot diffusion has been compared with the former halftoning methods with parallelism in terms of image quality, processing efficiency, periodicity, and memory consumption; the proposed dot diffusion exhibits as a very competitive candidate in the printing/display market.

  18. Nondestructive evaluation of Shuttle Columbia tiles

    NASA Technical Reports Server (NTRS)

    Davis, Richard M.; Moslehy, Faissal A.; Clarke, Margaret M.; Mauceri, A. J.

    1992-01-01

    The NDE of Orbiter Vehicle-102 tile bonds, performed in August 1991, is described. The evaluation was carried out in order to help NASA develop fast, reliable methods to diagnose problems in tile bonding other than the present 'pull' and 'wiggle' tests. The NDE did not find any indication of bond problems, and all bonds were classified as 'nominal'. The feasibility of using NDE techniques in a dynamic, real-world environment without interfering with Shuttle rework schedules is shown. The data will be useful in verifying analytical models of tile behavior developed at the University of Central Florida. The need for a tile test bed containing known tile misbonds is suggested.

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

    PubMed Central

    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. PMID:28085937

  20. Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization.

    PubMed

    Sabath, Daniel E; Bender, Michael A; Sankaran, Vijay G; Vamos, Esther; Kentsis, Alex; Yi, Hye-Son; Greisman, Harvey A

    2016-01-01

    Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most β-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volume. A small number of deletions accounts for most α-thalassemias; in contrast, there are no predominant HBB deletions causing β-thalassemia. To facilitate the identification and characterization of deletions of the HBA and HBB globin loci, we performed array-based comparative genomic hybridization using a custom oligonucleotide microarray. We accurately mapped the breakpoints of known and previously uncharacterized HBB deletions defining previously uncharacterized deletion breakpoints by PCR amplification and sequencing. The array also successfully identified the common HBA deletions --(SEA) and --(FIL). In summary, comparative genomic hybridization can be used to characterize deletions of the HBA and HBB loci, allowing high-resolution characterization of novel deletions that are not readily detected by PCR-based methods. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  1. Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization

    PubMed Central

    Sabath, Daniel E.; Bender, Michael A.; Sankaran, Vijay G.; Vamos, Esther; Kentsis, Alex; Yi, Hye-Son; Greisman, Harvey A.

    2017-01-01

    Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most β-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volume. A small number of deletions accounts for most α-thalassemias; in contrast, there are no predominant HBB deletions causing β-thalassemia. To facilitate the identification and characterization of deletions of the HBA and HBB globin loci, we performed array-based comparative genomic hybridization using a custom oligonucleotide microarray. We accurately mapped the breakpoints of known and previously uncharacterized HBB deletions defining previously uncharacterized deletion breakpoints by PCR amplification and sequencing. The array also successfully identified the common HBA deletions --SEA and --FIL. In summary, comparative genomic hybridization can be used to characterize deletions of the HBA and HBB loci, allowing high-resolution characterization of novel deletions that are not readily detected by PCR-based methods. PMID:26612711

  2. Foam on Tile Impact Modeling for the Space Shuttle Program

    NASA Technical Reports Server (NTRS)

    Stellingwerf, R. F.; Robinson, J. H.; Richardson, S.; Evans, S. W.; Stallworth, R.; Hovater, M.

    2003-01-01

    Following the breakup of the Space Shuttle Columbia during reentry a NASA-wide investigation team was formed to examine the probable damage inflicted on Orbiter Thermal Protection System (TPS) elements by impact of External Tank insulating foam projectiles. Our team was to apply rigorous, physics-based analysis techniques to help determine parameters of interest for an experimental test program, utilize validated codes to investigate the full range of impact scenarios, and use analysis derived models to predict aero-thermal-structural responses to entry conditions. We were to operate on a non-interference basis with the j Team, and were to supply significant findings to that team and to the Orbiter Vehicle Engineering Working Group, being responsive to any solicitations for support from these entities. The authors formed a working sub-group within the larger team to apply the Smooth Particle Hydrodynamics code SPHC to the damage estimation problem. Numerical models of the LI-900 TPS tiles and of the BX-250 foam were constructed and used as inputs into the code. Material properties needed to properly model the tiles and foam were obtained from other working sub-groups who performed tests on these items for this purpose. Two- and three- dimensional models of the tiles were constructed, including the glass outer layer, the densified lower layer of LI-900 insulation, the Nomex felt Strain Isolation Pad (SIP) mounting layer, and the underlying aluminum 2024 vehicle skin. A model for the BX-250 foam including porous compression, elastic rebound, and surface erosion was developed. Code results for the tile damage and foam behavior were extensively validated through comparison with the Southwest Research Institute (SwRI) foam-on-tile impact experiments carried out in 1999. These tests involved small projectiles striking individual tiles and small tile arrays. Following code and model validation we simulated impacts of larger ET foam projectiles on the TPS tile systems used

  3. Foam on Tile Impact Modeling for the Space Shuttle Program

    NASA Technical Reports Server (NTRS)

    Stellingwerf, R. F.; Robinson, J. H.; Richardson, S.; Evans, S. W.; Stallworth, R.; Hovater, M.

    2003-01-01

    Following the breakup of the Space Shuttle Columbia during reentry a NASA-wide investigation team was formed to examine the probable damage inflicted on Orbiter Thermal Protection System (TPS) elements by impact of External Tank insulating foam projectiles. Our team was to apply rigorous, physics-based analysis techniques to help determine parameters of interest for an experimental test program, utilize validated codes to investigate the full range of impact scenarios, and use analysis derived models to predict aero-thermal-structural responses to entry conditions. We were to operate on a non-interference basis with the j Team, and were to supply significant findings to that team and to the Orbiter Vehicle Engineering Working Group, being responsive to any solicitations for support from these entities. The authors formed a working sub-group within the larger team to apply the Smooth Particle Hydrodynamics code SPHC to the damage estimation problem. Numerical models of the LI-900 TPS tiles and of the BX-250 foam were constructed and used as inputs into the code. Material properties needed to properly model the tiles and foam were obtained from other working sub-groups who performed tests on these items for this purpose. Two- and three- dimensional models of the tiles were constructed, including the glass outer layer, the densified lower layer of LI-900 insulation, the Nomex felt Strain Isolation Pad (SIP) mounting layer, and the underlying aluminum 2024 vehicle skin. A model for the BX-250 foam including porous compression, elastic rebound, and surface erosion was developed. Code results for the tile damage and foam behavior were extensively validated through comparison with the Southwest Research Institute (SwRI) foam-on-tile impact experiments carried out in 1999. These tests involved small projectiles striking individual tiles and small tile arrays. Following code and model validation we simulated impacts of larger ET foam projectiles on the TPS tile systems used

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

    NASA Astrophysics Data System (ADS)

    Ryzhov, A.

    2016-12-01

    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.

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

    PubMed

    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.

  6. Summer Thermal Performance of Ventilated Roofs with Tiled Coverings

    NASA Astrophysics Data System (ADS)

    Bortoloni, M.; Bottarelli, M.; Piva, S.

    2017-01-01

    The thermal performance of a ventilated pitched roof with tiled coverings is analysed and compared with unventilated roofs. The analysis is carried out by means of a finite element numerical code, by solving both the fluid and thermal problems in steady-state. A whole one-floor building with a pitched roof is schematized as a 2D computational domain including the air-permeability of tiled covering. Realistic data sets for wind, temperature and solar radiation are used to simulate summer conditions at different times of the day. The results demonstrate that the batten space in pitched roofs is an effective solution for reducing the solar heat gain in summer and thus for achieving better indoor comfort conditions. The efficiency of the ventilation is strictly linked to the external wind conditions and to buoyancy forces occurring due to the heating of the tiles.

  7. Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation.

    PubMed

    Osoegawa, K; Vessere, G M; Utami, K H; Mansilla, M A; Johnson, M K; Riley, B M; L'Heureux, J; Pfundt, R; Staaf, J; van der Vliet, W A; Lidral, A C; Schoenmakers, E F P M; Borg, A; Schutte, B C; Lammer, E J; Murray, J C; de Jong, P J

    2008-02-01

    We analysed DNA samples isolated from individuals born with cleft lip and cleft palate to identify deletions and duplications of candidate gene loci using array comparative genomic hybridisation (array-CGH). Of 83 syndromic cases analysed we identified one subject with a previously unknown 2.7 Mb deletion at 22q11.21 coinciding with the DiGeorge syndrome region. Eighteen of the syndromic cases had clinical features of Van der Woude syndrome and deletions were identified in five of these, all of which encompassed the interferon regulatory factor 6 (IRF6) gene. In a series of 104 non-syndromic cases we found one subject with a 3.2 Mb deletion at chromosome 6q25.1-25.2 and another with a 2.2 Mb deletion at 10q26.11-26.13. Analyses of parental DNA demonstrated that the two deletion cases at 22q11.21 and 6q25.1-25.2 were de novo, while the deletion of 10q26.11-26.13 was inherited from the mother, who also has a cleft lip. These deletions appear likely to be causally associated with the phenotypes of the subjects. Estrogen receptor 1 (ESR1) and fibroblast growth factor receptor 2 (FGFR2) genes from the 6q25.1-25.2 and 10q26.11-26.13, respectively, were identified as likely causative genes using a gene prioritization software. We have shown that array-CGH analysis of DNA samples derived from cleft lip and palate subjects is an efficient and productive method for identifying candidate chromosomal loci and genes, complementing traditional genetic mapping strategies.

  8. Detection limit of intragenic deletions with targeted array comparative genomic hybridization

    PubMed Central

    2013-01-01

    Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

  9. Characterization of color texture: color texture based sorting of tiles

    NASA Astrophysics Data System (ADS)

    Bourada, Y.; Lafon, Dominique; Eterradossi, O.

    1998-09-01

    Many materials used by the building industry show a color texture which affects the product commercial value. This texture can be seen as the spatial arrangement of regions of acceptable color differences. This work describes an appearance based automated sorting via color texture analysis, using ceramic tiles as example. Textural analysis of the tiles digital images expressed in CIEL*a*b* color system is performed through the analysis of intrinsic features of each region and relationships between regions. Results obtained through the automated process are compared to a visual sorting which leads to calculation of application dependant color and texture tolerances.

  10. Developing tiled projection display systems

    SciTech Connect

    Hereld, M.; Judson, I. R.; Paris, J.; Stevens, R. L.

    2000-06-08

    Tiled displays are an emerging technology for constructing high-resolution semi-immersive visualization environments capable of presenting high-resolution images from scientific simulation [EVL, PowerWall]. In this way, they complement other technologies such as the CAVE [Cruz-Niera92] or ImmersaDesk, [Czernuszenko97], which by design give up pure resolution in favor of width of view and stereo. However, the largest impact may well be in using large-format tiled displays as one of possibly multiple displays in building ''information'' or ''active'' spaces that surround the user with diverse ways of interacting with data and multimedia information flows [IPSI, Childers00, Raskar98, ROME, Stanford, UNC]. These environments may prove to be the ultimate successor of the desktop metaphor for information technology work.

  11. Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation

    PubMed Central

    Lantieri, Francesca; Malacarne, Michela; Gimelli, Stefania; Santamaria, Giuseppe; Coviello, Domenico; Ceccherini, Isabella

    2017-01-01

    The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log2ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log2ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected. PMID:28287439

  12. Genome profiling of chondrosarcoma using oligonucleotide array-based comparative genomic hybridization.

    PubMed

    Hameed, Meera; Ulger, Celal; Yasar, Duygu; Limaye, Neha; Kurvathi, Rohini; Streck, Deanna; Benevenia, Joseph; Patterson, Francis; Dermody, James J; Toruner, Gokce A

    2009-07-15

    Chondrosarcomas of the bone are malignant hyaline cartilage-forming tumors with an annual incidence rate of 3.6% of all primary bone malignancies in the United States. Specimens of 25 chondrosarcomas (10 grade I, 9 grade II, 1 grade III, and 5 dedifferentiated) from 23 patients were collected from the Department of Pathology at the University Hospital at UMDNJ-New Jersey Medical School from 1996 to 2007. Array-based comparative genomic hybridization (array-CGH) studies were performed on frozen tumor specimens. Recurrent deletions observed in at least in six tumors were 5q13.2, 5q14.2 approximately q21.3, 6q12 approximately q13, 6q16 approximately q25.3, 9p24.2 approximately q12, and 9p21.3. There was a statistically significant association between high-grade tumor (grade III and dedifferentiated) and the recurrent genetic deletions at 5q14.2 approximately q21.3, 6q16 approximately q25.3, 9p24.2 approximately q12, and 9p21.3. There is consistency between increased levels of aneuploidy and the progression of chondrosarcoma from lower to higher grades.

  13. Shuttle Upgrade Program: Tile TPS

    NASA Technical Reports Server (NTRS)

    Leiser, Daniel B.; Stewart, David A.; DiFiore, Robert; Irby, Ed; Arnold, James (Technical Monitor)

    2001-01-01

    One of the areas where the thermal protection system on the Space Shuttle Orbiter could be improved is the RSI (Reusable Surface Insulation) tile. The improvement would be in damage resistance that would reduce the resultant maintenance and inspection required. It has performed very well in every other aspect. Improving the system's damage resistance has been the subject of much research over the past several years. One of the results of that research was a new system developed for damage prone areas on the orbiter (i.e., base heat shield). That system, designated as TUFI, Toughened Uni-Piece Fibrous Insulation, was successfully demonstrated as an experiment on the Orbiter and is now baselined for the base heat shield. This paper describes the results of a current research program to further improve the TUFI tile system, thus making it applicable to more areas on the orbiter. The way to remove the current limitations of the TUFI system (i.e., weight or thermal conductivity differences between it and the baseline tile (LI-900)) is to improve the characteristics of LI-900 or AETB-8. Specifically this paper describes the results of two efforts. The first shows performance data of an improved LI-900 system involving the application of TUFI and the second describes data that shows a reduced difference in thermal conductivity between the advanced TUFI substrate (AETB-8) now used on the orbiter and LI-900.

  14. Shuttle Upgrade Program: Tile TPS

    NASA Technical Reports Server (NTRS)

    Leiser, Daniel B.; Stewart, David A.; DiFiore, Robert; Irby, Ed; Arnold, James (Technical Monitor)

    2001-01-01

    One of the areas where the thermal protection system on the Space Shuttle Orbiter could be improved is the RSI (Reusable Surface Insulation) tile. The improvement would be in damage resistance that would reduce the resultant maintenance and inspection required. It has performed very well in every other aspect. Improving the system's damage resistance has been the subject of much research over the past several years. One of the results of that research was a new system developed for damage prone areas on the orbiter (i.e., base heat shield). That system, designated as TUFI, Toughened Uni-Piece Fibrous Insulation, was successfully demonstrated as an experiment on the Orbiter and is now baselined for the base heat shield. This paper describes the results of a current research program to further improve the TUFI tile system, thus making it applicable to more areas on the orbiter. The way to remove the current limitations of the TUFI system (i.e., weight or thermal conductivity differences between it and the baseline tile (LI-900)) is to improve the characteristics of LI-900 or AETB-8. Specifically this paper describes the results of two efforts. The first shows performance data of an improved LI-900 system involving the application of TUFI and the second describes data that shows a reduced difference in thermal conductivity between the advanced TUFI substrate (AETB-8) now used on the orbiter and LI-900.

  15. Pre- and postnatal genetic testing by array-comparative genomic hybridization: genetic counseling perspectives.

    PubMed

    Darilek, Sandra; Ward, Patricia; Pursley, Amber; Plunkett, Katie; Furman, Patti; Magoulas, Pilar; Patel, Ankita; Cheung, Sau Wai; Eng, Christine M

    2008-01-01

    Recently, a new genetic test has been developed that allows a more detailed examination of the genome when compared with a standard chromosome analysis. Array comparative genomic hybridization (CGH microarray; also known as chromosome microarray analysis) in effect, combines chromosome and fluorescence in situ hybridization analyses allowing detection not only of aneuploidies, but also of all known microdeletion and microduplication disorders, including telomere rearrangements. Since 2004, this testing has been available in the Medical Genetics Laboratory at Baylor College of Medicine for postnatal evaluation and diagnosis of individuals with suspected genomic disorders. Subsequently, to assess the feasibility of offering CGH microarray for prenatal diagnosis, a prospective study was conducted on 98 pregnancies in a clinical setting comparing the results obtained from array CGH with those obtained from a standard karyotype. This was followed by the availability of prenatal testing on a clinical basis in 2005. To date, we have analyzed over 8000 cases referred to our clinical laboratory, including approximately 300 prenatal cases. With the clinical introduction of any new testing strategy, and particularly one focused on genetic disorders, issues of patient education, result interpretation, and genetic counseling must be anticipated and strategies adopted to allow the implementation of the testing with maximum benefit and minimum risk. In this article, we describe our experience with over 8000 clinical prenatal and postnatal cases of CGH microarray ordered by our clinical service or referred to the Baylor Medical Genetics Laboratory and describe the strategies used to optimize patient and provider education, facilitate clinical interpretation of results, and provide counseling for unique clinical circumstances.

  16. Comparison between fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis in translocation carriers.

    PubMed

    Lee, Vivian C Y; Chow, Judy F C; Lau, Estella Y L; Yeung, William S B; Ho, P C; Ng, Ernest H Y

    2015-02-01

    To compare the pregnancy outcome of the fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis of translocation carriers. Historical cohort. A teaching hospital in Hong Kong. All preimplantation genetic diagnosis treatment cycles performed for translocation carriers from 2001 to 2013. Overall, 101 treatment cycles for preimplantation genetic diagnosis in translocation were included: 77 cycles for reciprocal translocation and 24 cycles for Robertsonian translocation. Fluorescent in-situ hybridisation and array comparative genomic hybridisation were used in 78 and 11 cycles, respectively. The ongoing pregnancy rate per initiated cycle after array comparative genomic hybridisation was significantly higher than that after fluorescent in-situ hybridisation in all translocation carriers (36.4% vs 9.0%; P=0.010). The miscarriage rate was comparable with both techniques. The testing method (array comparative genomic hybridisation or fluorescent in-situ hybridisation) was the only significant factor affecting the ongoing pregnancy rate after controlling for the women's age, type of translocation, and clinical information of the preimplantation genetic diagnosis cycles by logistic regression (odds ratio=1.875; P=0.023; 95% confidence interval, 1.090-3.226). This local retrospective study confirmed that comparative genomic hybridisation is associated with significantly higher pregnancy rates versus fluorescent in-situ hybridisation in translocation carriers. Array comparative genomic hybridisation should be the technique of choice in preimplantation genetic diagnosis cycles in translocation carriers.

  17. Array tomography: imaging stained arrays.

    PubMed

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. In this protocol, tissue arrays are imaged using conventional wide-field fluorescence microscopy. Images can be captured manually or, with the appropriate software and hardware, the process can be automated.

  18. Array tomography: production of arrays.

    PubMed

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time consuming and require some practice to perfect. This protocol describes the sectioning of embedded tissues and the mounting of the serial arrays. The procedures require some familiarity with the techniques used for ultramicrotome sectioning for electron microscopy.

  19. Customized Array Comparative Genomic Hybridization Analysis of 25 Phosphatase-encoding Genes in Colorectal Cancer Tissues

    PubMed Central

    LACZMANSKA, IZABELA; SKIBA, PAWEL; KARPINSKI, PAWEL; BEBENEK, MAREK; M. SASIADEK, MARIA

    2016-01-01

    Background/Aim: Molecular mechanisms of alterations in protein tyrosine phosphatases (PTPs) genes in cancer have been previously described and include chromosomal aberrations, gene mutations, and epigenetic silencing. However, little is known about small intragenic gains and losses that may lead to either changes in expression or enzyme activity and even loss of protein function. Materials and Methods: The aim of this study was to investigate 25 phosphatase genes using customized array comparative genomic hybridization in 16 sporadic colorectal cancer tissues. Results: The analysis revealed two unique small alterations: of 2 kb in PTPN14 intron 1 and of 1 kb in PTPRJ intron 1. We also found gains and losses of whole PTPs gene sequences covered by large chromosome aberrations. Conclusion: In our preliminary studies using high-resolution custom microarray we confirmed that PTPs are frequently subjected to whole-gene rearrangements in colorectal cancer, and we revealed that non-polymorphic intragenic changes are rare. PMID:28031238

  20. Malignant canine mammary tumours: Preliminary genomic insights using oligonucleotide array comparative genomic hybridisation analysis.

    PubMed

    Santos, Marta; Dias-Pereira, Patrícia; Williams, Christina; Lopes, Carlos; Breen, Matthew

    2017-03-28

    Neoplastic mammary disease in female dogs represents a major health concern for dog owners and veterinarians, but the genomic basis of the disease is poorly understood. In this study, we performed high resolution oligonucleotide array comparative genomic hybridisation (oaCGH) to assess genome wide DNA copy number changes in 10 malignant canine mammary tumours from seven female dogs, including multiple tumours collected at one time from each of three female dogs. In all but two tumours, genomic imbalances were detected, with losses being more common than gains. Canine chromosomes 9, 22, 26, 27, 34 and X were most frequently affected. Dissimilar oaCGH ratio profiles were observed in multiple tumours from the same dogs, providing preliminary evidence for probable independent pathogenesis. Analysis of adjacent samples of one tumour revealed regional differences in the number of genomic imbalances, suggesting heterogeneity within tumours.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  2. Whole Genome Amplification of Labeled Viable Single Cells Suited for Array-Comparative Genomic Hybridization.

    PubMed

    Kroneis, Thomas; El-Heliebi, Amin

    2015-01-01

    Understanding details of a complex biological system makes it necessary to dismantle it down to its components. Immunostaining techniques allow identification of several distinct cell types thereby giving an inside view of intercellular heterogeneity. Often staining reveals that the most remarkable cells are the rarest. To further characterize the target cells on a molecular level, single cell techniques are necessary. Here, we describe the immunostaining, micromanipulation, and whole genome amplification of single cells for the purpose of genomic characterization. First, we exemplify the preparation of cell suspensions from cultured cells as well as the isolation of peripheral mononucleated cells from blood. The target cell population is then subjected to immunostaining. After cytocentrifugation target cells are isolated by micromanipulation and forwarded to whole genome amplification. For whole genome amplification, we use GenomePlex(®) technology allowing downstream genomic analysis such as array-comparative genomic hybridization.

  3. Tile profiling analysis of samples from the JET ITER-like wall and carbon wall

    NASA Astrophysics Data System (ADS)

    Heinola, K.; Ayres, C. F.; Baron-Wiechec, A.; Coad, J. P.; Likonen, J.; Matthews, G. F.; Widdowson, A.; Contributors, JET-EFDA

    2014-04-01

    A complete global balance for material transport in JET requires knowledge of the net erosion in the main chamber, net deposition in the divertor and the amount of dust in the divertor region. Following the end of the first JET ITER-like wall campaign a set of tiles has been removed from the main chamber and the divertor. This paper describes the initial tile surface profiling results for evaluating the erosion in the main chamber and deposition in the divertor. Tile profiling was performed on upper dump plate tiles and inner wall guard limiters made of beryllium and on inner divertor tiles made of tungsten coated carbon (C)-fibre composites. Additionally, the mass of dust collected from the JET divertor is also reported. Present results are compared with JET-C campaign results with the all-carbon C wall.

  4. Non-invasive prenatal screening versus prenatal diagnosis by array comparative genomic hybridization: a comparative retrospective study.

    PubMed

    Sotiriadis, Alexandros; Papoulidis, Ioannis; Siomou, Elisavet; Papageorgiou, Elena; Eleftheriades, Makarios; Papadopoulos, Vasilios; Alexiou, Maria; Manolakos, Emmanouil; Athanasiadis, Apostolos

    2017-06-01

    To calculate the proportion of array comparative genomic hybridization (aCGH) pathogenic results, that would not be detectable by non-invasive prenatal screening (NIPS). This is a comparative study using data from 2779 fetuses, which underwent invasive prenatal diagnosis, and the samples were analyzed using aCGH. The simulated NIPS assay would test for trisomies 21, 18, 13, monosomy X, 47, XXX, 47, XYY, and 47, XXY. Indications for invasive testing were grouped into categories and the absolute, relative rates of pathogenic/likely pathogenic results of aCGH analysis that would not be detectable by NIPS were calculated. The expected rate of aCGH-detected abnormalities that would not be detectable by NIPS was 28.0% (95% CI 14.3-47.6) for nuchal translucency (NT) 95 to 99th centile; 14.3% (95% 5.0-34.6) for NT > 99th centile; 34.2% (95% CI 21.1-50.1) for high-risk first-trimester results (regardless of NT); 52.4% (95% CI 32.4-71.7) for second-trimester markers; and 50.0% (95% CI 26.8-73.2) for advanced maternal age. The overall rate of aCGH pathogenic/likely pathogenic results was 5.0% and 44.0% (95% CI 36.0-52.2) of them would not be detected by NIPS. Approximately half of the abnormal aCGH results would not be detectable by standard NIPS assays, highlighting the necessity of pre-test counseling, and illustrating the limitations of NIPS. © 2017 John Wiley & Sons, Ltd. © 2017 John Wiley & Sons, Ltd.

  5. Global Swath and Gridded Data Tiling

    NASA Technical Reports Server (NTRS)

    Thompson, Charles K.

    2012-01-01

    This software generates cylindrically projected tiles of swath-based or gridded satellite data for the purpose of dynamically generating high-resolution global images covering various time periods, scaling ranges, and colors called "tiles." It reconstructs a global image given a set of tiles covering a particular time range, scaling values, and a color table. The program is configurable in terms of tile size, spatial resolution, format of input data, location of input data (local or distributed), number of processes run in parallel, and data conditioning.

  6. Tetromino tilings and the Tutte polynomial

    NASA Astrophysics Data System (ADS)

    Lykke Jacobsen, Jesper

    2007-02-01

    We consider tiling rectangles of size 4m × 4n by T-shaped tetrominoes. Each tile is assigned a weight that depends on its orientation and position on the lattice. For a particular choice of the weights, the generating function of tilings is shown to be the evaluation of the multivariate Tutte polynomial ZG(Q, v) (known also to physicists as the partition function of the Q-state Potts model) on an (m - 1) × (n - 1) rectangle G, where the parameter Q and the edge weights v can take arbitrary values depending on the tile weights.

  7. Multilayer Impregnated Fibrous Thermal Insulation Tiles

    NASA Technical Reports Server (NTRS)

    Tran, Huy K.; Rasky, Daniel J.; Szalai, Christine e.; Hsu, Ming-ta; Carroll, Joseph A.

    2007-01-01

    The term "secondary polymer layered impregnated tile" ("SPLIT") denotes a type of ablative composite-material thermal- insulation tiles having engineered, spatially non-uniform compositions. The term "secondary" refers to the fact that each tile contains at least two polymer layers wherein endothermic reactions absorb considerable amounts of heat, thereby helping to prevent overheating of an underlying structure. These tiles were invented to afford lighter-weight alternatives to the reusable thermal-insulation materials heretofore variously used or considered for use in protecting the space shuttles and other spacecraft from intense atmospheric-entry heating.

  8. Array-Based Comparative Genomic Hybridization for the Genomewide Detection of Submicroscopic Chromosomal Abnormalities

    PubMed Central

    Vissers, Lisenka E. L. M. ; de Vries, Bert B. A. ; Osoegawa, Kazutoyo ; Janssen, Irene M. ; Feuth, Ton ; Choy, Chik On ; Straatman, Huub ; van der Vliet, Walter ; Huys, Erik H. L. P. G. ; van Rijk, Anke ; Smeets, Dominique ; van Ravenswaaij-Arts, Conny M. A. ; Knoers, Nine V. ; van der Burgt, Ineke ; de Jong, Pieter J. ; Brunner, Han G. ; van Kessel, Ad Geurts ; Schoenmakers, Eric F. P. M. ; Veltman, Joris A. 

    2003-01-01

    Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using ∼3,500 flourescent in situ hybridization–verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome. PMID:14628292

  9. Application of a target array Comparative Genomic Hybridization to prenatal diagnosis

    PubMed Central

    2010-01-01

    Background While conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization (array CGH) technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis. We have investigated the value of our own designed DNA chip as a prenatal diagnostic tool for detecting submicroscopic deletions/duplications and chromosome aneuploidies. Methods We designed a target bacterial artificial chromosome (BAC)-based aCGH platform (MacArray™ M-chip), which specifically targets submicroscopic deletions/duplications for 26 known genetic syndromes of medical significance observed prenatally. To validate the DNA chip, we obtained genomic DNA from 132 reference materials generated from patients with 22 genetic diseases and 94 clinical amniocentesis samples obtained for karyotyping. Results In the 132 reference materials, all known genomic alterations were successfully identified. In the 94 clinical samples that were also subjected to conventional karyotyping, three cases of balanced chromosomal aberrations were not detected by aCGH. However, we identified eight cases of microdeletions in the Yq11.23 chromosomal region that were not found by conventional karyotyping. This region harbors the DAZ gene, and deletions may lead to non-obstructive spermatogenesis. Conclusions We have successfully designed and applied a BAC-based aCGH platform for prenatal diagnosis. This platform can be used in conjunction with conventional karyotyping and will provide rapid and accurate diagnoses for the targeted genomic regions while eliminating the need to interpret clinically-uncertain genomic regions. PMID:20576126

  10. Comparative study of sampling strategies for sparse photon multispectral lidar imaging: towards mosaic filter arrays

    NASA Astrophysics Data System (ADS)

    Tobin, Rachael; Altmann, Yoann; Ren, Ximing; McCarthy, Aongus; Lamb, Robert A.; McLaughlin, Stephen; Buller, Gerald S.

    2017-09-01

    In this paper, we investigate the recovery of range and spectral profiles associated with remote three-dimensional scenes sensed via single-photon multispectral lidar (MSL). We consider two different spatial/spectral sampling strategies and compare their performance for a similar overall number of detected photons. For a regular spatial grid of pixels, the first strategy consists of sampling all the spatial locations of the grid for each of the L wavelengths. The second strategy is consistent with the use of mosaic filter-based arrays and consists of acquiring only one wavelength (out of L) per spatial location. Despite the reduction of spectral content observed in each location, the second strategy has clear potential advantages for fast multispectral imaging using only a single frame read out. We propose a fully automated computational method, adapted for each of the two sampling strategies in order to recover the target range profile, as well as the reflectivity profiles associated with the different wavelengths. These strategies were also assessed with high ambient background. The performance of the two sampling strategies is illustrated using a single-photon MSL system with L = 4 wavelengths (473, 532, 589 and 640 nm). The results presented demonstrate that although the first strategy usually provides more accurate results, the second strategy does not exhibit a significant performance degradation, particularly for sparse photon data (down to 1 photon per pixel on average). These results suggest a way forward for the integration of single-photon detector arrays with mosaic filters for use in a range of emerging photon-starved two-dimensional and three-dimensional imaging applications.

  11. Detection of copy number variations in melanocytic lesions utilising array based comparative genomic hybridisation.

    PubMed

    Mesbah Ardakani, Nima; Thomas, Carla; Robinson, Cleo; Mina, Kym; Harvey, Nathan Tobias; Amanuel, Benhur; Wood, Benjamin Andrew

    2017-04-01

    Distinction between melanocytic naevi and melanoma occasionally poses a diagnostic challenge in ambiguous cases showing overlapping histological features. Melanomas are characterised by the presence of multiple genomic copy number variants (CNVs), while this is not a feature of naevi. We assessed the feasibility and utility of array-based comparative genomic hybridisation (aCGH) to assess CNVs in melanocytic lesions. DNA was extracted from formalin fixed, paraffin embedded (FFPE) sections of unambiguous naevi (n=19) and melanomas (n=19). The test DNA and gender mismatched human reference DNA were differentially labelled with fluorophores. Equal quantities of the two DNA samples were mixed and co-hybridised to a SurePrint G3 Human CGH 8x60K array, and digitally scanned to capture and quantify the relative fluorescence intensities. The ratio of the fluorescence intensities was analysed by Cytogenomics software (Agilent). Frequent large CNVs were identified in 94.7% of melanoma samples, including losses of 9p (73.6%), 9q (52.6%), 10q (36.8%), 11q (36.8%), 3p (21%), and 10p (21%), and gains of 6p (42.1%), 7p (42.1%), 1q (36.8%), 8q (31.5%) and 20q (21%). Only one naevus showed two large copy number changes. Overall aCGH showed a specificity and sensitivity of 94.7% in separating naevi from melanomas. Based on our results, aCGH can be successfully used to analyse CNVs of melanocytic lesions utilising FFPE derived biopsy samples, providing a potentially useful adjunctive test for the classification of diagnostically challenging melanocytic proliferations. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  12. Array-Based Genomic Comparative Hybridization Analysis of Field Strains of Mycoplasma hyopneumoniae▿ †

    PubMed Central

    Madsen, Melissa L.; Oneal, Michael J.; Gardner, Stuart W.; Strait, Erin L.; Nettleton, Dan; Thacker, Eileen L.; Minion, F. Chris

    2007-01-01

    Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia and a major factor in the porcine respiratory disease complex. A clear understanding of the mechanisms of pathogenesis does not exist, although it is clear that M. hyopneumoniae adheres to porcine ciliated epithelium by action of a protein called P97. Previous studies have shown variation in the gene encoding the P97 cilium adhesin in different strains of M. hyopneumoniae, but the extent of genetic variation among field strains across the genome is not known. Since M. hyopneumoniae is a worldwide problem, it is reasonable to expect that a wide range of genetic variability may exist given all of the different breeds and housing conditions. This variation may impact the overall virulence of a single strain. Using microarray technology, this study examined the potential variation of 14 field strains compared to strain 232, on which the array was based. Genomic DNA was obtained, amplified with TempliPhi, and labeled indirectly with Alexa dyes. After genomic hybridization, the arrays were scanned and data were analyzed using a linear statistical model. The results indicated that genetic variation could be detected in all 14 field strains but across different loci, suggesting that variation occurs throughout the genome. Fifty-nine percent of the variable loci were hypothetical genes. Twenty-two percent of the lipoprotein genes showed variation in at least one field strain. A permutation test identified a location in the M. hyopneumoniae genome where there is spatial clustering of variability between the field strains and strain 232. PMID:17873054

  13. Positive feedback fishery: Population consequences of `crab-tiling' on the green crab Carcinus maenas

    NASA Astrophysics Data System (ADS)

    Sheehan, E. V.; Thompson, R. C.; Coleman, R. A.; Attrill, M. J.

    2008-11-01

    Collection of marine invertebrates for use as fishing bait is a substantial activity in many parts of the world, often with unknown ecological consequences. As new fisheries develop, it is critical for environmental managers to have high quality ecological information regarding the potential impacts, in order to develop sound management strategies. Crab-tiling is a largely unregulated and un-researched fishery, which operates commercially in the south-west UK. The target species is the green crab Carcinus maenas. Those crabs which are pre-ecdysis and have a carapace width greater than 40 mm are collected to be sold to recreational anglers as bait. Collection involves laying artificial structures on intertidal sandflats and mudflats in estuaries. Crabs use these structures as refugia and are collected during low tide. However, the effect that this fishery has on populations of C. maenas is not known. The impact of crab-tiling on C. maenas population structure was determined by sampling crabs from tiled estuaries and non-tiled estuaries using baited drop-nets. A spatially and temporarily replicated, balanced design was used to compare crab abundance, sizes and sex ratios between estuaries. Typically, fisheries are associated with a reduction in the abundance of the target species. Crab-tiling, however, significantly increased C. maenas abundance. This was thought to be a result of the extra habitat in tiled estuaries, which probably provides protection from natural predators, such as birds and fish. Although crabs were more abundant in tiled estuaries than non-tiled estuaries, the overall percentage of reproductively active crabs in non-tiled estuaries was greater than in tiled estuaries. As with most exploited fisheries stocks, crabs in exploited (tiled) estuaries tended to be smaller, with a modal carapace width of 20-29 mm rather than 30-39 mm in non-tiled estuaries. The sex ratio of crabs however; was not significantly different between tiled and non-tiled

  14. Thermal Characterization of TPS Tiles

    SciTech Connect

    Kacmar, C. J.; LaCivita, K. J.; Jata, K. V.; Sathish, S.

    2006-03-06

    The Thermal Protection System (TPS) used on space shuttles protects the metallic structure from the large amounts of heat created during travel through the atmosphere, both on takeoff and reentry. The shuttle experiences high thermo-acoustic loading and impact damage from micro-meteorites, which can cause disbonds, delaminations, chips, cracks, and other defects to the TPS system. To enhance durability and damage tolerance, new TPS tiles with an added protective ceramic-matrix-composite layer are being developed. This paper explores the use of pulsed thermography as a quick, diverse, non-destructive technique, to characterize the TPS system. The pulsed thermography images obtained are presented and analyzed.

  15. Liquid scintillator tiles for calorimetry

    NASA Astrophysics Data System (ADS)

    Amouzegar, M.; Belloni, A.; Bilki, B.; Calderon, J.; De Barbaro, P.; Eno, S. C.; Hatakeyama, K.; Hirschauer, J.; Jeng, G. Y.; Pastika, N. J.; Pedro, K.; Rumerio, Paolo; Samuel, J.; Sharp, E.; Shin, Y. H.; Tiras, E.; Vishnevskiy, D.; Wetzel, J.; Yang, Z.; Yao, Y.; Youn, S. W.

    2016-11-01

    Future experiments in high energy and nuclear physics may require large, inexpensive calorimeters that can continue to operate after receiving doses of 50 Mrad or more. The light output of liquid scintillators suffers little degradation under irradiation. However, many challenges exist before liquids can be used in sampling calorimetry, especially regarding developing a packaging that has sufficient efficiency and uniformity of light collection, as well as suitable mechanical properties. We present the results of a study of a scintillator tile based on the EJ-309 liquid scintillator using cosmic rays and test beam on the light collection efficiency and uniformity, and some preliminary results on radiation hardness.

  16. Liquid scintillator tiles for calorimetry

    SciTech Connect

    Amouzegar, M.; Belloni, A.; Bilki, B.; Calderon, J.; Barbaro, P. De; Eno, S. C.; Hatakeyama, K.; Hirschauer, J.; Jeng, G. Y.; Pastika, N. J.; Pedro, K.; Rumerio, Paolo; Samuel, J.; Sharp, E.; Shin, Y. H.; Tiras, E.; Vishnevskiy, D.; Wetzel, J.; Yang, Z.; Yao, Y.; Youn, S. W.

    2016-11-28

    Future experiments in high energy and nuclear physics may require large, inexpensive calorimeters that can continue to operate after receiving doses of 50 Mrad or more. Also, the light output of liquid scintillators suffers little degradation under irradiation. However, many challenges exist before liquids can be used in sampling calorimetry, especially regarding developing a packaging that has sufficient efficiency and uniformity of light collection, as well as suitable mechanical properties. We present the results of a study of a scintillator tile based on the EJ-309 liquid scintillator using cosmic rays and test beam on the light collection efficiency and uniformity, and some preliminary results on radiation hardness.

  17. [Attention deficit hyperactivity disorder analyzed with array comparative genome hybridization method. Case report].

    PubMed

    Duga, Balázs; Czakó, Márta; Komlósi, Katalin; Hadzsiev, Kinga; Sümegi, Katalin; Kisfali, Péter; Melegh, Márton; Melegh, Béla

    2014-10-05

    One of the most common psychiatric disorders during childhood is attention deficit hyperactivity disorder, which affects 5-6% of children worldwide. Symptoms include attention deficit, hyperactivity, forgetfulness and weak impulse control. The exact mechanism behind the development of the disease is unknown. However, current data suggest that a strong genetic background is responsible, which explains the frequent occurrence within a family. Literature data show that copy number variations are very common in patients with attention deficit hyperactivity disorder. The authors present a patient with attention deficit hyperactivity disorder who proved to have two approximately 400 kb heterozygous microduplications at 6p25.2 and 15q13.3 chromosomal regions detected by comparative genomic hybridization methods. Both duplications affect genes (6p25.2: SLC22A23; 15q13.3: CHRNA7) which may play a role in the development of attention deficit hyperactivity disorder. This case serves as an example of the wide spectrum of indication of the array comparative genome hybridization method.

  18. Allelic genome structural variations in maize detected by array comparative genome hybridization.

    PubMed

    Beló, André; Beatty, Mary K; Hondred, David; Fengler, Kevin A; Li, Bailin; Rafalski, Antoni

    2010-01-01

    DNA polymorphisms such as insertion/deletions and duplications affecting genome segments larger than 1 kb are known as copy-number variations (CNVs) or structural variations (SVs). They have been recently studied in animals and humans by using array-comparative genome hybridization (aCGH), and have been associated with several human diseases. Their presence and phenotypic effects in plants have not been investigated on a genomic scale, although individual structural variations affecting traits have been described. We used aCGH to investigate the presence of CNVs in maize by comparing the genome of 13 maize inbred lines to B73. Analysis of hybridization signal ratios of 60,472 60-mer oligonucleotide probes between inbreds in relation to their location in the reference genome (B73) allowed us to identify clusters of probes that deviated from the ratio expected for equal copy-numbers. We found CNVs distributed along the maize genome in all chromosome arms. They occur with appreciable frequency in different germplasm subgroups, suggesting ancient origin. Validation of several CNV regions showed both insertion/deletions and copy-number differences. The nature of CNVs detected suggests CNVs might have a considerable impact on plant phenotypes, including disease response and heterosis.

  19. 2D capacitive micromachined ultrasound transducer using novel tiling based on silicon frame

    NASA Astrophysics Data System (ADS)

    Kim, Youngil; Cho, Kyungil; Kim, Baehyung; Lee, Seungheun; Jeon, Taeho; Song, Jongkeun

    2013-03-01

    In this study, we showed the new transducer and probe integration of 2D ultrasound probe using cMUT. cMUT ultrasound probe having 8192 elements is assembled with tiling frame. Flip chip bonded cMUT-ASIC tiles were arrayed along 2×8 directions to enlarge lateral aperture. Tiling gap between two tiles was under 100μm. RTV layer that has 1mm thick is used in 2-D probe system as a lens and protection layer. Thermal module is also analyzed by using the thermal network analysis, which is realized with the air fans and the fins. Designed PCB circuit for tiling module which is considered with cooling spread concept is 5cm × 5cm dimension. Uniformity and performance of tiled ultrasound transducer were tested under soybean oil at 3MHz frequency successfully. The measured 256 elements distribution has only 4.45% deviation. If we can remove the side edge error, the deviation will be under 3%. The performance after RTV lensing showed 35% attenuation in Tx and 35~45% attenuation in Rx.

  20. Revealing Transcriptome Landscape of Mouse Spermatogonial Cells by Tiling Microarray

    PubMed Central

    Lee, Tin-Lap.; Rennert, Owen M.; Chan, Wai-Yee.

    2014-01-01

    Summary Spermatogenesis is a highly regulated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific events through tightly regulated gene expression programs. In the past decade the advent of microarray technologies has allowed functional genomic studies of male germ cell development, resulting in the identification of genes governing various processes. A major limitation with conventional gene expression microarray is that there is a bias from gene probe design. The gene probes for expression microarrays are usually represented by a small number probes located at the 3’ end of a transcirpt. Tiling microarrays eliminate such issue by interrogating the genome in an unbiased fashion through probes tiled for the entire genome. These arrays provide a higher genomic resolution and allow identification of novel transcripts. To reveal the complexity of the genomic landscape of developing male germ cells, we applied tiling microarray to evaluate the transcriptome in spermatogonial cells. Over 50% of the mouse and rat genome are expressed during testicular development. More than 47% of transcripts are uncharacterized. The results suggested the transcription machinery in spermaotogonial cells are more complex than previously envisioned. PMID:22144238

  1. Effects of thermal blooming on systems comprised of tiled subapertures

    NASA Astrophysics Data System (ADS)

    Leakeas, Charles L.; Bartell, Richard J.; Krizo, Matthew J.; Fiorino, Steven T.; Cusumano, Salvatore J.; Whiteley, Matthew R.

    2010-04-01

    Laser weapon systems comprise of tiled subapertures are rapidly emerging in the directed energy community. The Air Force Institute of Technology Center for Directed Energy (AFIT/CDE), under sponsorship of the HEL Joint Technology Office has developed performance models of such laser weapon system configurations consisting of tiled arrays of both slab and fiber subapertures. These performance models are based on results of detailed waveoptics analyses conducted using WaveTrain. Previous performance model versions developed in this effort represent system characteristics such as subaperture shape, aperture fill factor, subaperture intensity profile, subaperture placement in the primary aperture, subaperture mutual coherence (piston), subaperture differential jitter (tilt), and beam quality wave-front error associated with each subaperture. The current work is a prerequisite for the development of robust performance models for turbulence and thermal blooming effects for tiled systems. Emphasis is placed on low altitude tactical scenarios. The enhanced performance model developed will be added to AFIT/CDE's HELEEOS parametric one-on-one engagement level model via the Scaling for High Energy Laser and Relay Engagement (SHaRE) toolbox.

  2. A brief introduction to tiling microarrays: principles, concepts, and applications.

    PubMed

    Lemetre, Christophe; Zhang, Zhengdong D

    2013-01-01

    Technological achievements have always contributed to the advancement of biomedical research. It has never been more so than in recent times, when the development and application of innovative cutting-edge technologies have transformed biology into a data-rich quantitative science. This stunning revolution in biology primarily ensued from the emergence of microarrays over two decades ago. The completion of whole-genome sequencing projects and the advance in microarray manufacturing technologies enabled the development of tiling microarrays, which gave unprecedented genomic coverage. Since their first description, several types of application of tiling arrays have emerged, each aiming to tackle a different biological problem. Although numerous algorithms have already been developed to analyze microarray data, new method development is still needed not only for better performance but also for integration of available microarray data sets, which without doubt constitute one of the largest collections of biological data ever generated. In this chapter we first introduce the principles behind the emergence and the development of tiling microarrays, and then discuss with some examples how they are used to investigate different biological problems.

  3. Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization

    USDA-ARS?s Scientific Manuscript database

    This study was designed to evaluate the feasibility of using a targeted array-CGH strategy for prenatal diagnosis of genomic imbalances in a clinical setting of current pregnancies. Women undergoing prenatal diagnosis were counseled and offered array-CGH (BCM V4.0) in addition to routine chromosome ...

  4. Parametric Multi-Level Tiling of Imperfectly Nested Loops

    SciTech Connect

    Hartono, Albert; Baskaran, Muthu M.; Bastoul, Cedric; Cohen, Albert; Krishnamoorthy, Sriram; Norris, Boyana; Ramanujam, J.; Sadayappan, Ponnuswamy

    2009-05-18

    Tiling is a critical loop transformation for generating high-performance code on modern architectures. Efficient generation of multilevel tiled code is essential to exploit several levels of parallelism and/or to maximize data reuse in deep memory hierarchies. Tiled loops with parameterized tile sizes (not compile time constants) facilitate runtime feedback and dynamic optimizations used in iterative compilation and automatic tuning. The existing parametric multilevel tiling approach has focused on transformation for perfectly nested loops, where all assignment statements are contained inside the innermost loop of a loop nest. Previous solutions to tiling for imperfect loop nests are limited to the case where tile sizes are fixed. In this paper, we present an approach to parameterized multilevel tiling for imperfectly nested loops. Our tiling algorithm generates loops that iterate over full rectangular tiles that are amenable for potential compiler optimizations such as register tiling. Experimental results using a number of computational benchmarks demonstrate the effectiveness of our tiling approach.

  5. Programmable disorder in random DNA tilings

    NASA Astrophysics Data System (ADS)

    Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

    2016-11-01

    Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures.

  6. Programmable disorder in random DNA tilings

    NASA Astrophysics Data System (ADS)

    Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu

    2017-03-01

    Scaling up the complexity and diversity of synthetic molecular structures will require strategies that exploit the inherent stochasticity of molecular systems in a controlled fashion. Here we demonstrate a framework for programming random DNA tilings and show how to control the properties of global patterns through simple, local rules. We constructed three general forms of planar network—random loops, mazes and trees—on the surface of self-assembled DNA origami arrays on the micrometre scale with nanometre resolution. Using simple molecular building blocks and robust experimental conditions, we demonstrate control of a wide range of properties of the random networks, including the branching rules, the growth directions, the proximity between adjacent networks and the size distribution. Much as combinatorial approaches for generating random one-dimensional chains of polymers have been used to revolutionize chemical synthesis and the selection of functional nucleic acids, our strategy extends these principles to random two-dimensional networks of molecules and creates new opportunities for fabricating more complex molecular devices that are organized by DNA nanostructures.

  7. An efficient analog Hamming distance comparator realized with a unipolar memristor array: a showcase of physical computing

    PubMed Central

    Ge, Ning; Yoon, Jung Ho; Hu, Miao; Merced-Grafals, E. J.; Davila, Noraica; Strachan, John Paul; Li, Zhiyong; Holder, Helen; Xia, Qiangfei; Williams, R. Stanley; Zhou, Xing; Yang, J. Joshua

    2017-01-01

    We propose and demonstrate a novel physical computing paradigm based on an engineered unipolar memristor that exhibits symmetric SET switching with respect to voltage polarity. A one-dimensional array of these devices was sufficient to demonstrate an efficient Hamming distance comparator for two strings of analog states represented by voltages from the physical world. The comparator first simultaneously applies the two sets of voltages to the array of memristors, each of which is initially in its high resistance state and switches to its low resistance state only if the two voltages applied on that memristor differ by more than the switching threshold. An accurate analog representation of the Hamming distance is then obtained by applying a reading voltage to the memristors and summing all the resultant currents. The comparator with a small footprint can directly process analog signals and store computation results without power, representing a promising application for analog computing based on memristor crossbar arrays. PMID:28054642

  8. An efficient analog Hamming distance comparator realized with a unipolar memristor array: a showcase of physical computing

    NASA Astrophysics Data System (ADS)

    Ge, Ning; Yoon, Jung Ho; Hu, Miao; Merced-Grafals, E. J.; Davila, Noraica; Strachan, John Paul; Li, Zhiyong; Holder, Helen; Xia, Qiangfei; Williams, R. Stanley; Zhou, Xing; Yang, J. Joshua

    2017-01-01

    We propose and demonstrate a novel physical computing paradigm based on an engineered unipolar memristor that exhibits symmetric SET switching with respect to voltage polarity. A one-dimensional array of these devices was sufficient to demonstrate an efficient Hamming distance comparator for two strings of analog states represented by voltages from the physical world. The comparator first simultaneously applies the two sets of voltages to the array of memristors, each of which is initially in its high resistance state and switches to its low resistance state only if the two voltages applied on that memristor differ by more than the switching threshold. An accurate analog representation of the Hamming distance is then obtained by applying a reading voltage to the memristors and summing all the resultant currents. The comparator with a small footprint can directly process analog signals and store computation results without power, representing a promising application for analog computing based on memristor crossbar arrays.

  9. On the Challenge of Keeping ATLAS Tile Calorimeter Raw Data

    NASA Astrophysics Data System (ADS)

    Tsiskaridze, V. K.

    2012-08-01

    The Tile Calorimeter (TileCal) for the ATLAS experiment at the CERN Large Hadron Collider (LHC) is currently taking data with proton-proton collisions. The TileCal read-out system was initially designed to reconstruct the data in real-time and to store for each channel the signal amplitude, time and quality factor at the required high rate. This approach implied discarding 80% of the raw data that correspond to noise or small signals. Practical experience operating in this scheme with increasing rate have led to several modifications and understanding that some kind of data compression is helpful during data processing and storing. An alternate approach is to use online reconstruction for Level 2 triggering only and to implement a data flow lossless compression scheme for further offiine analysis. A new version of the lossless compression algorithm is proposed which allows to both save the complete raw data and to feed the trigger with the reconstructed signal amplitude and time. It does not increase the data flow as compared to the existing approach and the size of the data fragments transmitted is more stable. We will describe the lossless compression algorithm as a possible upgrade of the Tile data acquisition and highlight some details of the implementation. We will report on its testing and validation and on the overall performance measured on high rate tests, calibration and √ {s} = 7 TeV proton-proton collisions runs.

  10. Wind-Resistant Filler for Tile Gaps

    NASA Technical Reports Server (NTRS)

    Bellavia, J.; Quigley, I. A.; Callahan, T. S.

    1982-01-01

    Filler developed for gaps between insulating tiles on Space Shuttle finds application in industries that use tiles for thermal or environmental protection. Filler consists of tight-fitting ceramic tubes and fibrous alumina. Combination resists high wind loads while providing requisite heat protection. Quartz-thread stitching holds envelope together.

  11. Bonding Heat-Resistant Fabric to Tile

    NASA Technical Reports Server (NTRS)

    Holt, J. W.; Smiser, L. W.

    1985-01-01

    Acid etching, densification, and silica cement ensure strong bond. Key step in preparation for bonding to glazed tile is etching quartz fabric and tile with acid. This increases adhesion of silica cement used to form bond. Procedures use high-temperature materials exclusively and therefore suitable for securing flexible seals and heat barriers around doors and viewing ports in furnaces and kilns.

  12. The Sad Case of the Columbine Tiles.

    ERIC Educational Resources Information Center

    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…

  13. The Sad Case of the Columbine Tiles.

    ERIC Educational Resources Information Center

    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…

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

    NASA Astrophysics Data System (ADS)

    Carrió, F.; Moreno, P.; Valero, A.

    2016-03-01

    The Tile Calorimeter PreProcessor 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 Demonstrator project for the Phase II Upgrade as the first stage of the back-end electronics. The TilePPr demonstrator has been conceived to receive and process the data coming from the front-end electronics of the TileCal Demonstrator module, as well as to configure it. Moreover, the TilePPr demonstrator handles the communication with the Detector Control System to monitor and control the front-end electronics. The TilePPr demonstrator represents 1/8 of the final TilePPr that will be designed and installed into the detector for the ATLAS Phase II Upgrade.

  15. Detection of ultra-high energy neutrino interactions in ice: comparing radio detector array designs

    NASA Astrophysics Data System (ADS)

    Bechtol, Keith; Vieregg, Abigail

    2014-08-01

    Ultra-high energy (UHE, >10^18 eV) cosmic neutrinos are anticipated to reveal the most distant, most obscured, and highest energy particle accelerators in the Universe. An almost guaranteed flux of UHE neutrinos is predicted from the interactions of UHE cosmic rays with the cosmic microwave background, and additional contributions may arise from prompt emission at individual sources. The spectrum of UHE neutrinos is a sensitive discriminator of the cosmological evolution of UHE sources, as well as the composition of UHE cosmic rays. At the same time, UHE neutrinos will enable several tests of fundamental physics, including constraints on the neutrino-nucleon interaction cross section at center-of-momentum energies ~100 TeV, and searches for Lorentz invariance violation.Theoretical predictions and subsequent laboratory measurements of coherent radio emission from showers initiated by neutrino interactions in dielectric media (e.g., ice, sand, salt, lunar regolith) have motivated diverse experimental approaches involving "detectors" comprised of up to millions of cubic kilometers of natural materials. I will discuss simulation results comparing the expected performance of several proposed radio detector array designs with subterranean, ice shelf, and above ice configurations.

  16. Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors.

    PubMed

    Voortman, Johannes; Lee, Jih-Hsiang; Killian, Jonathan Keith; Suuriniemi, Miia; Wang, Yonghong; Lucchi, Marco; Smith, William I; Meltzer, Paul; Wang, Yisong; Giaccone, Giuseppe

    2010-07-20

    The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on array comparative genomic hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal carcinoids. In contrast to the relatively conserved karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. In SCLC tumors, as well as bronchial carcinoids and carcinoids of gastrointestinal origin, recurrent CN alterations were observed in 203 genes, including the RB1 gene and 59 microRNAs of which 51 locate in the DLK1-DIO3 domain. These findings suggest the existence of partially shared CN alterations in these tumor types. In contrast, CN alterations of the TP53 gene and the MYC family members were predominantly observed in SCLC. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resembles that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics-based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC.

  17. Statistical methods for detecting genomic alterations through array-based comparative genomic hybridization (CGH).

    PubMed

    Wang, Yuedong; Guo, Sun-Wei

    2004-01-01

    Array-based comparative genomic hybridization (ABCGH) is an emerging high-resolution and high-throughput molecular genetic technique that allows genome-wide screening for chromosome alterations associated with tumorigenesis. Like the cDNA microarrays, ABCGH uses two differentially labeled test and reference DNAs which are cohybridized to cloned genomic fragments immobilized on glass slides. The hybridized DNAs are then detected in two different fluorochromes, and the significant deviation from unity in the ratios of the digitized intensity values is indicative of copy-number differences between the test and reference genomes. Proper statistical analyses need to account for many sources of variation besides genuine differences between the two genomes. In particular, spatial correlations, the variable nature of the ratio variance and non-Normal distribution call for careful statistical modeling. We propose two new statistics, the standard t-statistic and its modification with variances smoothed along the genome, and two tests for each statistic, the standard t-test and a test based on the hybrid adaptive spline (HAS). Simulations indicate that the smoothed t-statistic always improves the performance over the standard t-statistic. The t-tests are more powerful in detecting isolated alterations while those based on HAS are more powerful in detecting a cluster of alterations. We apply the proposed methods to the identification of genomic alterations in endometrium in women with endometriosis.

  18. New Tools for Embryo Selection: Comprehensive Chromosome Screening by Array Comparative Genomic Hybridization

    PubMed Central

    Cobo, Ana Cristina; Milán, Miguel; Al-Asmar, Nasser; García-Herrero, Sandra; Mir, Pere; Simón, Carlos

    2014-01-01

    The objective of this study was to evaluate the usefulness of comprehensive chromosome screening (CCS) using array comparative genomic hybridization (aCGH). The study included 1420 CCS cycles for recurrent miscarriage (n = 203); repetitive implantation failure (n = 188); severe male factor (n = 116); previous trisomic pregnancy (n = 33); and advanced maternal age (n = 880). CCS was performed in cycles with fresh oocytes and embryos (n = 774); mixed cycles with fresh and vitrified oocytes (n = 320); mixed cycles with fresh and vitrified day-2 embryos (n = 235); and mixed cycles with fresh and vitrified day-3 embryos (n = 91). Day-3 embryo biopsy was performed and analyzed by aCGH followed by day-5 embryo transfer. Consistent implantation (range: 40.5–54.2%) and pregnancy rates per transfer (range: 46.0–62.9%) were obtained for all the indications and independently of the origin of the oocytes or embryos. However, a lower delivery rate per cycle was achieved in women aged over 40 years (18.1%) due to the higher percentage of aneuploid embryos (85.3%) and lower number of cycles with at least one euploid embryo available per transfer (40.3%). We concluded that aneuploidy is one of the major factors which affect embryo implantation. PMID:24877108

  19. Clinical validity of karyotyping for the diagnosis of chromosomal imbalance following array comparative genomic hybridisation.

    PubMed

    Gekas, Jean; Vallée, Maud; Castonguay, Lysanne; Laframboise, Rachel; Maranda, Bruno; Piedboeuf, Bruno; Rousseau, François

    2011-12-01

    Array comparative genomic hybridisation (aCGH) represents a major advance in the ability to detect chromosomal imbalances (CI). A recent meta-analysis recommended aCGH for replacing karyotyping for patients with unexplained disabilities. However, favouring aCGH over karyotyping must be based on solid evidence due to the major implications of selecting a preferential diagnostic tool. A prospective study of 376 samples was conducted to assess the relevance of karyotyping after a first-tier aCGH in patients with unexplained disabilities. aCGH detected CI in 28.7% of the cases. Out of 376 patients, 288 had undergone parallel karyotyping testing: 69.8% (201/288) showed similar results for both aCGH and karyotyping. For patients with a CI detected by aCGH, 7.9% (7/89) showed similar results for both aCGH and karyotyping. Among 20 patients with abnormal karyotyping, 13 showed dissimilar results compared to aCGH analysis: 4 patients (1.4%) had balanced rearrangements and 9 patients (3.1%) had additional chromosomal anomalies unseen using aCGH. This rate of unseen chromosomal anomalies is far superior to the previously estimated 0.5-0.78% prevalence and affects 10.1% (9/89) of patients with CI detected by aCGH in the tested population. Since the clinical significance of CI identified by aCGH might be influenced by such discrepancies between the two methods, these may in turn have an impact on clinical diagnosis and patient counselling. It is proposed that each genetic laboratory should evaluate the relevance of karyotyping for all first-tier abnormal aCGH results in order to include the genomic (chromosomal) aspects of the aCGH findings in the diagnosis.

  20. Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization.

    PubMed

    Repnikova, Elena A; Rosenfeld, Jill A; Bailes, Andrea; Weber, Cecilia; Erdman, Linda; McKinney, Aimee; Ramsey, Sarah; Hashimoto, Sayaka; Lamb Thrush, Devon; Astbury, Caroline; Reshmi, Shalini C; Shaffer, Lisa G; Gastier-Foster, Julie M; Pyatt, Robert E

    2013-09-01

    Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci.

  1. Array comparative genomic hybridization and cytogenetic analysis in pediatric acute leukemias.

    PubMed

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

    2011-10-01

    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 complementary use of microarray

  2. Geant4 simulation of optical photon transport in scintillator tile with direct readout by silicon photomultiplier

    NASA Astrophysics Data System (ADS)

    Korpachev, S.; Chadeeva, M.

    2017-01-01

    The direct coupling of silicon photomultiplier to the scintillator tile is considered to be the main option for active elements of the highly granular hadron calorimeter developed for future linear collider experiments. In this study, the response of the scintillator-SiPM system to minimum ionising particles was simulated using the optical photon transport functionality available in the Geant4 package. The uniformity of response for both flat tile and tile with dimple was estimated from the simulations and compared to the experimental results obtained in the previous studies.

  3. BICEP3 performance overview and planned Keck Array upgrade

    NASA Astrophysics Data System (ADS)

    Grayson, J. A.; Ade, P. A. R.; Ahmed, Z.; Alexander, K. D.; Amiri, M.; Barkats, D.; Benton, S. J.; Bischoff, C. A.; Bock, J. J.; Boenish, H.; Bowens-Rubin, R.; Buder, I.; Bullock, E.; Buza, V.; Connors, J.; Filippini, J. P.; Fliescher, S.; Halpern, M.; Harrison, S.; Hilton, G. C.; Hristov, V. V.; Hui, H.; Irwin, K. D.; Kang, J.; Karkare, K. S.; Karpel, E.; Kefeli, S.; Kernasovskiy, S. A.; Kovac, J. M.; Kuo, C. L.; Leitch, E. M.; Lueker, M.; Megerian, K. G.; Monticue, V.; Namikawa, T.; Netterfield, C. B.; Nguyen, H. T.; O'Brient, R.; Ogburn, R. W.; Pryke, C.; Reintsema, C. D.; Richter, S.; Schwarz, R.; Sorenson, C.; Sheehy, C. D.; Staniszewski, Z. K.; Steinbach, B.; Teply, G. P.; Thompson, K. L.; Tolan, J. E.; Tucker, C.; Turner, A. D.; Vieregg, A. G.; Wandui, A.; Weber, A. C.; Wiebe, D. V.; Willmert, J.; Wu, W. L. K.; Yoon, K. W.

    2016-07-01

    Bicep3 is a 520mm aperture, compact two-lens refractor designed to observe the polarization of the cosmic microwave background (CMB) at 95 GHz. Its focal plane consists of modularized tiles of antenna-coupled transition edge sensors (TESs), similar to those used in Bicep2 and the Keck Array. The increased per-receiver optical throughput compared to Bicep2/Keck Array, due to both its faster f=1:7 optics and the larger aperture, more than doubles the combined mapping speed of the Bicep/Keck program. The Bicep3 receiver was recently upgraded to a full complement of 20 tiles of detectors (2560 TESs) and is now beginning its second year of observation (and first science season) at the South Pole. We report on its current performance and observing plans. Given its high per-receiver throughput while maintaining the advantages of a compact design, Bicep3- class receivers are ideally suited as building blocks for a 3rd-generation CMB experiment, consisting of multiple receivers spanning 35 GHz to 270 GHz with total detector count in the tens of thousands. We present plans for such an array, the new "BICEP Array" that will replace the Keck Array at the South Pole, including design optimization, frequency coverage, and deployment/observing strategies.

  4. High-Resolution Array Comparative Genomic Hybridization Utility in Polish Newborns with Isolated Cleft Lip and Palate.

    PubMed

    Szczałuba, Krzysztof; Nowakowska, Beata A; Sobecka, Katarzyna; Smyk, Marta; Castaneda, Jennifer; Dudkiewicz, Zofia; Kutkowska-Kaźmierczak, Anna; Sąsiadek, Maria M; Śmigiel, Robert; Bocian, Ewa

    2015-01-01

    Cleft lip with or without cleft palate is one of the most common birth defects of unknown etiology. A fraction of its genetic causes is attributable to copy number variations detected by array comparative genomic hybridization. The value of array comparative genomic hybridization screening as a first-tier test in the newborn population with multiple congenital anomalies has now been accepted. Due to unspecific clinical picture at this age, it can also be applied to neonates with isolated anomalies. Our purpose was to assess utility of array comparative genomic hybridization in the population of newborns with isolated cleft lip and palate. We conducted the study in a group of 52 Polish newborns with apparently isolated cleft lip and palate. In the study group, we found 8 rearrangements. Of these, 2 de novo events have been noted that potentially explain the phenotype. In addition, 2 novel candidate genes for cleft lip and palate, CHN2 and CDH19, are suggested. Given the high number of inherited potentially benign changes, we question the clinical utility of array comparative genomic hybridization in the newborn population with isolated cleft lip and palate, at the same time pointing to the need of skilled professional's clinical assessment at a later age. However, the value of this technology in searching for the cause of isolated anomalies cannot be underestimated. © 2015 S. Karger AG, Basel.

  5. Liquid scintillator tiles for calorimetry

    DOE PAGES

    Amouzegar, M.; Belloni, A.; Bilki, B.; ...

    2016-11-28

    Future experiments in high energy and nuclear physics may require large, inexpensive calorimeters that can continue to operate after receiving doses of 50 Mrad or more. Also, the light output of liquid scintillators suffers little degradation under irradiation. However, many challenges exist before liquids can be used in sampling calorimetry, especially regarding developing a packaging that has sufficient efficiency and uniformity of light collection, as well as suitable mechanical properties. We present the results of a study of a scintillator tile based on the EJ-309 liquid scintillator using cosmic rays and test beam on the light collection efficiency and uniformity,more » and some preliminary results on radiation hardness.« less

  6. Damage to JET beryllium tiles

    NASA Astrophysics Data System (ADS)

    Deksnis, E.; Cheetham, A.; Hwang, A.; Lomas, P.; Pick, M.; Summers, D. D. R.

    1990-12-01

    JET has operated with beryllium limiters such that up to 180 MJ could be coupled to the plasma. Approximately 2-4% of the surface of the limiter has been melted near the plasma contact point. Another 10-15% of the surface shows evidence of edge heating. Some 5% of tiles have been subjected to abnormal loads at points distant from the contact area. Damage shows strong correlation of localised heating of the limiter with toroidal field ripple. Edge heating rates of 260 Mw/m 2 have not caused gross mechanical failure of the limiter. The mechanical damage comprises fatigue cracks analogous to those due to sustained loading at low power levels.

  7. Diminished effect of maternal age on implantation after preimplantation genetic diagnosis with array comparative genomic hybridization.

    PubMed

    Harton, Gary L; Munné, Santiago; Surrey, Mark; Grifo, Jamie; Kaplan, Brian; McCulloh, David H; Griffin, Darren K; Wells, Dagan

    2013-12-01

    To assess the relationship between maternal age, chromosome abnormality, implantation, and pregnancy loss. Multicenter retrospective study. IVF centers in the United States. IVF patients undergoing chromosome screening. Embryo biopsy on day 3 or day 5/6 with preimplantation genetic diagnosis (PGD) by array comparative genomic hybridization. Aneuploidy, implantation, pregnancy, and loss rates. Aneuploidy rates increased with maternal age from 53% to 93% for day 3 biopsies and from 32% to 85% for blastocyst biopsies. Implantation rates for euploid embryos for ages <35-42 years did not decrease after PGD: ranges 44%-32% for day 3 and 51%-40% for blastocyst. Ongoing pregnancy rates per transfer did not decrease for maternal ages <42 years after PGD with day 3 biopsy (48.5%-38.1%) or blastocyst biopsy (64.4%-54.5%). Patients >42 years old had implantation rates of 23.3% (day 3), 27.7% (day 5/6), and the pregnancy rate with day 3 biopsy was 9.3% and with day 5 biopsy 10.3%. Selective transfer of euploid embryos showed that implantation and pregnancy rates were not significantly different between reproductively younger and older patients up to age 42 years. Some patients who start an IVF cycle planning to have chromosome screening do not have euploid embryos available for transfer, a situation that increases with advancing maternal age. Mounting data suggests that the dramatic decline in IVF treatment success rates with female age is primarily caused by aneuploidy. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  8. Application of array-comparative genomic hybridization in tetralogy of Fallot.

    PubMed

    Liu, Lin; Wang, Hong-Dan; Cui, Cun-Ying; Wu, Dong; Li, Tao; Fan, Tai-Bing; Peng, Bang-Tian; Zhang, Lian-Zhong; Wang, Cheng-Zeng

    2016-12-01

    To explore the underlying pathogenesis and provide references for genetic counseling and prenatal gene diagnosis, we analyzed the chromosome karyotypes and genome-wide copy number variations (CNVs) in 86 patients with tetralogy of Fallot (TOF) by G-banding karyotype analysis and array-comparative genomic hybridization (aCGH), respectively. And then quantitative polymerase chain reaction was used to validate these candidate CNVs. Based on their different properties, CNVs were categorized into benign CNVs, suspiciously pathogenic CNVs, and indefinite CNVs. Data analysis was based on public databases such as UCSC, DECIPHER, DGV, ISCA, and OMIM.The karyotype was normal in all the 86 patients with TOF. CNVs were detected in 11 patients by aCGH and quantitative polymerase chain reaction. Patient no. 0001, 0010, and 0029 had 2.52-Mb deletion in the chromosome 22q11.21 region; patient no. 0008 had both 595- and 428-kb duplications, respectively, in 12p12.3p12.2 and 14q23.2q23.3 regions; patient no. 0009 had 1.46-Mb duplication in the 1q21.1q21.2 region; patient no. 0016 had 513-kb duplication in the 1q42.13 region; patient no. 0024 had 292-kb duplication in the 16q11.2 region; patient no. 0026 had 270-kb duplication in the 16q24.1 region; patient no. 0028 had 222-kb deletion in the 7q31.1 region; patient no. 0033 had 1.73-Mb duplication in the 17q12 region; and patient no. 0061 had 5.79-Mb deletion in the 1p36.33p36.31 region.aCGH can accurately detect CNVs in the patients with TOF. This is conducive to genetic counseling and prenatal diagnosis for TOF and provides a new clue and theoretical basis for exploring the pathogenesis of congenital heart disease.

  9. Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties

    PubMed Central

    2010-01-01

    Background Trichoderma reesei is the main industrial producer of cellulases and hemicellulases that are used to depolymerize biomass in a variety of biotechnical applications. Many of the production strains currently in use have been generated by classical mutagenesis. In this study we characterized genomic alterations in high-producing mutants of T. reesei by high-resolution array comparative genomic hybridization (aCGH). Our aim was to obtain genome-wide information which could be utilized for better understanding of the mechanisms underlying efficient cellulase production, and would enable targeted genetic engineering for improved production of proteins in general. Results We carried out an aCGH analysis of four high-producing strains (QM9123, QM9414, NG14 and Rut-C30) using the natural isolate QM6a as a reference. In QM9123 and QM9414 we detected a total of 44 previously undocumented mutation sites including deletions, chromosomal translocation breakpoints and single nucleotide mutations. In NG14 and Rut-C30 we detected 126 mutations of which 17 were new mutations not documented previously. Among these new mutations are the first chromosomal translocation breakpoints identified in NG14 and Rut-C30. We studied the effects of two deletions identified in Rut-C30 (a deletion of 85 kb in the scaffold 15 and a deletion in a gene encoding a transcription factor) on cellulase production by constructing knock-out strains in the QM6a background. Neither the 85 kb deletion nor the deletion of the transcription factor affected cellulase production. Conclusions aCGH analysis identified dozens of mutations in each strain analyzed. The resolution was at the level of single nucleotide mutation. High-density aCGH is a powerful tool for genome-wide analysis of organisms with small genomes e.g. fungi, especially in studies where a large set of interesting strains is analyzed. PMID:20642838

  10. Microphthalmia with linear skin defects (MLS) syndrome evaluated by prenatal karyotyping, FISH and array comparative genomic hybridization.

    PubMed

    Cain, Colyn Cargile; Saul, Daniel; Attanasio, Lisa; Oehler, Erin; Hamosh, Ada; Blakemore, Karin; Stetten, Gail

    2007-04-01

    To explore the utility of comparative genomic hybridization to BAC arrays (array CGH) for prenatal diagnosis of microphthalmia and linear skin defects syndrome. We used karyotype analysis, FISH and array CGH to investigate an X;Y translocation. Replication studies were done on cultured amniocytes and lymphoblasts. We describe a severe case of MLS syndrome that presented prenatally with multiple anomalies including cystic hygroma, microphthalmia, intrauterine growth restriction and a complex congenital heart defect. Cytogenetic analysis of amniocytes revealed an unbalanced de novo translocation between chromosomes X and Y [karyotype 46,X,der(X)t(X;Y)(p22.3;q11.2).ish der(X)(DXZ1+,DMD+,KAL-,STS-,SRY-),22q11.2 (Tuple1 x 2)]. MLS diagnosis was made at birth and the prenatal karyotype was confirmed. Replication studies showed the derivative X chromosome was the inactive X. Array CGH confirmed the X and Y imbalances seen in the karyotype and also showed twelve BACs in the MLS region were deleted as a result of the translocation. FISH with BAC clones verified the array findings and placed the X breakpoint in Xp22.2, resulting in the amended karyotype, 46,X,der(X)t(X;Y)(p22.2;q11.2).ish der(X)(DXZ1+,DMD+,KAL-,STS-,SRY-),22q11.2(Tuple1 x 2) arr cgh Xp22.33p22.2(LLNOYCO3M15D10 -->GS1-590J6)x 1,Yq11.222q23(RP11-20H21-->RP11-79J10)x 1. The sensitivity of array CGH was valuable in detecting monosomy of the MLS critical region. Array CGH should be considered for the prenatal diagnosis of this syndrome. Copyright (c) 2007 John Wiley & Sons, Ltd.

  11. Comparative efficiency analysis of fiber-array and conventional beam director systems in volume turbulence.

    PubMed

    Vorontsov, Mikhail; Filimonov, Grigory; Ovchinnikov, Vladimir; Polnau, Ernst; Lachinova, Svetlana; Weyrauch, Thomas; Mangano, Joseph

    2016-05-20

    The performance of two prominent laser beam projection system types is analyzed through wave-optics numerical simulations for various atmospheric turbulence conditions, propagation distances, and adaptive optics (AO) mitigation techniques. Comparisons are made between different configurations of both a conventional beam director (BD) using a monolithic-optics-based Cassegrain telescope and a fiber-array BD that uses an array of densely packed fiber collimators. The BD systems considered have equal input power and aperture diameters. The projected laser beam power inside the Airy size disk at the target plane is used as the performance metric. For the fiber-array system, both incoherent and coherent beam combining regimes are considered. We also present preliminary results of side-by-side atmospheric beam projection experiments over a 7-km propagation path using both the AO-enhanced beam projection system with a Cassegrain telescope and the coherent fiber-array BD composed of 21 densely packed fiber collimators. Both wave-optics numerical simulation and experimental results demonstrate that, for similar system architectures and turbulence conditions, coherent fiber-array systems are more efficient in mitigation of atmospheric turbulence effects and generation of a hit spot of the smallest possible size on a remotely located target.

  12. Solar-energy treatment of ceramic tiles

    NASA Astrophysics Data System (ADS)

    Harris, J. N.; Clayton, M. E.

    1981-12-01

    The 400 kW Advanced Components Test Facility was used to provide a concentrated source of solar energy for firing ceramic wall tile. A domed top cylindrical cavity with a white refractory fiber lining provided diffuse reflection of the concentrated solar beam directly onto the upper surface of the unfired wall tile. The tile were placed directly on the cavity floor in a circular pattern, centered at 450 intervals so that eight tile could be fired at one time. The tile and cavity walls were instrumented with thermocouples, and pyrometric cones were used to determine temperature distribution within the cavity. The glazed and unglazed solar fired titles were tested for flatness, modulus of rupture, water absorption, porosity, bulk density, apparent specific gravity, percent linear thermal expansion and crystalline phases present in the fired bodies. The major problems encountered are: cracking by thermal shock, and uneven shrinkage and glaze maturity across individual tile. The cavity failed to provide even heating at all eight tile positions.

  13. Comparative Study on Synthesizing Reconfigurable Time- Modulated Linear Arrays using Differential Evolution, Artificial Bee Colony and Particle Swarm Optimization

    NASA Astrophysics Data System (ADS)

    Mandal, S. K.; Singh, Harshavardhan; Mahanti, G. K.; Ghatak, Rowdra

    2014-10-01

    This paper presents a new technique based on optimization tools to design phase only, digitally controlled, reconfigurable antenna arrays through time modulation. In the proposed approach, the on-time durations of the time-modulated elements and the static amplitudes of the array elements are perturbed in such a way that the same on-time sequence and discrete values of static amplitudes for four bit digital attenuators produces either a pencil or a flat-top beam pattern, depending on the suitable discrete phase distributions of five bit digital phase shifters. In order to illustrate the technique, three optimization tools: differential evolution (DE), artificial bee colony (ABC), and particle swarm optimization (PSO) are employed and their performances are compared. The numerical results for a 20-element linear array are presented.

  14. Fibrous-Ceramic/Aerogel Composite Insulating Tiles

    NASA Technical Reports Server (NTRS)

    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

  15. Aerogel: Tile Composites Toughen a Brittle Superinsulation

    NASA Technical Reports Server (NTRS)

    White, Susan; Rasky, Daniel; Arnold, James O. (Technical Monitor)

    1998-01-01

    Pure aerogels, though familiar in the laboratory for decades as exotic lightweight insulators with unusual physical properties, have had limited industrial applications due to their low strength and high brittleness. Composites formed of aerogels and the ceramic fiber matrices like those used as space shuttle tiles bypass the fragility of pure aerogels and can enhance the performance of space shuttle tiles in their harsh operating environment. Using a layer of aerogel embedded in a tile may open up a wide range of applications where thermal insulation, gas convection control and mechanical strength matter.

  16. The TileCal Laser Calibration System

    NASA Astrophysics Data System (ADS)

    Giangiobbe, Vincent; ATLAS Tile Calorimeter Group

    TileCal is the central hadronic calorimeter of the ATLAS detector operating at LHC. It is a sampling calorimeter whose active material is made of scintillating plastic tiles. Scintillation light is read by photomultipliers. A Laser system is used to monitor their gain stability. During dedicated calibration runs the Laser system sends via long optical fibers, a monitored amount of light simultaneously to all the ≈10000 photomultipliers of TileCal. This note describes two complementary methods to measure the stability of the photomultipliers gain using the Laser calibration runs. The results of validation tests are presented for both methods and theirrespective performances and limitations are discussed.

  17. Remotely replaceable tokamak plasma limiter tiles

    DOEpatents

    Gallix, R.

    1987-12-09

    U-shaped tiles placed end-to-end over a pair of parallel runners have two rods which engage L-shaped slots. 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 wall. Resilient contact strips under the parallel sides of the U-shaped tile assure thermal and electrical contact with the wall. 6 figs.

  18. Triangulations (tilings) and certain block triangular matrices

    SciTech Connect

    Dantzig, G.B.; Hoffman, A.J.; Hu, T.C.

    1983-09-01

    The problem is to find a tiling (triangularization) of a convex n polytope (or combinatorially an n-gon) such that the partition uses the minimum number of tiles. We show that a certain linear program can be formulated whose optimal solution is always in integers and corresponds to a tiling. Moreover the system is in the form of a block-triangular Leontief-Substitution System that is readily solved by a O(n/sup 3/) algorithm consisting of a single forward and backward pass through data.

  19. The challenging scales of the bird: Shuttle tile structural integrity

    NASA Technical Reports Server (NTRS)

    Schneider, W. C.; Miller, G. J.

    1985-01-01

    The principal design issues, tests, and analyses required to solve the tile integrity problem on the space shuttle orbiters are addressed. Proof testing of installed tiles is discussed along with an airflow test of special tiles. Orbiter windshield tiles are considered in terms of changes necessary to ensure acceptable margins of safety for flight.

  20. Measuring phased-array antenna beampatterns with high dynamic range for the Murchison Widefield Array using 137 MHz ORBCOMM satellites

    NASA Astrophysics Data System (ADS)

    Neben, A. R.; Bradley, R. F.; Hewitt, J. N.; Bernardi, G.; Bowman, J. D.; Briggs, F.; Cappallo, R. J.; Deshpande, A. A.; Goeke, R.; Greenhill, L. J.; Hazelton, B. J.; Johnston-Hollitt, M.; Kaplan, D. L.; Lonsdale, C. J.; McWhirter, S. R.; Mitchell, D. A.; Morales, M. F.; Morgan, E.; Oberoi, D.; Ord, S. M.; Prabu, T.; Shankar, N. Udaya; Srivani, K. S.; Subrahmanyan, R.; Tingay, S. J.; Wayth, R. B.; Webster, R. L.; Williams, A.; Williams, C. L.

    2015-07-01

    Detection of the fluctuations in a 21 cm line emission from neutral hydrogen during the Epoch of Reionization in thousand hour integrations poses stringent requirements on calibration and image quality, both of which necessitate accurate primary beam models. The Murchison Widefield Array (MWA) uses phased-array antenna elements which maximize collecting area at the cost of complexity. To quantify their performance, we have developed a novel beam measurement system using the 137 MHz ORBCOMM satellite constellation and a reference dipole antenna. Using power ratio measurements, we measure the in situ beampattern of the MWA antenna tile relative to that of the reference antenna, canceling the variation of satellite flux or polarization with time. We employ angular averaging to mitigate multipath effects (ground scattering) and assess environmental systematics with a null experiment in which the MWA tile is replaced with a second-reference dipole. We achieve beam measurements over 30 dB dynamic range in beam sensitivity over a large field of view (65% of the visible sky), far wider and deeper than drift scans through astronomical sources allow. We verify an analytic model of the MWA tile at this frequency within a few percent statistical scatter within the full width at half maximum. Toward the edges of the main lobe and in the sidelobes, we measure tens of percent systematic deviations. We compare these errors with those expected from known beamforming errors.

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

    PubMed

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

    2015-03-01

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

  2. High-Strength, Low-Shrinkage Ceramic Tiles

    NASA Technical Reports Server (NTRS)

    Wheeler, W. H.; Creedon, J. F.

    1986-01-01

    Addition of refractory fibers and whiskers to insulating tiles composed primarily of fibrous silica, such as those used on the skin of Space Shuttle orbiter, greatly improves properties. New composition suitable for lightweight, thermally-stable mirror blanks and as furnace and kiln insulation. Improved tiles made with current tile-fabrication processes. For given density, tiles containing silicon carbide and boron additives stronger in flexure than tiles made from silica alone. In addition, tiles with additives nearly immune to heat distortion, whereas pure-silica tiles shrink and become severely distorted.

  3. Hetero-oligonucleotide Nanoscale Tiles Capable of Two-Dimensional Lattice Formation as Testbeds for a Rapid, Affordable Purification Methodology

    DTIC Science & Technology

    2013-01-01

    SUBJECT TERMS DNA nanotechnology, purification, origami , 2d arrays Philip S. Lukeman St. John’s University, New York 8000 Utopia Parkway Queens, NY... origami ; DNA double-crossover (“DX”) tile based arrays5 have been constructed using PNA6 and LNA7 oligonucleotides. RNA/ DNA duplexes have been used8 for...the assembly of multiply armed tiles9 and as a template10 to fold DNA origami ;11 all-RNA systems known as ‘tecto-RNA’ have been used to generate a wide

  4. Analysis of Molecular Cytogenetic Alteration in Rhabdomyosarcoma by Array Comparative Genomic Hybridization

    PubMed Central

    Liu, Chunxia; Li, Dongliang; Jiang, Jinfang; Hu, Jianming; Zhang, Wei; Chen, Yunzhao; Cui, Xiaobin; Qi, Yan; Zou, Hong; Zhang, WenJie; Li, Feng

    2014-01-01

    Rhabdomyosarcoma (RMS) is the most common pediatric soft tissue sarcoma with poor prognosis. The genetic etiology of RMS remains largely unclear underlying its development and progression. To reveal novel genes more precisely and new therapeutic targets associated with RMS, we used high-resolution array comparative genomic hybridization (aCGH) to explore tumor-associated copy number variations (CNVs) and genes in RMS. We confirmed several important genes by quantitative real-time polymerase chain reaction (QRT-PCR). We then performed bioinformatics-based functional enrichment analysis for genes located in the genomic regions with CNVs. In addition, we identified miRNAs located in the corresponding amplification and deletion regions and performed miRNA functional enrichment analysis. aCGH analyses revealed that all RMS showed specific gains and losses. The amplification regions were 12q13.12, 12q13.3, and 12q13.3–q14.1. The deletion regions were 1p21.1, 2q14.1, 5q13.2, 9p12, and 9q12. The recurrent regions with gains were 12q13.3, 12q13.3–q14.1, 12q14.1, and 17q25.1. The recurrent regions with losses were 9p12–p11.2, 10q11.21–q11.22, 14q32.33, 16p11.2, and 22q11.1. The mean mRNA level of GLI1 in RMS was 6.61-fold higher than that in controls (p = 0.0477) by QRT-PCR. Meanwhile, the mean mRNA level of GEFT in RMS samples was 3.92-fold higher than that in controls (p = 0.0354). Bioinformatic analysis showed that genes were enriched in functions such as immunoglobulin domain, induction of apoptosis, and defensin. Proto-oncogene functions were involved in alveolar RMS. miRNAs that located in the amplified regions in RMS tend to be enriched in oncogenic activity (miR-24 and miR-27a). In conclusion, this study identified a number of CNVs in RMS and functional analyses showed enrichment for genes and miRNAs located in these CNVs regions. These findings may potentially help the identification of novel biomarkers and/or drug targets implicated in diagnosis of

  5. Application of array-comparative genomic hybridization in tetralogy of Fallot

    PubMed Central

    Liu, Lin; Wang, Hong-Dan; Cui, Cun-Ying; Wu, Dong; Li, Tao; Fan, Tai-Bing; Peng, Bang-Tian; Zhang, Lian-Zhong; Wang, Cheng-Zeng

    2016-01-01

    Abstract To explore the underlying pathogenesis and provide references for genetic counseling and prenatal gene diagnosis, we analyzed the chromosome karyotypes and genome-wide copy number variations (CNVs) in 86 patients with tetralogy of Fallot (TOF) by G-banding karyotype analysis and array-comparative genomic hybridization (aCGH), respectively. And then quantitative polymerase chain reaction was used to validate these candidate CNVs. Based on their different properties, CNVs were categorized into benign CNVs, suspiciously pathogenic CNVs, and indefinite CNVs. Data analysis was based on public databases such as UCSC, DECIPHER, DGV, ISCA, and OMIM. The karyotype was normal in all the 86 patients with TOF. CNVs were detected in 11 patients by aCGH and quantitative polymerase chain reaction. Patient no. 0001, 0010, and 0029 had 2.52-Mb deletion in the chromosome 22q11.21 region; patient no. 0008 had both 595- and 428-kb duplications, respectively, in 12p12.3p12.2 and 14q23.2q23.3 regions; patient no. 0009 had 1.46-Mb duplication in the 1q21.1q21.2 region; patient no. 0016 had 513-kb duplication in the 1q42.13 region; patient no. 0024 had 292-kb duplication in the 16q11.2 region; patient no. 0026 had 270-kb duplication in the 16q24.1 region; patient no. 0028 had 222-kb deletion in the 7q31.1 region; patient no. 0033 had 1.73-Mb duplication in the 17q12 region; and patient no. 0061 had 5.79-Mb deletion in the 1p36.33p36.31 region. aCGH can accurately detect CNVs in the patients with TOF. This is conducive to genetic counseling and prenatal diagnosis for TOF and provides a new clue and theoretical basis for exploring the pathogenesis of congenital heart disease. PMID:27930557

  6. Comparative evaluation of different DNA extraction methods for HPV genotyping by linear array and INNO-LiPA.

    PubMed

    Donà, Maria Gabriella; Benevolo, Maria; Pimpinelli, Fulvia; Battista, Mara; Rollo, Francesca; Stivali, Francesca; Moscarelli, Antonella; Giuliani, Massimo; Di Carlo, Aldo; Vocaturo, Amina

    2011-06-01

    In order to investigate the influence of DNA extraction on two PCR-based HPV genotyping tests (Linear Array, Roche and INNO-LiPA Extra, Innogenetics), three different procedures were used to purify DNA from 28 cervico-vaginal samples tested previously by the Hybrid Capture 2: the AmpliLute Liquid Media Extraction kit (Roche), the QIAamp DNA Blood mini kit (QIAGEN), and the NucliSENS EasyMAG automated platform (bioMérieux). All HC2-positive samples were found positive by both assays, independently of the extract used. Type-specific concordance (i.e., identical HPV type-specific profile in all the extracts of the same sample) was observed in 55% and 75% of the cases testing samples by the Linear Array and the INNO-LiPA, respectively. Using the DNA extracted with the two manual methods the results were concordant in 75% of the cases both for the Linear Array and the INNO-LiPA. When comparing the Linear Array results obtained on either of the two manual extracts with those obtained following automated extraction, 65% of the samples showed type-specific concordance in both cases. The INNO-LiPA results were concordant in 80% of the cases comparing the AmpliLute versus the automated extract, while concordant results were observed in 90% of the cases when comparing the QIAGEN versus the automated extract. In conclusion, the Linear Array and INNO-LiPA results are affected by the method of DNA extraction. Consequently, different HPV type-specific profiles may be observed using different extracts of the same sample. The use of consistent protocols for DNA purification is a priority to guarantee intra-assay reproducibility over time.

  7. Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile

    PubMed Central

    2010-01-01

    Background Clostridium difficile is a Gram-positive, anaerobic, spore-forming bacterium that is responsible for C. difficile associated disease in humans and is currently the most common cause of nosocomial diarrhoea in the western world. This current status has been linked to the emergence of a highly virulent PCR-ribotype 027 strain. The aim of this work was to identify regions of sequence divergence that may be used as genetic markers of hypervirulent PCR-ribotype 027 strains and markers of the sequenced strain, CD630 by array comparative hybridisation. Results In this study, we examined 94 clinical strains of the most common PCR-ribotypes isolated in mainland Europe and the UK by array comparative genomic hybridisation. Our array was comprehensive with 40,097 oligonucleotides covering the C. difficile 630 genome and revealed a core genome for all the strains of 32%. The array also covered genes unique to two PCR-ribotype 027 strains, relative to C. difficile 630 which were represented by 681 probes. All of these genes were also found in the commonly occuring PCR-ribotypes 001 and 106, and the emerging hypervirulent PCR-ribotype 078 strains, indicating that these are markers for all highly virulent strains. Conclusions We have fulfilled the aims of this study by identifying markers for CD630 and markers associated with hypervirulence, albeit genes that are not just indicative of PCR-ribotype 027 strains. We have also extended this study and have defined a more stringent core gene set compared to those previously published due to the comprehensive array coverage. Further to this we have defined a list of genes absent from non-toxinogenic strains and defined the nature of the specific toxin deletion in the strain CD37. PMID:20565959

  8. Increasing live birth rate by preimplantation genetic screening of pooled polar bodies using array comparative genomic hybridization.

    PubMed

    Feichtinger, Michael; Stopp, Tina; Göbl, Christian; Feichtinger, Elisabeth; Vaccari, Enrico; Mädel, Ulrike; Laccone, Franco; Stroh-Weigert, Monika; Hengstschläger, Markus; Feichtinger, Wilfried; Neesen, Jürgen

    2015-01-01

    Meiotic errors during oocyte maturation are considered the major contributors to embryonic aneuploidy and failures in human IVF treatment. Various technologies have been developed to screen polar bodies, blastomeres and trophectoderm cells for chromosomal aberrations. Array-CGH analysis using bacterial artificial chromosome (BAC) arrays is widely applied for preimplantation genetic diagnosis (PGD) using single cells. Recently, an increase in the pregnancy rate has been demonstrated using array-CGH to evaluate trophectoderm cells. However, in some countries, the analysis of embryonic cells is restricted by law. Therefore, we used BAC array-CGH to assess the impact of polar body analysis on the live birth rate. A disadvantage of polar body aneuploidy screening is the necessity of the analysis of both the first and second polar bodies, resulting in increases in costs for the patient and complex data interpretation. Aneuploidy screening results may sometimes be ambiguous if the first and second polar bodies show reciprocal chromosomal aberrations. To overcome this disadvantage, we tested a strategy involving the pooling of DNA from both polar bodies before DNA amplification. We retrospectively studied 351 patients, of whom 111 underwent polar body array-CGH before embryo transfer. In the group receiving pooled polar body array-CGH (aCGH) analysis, 110 embryos were transferred, and 29 babies were born, corresponding to live birth rates of 26.4% per embryo and 35.7% per patient. In contrast, in the control group, the IVF treatment was performed without preimplantation genetic screening (PGS). For this group, 403 embryos were transferred, and 60 babies were born, resulting in live birth rates of 14.9% per embryo and 22.7% per patient. In conclusion, our data show that in the aCGH group, the use of aneuploidy screening resulted in a significantly higher live birth rate compared with the control group, supporting the benefit of PGS for IVF couples in addition to the

  9. A comprehensive survey of brane tilings

    NASA Astrophysics Data System (ADS)

    Franco, Sebastián; He, Yang-Hui; Sun, Chuang; Xiao, Yan

    2017-08-01

    An infinite class of 4d 𝒩 = 1 gauge theories can be engineered on the worldvolume of D3-branes probing toric Calabi-Yau 3-folds. This kind of setup has multiple applications, ranging from the gauge/gravity correspondence to local model building in string phenomenology. Brane tilings fully encode the gauge theories on the D3-branes and have substantially simplified their connection to the probed geometries. The purpose of this paper is to push the boundaries of computation and to produce as comprehensive a database of brane tilings as possible. We develop efficient implementations of brane tiling tools particularly suited for this search. We present the first complete classification of toric Calabi-Yau 3-folds with toric diagrams up to area 8 and the corresponding brane tilings. This classification is of interest to both physicists and mathematicians alike.

  10. Notch sensitivity of space shuttle tile materials

    NASA Technical Reports Server (NTRS)

    Newman, J. C., Jr.

    1980-01-01

    Tests were conducted at room temperature to determine the notch sensitivity of the thermal protection tile for the space shuttle. Two types of RSI tile were studied: LI-900 and LI-2200. Three point bend specimens were cut from discarded tiles in the in-plane (ip) and through-the-thickness (ttt) directions. They were tested with or without a sharp notch. The LI-900 (ip and ttt) specimens were not very notch sensitive, but the LI-2200 (ip and ttt) specimens were. The LI-2200 material showed about a 35 percent reduction in strength due to the presence of the notch. This reduction in strength should be considered in the design of mechanically fastened tile concepts.

  11. VB Platinum Tile & Carpet, Inc. Information Sheet

    EPA Pesticide Factsheets

    VB Platinum Tile & Carpet, Inc. (the Company) is located in Bristow, Virginia. The settlement involves renovation activities conducted at a property constructed prior to 1978, located in Washington, DC.

  12. Radioactivity in zircon and building tiles

    SciTech Connect

    Wen Deng; Kaizhen Tian; Daifu Chen; Yiyun Zhang

    1997-08-01

    Zircon (ZrSiO{sub 4}) is commonly used in The manufacture of glazed tiles. In this study we found high concentrations of the radionuclides {sup 226}Ra, {sup 232}tH, {sup 40}k in zircon sand. The average radium equivalent (A{sub Ra} + 1.26 A{sub Th} + 0.086 A{sub k}) in zircon sand is 17,500 Bq kg{sup -1}, which is 106 times as much as that in ordinary building materials. The external radiation ({gamma} + {beta}) dose rates from 1.1 to 4.9 x 10{sup -2} mGy h{sup -1} with an average of 2.1 x 10{sup -2} mGy h{sup -1}. Although no elevated {gamma}-ray radiation or radon exhalation rate was detected in rooms decorated with glazed tiles, which is characteristic of combined {alpha}, {beta} and {gamma} emitting thin materials, the average {gamma} radiation dose rate at the surface of the tile stacks in shops is 1.5 times as much as the indoor background level. The average area density of total {beta} emitting radionuclides in glazed floor tiles and glazed wall tiles is 0.30 Bq cm{sup -2} and 0.28 Bq cm{sup -2}, respectively. It was estimated that the average {beta} dose rates in tissue at a depth 7 mg cm{sup -2} with a distance 20-100 cm from the floor tiles were 3.2 to 0.9 x 10{sup -7} Gy h{sup -1}. The study indicates that the {beta}-rays from glazed tiles might be one of the main factors leading to an increase in ionizing radiation received by the general public. Workers in glazed tile manufacturing factories and in tile shops or stores may be exposed to elevated levels of both {beta}-rays and {gamma}-rays from zircon sand or glazed tile stacks. No elevated radiation from unglazed tiles was detected. 10 refs., 1 fig., 3 tabs.

  13. Radioactivity in zircon and building tiles.

    PubMed

    Deng, W; Tian, K; Zhang, Y; Chen, D

    1997-08-01

    Zircon (ZrSiO4) is commonly used in the manufacture of glazed tiles. In this study we found high concentrations of the radionuclides 226Ra, 232Th, 40K in zircon sand. The average radium equivalent (A(Ra) + 1.26 A(Th) + 0.086 A(k)) in zircon sand is 17,500 Bq kg(-1), which is 106 times as much as that in ordinary building materials. The external radiation (gamma + beta) dose rates in air at 5 cm from the surface of piles of zircon sand sacks range from 1.1 to 4.9 x 10(-2) mGy h(-1) with an average of 2.1 x 10(-2) mGy h(-1). Although no elevated gamma-ray radiation or radon exhalation rate was detected in rooms decorated with glazed tiles, which is characteristic of combined alpha, beta and gamma emitting thin materials, the average gamma-ray radiation dose rate at the surface of the tile stacks in shops is 1.5 times as much as the indoor background level. The average area density of total beta emitting radionuclides in glazed floor tiles and glazed wall tiles is 0.30 Bq cm(-2) and 0.28 Bq cm(-2), respectively. It was estimated that the average beta dose rates in tissue at a depth 7 mg cm(-2) with a distance 20-100 cm from the floor tiles were 3.2 to 0.9 x 10(-7) Gy h(-1). The study indicates that the beta-rays from glazed tiles might be one of the main factors leading to an increase in ionizing radiation received by the general public. Workers in glazed tile manufacturing factories and in tile shops or stores may be exposed to elevated levels of both beta-rays and gamma-rays from zircon sand or glazed tile stacks. No elevated radiation from unglazed tiles was detected.

  14. Heat Transfer Measurement and Modeling in Rigid High-Temperature Reusable Surface Insulation Tiles

    NASA Technical Reports Server (NTRS)

    Daryabeigi, Kamran; Knutson, Jeffrey R.; Cunnington, George R.

    2011-01-01

    Heat transfer in rigid reusable surface insulations was investigated. Steady-state thermal conductivity measurements in a vacuum were used to determine the combined contribution of radiation and solid conduction components of heat transfer. Thermal conductivity measurements at higher pressures were then used to estimate the effective insulation characteristic length for gas conduction modeling. The thermal conductivity of the insulation can then be estimated at any temperature and pressure in any gaseous media. The methodology was validated by comparing estimated thermal conductivities with published data on a rigid high-temperature silica reusable surface insulation tile. The methodology was also applied to the alumina enhanced thermal barrier tiles. Thermal contact resistance for thermal conductivity measurements on rigid tiles was also investigated. A technique was developed to effectively eliminate thermal contact resistance on the rigid tile s cold-side surface for the thermal conductivity measurements.

  15. Manufacture of ceramic tiles from fly ash

    DOEpatents

    Hnat, James G.; Mathur, Akshay; Simpson, James C.

    1999-01-01

    The present invention relates to a process for forming glass-ceramic tiles. Fly ash containing organic material, metal contaminants, and glass forming materials is oxidized under conditions effective to combust the organic material and partially oxidize the metallic contaminants and the glass forming materials. The oxidized glass forming materials are vitrified to form a glass melt. This glass melt is then formed into tiles containing metallic contaminants.

  16. Manufacture of ceramic tiles from fly ash

    DOEpatents

    Hnat, J.G.; Mathur, A.; Simpson, J.C.

    1999-08-10

    The present invention relates to a process for forming glass-ceramic tiles. Fly ash containing organic material, metal contaminants, and glass forming materials is oxidized under conditions effective to combust the organic material and partially oxidize the metallic contaminants and the glass forming materials. The oxidized glass forming materials are vitrified to form a glass melt. This glass melt is then formed into tiles containing metallic contaminants. 6 figs.

  17. Laser Scanner for Tile-Cavity Measurement

    NASA Technical Reports Server (NTRS)

    Yoshino, Stanley Y.; Wykes, Donald H.; Hagen, George R.; Lotgering, Gene E.; Gaynor, Michael B.; Westerlund, Paul G.; Baal, Thomas A.

    1987-01-01

    Irregular surfaces mapped and digitized for numerical-control machinery. Fast, accurate laser scanning system measures size and shape of cavity without making any physical contact with cavity and walls. Measurements processed into control signals for numerically controlled machining of tile or block to fit cavity. System generates map of grid points representing cavity and portion of outer surface surrounding cavity. Map data used to control milling machine, which cuts tile or block to fit in cavity.

  18. Laser Scanner for Tile-Cavity Measurement

    NASA Technical Reports Server (NTRS)

    Yoshino, Stanley Y.; Wykes, Donald H.; Hagen, George R.; Lotgering, Gene E.; Gaynor, Michael B.; Westerlund, Paul G.; Baal, Thomas A.

    1987-01-01

    Irregular surfaces mapped and digitized for numerical-control machinery. Fast, accurate laser scanning system measures size and shape of cavity without making any physical contact with cavity and walls. Measurements processed into control signals for numerically controlled machining of tile or block to fit cavity. System generates map of grid points representing cavity and portion of outer surface surrounding cavity. Map data used to control milling machine, which cuts tile or block to fit in cavity.

  19. Cutting Symmetrical Recesses In Soft Ceramic Tiles

    NASA Technical Reports Server (NTRS)

    Nesotas, Tony C.; Tyler, Brent

    1989-01-01

    Simple tool cuts hemispherical recesses in soft ceramic tiles. Designed to expose wires of thermocouples embedded in tiles without damaging leads. Creates neat, precise holes around wires. End mill includes axial hole to accommodate thermocouple wires embedded in material to be cut. Wires pass into hole without being bent or broken. Dimensions in inches. Used in place of such tools as dental picks, tweezers, spatulas, and putty knives.

  20. Cutting Symmetrical Recesses In Soft Ceramic Tiles

    NASA Technical Reports Server (NTRS)

    Nesotas, Tony C.; Tyler, Brent

    1989-01-01

    Simple tool cuts hemispherical recesses in soft ceramic tiles. Designed to expose wires of thermocouples embedded in tiles without damaging leads. Creates neat, precise holes around wires. End mill includes axial hole to accommodate thermocouple wires embedded in material to be cut. Wires pass into hole without being bent or broken. Dimensions in inches. Used in place of such tools as dental picks, tweezers, spatulas, and putty knives.

  1. Performance of the TFTR moveable limiter tiles

    NASA Astrophysics Data System (ADS)

    Ulrickson, M.; Cecchi, J. L.; Doyle, B. L.; Dylla, H. F.; Medley, S. S.; Owens, D. K.; Trester, P.

    1985-08-01

    The movable limiter for the Tokamak Fusion Test Reactor (TFTR) is composed of an Inconel X-750 backing plate covered with titanium carbide coated graphite tiles. It has been used for ohmic heating discharges at input powers up to about 2 MW for durations up to 3 s. Even though these levels were well within the design requirements, discharges showed high levels (up to 1%) of titanium contamination. It was observed that certain tiles were showing substantial coating removal which became progressively worse as more discharges were made. After about 800 discharges the tiles were removed. A few of the tiles were examined in the Sandia external beam facility. This analysis showed that the TiC coating was completely removed over large areas. There was also evidence of plasma deposited material on the tiles. The thickness of the remaining coating from this beam analysis agreed with the thickness determined from sectioning control coupons from the production runs. There was a weak correlation between damage and coating thickness. The correlation was such that there was a higher probability of coating failure as the coating thickness increased from 15 μm to 40 μm. Test were done using the ASTM-C-633 procedure for measuring coating bond strength. The adhesion strength agreed well with the behavior observed in TFTR. The coating has been removed, and the tiles reinstalled.

  2. Quasicrystalline tilings with nematic colloidal platelets.

    PubMed

    Dontabhaktuni, Jayasri; Ravnik, Miha; Žumer, Slobodan

    2014-02-18

    Complex nematic fluids have the remarkable capability for self-assembling regular colloidal structures of various symmetries and dimensionality according to their micromolecular orientational order. Colloidal chains, clusters, and crystals were demonstrated recently, exhibiting soft-matter functionalities of robust binding, spontaneous chiral symmetry breaking, entanglement, shape-driven and topological driven assembly, and even memory imprinting. However, no quasicrystalline structures were found. Here, we show with numerical modeling that quasicrystalline colloidal lattices can be achieved in the form of original Penrose P1 tiling by using pentagonal colloidal platelets in layers of nematic liquid crystals. The tilings are energetically stabilized with binding energies up to 2500 kBT for micrometer-sized platelets and further allow for hierarchical substitution tiling, i.e., hierarchical pentagulation. Quasicrystalline structures are constructed bottom-up by assembling the boat, rhombus, and star maximum density clusters, thus avoiding other (nonquasicrystalline) stable or metastable configurations of platelets. Central to our design of the quasicrystalline tilings is the symmetry breaking imposed by the platelet shape and the surface anchoring conditions at the colloidal platelets, which are misaligning and asymmetric over two perpendicular mirror planes. Finally, the design of the quasicrystalline tilings as platelets in nematic liquid crystals is inherently capable of a continuous variety of length scales of the tiling, ranging over three orders of magnitude in the typical length (from ~ 10 nm to ~ 10 μm), which could allow for the design of quasicrystalline photonics at multiple frequency ranges.

  3. Quasicrystalline tilings with nematic colloidal platelets

    PubMed Central

    Dontabhaktuni, Jayasri; Ravnik, Miha; Žumer, Slobodan

    2014-01-01

    Complex nematic fluids have the remarkable capability for self-assembling regular colloidal structures of various symmetries and dimensionality according to their micromolecular orientational order. Colloidal chains, clusters, and crystals were demonstrated recently, exhibiting soft-matter functionalities of robust binding, spontaneous chiral symmetry breaking, entanglement, shape-driven and topological driven assembly, and even memory imprinting. However, no quasicrystalline structures were found. Here, we show with numerical modeling that quasicrystalline colloidal lattices can be achieved in the form of original Penrose P1 tiling by using pentagonal colloidal platelets in layers of nematic liquid crystals. The tilings are energetically stabilized with binding energies up to 2500 kBT for micrometer-sized platelets and further allow for hierarchical substitution tiling, i.e., hierarchical pentagulation. Quasicrystalline structures are constructed bottom-up by assembling the boat, rhombus, and star maximum density clusters, thus avoiding other (nonquasicrystalline) stable or metastable configurations of platelets. Central to our design of the quasicrystalline tilings is the symmetry breaking imposed by the platelet shape and the surface anchoring conditions at the colloidal platelets, which are misaligning and asymmetric over two perpendicular mirror planes. Finally, the design of the quasicrystalline tilings as platelets in nematic liquid crystals is inherently capable of a continuous variety of length scales of the tiling, ranging over three orders of magnitude in the typical length (from to ), which could allow for the design of quasicrystalline photonics at multiple frequency ranges. PMID:24550269

  4. DNA-Tile Structures Induce Ionic Currents through Lipid Membranes.

    PubMed

    Göpfrich, Kerstin; Zettl, Thomas; Meijering, Anna E C; Hernández-Ainsa, Silvia; Kocabey, Samet; Liedl, Tim; Keyser, Ulrich F

    2015-05-13

    Self-assembled DNA nanostructures have been used to create man-made transmembrane channels in lipid bilayers. Here, we present a DNA-tile structure with a nominal subnanometer channel and cholesterol-tags for membrane anchoring. With an outer diameter of 5 nm and a molecular weight of 45 kDa, the dimensions of our synthetic nanostructure are comparable to biological ion channels. Because of its simple design, the structure self-assembles within a minute, making its creation scalable for applications in biology. Ionic current recordings demonstrate that the tile structures enable ion conduction through lipid bilayers and show gating and voltage-switching behavior. By demonstrating the design of DNA-based membrane channels with openings much smaller than that of the archetypical six-helix bundle, our work showcases their versatility inspired by the rich diversity of natural membrane components.

  5. Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms

    PubMed Central

    Dapas, Matthew; Kandpal, Manoj; Bi, Yingtao

    2017-01-01

    Abstract Given that the majority of multi-exon genes generate diverse functional products, it is important to evaluate expression at the isoform level. Previous studies have demonstrated strong gene-level correlations between RNA sequencing (RNA-seq) and microarray platforms, but have not studied their concordance at the isoform level. We performed transcript abundance estimation on raw RNA-seq and exon-array expression profiles available for common glioblastoma multiforme samples from The Cancer Genome Atlas using different analysis pipelines, and compared both the isoform- and gene-level expression estimates between programs and platforms. The results showed better concordance between RNA-seq/exon-array and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) platforms for fold change estimates than for raw abundance estimates, suggesting that fold change normalization against a control is an important step for integrating expression data across platforms. Based on RT-qPCR validations, eXpress and Multi-Mapping Bayesian Gene eXpression (MMBGX) programs achieved the best performance for RNA-seq and exon-array platforms, respectively, for deriving the isoform-level fold change values. While eXpress achieved the highest correlation with the RT-qPCR and exon-array (MMBGX) results overall, RSEM was more highly correlated with MMBGX for the subset of transcripts that are highly variable across the samples. eXpress appears to be most successful in discriminating lowly expressed transcripts, but IsoformEx and RSEM correlate more strongly with MMBGX for highly expressed transcripts. The results also reinforce how potentially important isoform-level expression changes can be masked by gene-level estimates, and demonstrate that exon arrays yield comparable results to RNA-seq for evaluating isoform-level expression changes. PMID:26944083

  6. Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis

    PubMed Central

    Zhao, Qiu-jiong; Bai, Shao-cong; Cheng, Cheng; Tao, Ben-zhang; Wang, Le-kai; Liang, Shuang; Yin, Ling; Hang, Xing-yi; Shang, Ai-jia

    2016-01-01

    Copy number variations have been found in patients with neural tube abnormalities. In this study, we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy parents. Of eight copy number variations, four were non-polymorphic. These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes, and microcephaly. Gene function enrichment analysis revealed that COX8C, a gene associated with metabolic disorders of the nervous system, was located in the copy number variation region of Patient 1. Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome. Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease. PMID:27651783

  7. 2q23.1 microdeletion identified by array comparative genomic hybridisation: an emerging phenotype with Angelman-like features?

    PubMed Central

    Jaillard, Sylvie; Dubourg, Christèle; Gérard-Blanluet, Marion; Delahaye, Andrée; Pasquier, Laurent; Dupont, Céline; Henry, Catherine; Tabet, Anne-Claude; Lucas, Josette; Aboura, Azzedine; David, Véronique; Benzacken, Brigitte; Odent, Sylvie; Pipiras, Eva

    2009-01-01

    Background Genome-wide screening of patients with mental retardation using Array Comparative Genomic Hybridization (array-CGH) has identified several novel imbalances. With this genotype-first approach, the 2q22.3q23.3 deletion was recently described as a novel microdeletion syndrome. We report two unrelated patients with a de novo interstitial deletion mapping in this genomic region and presenting similar “pseudo-Angelman” phenotypes, including severe psychomotor retardation, speech impairment, epilepsy, microcephaly, ataxia and behavioural disabilities. Methods The microdeletions were identified by array-CGH using oligonucleotide and BAC-arrays, and further confirmed by Fluorescence In Situ Hybridization (FISH) and semi-quantitative PCR. Results The boundaries and sizes of the deletions in the two patients were different but an overlapping region of about 250 kb was defined, which mapped to 2q23.1 and included two genes: MBD5 and EPC2. The SIP1 gene associated with the Mowat Wilson syndrome was not included in the deleted genomic region. Discussion Haploinsufficiency of one of the deleted genes (MBD5 or EPC2) could be responsible for the common clinical features observed in the 2q23.1 microdeletion syndrome and this hypothesis needs further investigation. PMID:18812405

  8. Differential analysis for high density tiling microarray data.

    PubMed

    Ghosh, Srinka; Hirsch, Heather A; Sekinger, Edward A; Kapranov, Philipp; Struhl, Kevin; Gingeras, Thomas R

    2007-09-24

    High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program. We have proposed a novel approach, based on a piece-wise function - to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias. The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value < 0.003; it is most significant at the 5' end of genes, at a p-value < 10-13. The prototype R code has been made available as supplementary material [see Additional file 1].

  9. Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework.

    PubMed

    Antonopoulos, Georgios C; Steltner, Benjamin; Heisterkamp, Alexander; Ripken, Tammo; Meyer, Heiko

    2015-01-01

    A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available.

  10. Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework

    PubMed Central

    Antonopoulos, Georgios C.; Steltner, Benjamin; Heisterkamp, Alexander; Ripken, Tammo; Meyer, Heiko

    2015-01-01

    A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available. PMID:26599984

  11. Effect of tillage on macropore flow and phosphorus transport to tile drains

    NASA Astrophysics Data System (ADS)

    Williams, Mark R.; King, Kevin W.; Ford, William; Buda, Anthony R.; Kennedy, Casey D.

    2016-04-01

    Elevated phosphorus (P) concentrations in subsurface drainage water are thought to be the result of P bypassing the soil matrix via macropore flow. The objectives of this study were to quantify event water delivery to tile drains via macropore flow paths during storm events and to determine the effect of tillage practices on event water and P delivery to tiles. Tile discharge, total dissolved P (DP) and total P (TP) concentrations, and stable oxygen and deuterium isotopic signatures were measured from two adjacent tile-drained fields in Ohio, USA during seven spring storms. Fertilizer was surface-applied to both fields and disk tillage was used to incorporate the fertilizer on one field while the other remained in no-till. Median DP concentration in tile discharge prior to fertilizer application was 0.08 mg L-1 in both fields. Following fertilizer application, median DP concentration was significantly greater in the no-tilled field (1.19 mg L-1) compared to the tilled field (0.66 mg L-1), with concentrations remaining significantly greater in the no-till field for the remainder of the monitored storms. Both DP and TP concentrations in the no-till field were significantly related to event water contributions to tile discharge, while only TP concentration was significantly related to event water in the tilled field. Event water accounted for between 26 and 69% of total tile discharge from both fields, but tillage substantially reduced maximum contributions of event water. Collectively, these results suggest that incorporating surface-applied fertilizers has the potential to substantially reduce the risk of P transport from tile-drained fields.

  12. Managing tile drainage, subirrigation, and nitrogen fertilization to enhance crop yields and reduce nitrate loss.

    PubMed

    Drury, C F; Tan, C S; Reynolds, W D; Welacky, T W; Oloya, T O; Gaynor, J D

    2009-01-01

    Improving field-crop use of fertilizer nitrogen is essential for protecting water quality and increasing crop yields. The objective of this study was to determine the effectiveness of controlled tile drainage (CD) and controlled tile drainage with subsurface irrigation (CDS) for mitigating off-field nitrate losses and enhancing crop yields. The CD and CDS systems were compared on a clay loam soil to traditional unrestricted tile drainage (UTD) under a corn (Zea Mays L.)-soybean (Glycine Max. (L.) Merr.) rotation at two nitrogen (N) fertilization rates (N1: 150 kg N ha(-1) applied to corn, no N applied to soybean; N2: 200 kg N ha(-1) applied to corn, 50 kg N ha(-1) applied to soybean). The N concentrations in tile flow events with the UTD treatment exceeded the provisional long-term aquatic life limit (LT-ALL) for freshwater (4.7 mg N L(-1)) 72% of the time at the N1 rate and 78% at the N2 rate, whereas only 24% of tile flow events at N1 and 40% at N2 exceeded the LT-ALL for the CDS treatment. Exceedances in N concentration for surface runoff and tile drainage were greater during the growing season than the non-growing season. At the N1 rate, CD and CDS reduced average annual N losses via tile drainage by 44 and 66%, respectively, relative to UTD. At the N2 rate, the average annual decreases in N loss were 31 and 68%, respectively. Crop yields from CDS were increased by an average of 2.8% relative to UTD at the N2 rate but were reduced by an average of 6.5% at the N1 rate. Hence, CD and CDS were effective for reducing average nitrate losses in tile drainage, but CDS increased average crop yields only when additional N fertilizer was applied.

  13. Tiling patterns from ABC star molecules: 3-colored foams?

    PubMed

    Kirkensgaard, Jacob J K; Pedersen, Martin C; Hyde, Stephen T

    2014-10-07

    We present coarse-grained simulations of the self-assembly of 3-armed ABC star polyphiles. In systems of star polyphiles with two arms of equal length the simulations corroborate and expand previous findings from related miktoarm star terpolymer systems on the formation of patterns containing columnar domains whose sections are 2D planar tilings. However, the systematic variation of face topologies as the length of the third (unequal) arm is varied differs from earlier findings regarding the compositional dependence. We explore 2D 3-colored foams to establish the optimal patterns based on interfacial energy alone. A generic construction algorithm is described that accounts for all observed 2D tiling patterns and suggests other patterns likely to be found beyond the range of the simulations reported here. Patterns resulting from this algorithm are relaxed using Surface Evolver calculations to form 2D foams with minimal interfacial length as a function of composition. This allows us to estimate the interfacial enthalpic contributions to the free energy of related star molecular assemblies assuming strong segregation. We compare the resulting phase sequence with a number of theoretical results from particle-based simulations and field theory, allowing us to tease out relative enthalpic and entropic contributions as a function of the chain lengths making up the star molecules. Our results indicate that a richer polymorphism is to be expected in systems not dominated by chain entropy. Further, analysis of corresponding planar tiling patterns suggests that related two-periodic columnar structures are unlikely hypothetical phases in 4-arm star polyphile melts in the absence of sufficient arm configurational freedom for minor domains to form lens-shaped di-gons, which require higher molecular weight polymeric arms. Finally, we discuss the possibility of forming a complex tiling pattern that is a quasi-crystalline approximant for 3-arm star polyphiles with unequal arm

  14. Defect detection for end surface of ferrite magnetic tile

    NASA Astrophysics Data System (ADS)

    Tao, Jiayuan; Wang, Yuwei; Wang, Keyi

    2016-09-01

    A visual automatic detection method is proposed for defect detection on end surface of ferrite magnetic tile to tackle the disadvantages generated by human work which has low efficiency and unstable accuracy. Because the defects on end surface of ferrite magnetic tile with dark colors and low contrasts are negative for defect detection, uniform illumination is provided by LED light source and a dedicated optical system is designed to extract defects conveniently. The approach uses comparison of the fitting and actual edge curves to detect defects mainly with most defects located on the edge. Firstly improved adaptive median filter is used as the image preprocessing. Subsequently the appropriate threshold is calculated by Otsu algorithm based on the extreme points in the gray-level histogram to segment the preprocessing image. Then the Sobel operator can be used to extract the edge of end surface precisely. Finally through comparing the ideal fitting and actual edge curves of end surface, to detect the defects with some relevant features. Experimental results show that the proposed scheme could detect defects on the end surface of ferrite magnetic tile efficiency and accurately with 93.33% accuracy rate, 2.30% false acceptance rate and 8.45% correct rejection rate.

  15. Development of Microplasma Arrays for High Efficiency Lighting Tiles

    DTIC Science & Technology

    2012-02-01

    other three lamps. At this moment, the bill of materials ( BOM ) for the microplasma lamp is expected to be in the middle of LED fixtures and mercury...incorporates an internal spacer structure fabricated from various materials (currently from glass). Areal capacitance is the primary drawback of such...Mason ( Material Scientist), Youngwha Kim (Intern), Kyle Moon (Intern) B. University of Illinois (Subcontract) Prof. J. Gary Eden (Co-PI), Dr. Jin

  16. Acoustic generation of underwater cavities-Comparing modeled and measured acoustic signals generated by seismic air gun arrays.

    PubMed

    Khodabandeloo, Babak; Landrø, Martin; Hanssen, Alfred

    2017-04-01

    Underwater vapor cavities can be generated by acoustic stimulation. When the acoustic signals from several air guns are reflected from the sea surface, the pressure drop at some locations is sufficient for cavity growth and subsequent collapse. In this paper the generation of multiple water vapor cavities and their collapses are numerically modeled and the results are validated by comparing with field data from a seismic air gun array test. In a first modeling attempt where cavity interaction is neglected, a correspondence between measured and modeled data is found. Then, this correspondence is improved by assuming that the acoustic signal generated by the other cavities changes the hydrostatic pressure surrounding each cavity. This modeling can be used to estimate the amount and strength of high frequency signals generated by typical marine air gun arrays, given that a calibration step is performed prior to the modeling.

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

    USGS Publications Warehouse

    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

  18. Symmetry groups associated with tilings on a flat torus.

    PubMed

    Loyola, Mark L; De Las Peñas, Ma Louise Antonette N; Estrada, Grace M; Santoso, Eko Budi

    2015-01-01

    This work investigates symmetry and color symmetry properties of Kepler, Heesch and Laves tilings embedded on a flat torus and their geometric realizations as tilings on a round torus in Euclidean 3-space. The symmetry group of the tiling on the round torus is determined by analyzing relevant symmetries of the planar tiling that are transformed to axial symmetries of the three-dimensional tiling. The focus on studying tilings on a round torus is motivated by applications in the geometric modeling of nanotori and the determination of their symmetry groups.

  19. Dynamic Moire methods for detection of loosened space shuttle tiles

    NASA Astrophysics Data System (ADS)

    Snow, W. L.; Burner, A. W.; Goad, W. K.

    1981-09-01

    Moire fringe methods for detecting loose space shuttle tiles were investigated with a test panel consisting of a loose tile surrounded by four securely bonded tiles. The test panel was excited from 20 to 150 Hz with in-plane sinusoidal acceleration of 2 g (peak). If the shuttle orbiter can be subjected to periodic excitation of 1 to 2 g (peak) and rigid-body periodic displacements do not mask the change in the Moire pattern due to tile looseness, then the use of projected Moire fringes to detect out-of-plane rockin appears to be the most viable indicator of tile looseness since no modifications to the tiles are required.

  20. Tiled WMS/KML Server V2

    NASA Technical Reports Server (NTRS)

    Plesea, Lucian

    2012-01-01

    This software is a higher-performance implementation of tiled WMS, with integral support for KML and time-varying data. This software is compliant with the Open Geospatial WMS standard, and supports KML natively as a WMS return type, including support for the time attribute. Regionated KML wrappers are generated that match the existing tiled WMS dataset. Ping and JPG formats are supported, and the software is implemented as an Apache 2.0 module that supports a threading execution model that is capable of supporting very high request rates. The module intercepts and responds to WMS requests that match certain patterns and returns the existing tiles. If a KML format that matches an existing pyramid and tile dataset is requested, regionated KML is generated and returned to the requesting application. In addition, KML requests that do not match the existing tile datasets generate a KML response that includes the corresponding JPG WMS request, effectively adding KML support to a backing WMS server.

  1. Performance of the ATLAS Tile Calorimeter

    NASA Astrophysics Data System (ADS)

    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.

  2. Characterization of genomic alterations in radiation-associated breast cancer among childhood cancer survivors, using comparative genomic hybridization (CGH) arrays.

    PubMed

    Yang, Xiaohong R; Killian, J Keith; Hammond, Sue; Burke, Laura S; Bennett, Hunter; Wang, Yonghong; Davis, Sean R; Strong, Louise C; Neglia, Joseph; Stovall, Marilyn; Weathers, Rita E; Robison, Leslie L; Bhatia, Smita; Mabuchi, Kiyohiko; Inskip, Peter D; Meltzer, Paul

    2015-01-01

    Ionizing radiation is an established risk factor for breast cancer. Epidemiologic studies of radiation-exposed cohorts have been primarily descriptive; molecular events responsible for the development of radiation-associated breast cancer have not been elucidated. In this study, we used array comparative genomic hybridization (array-CGH) to characterize genome-wide copy number changes in breast tumors collected in the Childhood Cancer Survivor Study (CCSS). Array-CGH data were obtained from 32 cases who developed a second primary breast cancer following chest irradiation at early ages for the treatment of their first cancers, mostly Hodgkin lymphoma. The majority of these cases developed breast cancer before age 45 (91%, n = 29), had invasive ductal tumors (81%, n = 26), estrogen receptor (ER)-positive staining (68%, n = 19 out of 28), and high proliferation as indicated by high Ki-67 staining (77%, n = 17 out of 22). Genomic regions with low-copy number gains and losses and high-level amplifications were similar to what has been reported in sporadic breast tumors, however, the frequency of amplifications of the 17q12 region containing human epidermal growth factor receptor 2 (HER2) was much higher among CCSS cases (38%, n = 12). Our findings suggest that second primary breast cancers in CCSS were enriched for an "amplifier" genomic subgroup with highly proliferative breast tumors. Future investigation in a larger irradiated cohort will be needed to confirm our findings.

  3. A customized high-resolution array-comparative genomic hybridization to explore copy number variations in Parkinson's disease.

    PubMed

    La Cognata, Valentina; Morello, Giovanna; Gentile, Giulia; D'Agata, Velia; Criscuolo, Chiara; Cavalcanti, Francesca; Cavallaro, Sebastiano

    2016-10-01

    Parkinson's disease (PD), the second most common progressive neurodegenerative disorder, was long believed to be a non-genetic sporadic syndrome. Today, only a small percentage of PD cases with genetic inheritance patterns are known, often complicated by reduced penetrance and variable expressivity. The few well-characterized Mendelian genes, together with a number of risk factors, contribute to the major sporadic forms of the disease, thus delineating an intricate genetic profile at the basis of this debilitating and incurable condition. Along with single nucleotide changes, gene-dosage abnormalities and copy number variations (CNVs) have emerged as significant disease-causing mutations in PD. However, due to their size variability and to the quantitative nature of the assay, CNV genotyping is particularly challenging. For this reason, innovative high-throughput platforms and bioinformatics algorithms are increasingly replacing classical CNV detection methods. Here, we report the design strategy, development, validation and implementation of NeuroArray, a customized exon-centric high-resolution array-based comparative genomic hybridization (aCGH) tailored to detect single/multi-exon deletions and duplications in a large panel of PD-related genes. This targeted design allows for a focused evaluation of structural imbalances in clinically relevant PD genes, combining exon-level resolution with genome-wide coverage. The NeuroArray platform may offer new insights in elucidating inherited potential or de novo structural alterations in PD patients and investigating new candidate genes.

  4. 2q23.1 microdeletion identified by array comparative genomic hybridisation: an emerging phenotype with Angelman-like features?

    PubMed

    Jaillard, S; Dubourg, C; Gérard-Blanluet, M; Delahaye, A; Pasquier, L; Dupont, C; Henry, C; Tabet, A-C; Lucas, J; Aboura, A; David, V; Benzacken, B; Odent, S; Pipiras, E

    2009-12-01

    Genome-wide screening of patients with mental retardation using array comparative genomic hybridisation (CGH) has identified several novel imbalances. With this genotype-first approach, the 2q22.3q23.3 deletion was recently described as a novel microdeletion syndrome. The authors report two unrelated patients with a de novo interstitial deletion mapping in this genomic region and presenting similar "pseudo-Angelman" phenotypes, including severe psychomotor retardation, speech impairment, epilepsy, microcephaly, ataxia, and behavioural disabilities. The microdeletions were identified by array CGH using oligonucleotide and bacterial artificial chromosome (BAC) arrays, and further confirmed by fluorescence in situ hybridisation (FISH) and semi-quantitative polymerase chain reaction (PCR). The boundaries and sizes of the deletions in the two patients were different but an overlapping region of about 250 kb was defined, which mapped to 2q23.1 and included two genes: MBD5 and EPC2. The SIP1 gene associated with the Mowat-Wilson syndrome was not included in the deleted genomic region. Haploinsufficiency of one of the deleted genes (MBD5 or EPC2) could be responsible for the common clinical features observed in the 2q23.1 microdeletion syndrome, and this hypothesis needs further investigation.

  5. Characterization of Genomic Alterations in Radiation-Associated Breast Cancer among Childhood Cancer Survivors, Using Comparative Genomic Hybridization (CGH) Arrays

    PubMed Central

    Yang, Xiaohong R.; Killian, J. Keith; Hammond, Sue; Burke, Laura S.; Bennett, Hunter; Wang, Yonghong; Davis, Sean R.; Strong, Louise C.; Neglia, Joseph; Stovall, Marilyn; Weathers, Rita E.; Robison, Leslie L.; Bhatia, Smita; Mabuchi, Kiyohiko; Inskip, Peter D.; Meltzer, Paul

    2015-01-01

    Ionizing radiation is an established risk factor for breast cancer. Epidemiologic studies of radiation-exposed cohorts have been primarily descriptive; molecular events responsible for the development of radiation-associated breast cancer have not been elucidated. In this study, we used array comparative genomic hybridization (array-CGH) to characterize genome-wide copy number changes in breast tumors collected in the Childhood Cancer Survivor Study (CCSS). Array-CGH data were obtained from 32 cases who developed a second primary breast cancer following chest irradiation at early ages for the treatment of their first cancers, mostly Hodgkin lymphoma. The majority of these cases developed breast cancer before age 45 (91%, n = 29), had invasive ductal tumors (81%, n = 26), estrogen receptor (ER)-positive staining (68%, n = 19 out of 28), and high proliferation as indicated by high Ki-67 staining (77%, n = 17 out of 22). Genomic regions with low-copy number gains and losses and high-level amplifications were similar to what has been reported in sporadic breast tumors, however, the frequency of amplifications of the 17q12 region containing human epidermal growth factor receptor 2 (HER2) was much higher among CCSS cases (38%, n = 12). Our findings suggest that second primary breast cancers in CCSS were enriched for an “amplifier” genomic subgroup with highly proliferative breast tumors. Future investigation in a larger irradiated cohort will be needed to confirm our findings. PMID:25764003

  6. Identification of DNA copy-number aberrations by array-comparative genomic hybridization in patients with schizophrenia.

    PubMed

    Moon, Ho Jin; Yim, Sung-Vin; Lee, Woon Kyu; Jeon, Yang-Whan; Kim, Young Hoon; Ko, Young Jin; Lee, Kwang-Soo; Lee, Kweon-Haeng; Han, Sang-Ick; Rha, Hyoung Kyun

    2006-06-02

    Chromosomal abnormalities are implicated as important markers for the pathogenesis in patients with schizophrenia. In this study, with using bacterial artificial chromosome (BAC) array-based comparative genomic hybridization (CGH), we analyzed DNA copy-number changes among 30 patients with schizophrenia. The most frequent changes were partial gain of Xq23 (52%) and loss of 3q13.12 (32%). Other frequent gains were found in: 1p, 6q, 10p, 11p, 11q, 14p, and 15q regions, and frequent losses were found in: 2p, 9q, 10q, 14q, 20q, and 22q regions. The set of abnormal regions was confirmed by real-time PCR (9q12, 9q34.2, 11p15.4, 14q32.33, 15q15.1, 22q11.21, and Xq23). All real-time PCR results were consistent with the array-CGH results. Therefore, it is suggested that array-CGH and real-time PCR analysis could be used as powerful tools in screening for schizophrenia-related genes. Our results might be useful for further exploration of candidate genomic regions in the pathogenesis of schizophrenia.

  7. Crosslinking in viral capsids via tiling theory.

    PubMed

    Twarock, R; Hendrix, R W

    2006-06-07

    A vital part of a virus is its protein shell, called the viral capsid, that encapsulates and hence protects the viral genome. It has been shown in Twarock [2004. A tiling approach to vius capsids assembly explaining a structural puzzle in virology. J. Theor. Biol. 226, 477-482] that the surface structures of viruses with icosahedrally symmetric capsids can be modelled in terms of tilings that encode the locations of the protein subunits. This theory is extended here to multi-level tilings in order to model crosslinking structures. The new framework is demonstrated for the case of bacteriophage HK97, and it is shown, how the theory can be used in general to decide if crosslinking, and what type of crosslinking, is compatible from a mathematical point of view with the geometrical surface structure of a virus.

  8. Remotely replaceable tokamak plasma limiter tiles

    DOEpatents

    Tsuo, Simon , Langford, Alison A.

    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.

  9. Improved blood culture identification by FilmArray in cultures from regional hospitals compared with teaching hospital cultures.

    PubMed

    Inglis, Timothy J J; Bzdyl, Nicole; Chua, I-Ly Joanna; Urosevic, Nadezda M; Leung, Michael J; Geelhoed, Elizabeth

    2016-01-01

    Rapid identification of bacteria isolated from blood cultures by direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now in wide spread use in major centres but is not yet feasible in smaller hospital laboratories. A FilmArray multiplex PCR panel for blood culture isolate identification (BCID) provides an alternative approach to near point-of-care microbial identification in regional hospitals. We assessed the accuracy and time to identification of the BCID FilmArray in a consecutive series of 149 blood cultures from 143 patients in a teaching hospital and smaller regional hospitals, currently identified by direct MALDI-TOF and proprietary molecular methods. The BCID FilmArray contained 18 of 34 species and 20 of 23 species isolated from teaching and regional hospital, respectively. Overall, 85 % of the teaching hospital and 100 % of the regional hospital monomicrobial blood cultures were identified, compared with 60 and 68 %, respectively, for direct MALDI-TOF on the same cultures. There were no incorrect results from blood cultures containing Staphylococcus aureus, streptococci, Pseudomonas aeruginosa or Enterobacteriaceae. The three discrepant results were all in mixed cultures. The mean reduction in time to identification of blood culture isolates was 53 h, which did not include the time required to transport cultures from regional centres to a central laboratory. The overall performance of the BCID FilmArray is stronger in blood cultures from smaller regional hospitals that encounter a narrower range of bacterial species dominated by the commonest species. This approach is more suited to smaller clinical laboratories than the MALDI-TOF direct method.

  10. Comparison of array comparative genomic hybridization and quantitative real-time PCR-based aneuploidy screening of blastocyst biopsies.

    PubMed

    Capalbo, Antonio; Treff, Nathan R; Cimadomo, Danilo; Tao, Xin; Upham, Kathleen; Ubaldi, Filippo Maria; Rienzi, Laura; Scott, Richard T

    2015-07-01

    Comprehensive chromosome screening (CCS) methods are being extensively used to select chromosomally normal embryos in human assisted reproduction. Some concerns related to the stage of analysis and which aneuploidy screening method to use still remain. In this study, the reliability of blastocyst-stage aneuploidy screening and the diagnostic performance of the two mostly used CCS methods (quantitative real-time PCR (qPCR) and array comparative genome hybridization (aCGH)) has been assessed. aCGH aneuploid blastocysts were rebiopsied, blinded, and evaluated by qPCR. Discordant cases were subsequently rebiopsied, blinded, and evaluated by single-nucleotide polymorphism (SNP) array-based CCS. Although 81.7% of embryos showed the same diagnosis when comparing aCGH and qPCR-based CCS, 18.3% (22/120) of embryos gave a discordant result for at least one chromosome. SNP array reanalysis showed that a discordance was reported in ten blastocysts for aCGH, mostly due to false positives, and in four cases for qPCR. The discordant aneuploidy call rate per chromosome was significantly higher for aCGH (5.7%) compared with qPCR (0.6%; P<0.01). To corroborate these findings, 39 embryos were simultaneously biopsied for aCGH and qPCR during blastocyst-stage aneuploidy screening cycles. 35 matched including all 21 euploid embryos. Blinded SNP analysis on rebiopsies of the four embryos matched qPCR. These findings demonstrate the high reliability of diagnosis performed at the blastocyst stage with the use of different CCS methods. However, the application of aCGH can be expected to result in a higher aneuploidy rate than other contemporary methods of CCS.

  11. Degenerate polygonal tilings in simple animal tissues

    NASA Astrophysics Data System (ADS)

    Ziherl, Primoz; Hocevar, Ana

    2009-03-01

    We study 2D polygonal tilings as models of the en-face structure of single-layer biological tissues. Using numerical simulations, we explore the phase diagram of equilibrium tilings of equal-area, equal-perimeter convex polygons whose energy is independent of their shape. We identify 3 distinct phases, which are all observed in simple epithelial tissues: The disordered phase of polygons with 4-9 sides, the hexatic phase, and the hexagonal phase with perfect 6-fold coordination. We quantify their structure using Edwards' statistical mechanics of cellular systems.

  12. Improvement of PVC floor tiles by gamma radiation

    NASA Astrophysics Data System (ADS)

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

    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. The 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.

  13. INTERIOR VIEW OF BATHROOM 1. SHOWING ORIGINAL MOSAIC PATTERN TILE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    INTERIOR VIEW OF BATHROOM 1. SHOWING ORIGINAL MOSAIC PATTERN TILE FLOOR, TILE WAINSCOT AND SHOWER SURROUND, AND CERAMIC ACCESSORIES. VIEW FACING EAST. - Hickam Field, Officers' Housing Type J, 701 Beard Street, Honolulu, Honolulu County, HI

  14. 2. MORAVIAN POTTERY AND TILE WORKS, VIEW FROM THE SOUTHWEST. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. MORAVIAN POTTERY AND TILE WORKS, VIEW FROM THE SOUTHWEST. INDIAN HOUSE WING AT THE LEFT. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  15. 37. PRESSING TILES FROM PLASTER MOLDS, USING A HAND PRESS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    37. PRESSING TILES FROM PLASTER MOLDS, USING A HAND PRESS CONSTRUCTED IN 1986. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  16. A Comparative Analysis for Verification of IMRT and VMAT Treatment Plans using a 2-D and 3-D Diode Array

    NASA Astrophysics Data System (ADS)

    Dance, Michael J.

    With the added complexity of current radiation treatment dose delivery modalities such as IMRT (Intensity Modulated Radiation Therapy) and VMAT (Volumetric Modulated Arc Therapy), quality assurance (QA) of these plans become multifaceted and labor intensive. To simplify the patient specific quality assurance process, 2D or 3D diode arrays are used to measure the radiation fluence for IMRT and VMAT treatments which can then be quickly and easily compared against the planned dose distribution. Because the arrays that can be used for IMRT and VMAT patient-specific quality assurance are of different geometry (planar vs. cylindrical), the same IMRT or VMAT treatment plan measured by two different arrays could lead to different measured radiation fluences, regardless of the output and performance of linear accelerator. Thus, the purpose of this study is to compare patient specific QA results as measured by the MapCHECK 2 and ArcCHECK diode arrays for the same IMRT and VMAT treatment plans to see if one diode array consistently provides a closer comparison to reference data. Six prostate and three thoracic spine IMRT treatment plans as well as three prostate and three thoracic spine VMAT treatment plans were produced. Radiotherapy plans for this study were generated using the Pinnacle TPS v9.6 (Philips Radiation Oncology Systems, Fitchburg, WI) using 6 MV, 6 MV FFF, and 10 MV x-ray beams from a Varian TrueBeam linear accelerator (Varian Medical Systems, Palo Alto, CA) with a 120-millenium multi-leaf collimator (MLC). Each IMRT and VMAT therapy plan was measured on Sun Nuclear's MapCHECK 2 and ArcCHECK diode arrays. IMRT measured data was compared with planned dose distribution using Sun Nuclear's 3DVH quality assurance software program using gamma analysis and dose-volume histograms for target volumes and critical structures comparison. VMAT arc plans measured on the MapCHECK 2 and ArcCHECK were compared using beam-by-beam analysis with the gamma evaluation method with

  17. Male with mosaicism for supernumerary ring X chromosome: analysis of phenotype and characterization of genotype using array comparative genome hybridization.

    PubMed

    Baker, Peter R; Tsai, Anne Chun-Hui; Springer, Michelle; Swisshelm, Karen; March, Jennifer; Brown, Kathleen; Bellus, Gary

    2010-09-01

    Supernumerary, derivative, and ring X chromosomes are relatively common in Turner syndrome females but have been reported rarely in males. To date, less than 10 cases have been published, of which only 2 have been partially characterized in defining the breakpoints and genetic content of the derivative X chromosome. We describe a male with mosaicism for a supernumerary X chromosome (46,XY/47,XY, r(X)) who has multiple congenital anomalies, including features of craniofrontonasal dysplasia (Mendelian Inheritance in Man 304110) and the presence of ectopic female reproductive organs. Using comparative genomic hybridization array mapping, we determined that the derivative X is composed of a 24-Mb fragment that contains the regions Xp11.3 through Xq13.1 and lacks the XIST gene. This is the first report to describe a detailed molecular characterization of a ring X chromosome in a male by comparative genomic hybridization array analysis. We compare the clinical and molecular findings in this patient to other 46,XY, r(X) patients reported in the literature and discuss the potential role of disomy for known genes contained on the ring X chromosome.

  18. Recycling of Malaysia's electric arc furnace (EAF) slag waste into heavy-duty green ceramic tile.

    PubMed

    Teo, Pao-Ter; Anasyida, Abu Seman; Basu, Projjal; Nurulakmal, Mohd Sharif

    2014-12-01

    flexural strength, lowest apparent porosity and water absorption of EAF slag based tile was attained at the composition of 40 wt.% EAF slag--30 wt.% ball clay--10 wt.% feldspar--20 wt.% silica. The properties of ceramic tile made with EAF slag waste (up to 40 wt.%), especially flexural strength are comparable to those of commercial ceramic tile and are, therefore, suitable as high flexural strength and heavy-duty green ceramic floor tile. Continuous development is currently underway to improve the properties of tile so that this recycling approach could be one of the potential effective, efficient and sustainable solutions in sustaining our nature.

  19. Preimplantation Genetic Diagnosis for Aneuploidy and Translocations Using Array Comparative Genomic Hybridization

    PubMed Central

    Munné, Santiago

    2012-01-01

    At least 50% of human embryos are abnormal, and that increases to 80% in women 40 years or older. These abnormalities result in low implantation rates in embryos transferred during in vitro fertilization procedures, from 30% in women <35 years to 6% in women 40 years or older. Thus selecting normal embryos for transfer should improve pregnancy results. The genetic analysis of embryos is called Preimplantation Genetic Diagnosis (PGD) and for chromosome analysis it was first performed using FISH with up to 12 probes analyzed simultaneously on single cells. However, suboptimal utilization of the technique and the complexity of fixing single cells produced conflicting results. PGD has been invigorated by the introduction of microarray testing which allows for the analysis of all 24 chromosome types in one test, without the need of cell fixation, and with staggering redundancy, making the test much more robust and reliable. Recent data published and presented at scientific meetings has been suggestive of increased implantation rates and pregnancy rates following microarray testing, improvements in outcome that have been predicted for quite some time. By using markers that cover most of the genome, not only aneuploidy can be detected in single cells but also translocations. Our validation results indicate that array CGH has a 6Mb resolution in single cells, and thus the majority of translocations can be analyzed since this is also the limit of karyotyping. Even for translocations with smaller exchanged fragments, provided that three out of the four fragments are above 6Mb, the translocation can be detected. PMID:23448851

  20. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers.

    PubMed

    Chin, S-F; Wang, Y; Thorne, N P; Teschendorff, A E; Pinder, S E; Vias, M; Naderi, A; Roberts, I; Barbosa-Morais, N L; Garcia, M J; Iyer, N G; Kranjac, T; Robertson, J F R; Aparicio, S; Tavaré, S; Ellis, I; Brenton, J D; Caldas, C

    2007-03-22

    We analysed 148 primary breast cancers using BAC-arrays containing 287 clones representing cancer-related gene/loci to obtain genomic molecular portraits. Gains were detected in 136 tumors (91.9%) and losses in 123 tumors (83.1%). Eight tumors (5.4%) did not have any genomic aberrations in the 281 clones analysed. Common (more than 15% of the samples) gains were observed at 8q11-qtel, 1q21-qtel, 17q11-q12 and 11q13, whereas common losses were observed at 16q12-qtel, 11ptel-p15.5, 1p36-ptel, 17p11.2-p12 and 8ptel-p22. Patients with tumors registering either less than 5% (median value) or less than 11% (third quartile) total copy number changes had a better overall survival (log-rank test: P=0.0417 and P=0.0375, respectively). Unsupervised hierarchical clustering based on copy number changes identified four clusters. Women with tumors from the cluster with amplification of three regions containing known breast oncogenes (11q13, 17q12 and 20q13) had a worse prognosis. The good prognosis group (Nottingham Prognostic Index (NPI)

  1. Clinical utility of array comparative genomic hybridization: uncovering tumor susceptibility in individuals with developmental delay.

    PubMed

    Adam, Margaret P; Justice, April N; Schelley, Susan; Kwan, Andrea; Hudgins, Louanne; Martin, Christa L

    2009-01-01

    Microarray-based comparative genomic hybridization can determine genome-wide copy number alterations at the kilobase level. We highlight the clinical utility of microarray-based comparative genomic hybridization in determining tumor susceptibility in 3 patients with dysmorphic features and developmental delay, likely decreasing both morbidity and mortality in these patients.

  2. 90. TILES OF THE NEW WORLD PANEL, NORTH WALL OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    90. TILES OF THE NEW WORLD PANEL, NORTH WALL OF THE INDIAN HOUSE. THE RELIEF BROCADE TILES ILLUSTRATE SCENES OF NATIVE AMERICAN HISTORY AND CULTURE, AND THE EARLY EUROPEAN EXPLORATION OF THE NEW WORLD. SAME VIEW AS PA-107-21. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  3. 21. TILES OF THE NEW WORLD PANEL, NORTH WALL OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    21. TILES OF THE NEW WORLD PANEL, NORTH WALL OF THE INDIAN HOUSE. THE RELIEF BROCADE TILES ILLUSTRATE SCENES OF NATIVE AMERICAN HISTORY AND CULTURE, AND THE EARLY EUROPEAN EXPLORATION OF THE NEW WORLD. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  4. Two Views of Islam: Ceramic Tile Design and Miniatures.

    ERIC Educational Resources Information Center

    Macaulay, Sara Grove

    2001-01-01

    Describes an art project focusing on Islamic art that consists of two parts: (1) ceramic tile design; and (2) Islamic miniatures. Provides background information on Islamic art and step-by-step instructions for designing the Islamic tile and miniature. Includes learning objectives and resources on Islamic tile miniatures. (CMK)

  5. Two Views of Islam: Ceramic Tile Design and Miniatures.

    ERIC Educational Resources Information Center

    Macaulay, Sara Grove

    2001-01-01

    Describes an art project focusing on Islamic art that consists of two parts: (1) ceramic tile design; and (2) Islamic miniatures. Provides background information on Islamic art and step-by-step instructions for designing the Islamic tile and miniature. Includes learning objectives and resources on Islamic tile miniatures. (CMK)

  6. On the Penrose and Taylor–Socolar hexagonal tilings

    PubMed Central

    Lee, Jeong-Yup; Moody, Robert V.

    2017-01-01

    The intimate relationship between the Penrose and the Taylor–Socolar tilings is studied, within both the context of double hexagon tiles and the algebraic context of hierarchical inverse sequences of triangular lattices. This unified approach produces both types of tilings together, clarifies their relationship and offers straightforward proofs of their basic properties. PMID:28447596

  7. Production and characterization of glazed tiles containing incinerated sewage sludge.

    PubMed

    Lin, D F; Chang, W C; Yuan, C; Luo, H L

    2008-01-01

    In this article, glaze with different colorants was applied to tile specimens manufactured by incinerated sewage sludge ash (ISSA) and clay. Improvements using different amounts of colorants, and glaze components and concentrations on tile bodies were investigated. Four different proportions of clay (by weight ratio) were replaced by ISSA. Tiles of size 12 cm x 6 cm x 1 cm were made and left in an electric furnace to make biscuit tiles at 800 degrees C. Afterwards, four colorants, Fe2O3 (red), V2O5 (yellow), CoCO3 (blue), and MnO2 (purple), and four different glaze concentrations were applied on biscuit tile specimens. These specimens were later sintered into glazed tiles at 1050 degrees C. The study shows that replacement of clay by sludge ash had adverse effects on properties of tiles. Water absorption increased and bending strength reduced with increased amounts of ash. However, both water absorption and bending strength improved for glazed ash tiles. Abrasion of grazed tiles reduced noticeably from 0.001 to 0.002 g. This implies glaze can enhance abrasion resistance of tiles. Effects like lightfastness and acid-alkali resistance improved as different glazes were applied on tiles. In general, red glazed tiles showed the most stable performance, followed by blue, yellow, and purple.

  8. Thermal-Structural Analysis of PICA Tiles for Solar Tower Test

    NASA Technical Reports Server (NTRS)

    Agrawal, Parul; Empey, Daniel M.; Squire, Thomas H.

    2009-01-01

    Thermal protection materials used in spacecraft heatshields are subjected to severe thermal and mechanical loading environments during re-entry into earth atmosphere. In order to investigate the reliability of PICA tiles in the presence of high thermal gradients as well as mechanical loads, the authors designed and conducted solar-tower tests. This paper presents the design and analysis work for this tests series. Coupled non-linear thermal-mechanical finite element analyses was conducted to estimate in-depth temperature distribution and stress contours for various cases. The first set of analyses performed on isolated PICA tile showed that stresses generated during the tests were below the PICA allowable limit and should not lead to any catastrophic failure during the test. The tests results were consistent with analytical predictions. The temperature distribution and magnitude of the measured strains were also consistent with predicted values. The second test series is designed to test the arrayed PICA tiles with various gap-filler materials. A nonlinear contact method is used to model the complex geometry with various tiles. The analyses for these coupons predict the stress contours in PICA and inside gap fillers. Suitable mechanical loads for this architecture will be predicted, which can be applied during the test to exceed the allowable limits and demonstrate failure modes. Thermocouple and strain-gauge data obtained from the solar tower tests will be used for subsequent analyses and validation of FEM models.

  9. Modeling of the Thermal Footprint at the Strike Point and Fast Thermocouples in Carbon Tiles

    NASA Astrophysics Data System (ADS)

    Nygren, R. E.; Watkins, J. G.; Buchenauer, D. A.; Makowski, M. A.; Leonard, A. W.

    2013-10-01

    Thermal broadening can complicate interpretation of IR images at the strike point because the peaked profile of surface temperature widens as the tile heats due to lateral conduction away from the peak, so the instantaneous values of λq extracted from IR images increases during the shot. Detailed 3D thermal analyses of divertor tiles complement data from edge probes, fast thermocouples (FTCs) and IR thermography and aids interpretation. But the surface temperature reflects the integrated heat load over time, so changes in power or movement of the plasma complicates this interpretation. The array of 16 embedded FTCs in DIII-D divertor tiles are 8 mm below the surface.The poster focuses on the degree to which the FTCs can help resolve the absolute value of the surface temperature and the extracted profile of surface temperature and related peaked heat load.We include a series of detailed 3D thermal analyses of one DIII-D tile exposed to a (theoretical) peaked heat load characterized by the commonly-used two-parameter fit. Work supported by the US DOE under DE-AC04-94AL85000, DE-AC52-07N27344 & DE-FC02-04ER54698.

  10. CFD-Predicted Tile Heating Bump Factors Due to Tile Overlay Repairs

    NASA Technical Reports Server (NTRS)

    Lessard, Victor R.

    2006-01-01

    A Computational Fluid Dynamics investigation of the Orbiter's Tile Overlay Repair (TOR) is performed to assess the aeroheating Damage Assessment Team's (DAT) existing heating correlation method for protuberance interference heating on the surrounding thermal protection system. Aerothermodynamic heating analyses are performed for TORs at the design reference damage locations body points 1800 and 1075 for a Mach 17.9 and a=39deg STS-107 flight trajectory point with laminar flow. Six different cases are considered. The computed peak heating bump factor on the surrounding tiles are below the DAT's heating bump factor values for smooth tile cases. However, for the uneven tiles cases the peak interference heating is shown to be considerably higher than the existing correlation prediction.

  11. Jagged Tiling for Intra-tile Parallelism and Fine-Grain Multithreading

    SciTech Connect

    Shrestha, Sunil; Manzano Franco, Joseph B.; Marquez, Andres; Feo, John T.; Gao, Guang R.

    2015-05-01

    In this paper, we have developed a novel methodology that takes into consideration multithreaded many-core designs to better utilize memory/processing resources and improve memory residence on tileable applications. It takes advantage of polyhedral analysis and transformation in the form of PLUTO, combined with a highly optimized finegrain tile runtime to exploit parallelism at all levels. The main contributions of this paper include the introduction of multi-hierarchical tiling techniques that increases intra tile parallelism; and a data-flow inspired runtime library that allows the expression of parallel tiles with an efficient synchronization registry. Our current implementation shows performance improvements on an Intel Xeon Phi board up to 32.25% against instances produced by state-of-the-art compiler frameworks for selected stencil applications.

  12. Development of a nondestructive vibration technique for bond assessment of Space Shuttle tiles

    NASA Technical Reports Server (NTRS)

    Moslehy, Faissal A.

    1994-01-01

    This final report describes the achievements of the above titled project. The project is funded by NASA-KSC (Grant No. NAG 10-0117) for the period of 1 Jan. to 31 Dec. 1993. The purpose of this project was to develop a nondestructive, noncontact technique based on 'vibration signature' of tile systems to quantify the bond conditions of the thermal protection system) tiles of Space Shuttle orbiters. The technique uses a laser rapid scan system, modal measurements, and finite element modeling. Finite element models were developed for tiles bonded to both clamped and deformable integrated skin-stringer orbiter mid-fuselage. Results showed that the size and location of a disbonded tile can be determined from frequency and mode shape information. Moreover, a frequency response survey was used to quickly identify the disbonded tiles. The finite element results were compared with experimentally determined frequency responses of a 17-tile test panel, where a rapidscan laser system was employed. An excellent degree of correlation between the mathematical simulation and experimental results was realized. An inverse solution for single-tile assemblies was also derived and is being implemented into a computer program that can interact with the modal testing software. The output of the program displays the size and location of disbond. This program has been tested with simulated input (i.e., finite element data), and excellent agreement between predicted and simulated disbonds was shown. Finally, laser vibration imaging and acoustic emission techniques were shown to be well suited for detecting and monitoring the progressive damage in Graphite/Epoxy composite materials.

  13. Performance of the ATLAS Tile Calorimeter

    NASA Astrophysics Data System (ADS)

    Heelan, Louise; ATLAS Collaboration

    2015-06-01

    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 requirements and it has given essential contribution to reconstructed objects and physics results. In addition, the data quality procedures used during the LHC data-taking are described and the outcome of the detector consolidation in the maintenance period is also presented.

  14. The ATLAS Tile Calorimeter performance at LHC

    NASA Astrophysics Data System (ADS)

    Molander, Simon

    2014-05-01

    This paper gives an overview of the performance of the Tile Calorimeter of the ATLAS detector at the Large Hadron Collider. Detector performances with respect to electronic noise and cell response are presented. In addition, an overview of the partially overlapping calibration systems is given.

  15. L-Tromino Tiling of Multilated Chessboards

    ERIC Educational Resources Information Center

    Gardner, Martin

    2009-01-01

    An "n" x "n" chessboard is called deficient if one square is missing from any spot on the board. Can all deficient boards with a number of cells divisible by 3 be tiled by bent (or L-shaped) trominoes? The answer is yes, with exception of the order-5 board. This paper deals with the general problem plus numerous related puzzles and proofs…

  16. Tile survey seen during EVA 3

    NASA Image and Video Library

    2005-08-03

    S114-E-6396 (3 August 2005) --- Space Shuttle Discovery’s underside thermal protection tiles are featured in this image photographed by astronaut Stephen K. Robinson, STS-114 mission specialist, during the mission’s third session of extravehicular activities (EVA). Lake Nasser along the Nile River, Egypt is visible near Discovery’s starboard wing.

  17. High Temperature Filler for Tile Gaps

    NASA Technical Reports Server (NTRS)

    Holt, J. W.; Wang, D. S.

    1983-01-01

    Gaps between ceramic tiles filled with ceramic-coated fabric that withstands temperatures as high as 2,000 degrees F (1,300 degrees C). Reusable high-temperature gap filler is made of fabric coated with ceramic slurry and bonded in place with room-temperature-vulcanized adhesive. Procedure used in kilns and furnaces.

  18. L-Tromino Tiling of Multilated Chessboards

    ERIC Educational Resources Information Center

    Gardner, Martin

    2009-01-01

    An "n" x "n" chessboard is called deficient if one square is missing from any spot on the board. Can all deficient boards with a number of cells divisible by 3 be tiled by bent (or L-shaped) trominoes? The answer is yes, with exception of the order-5 board. This paper deals with the general problem plus numerous related puzzles and proofs…

  19. TILE at Iowa: Adoption and Adaptation

    ERIC Educational Resources Information Center

    Florman, Jean C.

    2014-01-01

    This chapter introduces a University of Iowa effort to enhance and support active learning pedagogies in technology-enhanced (TILE) classrooms and three elements that proved essential to the campus-wide adoption of those pedagogies. It then describes the impact of those professional development efforts on the curricula and cultures of three…

  20. Lozenge Tilings, Glauber Dynamics and Macroscopic Shape

    NASA Astrophysics Data System (ADS)

    Laslier, Benoît; Toninelli, Fabio Lucio

    2015-09-01

    We study the Glauber dynamics on the set of tilings of a finite domain of the plane with lozenges of side 1/ L. Under the invariant measure of the process (the uniform measure over all tilings), it is well known (Cohn et al. J Am Math Soc 14:297-346, 2001) that the random height function associated to the tiling converges in probability, in the scaling limit , to a non-trivial macroscopic shape minimizing a certain surface tension functional. According to the boundary conditions, the macroscopic shape can be either analytic or contain "frozen regions" (Arctic Circle phenomenon Cohn et al. N Y J Math 4:137-165, 1998; Jockusch et al. Random domino tilings and the arctic circle theorem, arXiv:math/9801068, 1998). It is widely conjectured, on the basis of theoretical considerations (Henley J Statist Phys 89:483-507, 1997; Spohn J Stat Phys 71:1081-1132, 1993), partial mathematical results (Caputo et al. Commun Math Phys 311:157-189, 2012; Wilson Ann Appl Probab 14:274-325, 2004) and numerical simulations for similar models (Destainville Phys Rev Lett 88:030601, 2002; cf. also the bibliography in Henley (J Statist Phys 89:483-507, 1997) and Wilson (Ann Appl Probab 14:274-325, 2004), that the Glauber dynamics approaches the equilibrium macroscopic shape in a time of order L 2+ o(1). In this work we prove this conjecture, under the assumption that the macroscopic equilibrium shape contains no "frozen region".

  1. Preimplantation genetic diagnosis and screening by array comparative genomic hybridisation: experience of more than 100 cases in a single centre.

    PubMed

    Chow, J Fc; Yeung, W Sb; Lee, V Cy; Lau, E Yl; Ho, P C; Ng, E Hy

    2017-04-01

    Preimplantation genetic screening has been proposed to improve the in-vitro fertilisation outcome by screening for aneuploid embryos or blastocysts. This study aimed to report the outcome of 133 cycles of preimplantation genetic diagnosis and screening by array comparative genomic hybridisation. This study of case series was conducted in a tertiary assisted reproductive centre in Hong Kong. Patients who underwent preimplantation genetic diagnosis for chromosomal abnormalities or preimplantation genetic screening between 1 April 2012 and 30 June 2015 were included. They underwent in-vitro fertilisation and intracytoplasmic sperm injection. An embryo biopsy was performed on day-3 embryos and the blastomere was subject to array comparative genomic hybridisation. Embryos with normal copy numbers were replaced. The ongoing pregnancy rate, implantation rate, and miscarriage rate were studied. During the study period, 133 cycles of preimplantation genetic diagnosis for chromosomal abnormalities or preimplantation genetic screening were initiated in 94 patients. Overall, 112 cycles proceeded to embryo biopsy and 65 cycles had embryo transfer. The ongoing pregnancy rate per transfer cycle after preimplantation genetic screening was 50.0% and that after preimplantation genetic diagnosis was 34.9%. The implantation rates after preimplantation genetic screening and diagnosis were 45.7% and 41.1%, respectively and the miscarriage rates were 8.3% and 28.6%, respectively. There were 26 frozen-thawed embryo transfer cycles, in which vitrified and biopsied genetically transferrable embryos were replaced, resulting in an ongoing pregnancy rate of 36.4% in the screening group and 60.0% in the diagnosis group. The clinical outcomes of preimplantation genetic diagnosis and screening using comparative genomic hybridisation in our unit were comparable to those reported internationally. Genetically transferrable embryos replaced in a natural cycle may improve the ongoing pregnancy rate

  2. Hollow clay tile wall program summary report

    SciTech Connect

    Henderson, R.C.; Jones, W.D.

    1995-07-30

    Many of the Y-12 Plant buildings, constructed during the 1940s and 1950s, consist of steel ed concrete framing infilled with hollow clay tile (HCT). The infill was intended to provide for building enclosure and was not designed to have vertical or lateral load-carrying capacity. During the late 1970s and early 1980s, seismic and wind evaluations were performed on many of these buildings in conjunction with the preparation of a site-wide safety analysis report. This analytical work, based on the best available methodology, considered lateral load-carrying capacity of the HCT infill on the basis of building code allowable shear values. In parallel with the analysis effort, DOE initiated a program to develop natural phenomena capacity and performance criteria for existing buildings, but these criteria did not specify guidelines for determining the lateral force capacity of frames infilled with HCT. The evaluation of infills was, therefore, based on the provisions for the design of unreinforced masonry as outlined in standard masonry codes. When the results of the seismic and wind evaluations were compared with the new criteria, the projected building capacities fell short of the requirements. Apparently, if the buildings were to meet the new criteria, many millions of dollars would be required for building upgrades. Because the upgrade costs were significant, the assumptions and approaches used in the analyses were reevaluated. Four issues were identified: (1) Once the infilled walls cracked, what capacity (nonlinear response), if any, would the walls have to resist earthquake or wind loads applied in the plane of the infill (in-plane)? (2) Would the infilled walls remain within the steel or reinforced concrete framing when subjected to earthquake or high wind loads applied perpendicular to the infill (out-of-plane)? (3) What was the actual shear capacity of the HCT infill? (4) Was modeling the HCT infill as a shear wall the best approach?

  3. Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization.

    PubMed

    Yuan, Bo; Liu, Pengfei; Rogers, Jeffrey; Lupski, James R

    2016-06-01

    Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45 kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primates revealed dynamic copy number transitions of the human 45 kb LCR orthologues during primate evolution and therefore shed light on the origin of complexity at this locus. The original aCGH data are available at GEO under GSE73962.

  4. Preimplantation genetic diagnosis for chromosomal rearrangements with the use of array comparative genomic hybridization at the blastocyst stage.

    PubMed

    Christodoulou, Christodoulos; Dheedene, Annelies; Heindryckx, Björn; van Nieuwerburgh, Filip; Deforce, Dieter; De Sutter, Petra; Menten, Björn; Van den Abbeel, Etienne

    2017-01-01

    To establish the value of array comparative genomic hybridization (CGH) for preimplantation genetic diagnosis (PGD) in embryos of translocation carriers in combination with vitrification and frozen embryo transfer in nonstimulated cycles. Retrospective data analysis study. Academic centers for reproductive medicine and genetics. Thirty-four couples undergoing PGD for chromosomal rearrangements from October 2013 to December 2015. Trophectoderm biopsy at day 5 or day 6 of embryo development and subsequently whole genome amplification and array CGH were performed. This approach revealed a high occurrence of aneuploidies and structural rearrangements unrelated to the parental rearrangement. Nevertheless, we observed a benefit in pregnancy rates of these couples. We detected chromosomal abnormalities in 133/207 embryos (64.2% of successfully amplified), and 74 showed a normal microarray profile (35.7%). In 48 of the 133 abnormal embryos (36.1%), an unbalanced rearrangement originating from the parental translocation was identified. Interestingly, 34.6% of the abnormal embryos (46/133) harbored chromosome rearrangements that were not directly linked to the parental translocation in question. We also detected a combination of unbalanced parental-derived rearrangements and aneuploidies in 27 of the 133 abnormal embryos (20.3%). The use of trophectoderm biopsy at the blastocyst stage is less detrimental to the survival of the embryo and leads to a more reliable estimate of the genomic content of the embryo than cleavage-stage biopsy. In this small cohort PGD study, we describe the successful implementation of array CGH analysis of blastocysts in patients with a chromosomal rearrangement to identify euploid embryos for transfer. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  5. Comparative study on mode-identification algorithms using a phased-array system in a rectangular duct

    NASA Astrophysics Data System (ADS)

    Suzuki, Takao; Day, Benjamin J.

    2015-07-01

    To identify multiple acoustic duct modes, conventional beam-forming, CLEAN as well as L2 (i.e. pseudo-inverse) and L1 generalized-inverse beam-forming are applied to phased-array pressure data. A tone signal of a prescribed mode or broadband signal is generated upstream of a curved rectangular duct, and acoustic fields formed in both upstream and downstream stations of the test section are measured with identical wall-mounted microphone arrays. Sound-power distributions of several horizontal and vertical modes including upstream- and downstream-propagating waves can be identified with phased-array techniques, and the results are compared among the four approaches. The comparisons using synthetic data demonstrate that the L2 generalized-inverse algorithm can sufficiently suppress undesirable noise levels and detect amplitude distributions accurately in over-determined cases (i.e. the number of microphones is more than the number of cut-on modes) with minimum computational cost. As the number of cut-on modes exceeds the number of microphones (i.e. under-determined problems), the L1 algorithm is necessary to retain better accuracy. The comparison using test data acquired in the curved duct test rig (CDTR) at NASA Langley Research Center suggests that the L1 /L2 generalized-inverse approach as well as CLEAN can improve the dynamic range of the detected mode by as much as 10 dB relative to conventional beam-forming even with mean flow of M=0.5.

  6. Comparative evaluation of the FilmArray meningitis/encephalitis molecular panel in a pediatric population.

    PubMed

    Graf, Erin H; Farquharson, Maria Victoria; Cárdenas, Ana María

    2017-01-01

    We compared an FDA cleared molecular meningitis/encephalitis panel to lab developed viral PCRs and bacterial culture. Of the 67 viral PCR or bacterial culture-positive samples, 92.5% were positive for the same target by the panel. Of the 66 negative samples tested, no targets were detected by the panel, for an agreement of 96.2%.

  7. Tile-based Level of Detail for the Parallel Age

    SciTech Connect

    Niski, K; Cohen, J D

    2007-08-15

    Today's PCs incorporate multiple CPUs and GPUs and are easily arranged in clusters for high-performance, interactive graphics. We present an approach based on hierarchical, screen-space tiles to parallelizing rendering with level of detail. Adapt tiles, render tiles, and machine tiles are associated with CPUs, GPUs, and PCs, respectively, to efficiently parallelize the workload with good resource utilization. Adaptive tile sizes provide load balancing while our level of detail system allows total and independent management of the load on CPUs and GPUs. We demonstrate our approach on parallel configurations consisting of both single PCs and a cluster of PCs.

  8. Comparative Analysis on the Performance of a Short String of Series-Connected and Parallel-Connected Photovoltaic Array Under Partial Shading

    NASA Astrophysics Data System (ADS)

    Vijayalekshmy, S.; Rama Iyer, S.; Beevi, Bisharathu

    2015-09-01

    The output power from the photovoltaic (PV) array decreases and the array exhibit multiple peaks when it is subjected to partial shading (PS). The power loss in the PV array varies with the array configuration, physical location and the shading pattern. This paper compares the relative performance of a PV array consisting of a short string of three PV modules for two different configurations. The mismatch loss, shading loss, fill factor and the power loss due to the failure in tracking of the global maximum power point, of a series string with bypass diodes and short parallel string are analysed using MATLAB/Simulink model. The performance of the system is investigated for three different conditions of solar insolation for the same shading pattern. Results indicate that there is considerable power loss due to shading in a series string during PS than in a parallel string with same number of modules.

  9. Frequent deletion of the CDKN2A locus in chordoma: analysis of chromosomal imbalances using array comparative genomic hybridisation

    PubMed Central

    Hallor, K H; Staaf, J; Jönsson, G; Heidenblad, M; Vult von Steyern, F; Bauer, H C F; IJszenga, M; Hogendoorn, P C W; Mandahl, N; Szuhai, K; Mertens, F

    2007-01-01

    The initiating somatic genetic events in chordoma development have not yet been identified. Most cytogenetically investigated chordomas have displayed near-diploid or moderately hypodiploid karyotypes, with several numerical and structural rearrangements. However, no consistent structural chromosome aberration has been reported. This is the first array-based study characterising DNA copy number changes in chordoma. Array comparative genomic hybridisation (aCGH) identified copy number alterations in all samples and imbalances affecting 5 or more out of the 21 investigated tumours were seen on all chromosomes. In general, deletions were more common than gains and no high-level amplification was found, supporting previous findings of primarily losses of large chromosomal regions as an important mechanism in chordoma development. Although small imbalances were commonly found, the vast majority of these were detected in single cases; no small deletion affecting all tumours could be discerned. However, the CDKN2A and CDKN2B loci in 9p21 were homo- or heterozygously lost in 70% of the tumours, a finding corroborated by fluorescence in situ hybridisation, suggesting that inactivation of these genes constitute an important step in chordoma development. PMID:18071362

  10. Effects of chromosomal variations on pharmacokinetic activity of zolpidem in healthy volunteers: an array-based comparative genomic hybridization study.

    PubMed

    Moon, Ho-Jin; Choi, Jin Soo; Park, E-Jin; Kang, Chin-Yang; Jeon, Yang-Whan; Lee, Kweon-Haeng; Rha, Hyoung Kyun; Han, Sang-Ick

    2007-05-18

    Zolpidem has been known as a very safe and effective hypnotic drug used to treat a variety of patients with insomnia. Even though the same dose of the medicine is administered to each patient, the blood level of zolpidem and the time required to obtain peak concentration are not consistent among different people. We evaluated the relationship between the peak concentrations of zolpidem and chromosomal imbalances using a high-resolution genome-wide array-based comparative genomic hybridization (CGH) in 16 healthy volunteers in order to detect the genetic factors underlying the variations. The present study showed that chromosomal losses were detected in the 4q35.2, 9p13.1 and 9p12 regions, and those gains were indicated in the 2p14, 11q13.4 and 15q11.2 regions. The abnormal regions were confirmed by fluorescence in situ hybridization (FISH) and real-time PCR. It is suggested that array-CGH analysis may be used as a measure for pharmacogenomic applications in the patients with insomnia and for further exploration of candidate genomic regions implicated in sleep disturbances.

  11. Zoom-in array comparative genomic hybridization (aCGH) to detect germline rearrangements in cancer susceptibility genes.

    PubMed

    Staaf, Johan; Borg, Ake

    2010-01-01

    Disease predisposing germline mutations in cancer susceptibility genes may consist of large genomic rearrangements, including deletions or duplications that are challenging, to detect and characterize using standard PCR-based mutation screening methods. Such rearrangements range from single exons up to hundreds of kilobases of sequence in size. Array-based comparative genomic hybridization (aCGH) has evolved as a powerful technique to detect copy number alterations on a genome-wide scale. However, the conventional genome-wide approach of aCGH still provides only limited information about copy number status for individual exons. Custom-designed aCGH arrays focused on only a few target regions (zoom-in aCGH) may circumvent this drawback. Benefits of zoom-in aCGH include the possibility to target almost any region in the genome, and an unbiased coverage of exonic and intronic sequence facilitating convenient design of primers for sequence determination of the breakpoints. Furthermore, zoom-in aCGH can be streamlined for a particular application, for example, focusing on breast cancer susceptibility genes, with increased capacity using multiformat design.

  12. Salmonella and fecal indicator bacteria in tile waters draining poultry litter application fields in central Iowa

    NASA Astrophysics Data System (ADS)

    Hruby, C.; Soupir, M.

    2012-12-01

    E. coli and enterococci are commonly used as pathogen indicators in surface waters. Along with these indicators, pathogenic Salmonella are prevalent in poultry litter, and have the potential to be transported from land-application areas to tile waters and ultimately to impact waters that are used for drinking-water and recreation. The fate and transport of these bacteria to drainage tiles from application fields, and the correlation of fecal indicator bacteria to pathogens in this setting, is poorly understood. In this field study, samples were obtained from poultry litter, soil, and drainage tile waters below chisel-plowed and no-till cornfields in central Iowa where poultry litter was applied each year in late spring prior to planting. Litter was applied at three different rates; commercial fertilizer with no litter, a low application rate based on the nitrogen requirements of the corn (PL1), and double the low rate (PL2). This site is characterized by low sloping (0-9%) Clarion and Nicollet soils, which are derived from glacial till. Samples were collected from April to September for three years (2010-12) when tiles were flowing. Record high precipitation fell during the sampling period in 2010, while 2011 and 2012 were exceptionally dry years at this location. Grab samples were taken directly from flowing tiles after every rainfall event (>2 cm in less than 24 hours) and samples were collected hourly throughout selected events using an automatic sampling device. Concentrations of E. coli, enterococci and Salmonella spp. were quantified by membrane filtration and growth on selective agars. Peak bacteria concentrations following rainfall events were often one order of magnitude higher in tile waters discharging from no-till plots, despite the smaller size and lower tile flow rates at these plots compared to the chisel-plowed plots. Bacteria concentrations regularly varied by two orders of magnitude in response to rainfall events. Bacteria transport via macropores

  13. Uncertainty in tile drain locations: Implications for hydrologic modeling of agricultural watersheds

    NASA Astrophysics Data System (ADS)

    Ogden, F. L.; Pradhan, N.; Downer, C. W.

    2009-12-01

    Predictive capabilities for water quality in agricultural watersheds must include consideration of subsurface tile drains, which effectively short-circuit the groundwater system, and result in rapid delivery of dissolved constituents to streams. Discharges of nutrients in particular have a significant effect on receiving water quality. Given the importance of tile drainage systems on water quality, surprisingly little is known about their extent, location, connectivity, and flow capacity. Some studies have shown that infrared imagery can help identify the presence of tile drains in agricultural fields. In this study we apply the Gridded Surface-Subsurface Hydrologic Analysis (GSSHA) Model, which explicitly includes tile drain hydraulics coupled to the groundwater system, to explore the necessity of exact knowledge of the location of agricultural tile drains. Simulations begin with a deterministic system modeled after the Sugar Creek, Indiana, watershed that has been monitored by the USGS. Simulation results from the deterministic system are compared against simulations that include differing approximations of the extent, location, connectivity, and flow capacity of the subsurface drainage network. Results reveal the impact of uncertainty in subsurface drainage network properties on hydrologic predictability.

  14. A landsat data tiling and compositing approach optimized for change detection in the conterminous United States

    USGS Publications Warehouse

    Nelson, Kurtis; Steinwand, Daniel R.

    2015-01-01

    Annual disturbance maps are produced by the LANDFIRE program across the conterminous United States (CONUS). Existing LANDFIRE disturbance data from 1999 to 2010 are available and current efforts will produce disturbance data through 2012. A tiling and compositing approach was developed to produce bi-annual images optimized for change detection. A tiled grid of 10,000 × 10,000 30 m pixels was defined for CONUS and adjusted to consolidate smaller tiles along national borders, resulting in 98 non-overlapping tiles. Data from Landsat-5,-7, and -8 were re-projected to the tile extents, masked to remove clouds, shadows, water, and snow/ice, then composited using a cosine similarity approach. The resultant images were used in a change detection algorithm to determine areas of vegetation change. This approach enabled more efficient processing compared to using single Landsat scenes, by taking advantage of overlap between adjacent paths, and allowed an automated system to be developed for the entire process.

  15. A semi-analytical model for transient flow to a subsurface tile drain

    NASA Astrophysics Data System (ADS)

    Stillman, Jennifer S.; Haws, Nathan W.; Govindaraju, R. S.; Rao, P. Suresh C.

    2006-02-01

    The goal of this paper is to develop and test a semi-analytical model for event-based transient flow to a subsurface tile drain. A sharp-front theory was used to describe redistribution of infiltrated water in the vadose zone. New approximate analytical solutions in terms of Fourier series were sought for the Boussinesq equation describing subsurface saturated flow subject to time-dependent recharge. Both one and two-term solutions of the series approximation were compared with observed tile hydrograph data from the Purdue Water Quality Field Station (WQFS) in West Lafayette, Indiana. In general, the models were able to capture the peaks of the tile-drain hydrographs, as well as the times-to-peak and the times-of-initial-response to rainfall events. The models performed particularly well for rainfall events with single-burst hyetographs, and in the prediction of the first hydrograph peak from multiple-burst hyetographs, though subsequent peaks could not be captured as well. A further comparison of results from the one-term model with those from HYDRUS 2D suggested that the one-term model is adequate for estimating transient flow to a tile drain. The solution developed here holds promise for extension to larger watersheds where the hydrology is governed by tile drains.

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

    PubMed

    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.

  17. Bacillus subtilis RNase Y Activity In Vivo Analysed by Tiling Microarrays

    PubMed Central

    Rocca, Anna; Zig, Léna; Nicolas, Pierre; Putzer, Harald

    2013-01-01

    RNase Y is a key endoribonuclease affecting global mRNA stability in Bacillus subtilis. Its characterization provided the first evidence that endonucleolytic cleavage plays a major role in the mRNA metabolism of this organism. RNase Y shares important functional features with the RNA decay initiating RNase E from Escherichia coli, notably a similar cleavage specificity and a preference for 5′ monophosphorylated substrates. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. The downstream cleavage products are likely to be degraded by the 5′ exonucleolytic activity of RNases J1/J2 as we show for a specific case. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% were in common in all three studies. This highlights that experimental conditions and data analysis play an important role in identifying RNase Y substrates by global transcriptional profiling. Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allow an exceptionally detailed view of the turnover of hundreds of new RNA substrates. PMID:23326572

  18. De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism

    NASA Astrophysics Data System (ADS)

    Yu, Jinwen; Liu, Zhiyu; Jiang, Wen; Wang, Guansong; Mao, Chengde

    2015-01-01

    Rational, de novo design of RNA nanostructures can potentially integrate a wide array of structural and functional diversities. Such nanostructures have great promises in biomedical applications. Despite impressive progress in this field, all RNA building blocks (or tiles) reported so far are not geometrically well defined. They are generally flexible and can only assemble into a mixture of complexes with different sizes. To achieve defined structures, multiple tiles with different sequences are needed. In this study, we design an RNA tile that can homo-oligomerize into a uniform RNA nanostructure. The designed RNA nanostructure is characterized by gel electrophoresis, atomic force microscopy and cryogenic electron microscopy imaging. We believe that development along this line would help RNA nanotechnology to reach the structural control that is currently associated with DNA nanotechnology.

  19. Test procedure for measurement of masonry flexural bond strength (Bond Wrench Test). Hollow Clay Tile Wall Test Program

    SciTech Connect

    Hardin, E.J.; Wynn, C.C.

    1992-03-30

    This document describes a procedure for determining the flexural bond strength of in situ hollow clay tile bed joints by physical testing of selected joints. This procedure is based on the requirements of ASTM C1072-86. The principal objective of this test is to provide a simple and economical means for the determination of comparative values of flexural bond strength by physical testing of each joint of non-reinforced existing hollow clay tile masonry.

  20. LSAMP, a novel candidate tumor suppressor gene in human osteosarcomas, identified by array comparative genomic hybridization.

    PubMed

    Kresse, Stine H; Ohnstad, Hege O; Paulsen, Erik B; Bjerkehagen, Bodil; Szuhai, Karoly; Serra, Massimo; Schaefer, Karl-Ludwig; Myklebost, Ola; Meza-Zepeda, Leonardo A

    2009-08-01

    Osteosarcomas are the most common primary malignant tumor of bone, and almost all conventional osteosarcomas are high-grade tumors with complex karyotypes. We have examined DNA copy number changes in 36 osteosarcoma tumors and 20 cell lines using microarray-based comparative genomic hybridization. The most frequent minimal recurrent regions of gain identified in the tumor samples were in 1q21.2-q21.3 (78% of the samples), 1q21.3-q22 (78%), and 8q22.1 (72%). Minimal recurrent regions in 10q22.1-q22.2 (81%), 6q16.1 (67%), 13q14.2 (67%), and 13q21.1 (67%) were most frequently lost. A small region in 3q13.31 (2.1 Mb) containing the gene limbic system-associated membrane protein (LSAMP) was frequently deleted (56%). LSAMP has previously been reported to be a candidate tumor suppressor gene in other cancer types. The deletion was validated using fluorescence in situ hybridization, and the expression level and promoter methylation status of LSAMP were investigated using quantitative real-time reverse transcription PCR and methylation-specific PCR, respectively. LSAMP showed low expression compared to two normal bone samples in 6/15 tumors and 5/9 cell lines with deletion of 3q13.31, and also in 5/14 tumors and 3/11 cell lines with normal copy number or gain. Partial or full methylation of the investigated CpG island was identified in 3/30 tumors and 7/20 cell lines. Statistical analyses revealed that loss of 11p15.4-p15.3 and low expression of LSAMP (both P = 0.011) were significantly associated with poor survival. Our results show that LSAMP is a novel candidate tumor suppressor gene in osteosarcomas.

  1. Characterization of hemizygous deletions in citrus using array-comparative genomic hybridization and microsynteny comparisons with the poplar genome.

    PubMed

    Ríos, Gabino; Naranjo, Miguel A; Iglesias, Domingo J; Ruiz-Rivero, Omar; Geraud, Marion; Usach, Antonio; Talón, Manuel

    2008-08-09

    Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in

  2. Characterization of hemizygous deletions in Citrus using array-Comparative Genomic Hybridization and microsynteny comparisons with the poplar genome

    PubMed Central

    Ríos, Gabino; Naranjo, Miguel A; Iglesias, Domingo J; Ruiz-Rivero, Omar; Geraud, Marion; Usach, Antonio; Talón, Manuel

    2008-01-01

    Background Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background. Results Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues. Conclusion In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny

  3. Interactive Scientific Visualization of High-resolution Brain Imagery Over Networked Tiled Display

    NASA Astrophysics Data System (ADS)

    Son, Seokho; Hong, Junhee; Bae, Changhyeok; Jun, Sung Chan; Kim, Jong Won

    In this paper, we discuss our on-going efforts for an interactive scientific visualization of high-resolution brain imagery over networked tiled display. It targets to visualize a brain in both 2D and 3D. It also supports multiple highresolution displays of brain images by integrating networked tiled display while providing interactive control of display resolution and view direction. In order to construct an appropriate visualization system for brain imaging researches, we study and compare existing visualization systems using a networked tiled display. Based on this comparison, we integrate visualization features on our brain visualization system. Finally, to verify the usefulness of the proposed approach, an initial implementation of EIT brain image visualization is being made.

  4. Comparing passive source localization and tracking approaches with a towed horizontal receiver array in an ocean waveguide.

    PubMed

    Gong, Zheng; Tran, Duong D; Ratilal, Purnima

    2013-11-01

    Approaches for instantaneous passive source localization using a towed horizontal receiver array in a random range-dependent ocean waveguide are examined. They include: (1) Moving array triangulation, (2) array invariant, (3) bearings-only target motion analysis in modified polar coordinates via the extended Kalman filter, and (4) bearings-migration minimum mean-square error. These methods are applied to localize and track a vertical source array deployed in the far-field of a towed horizontal receiver array during the Gulf of Maine 2006 Experiment. The source transmitted intermittent broadband pulses in the 300 to 1200 Hz frequency range. A nonlinear matched-filter kernel designed to replicate the acoustic signal measured by the receiver array is applied to enhance the signal-to-noise ratio. The source localization accuracy is found to be highly dependent on source-receiver geometry and the localization approach. For a relatively stationary source drifting at speeds much slower than the receiver array tow-speed, the mean source position can be estimated by moving array triangulation with less than 3% error near broadside direction. For a moving source, the Kalman filter method gives the best performance with 5.5% error. The array invariant is the best approach for localizing sources within the endfire beam of the receiver array with 7% error.

  5. Firing ceramic tiles in solar energy equipment

    SciTech Connect

    Pasichnyi, V.V.; Berezhetskaya, V.Ya.; Chop, Yu.I.; Kashket, G.I.

    1987-03-01

    In the interest of satisfying the growing demand for glazed ceramic tiles and conserving the natural gas ordinarily used to fire them, the authors assess the feasibility of using a solar kiln for the process. Their design incorporates a parabolic reflector and a tracking system to continuously focus radiant solar energy on the tile. Their energy analysis includes such factors as solar thermal input, radiant heat transfer, and heat flow, the relationship between the firing time and the heat flow density, and the surface quality of the glaze and colorizer. Their results indicate that when the heat flow density rises above a level at which the specific expenditure of heat is no longer dependent on the color of the pigment, this expenditure or input comes to a quarter of what is currently needed using existing technologies and fuels.

  6. Anosov Diffeomorphisms and {γ}-Tilings

    NASA Astrophysics Data System (ADS)

    Almeida, João P.; Pinto, Alberto A.

    2016-07-01

    We consider a toral Anosov automorphism {G_γ:{mathbb{T}}_γto{mathbb{T}}_γ} given by {G_γ(x,y)=(ax+y,x)} in the { < v,w > } base, where {ainmathbb{N} backslash\\{1\\}}, {γ=1/(a+1/(a+1/ldots))}, {v=(γ,1)} and {w=(-1,γ)} in the canonical base of {{mathbb{R}}^2} and {{mathbb{T}}_γ={mathbb{R}}^2/(v{mathbb{Z}} × w{mathbb{Z}})}. We introduce the notion of {γ}-tilings to prove the existence of a one-to-one correspondence between (i) marked smooth conjugacy classes of Anosov diffeomorphisms, with invariant measures absolutely continuous with respect to the Lebesgue measure, that are in the isotopy class of {G_γ}; (ii) affine classes of {γ}-tilings; and (iii) {γ}-solenoid functions. Solenoid functions provide a parametrization of the infinite dimensional space of the mathematical objects described in these equivalences.

  7. Degenerate polygonal tilings in simple animal tissues

    NASA Astrophysics Data System (ADS)

    Hočevar, A.; Ziherl, P.

    2009-07-01

    The salient feature of one-cell-thick epithelia is their en face view, which reveals the polygonal cross section of the close-packed prismatic cells. The physical mechanisms that shape these tissues were hitherto explored using theories based on cell proliferation, which were either entirely topological or included certain morphogenetic forces. But mitosis itself may not be instrumental in molding the tissue. We show that the structure of simple epithelia can be explained by an equilibrium model where energy-degenerate polygons in an entropy-maximizing tiling are described by a single geometric parameter encoding their inflatedness. The two types of tilings found numerically—ordered and disordered—closely reproduce the patterns observed in Drosophila, Hydra, and Xenopus and they generalize earlier theoretical results. Free of a specific cell self-energy, cell-cell interaction, and cell division kinetics, our model provides an insight into the universality of living and inanimate two-dimensional cellular structures.

  8. Residual Mechanical Properties of Concrete Made with Crushed Clay Bricks and Roof Tiles Aggregate after Exposure to High Temperatures.

    PubMed

    Miličević, Ivana; Štirmer, Nina; Banjad Pečur, Ivana

    2016-04-19

    This paper presents the residual mechanical properties of concrete made with crushed bricks and clay roof tile aggregates after exposure to high temperatures. One referent mixture and eight mixtures with different percentages of replacement of natural aggregate by crushed bricks and roof tiles are experimentally tested. The properties of the concrete were measured before and after exposure to 200, 400, 600 and 800 °C. In order to evaluate the basic residual mechanical properties of concrete with crushed bricks and roof tiles after exposure to high temperatures, ultrasonic pulse velocity is used as a non-destructive test method and the results are compared with those of a destructive method for validation. The mixture with the highest percentage of replacement of natural aggregate by crushed brick and roof tile aggregate has the best physical, mechanical, and thermal properties for application of such concrete in precast concrete elements exposed to high temperatures.

  9. Residual Mechanical Properties of Concrete Made with Crushed Clay Bricks and Roof Tiles Aggregate after Exposure to High Temperatures

    PubMed Central

    Miličević, Ivana; Štirmer, Nina; Banjad Pečur, Ivana

    2016-01-01

    This paper presents the residual mechanical properties of concrete made with crushed bricks and clay roof tile aggregates after exposure to high temperatures. One referent mixture and eight mixtures with different percentages of replacement of natural aggregate by crushed bricks and roof tiles are experimentally tested. The properties of the concrete were measured before and after exposure to 200, 400, 600 and 800 °C. In order to evaluate the basic residual mechanical properties of concrete with crushed bricks and roof tiles after exposure to high temperatures, ultrasonic pulse velocity is used as a non-destructive test method and the results are compared with those of a destructive method for validation. The mixture with the highest percentage of replacement of natural aggregate by crushed brick and roof tile aggregate has the best physical, mechanical, and thermal properties for application of such concrete in precast concrete elements exposed to high temperatures. PMID:28773420

  10. Mapping Signal Processing Kernels to Tiled Architectures

    DTIC Science & Technology

    2007-11-02

    attractive alternatives to monolithic computer architecture designs because they allow a larger design to be built from smaller modules and limit the...Computer Architectures. ACM Transactions on Computer Systems, 2(4):289–308, November 1984. [12] Steven Swanson, Ken Michelson , Andrew Schwerin, and...Program MIT Lincoln LaboratoryHPEC 2004-3 JML 28 Sep 2004 Tiled Architectures • Monolithic single-chip architectures are becoming rare in the industry

  11. NASA TileWorld Simulator Program

    NASA Technical Reports Server (NTRS)

    Philips, Andrew; Bresina, John; Drummond, Mark

    1993-01-01

    NASA TileWorld (NTW) computer program formulated to further research on planning, scheduling, and control problems. Designed to focus on three particular attributes of real-world problems: exogenous events, uncertain outcomes of actions, and metric time. Written specifically for use by NASA, NTW modified easily to act as software base for other simulated environments. Written in Allegro Common Lisp for Sun-3-(TM) and Sun-4-series(TM) computers running SunOS(TM).

  12. Laser printing of enamels on tiles

    NASA Astrophysics Data System (ADS)

    Fernández-Pradas, J. M.; Restrepo, J. W.; Gómez, M. A.; Serra, P.; Morenza, J. L.

    2007-07-01

    A Nd:YAG laser beam is used as a tool to print patterns of coloured enamels on tile substrates. For this, the laser beam is scanned over a layer of raw enamel previously sprayed on the tile surface. The possibility to focus the laser energy to heat a small zone without affecting the rest of the piece presents some advantages in front of traditional furnace techniques in which the whole piece has to be heated; among them, energy saving and the possibility to apply enamels with higher melting temperatures than those of the substrate. In this work, we study the effects of laser irradiation of a green enamel, based in chromium oxide pigment and lead frit, deposited on a white tile substrate. Lines obtained with different combinations of laser beam power and scan speeds were investigated with the aim to optimize the process from the point of view of the quality of the patterns. For this purpose, the morphology of the lines and their cross-sections is studied. The results show that lines with good visual properties can be printed with the laser. The characteristics of the marked lines were found to be directly related with the accumulated energy density delivered. Moreover, there is a linear relationship between the accumulated energy density and the volume of melted material. A minimum accumulated energy density is required to melt a shallow zone of the glazed substrate to allow the adhesion of the enamelled lines.

  13. Foam-on-Tile Damage Model

    NASA Technical Reports Server (NTRS)

    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.

  14. Performance of the ATLAS Tile Calorimeter

    NASA Astrophysics Data System (ADS)

    Cole, Stephe

    2013-04-01

    The Tile Calorimeter is the central section (0 < |η| < 1.7) of the ATLAS hadronic calorimeter. It is a key detector for the measurement of hadrons, jets, tau leptons decaying hadronically, and missing transverse energy. Because of its very good signal to noise ratio it is also useful for the identification and reconstruction of muons. The calorimeter consists of thin steel plates and 460,000 scintillating tiles configured into 4900 cells, each viewed by two photomultipliers. The calorimeter response is monitored to better than 1% using radioactive source, laser, and electronic 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 pp collisions acquired during 2011 and 2012. Results on the calorimeter performance will be presented, including the absolute energy scale, time resolution, and associated stabilities. These results demonstrate that the Tile Calorimeter is performing well within the design requirements and is giving essential input to the physics results.

  15. High-density tiling microarray analysis of the full transcriptional activity of yeast.

    PubMed

    David, Lior; Clauder-Münster, Sandra; Steinmetz, Lars M

    2014-01-01

    Understanding the relationship between DNA sequence variation and phenotypic variation in complex or quantitative traits is one of the major challenges in modern biology. We are witnessing a deluge of DNA sequence information and association studies of genetic polymorphisms with phenotypes of interest in families and populations. In addition, it has become clear that large portions of eukaryotic genomes beyond protein-coding genes are transcribed, generating numerous noncoding RNA (ncRNA) molecules whose functions remain mostly unknown.DNA oligonucleotide microarrays constitute a powerful technology for studying the expression of genes in different organisms. The Saccharomyces cerevisiae tiling array presents a significant advance over previous array-based platforms. It has a high density of overlapping probes that start on average every 8 bp along each strand of the genome, enabling precise definition of transcript structure. Furthermore, the array includes probes specific for the polymorphic positions of another, distantly related yeast strain, allowing accurate measurement of allele-specific expression in a hybrid of the two strains. This technology thus allows high-resolution, quantitative, strand- and allele-specific measurements of transcription from a full eukaryotic genome. In this chapter, we describe the methods for extracting RNA, synthesizing first-strand cDNA, fragmenting, and labeling of samples for hybridization to the tiling array. Combining genome-wide information on variation in DNA sequence with variation in transcript structure and levels promises to increase our understanding of the genotype-to-phenotype relationship.

  16. Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing

    PubMed Central

    Watanabe, Kenneth A.; Homayouni, Arielle; Tufano, Tara; Lopez, Jennifer; Ringler, Patricia; Rushton, Paul; Shen, Qingxi J.

    2015-01-01

    Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation. PMID:26341416

  17. Low Noise Performance Perspectives Of Wideband Aperture Phased Arrays

    NASA Astrophysics Data System (ADS)

    Woestenburg, E. E. M.; Kuenen, J. C.

    2004-06-01

    A general analysis of phased array noise properties and measurements, applied to one square meter tiles of the Thousand Element Array (THEA), has resulted in a procedure to define the noise budget for a THEA-tile (Woestenburg and Dijkstra, 2003). The THEA system temperature includes LNA and receiver noise, antenna connecting loss, noise coupling between antenna elements and other possible contributions. This paper discusses the various noise contributions to the THEA system temperature and identifies the areas where improvement can be realized. We will present better understanding of the individual noise contributions using measurements and analysis of single antenna/receiver elements. An improved design for a 1-m2 Low Noise Tile (LNT) will be discussed and optimized low noise performance for the LNT is presented. We will also give future perspectives of the noise performance for such tiles, in relation to the requirements for SKA in the 1 GHz frequency range.

  18. Microbial Volatile Organic Compound Emissions from Stachybotrys chartarum growing on Gypsum Wallboard and Ceiling tile

    EPA Science Inventory

    This study compared seven toxigenic strains of S. chartarum found in water-damaged buildings to characterize the microbial volatile organic compound (MVOC) emissions profile while growing on gypsum wallboard (W) and ceiling tile (C) coupons. The inoculated coupons with their sub...

  19. Microbial Volatile Organic Compound Emissions from Stachybotrys chartarum growing on Gypsum Wallboard and Ceiling tile

    EPA Science Inventory

    This study compared seven toxigenic strains of S. chartarum found in water-damaged buildings to characterize the microbial volatile organic compound (MVOC) emissions profile while growing on gypsum wallboard (W) and ceiling tile (C) coupons. The inoculated coupons with their sub...

  20. Comparative particle recoveries by the retracting rotorod, rotoslide and Burkard spore trap sampling in a compact array

    NASA Astrophysics Data System (ADS)

    Solomon, W. R.; Burge, H. A.; Boise, J. R.; Becker, M.

    1980-06-01

    An array comprising 4 intermittent (retracting) rotorods, 3 (“swingshield”) rotoslides and one Burkard (Hirst) automatic volumetric spore trap was operated on an urban rooftop during 70 periods of 9, 15 or 24 hours in late summer. Standard sampling procedures were utilized and recoveries of pollens as well as spores of Alternaria, Epicoccum, Pithomyces and Ganoderma species compared. Differences between paired counts from each sampler type showed variances increasing with levels of particle prevalence (and deposition). In addition, minimal, non-random, side-to-side and intersampler differences were noted for both impactor types. Exclusion of particles between operating intervals by rotoslides and rotorods was virtually complete. Spore trap recoveries for all particle categories, per m3, exceeded those by both impactors. The greatest (7-fold) difference was noted for the smallest type examined ( Ganoderma). For ragweed pollen, an overall spore trap/impactor ratio approached 1.5. Rain effects were difficult to discern but seemed to influence rotoslides least. Overall differences between impactors were quite small but generally favored the rotoslide in this comparison. Our data confirm the relative advantages of suction traps for small particles. Both impactors and spore traps are suited to pollen and large spore collection, and, with some qualification, data from both may be compared.

  1. Additional information from array comparative genomic hybridization technology over conventional karyotyping in prenatal diagnosis: a systematic review and meta-analysis.

    PubMed

    Hillman, S C; Pretlove, S; Coomarasamy, A; McMullan, D J; Davison, E V; Maher, E R; Kilby, M D

    2011-01-01

    Array comparative genomic hybridization (CGH) is transforming clinical cytogenetics with its ability to interrogate the human genome at increasingly high resolution. The aim of this study was to determine whether array CGH testing in the prenatal population provides diagnostic information over conventional karyotyping. MEDLINE (1970 to December 2009), EMBASE (1980 to December 2009) and CINAHL (1982 to December 2009) databases were searched electronically. Studies were selected if array CGH was used on prenatal samples or if array CGH was used on postnatal samples following termination of pregnancy for structural abnormalities that were detected on an ultrasound scan. Of the 135 potential articles, 10 were included in this systematic review and eight were included in the meta-analysis. The pooled rate of extra information detected by array CGH when the prenatal karyotype was normal was meta-analyzed using a random-effects model. The pooled rate of receiving an array CGH result of unknown significance was also meta-analyzed. Array CGH detected 3.6% (95% CI, 1.5-8.5) additional genomic imbalances when conventional karyo-typing was 'normal', regardless of referral indication. This increased to 5.2% (95% CI, 1.9-13.9) more than karyotyping when the referral indication was a structural malformation on ultrasound. There appears to be an increased detection rate of chromosomal imbalances, compared with conventional karyotyping, when array CGH techniques are employed in the prenatal population. However, some are copy number imbalances that are not clinically significant. This carries implications for prenatal counseling and maternal anxiety.

  2. Experimental study of a very high frequency (162MHz) capacitively coupled multi-tile electrode plasma source

    NASA Astrophysics Data System (ADS)

    Sirse, Nishant; Ellingboe, Bert

    2015-09-01

    In the recent years, plasma discharges excited at very high frequency (30-500MHz) has attracted much attention due to its ability to perform etching and deposition of large area substrates. VHF discharges yield high plasma density and low electron temperature and enable enhanced plasma dissociation. However, the plasma chemistry and power coupling mechanism in VHF discharges is not fully understood. In this article, we present an experimental study on nitrogen plasma produced by a VHF (162 MHz) multi-tile electrode. Electron density profile and gas temperature (rotational and vibrational) are measured as a function of rf power (100-1500W) and gas pressure (50mTorr-1Torr). Tile centre and Tile edge data are presented to realize the power coupling mechanism at different position in the multi-tile electrode discharge. It is observed that the plasma density increases monotonically with a rise in VHF power level at both positions while decreasing with an increase in the operating gas pressure. At a low gas pressure (50mTorr), plasma density profile shows a maximum at the tile centre and minimum at the tile edge position, whereas, at high gas pressures (500mTorr - 1 Torr) edge effects are observed. Measured rotational temperature (~ 350-450 K) is slightly above room temperature. Vibrational temperature, measured from 6500-8000 K, is increasing initially with a rise in rf power (<1 kW) and then saturates (above 1 kW). Similar to the plasma density profile, high vibrational temperature is measured at the tile edge compared to the tile centre.

  3. 55. QUARRY TILE CUTTERS, SECOND FLOOR, NORTH WING. WORKERS PRESSED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    55. QUARRY TILE CUTTERS, SECOND FLOOR, NORTH WING. WORKERS PRESSED THE CUTTERS INTO SLABS OF CLAY, LIFTED THEM ONTO DRYING BOARDS AND PRESSED THE PLUNGERS TO RELEASE THE CUT TILES. REPRODUCTIONS CUTTERS ARE NOT USED IN PRODUCTION. WOODEN FORMS FOR PRODUCING CLAY SLABS WITH ROLLING PINS REST AGAINST THE WALL. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  4. Survival of Staphylococcus aureus exposed to UV radiation on the surface of ceramic tiles coated with TiO2.

    PubMed

    Szczawiński, J; Tomaszewski, H; Jackowska-Tracz, A; Szczawińska, M E

    2011-01-01

    The aim of this study was to determine and compare the antimicrobial activity of UV radiation of wavelength 253.7 nm (used in typical germicidal lamps) against Staphylococcus aureus on the surfaces of conventionally produced white ceramic wall tiles (matt and shiny) and the same tiles coated with TiO2 using three different methods: RF diode sputtering, atmospheric pressure chemical vapour deposition (APCVD) and spray pyrolysis deposition (SPD). Results clearly indicate that the bactericidal action of UV radiation is much stronger on the surfaces of tiles coated with TiO2 than on the tiles uncovered. The strongest bactericidal effect of UV radiation was found for film prepared by APCVD. Results of experiments for shiny and matt tiles did not differ statistically. The use of ceramic wall tiles coated with TiO2 films in hospitals, veterinary clinics, laboratories, food processing plants and other places where UV radiation is applied for disinfection should greatly improve the efficiency of this treatment.

  5. Use of thin film transistor liquid crystal display (TFT-LCD) waste glass in the production of ceramic tiles.

    PubMed

    Lin, Kae-Long

    2007-09-05

    In this study, we employ the following operating conditions: varied pressure (25 kgf/cm(2)), sintering temperature (900-1200 degrees C), sintering time (6h), percentage of thin film transistor liquid crystal display (TFT-LCD) waste glass by weight (0-50%) and temperature rising at a rate of 5 degrees C/min, to fabricate clay tiles. The sintering characteristics of the clay blended with TFT-LCD waste glass tiles are examined to evaluate the feasibility of the reuse of TFT-LCD waste glass. TFT-LCD waste glass contains large amounts of glass. The TCLP leaching concentrations all met the ROC EPAs current regulatory thresholds. The addition of TFT-LCD waste glass to the mixture, increased the apparent weight loss. The incorporation of 50% TFT-LCD waste glass resulted in a significant increase in the porosity ratio of the specimens compared to the porosity ratio of the ceramic tile containing TFT-LCD waste glass. The main constituent in both the clay tile and the clay with TFT-LCD waste glass samples is quartz. Increasing the temperature resulted in an increase in the flexural strength and resistance to abrasion in the tiles. The porosity ratio decreases as shrinkage increases. The relation between the porosity ratio and the hardness of the tiles used in the study is also shown.

  6. Chunking of Large Multidimensional Arrays

    SciTech Connect

    Rotem, Doron; Otoo, Ekow J.; Seshadri, Sridhar

    2007-02-28

    Data intensive scientific computations as well on-lineanalytical processing applications as are done on very large datasetsthat are modeled as k-dimensional arrays. The storage organization ofsuch arrays on disks is done by partitioning the large global array intofixed size hyper-rectangular sub-arrays called chunks or tiles that formthe units of data transfer between disk and memory. Typical queriesinvolve the retrieval of sub-arrays in a manner that accesses all chunksthat overlap the query results. An important metric of the storageefficiency is the expected number of chunks retrieved over all suchqueries. The question that immediately arises is "what shapes of arraychunks give the minimum expected number of chunks over a query workload?"In this paper we develop two probabilistic mathematical models of theproblem and provide exact solutions using steepest descent and geometricprogramming methods. Experimental results, using synthetic workloads onreal life data sets, show that our chunking is much more efficient thanthe existing approximate solutions.

  7. Electrochemical growth of controlled tip shapes of ZnO nanorod arrays on silicon substrate and enhanced photoluminescence emission from nanopyramid arrays compared with flat-head nanorods

    NASA Astrophysics Data System (ADS)

    Alimanesh, Mahmoud; Hassan, Z.; Zainal, Norzaini

    2017-10-01

    Zinc oxide (ZnO) nanorod arrays (NRAs) with different morphologies such as; perfect hexagon flat-head, pyramidal, compact pencil, nail-shaped, and high-compact ZnO nanorod thin films, were successfully grown on silicon substrates. These NRAs were formed on substrates using a simple low-temperature electrochemical method without adding any catalyst or template via the precursors of zinc nitrate hexahydrate [Zn(NO3)2·6H2O] and hexamethylenetetramine [HMT; C6H12N4] with an equal molar concentration of 0.025 mol/l. The morphologies of the ZnO nanorods (NRs) could be controlled and transformed successfully in to other morphologies by changing the growth conditions, such as; growth temperature and applied current density. Detailed structural investigations reveal that the synthesized various NRs are single crystalline with wurtzite hexagonal phase and preferentially grow along the c-axis direction. The room temperature photoluminescence spectra show that each spectrum consists of an ultraviolet (UV) band and a relative broad visible light emission and infrared emission peak. The enhanced light emission intensity at UV peak (∼375 nm) is observed significantly from ZnO nanopyramid (NP) arrays because of the conical shape of NP. The photoluminescence intensity of the UV peak from the NPs is found to be 1.5-17 times larger than those from the other various NRs.

  8. NASA TileWorld manual (system version 2.2)

    NASA Technical Reports Server (NTRS)

    Philips, Andrew B.; Bresina, John L.

    1991-01-01

    The commands are documented of the NASA TileWorld simulator, as well as providing information about how to run it and extend it. The simulator, implemented in Common Lisp with Common Windows, encodes a particular range in a spectrum of domains, for controllable research experiments. TileWorld consists of a two dimensional grid of cells, a set of polygonal tiles, and a single agent which can grasp and move tiles. In addition to agent executable actions, there is an external event over which the agent has not control; this event correspond to a 'gust of wind'.

  9. View of Chapel mosaic tile ceiling featuring "doves of heaven" ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of Chapel mosaic tile ceiling featuring "doves of heaven" motifs on a stepped concrete shell. - Flanders Field American Cemetery & Memorial, Chapel, Wortegemseweg 117, Waregem, West Flanders (Belgium)

  10. Comprehensive genome characterization of solitary fibrous tumors using high-resolution array-based comparative genomic hybridization.

    PubMed

    Bertucci, François; Bouvier-Labit, Corinne; Finetti, Pascal; Adélaïde, José; Metellus, Philippe; Mokhtari, Karima; Decouvelaere, Anne-Valérie; Miquel, Catherine; Jouvet, Anne; Figarella-Branger, Dominique; Pedeutour, Florence; Chaffanet, Max; Birnbaum, Daniel

    2013-02-01

    Solitary fibrous tumors (SFTs) are rare spindle cell tumors with limited therapeutic options. Their molecular basis is poorly known. No consistent cytogenetic abnormality has been reported. We used high-resolution whole-genome array-based comparative genomic hybridization (Agilent 244K oligonucleotide chips) to profile 47 samples, meningeal in >75% of cases. Few copy number aberrations (CNAs) were observed. Sixty-eight percent of samples did not show any gene CNA after exclusion of probes located in regions with referenced copy number variation (CNV). Only low-level CNAs were observed. The genomic profiles were very homogeneous among samples. No molecular class was revealed by clustering of DNA copy numbers. All cases displayed a "simplex" profile. No recurrent CNA was identified. Imbalances occurring in >20%, such as the gain of 8p11.23-11.22 region, contained known CNVs. The 13q14.11-13q31.1 region (lost in 4% of cases) was the largest altered region and contained the lowest percentage of genes with referenced CNVs. A total of 425 genes without CNV showed copy number transition in at least one sample, but only but only 1 in at least 10% of samples. The genomic profiles of meningeal and extra-meningeal cases did not show any differences.

  11. Molecular characterization of 20 small supernumerary marker chromosome cases using array comparative genomic hybridization and fluorescence in situ hybridization.

    PubMed

    Sun, Mingran; Zhang, Han; Li, Guiying; Guy, Carrie J; Wang, Xianfu; Lu, Xianglan; Gong, Fangchao; Lee, Jiyun; Hassed, Susan; Li, Shibo

    2017-09-04

    The variability of a small supernumerary marker chromosome (sSMC)-related phenotype is determined by the molecular component, the size, and shape of the marker chromosome. As fluorescence in situ hybridization has limitations regarding the resolution, efficiency, and accuracy. Recently, array comparative genomic hybridization (aCGH) was used for sSMC characterization. In this study, twenty cases with sSMCs were characterized by aCGH and FISH. Chromosomal origin of the marker chromosomes were successfully identified in seventeen of them. For the three cases with negative aCGH results, two of them were more likely due to that the sSMCs only contained centromere heterochromatin, whereas the reason for the remaining case with negative aCGH finding was uncertain. In order to establish a stronger genotype-phenotype correlation for clinical service in the future and avoid miss characterization, more sSMC cases were needed to be detailed characterized. This will help to clarify the variable clinical characteristics of sSMCs and provide additional information to aid clinical service and future research.

  12. Comparative Analysis of Human and Rodent Brain Primary Neuronal Culture Spontaneous Activity Using Micro-Electrode Array Technology.

    PubMed

    Napoli, Alessandro; Obeid, Iyad

    2016-03-01

    Electrical activity in embryonic brain tissue has typically been studied using Micro Electrode Array (MEA) technology to make dozens of simultaneous recordings from dissociated neuronal cultures, brain stem cell progenitors, or brain slices from fetal rodents. Although these rodent neuronal primary culture electrical properties are mostly investigated, it has not been yet established to what extent the electrical characteristics of rodent brain neuronal cultures can be generalized to those of humans. A direct comparison of spontaneous spiking activity between rodent and human primary neurons grown under the same in vitro conditions using MEA technology has never been carried out before and will be described in the present study. Human and rodent dissociated fetal brain neuronal cultures were established in-vitro by culturing on a glass grid of 60 planar microelectrodes neurons under identical conditions. Three different cultures of human neurons were produced from tissue sourced from a single aborted fetus (at 16-18 gestational weeks) and these were compared with seven different cultures of embryonic rat neurons (at 18 gestational days) originally isolated from a single rat. The results show that the human and rodent cultures behaved significantly differently. Whereas the rodent cultures demonstrated robust spontaneous activation and network activity after only 10 days, the human cultures required nearly 40 days to achieve a substantially weaker level of electrical function. These results suggest that rat neuron preparations may yield inferences that do not necessarily transfer to humans.

  13. Genetic characterization of dogs via chromosomal analysis and array-based comparative genomic hybridization (aCGH).

    PubMed

    Müller, M H; Reimann-Berg, N; Bullerdiek, J; Murua Escobar, H

    2012-01-01

    The results of cytogenetic and molecular cytogenetic investigations revealed similarities in genetic background and biological behaviour between tumours and genetic diseases of humans and dogs. These findings classify the dog a good and accepted model for human cancers such as osteosarcomas, mammary carcinomas, oral melanomas and others. With the appearance of new studies and advances in canine genome sequencing, the number of known homologies in diseases between these species raised and still is expected to increase. In this context, array-based comparative genomic hybridization (aCGH) provides a novel tool to rapidly characterize numerical aberrations in canine tumours or to detect copy number aberrations between different breeds. As it is possible to spot probes covering the whole genome on each chip to discover copy number aberrations of all chromosomes simultaneously, this method is time-saving and cost-effective - considering the relation of costs and the amount of data obtained. Complemented with traditional methods like karyotyping and fluorescence in situ hybridization (FISH) analyses, the aCGH is able to provide new insights into the underlying causes of canine carcinogenesis.

  14. 1p36 deletion syndrome confirmed by fluorescence in situ hybridization and array-comparative genomic hybridization analysis

    PubMed Central

    Kang, Dong Soo; Shin, Eunsim

    2016-01-01

    Pediatric epilepsy can be caused by various conditions, including specific syndromes. 1p36 deletion syndrome is reported in 1 in 5,000–10,000 newborns, and its characteristic clinical features include developmental delay, mental retardation, hypotonia, congenital heart defects, seizure, and facial dysmorphism. However, detection of the terminal deletion in chromosome 1p by conventional G-banded karyotyping is difficult. Here we present a case of epilepsy with profound developmental delay and characteristic phenotypes. A 7-year- and 6-month-old boy experienced afebrile generalized seizure at the age of 5 years and 3 months. He had recurrent febrile seizures since 12 months of age and showed severe global developmental delay, remarkable hypotonia, short stature, and dysmorphic features such as microcephaly; small, low-set ears; dark, straight eyebrows; deep-set eyes; flat nasal bridge; midface hypoplasia; and a small, pointed chin. Previous diagnostic work-up, including conventional chromosomal analysis, revealed no definite causes. However, array-comparative genomic hybridization analysis revealed 1p36 deletion syndrome with a 9.15-Mb copy loss of the 1p36.33-1p36.22 region, and fluorescence in situ hybridization analysis (FISH) confirmed this diagnosis. This case highlights the need to consider detailed chromosomal study for patients with delayed development and epilepsy. Furthermore, 1p36 deletion syndrome should be considered for patients presenting seizure and moderate-to-severe developmental delay, particularly if the patient exhibits dysmorphic features, short stature, and hypotonia. PMID:28018437

  15. 1p36 deletion syndrome confirmed by fluorescence in situ hybridization and array-comparative genomic hybridization analysis.

    PubMed

    Kang, Dong Soo; Shin, Eunsim; Yu, Jeesuk

    2016-11-01

    Pediatric epilepsy can be caused by various conditions, including specific syndromes. 1p36 deletion syndrome is reported in 1 in 5,000-10,000 newborns, and its characteristic clinical features include developmental delay, mental retardation, hypotonia, congenital heart defects, seizure, and facial dysmorphism. However, detection of the terminal deletion in chromosome 1p by conventional G-banded karyotyping is difficult. Here we present a case of epilepsy with profound developmental delay and characteristic phenotypes. A 7-year- and 6-month-old boy experienced afebrile generalized seizure at the age of 5 years and 3 months. He had recurrent febrile seizures since 12 months of age and showed severe global developmental delay, remarkable hypotonia, short stature, and dysmorphic features such as microcephaly; small, low-set ears; dark, straight eyebrows; deep-set eyes; flat nasal bridge; midface hypoplasia; and a small, pointed chin. Previous diagnostic work-up, including conventional chromosomal analysis, revealed no definite causes. However, array-comparative genomic hybridization analysis revealed 1p36 deletion syndrome with a 9.15-Mb copy loss of the 1p36.33-1p36.22 region, and fluorescence in situ hybridization analysis (FISH) confirmed this diagnosis. This case highlights the need to consider detailed chromosomal study for patients with delayed development and epilepsy. Furthermore, 1p36 deletion syndrome should be considered for patients presenting seizure and moderate-to-severe developmental delay, particularly if the patient exhibits dysmorphic features, short stature, and hypotonia.

  16. Using multivariate analyses to compare subsets of electrodes and potentials within an electrode array for predicting sugar concentrations in mixed solutions.

    SciTech Connect

    Stork, Christopher Lyle; Steen, William Arthur

    2008-04-01

    A non-selective electrode array is presented for the quantification of fructose, galactose, and glucose in mixed solutions. A unique feature of this electrode array relative to other published work is the wide diversity of electrode materials incorporated within the array, being constructed of 41 different metals and metal alloys. Cyclic voltammograms were acquired for solutions containing a single sugar at varying concentrations, and the correlation between current and sugar concentration was calculated as a function of potential and electrode array element. The correlation plots identified potential regions and electrodes that scaled most linearly with sugar concentration, and the number of electrodes used in building predictive models was reduced to 15. Partial least squares regression models relating electrochemical response to sugar concentration were constructed using data from single electrodes and multiple electrodes within the array, and the predictive abilities of these models were rigorously compared using a non-parametric Wilcoxon test. Models using single electrodes (Pt:Rh (90:10) for fructose, Au:Ni (82:18) for galactose, and Au for glucose) were judged to be statistically superior or indistinguishable from those built with multiple electrodes. Additionally, for each sugar, interval partial least squares regression successfully identified a subset of potentials within a given electrode that generated a model of statistically equivalent predictive ability relative to the full potential model. While including data from multiple electrodes offered no benefit in predicting sugar concentration, use of the array afforded the versatility and flexibility of selecting the best single electrode for each sugar.

  17. Complex tiling patterns in liquid crystals

    PubMed Central

    Tschierske, C.; Nürnberger, C.; Ebert, H.; Glettner, B.; Prehm, M.; Liu, F.; Zeng, X.-B.; Ungar, G.

    2012-01-01

    In this account recent progress in enhancing the complexity of liquid crystal self-assembly is highlighted. The discussed superstructures are formed mainly by polyphilic T-shaped and X-shaped molecules composed of a rod-like core, tethered with glycerol units at both ends and flexible non-polar chain(s) in lateral position, but also related inverted molecular structures are considered. A series of honeycomb phases composed of polygonal cylinders ranging from triangular to hexagonal, followed by giant cylinder honeycombs is observed for ternary T-shaped polyphiles on increasing the size of the lateral chain(s). Increasing the chain size further leads to new modes of lamellar organization followed by three-dimensional and two-dimensional structures incorporating branched and non-branched axial rod-bundles. Grafting incompatible chains to opposite sides of the rod-like core leads to quaternary X-shaped polyphiles. These form liquid crystalline honeycombs where different cells are filled with different material. Projected on an Euclidian plane, all honeycomb phases can be described either by uniformly coloured Archimedean and Laves tiling patterns (T-shaped polyphiles) or as multi-colour tiling patterns (X-shaped polyphiles). It is shown that geometric frustration, combined with the tendency to segregate incompatible chains into different compartments and the need to find a periodic tiling pattern, leads to a significant increase in the complexity of soft self-assembly. Mixing of different chains greatly enhances the number of possible ‘colours’ and in this way, periodic structures comprising up to seven distinct compartments can be generated. Relations to biological self-assembly are discussed shortly. PMID:24098852

  18. Direct AFM observation of individual micelles, tile decorations and tiling rules of a dodecagonal liquid quasicrystal

    NASA Astrophysics Data System (ADS)

    Zhang, Ruibin; Zeng, Xiangbing; Ungar, Goran

    2017-10-01

    We performed an atomic force microscopy study of the dendron-based dodecagonal quasicrystal, the material that had been reported in 2004 as the first soft quasicrystal. We succeeded in orienting the 12-fold axis perpendicular to the substrate, which allowed the imaging of the quasiperiodic xy plane. Thus for the first time we have been able to obtain direct real-space information not only on the arrangement of the tiles, but also on their ‘decorations’ by the individual spherical micelles or ‘nanoatoms’. The high-resolution patterns recorded confirm the square-triangle tiling, but the abundance of different nodes corresponds closely to random tiling rather than to any inflation rule. The previously proposed model of three types of decorated tiles, two triangular and one square, has been confirmed; the basic Frank–Kasper mode of alternating dense-sparse-dense-sparse layer stacking along z is confirmed too, each of the four sublayers being 2 nm thick. The consecutive dense layers are seen to be rotated by 90°, as expected. The 2 nm steps on the surface correspond to one layer of spheres, nonetheless with a dense layer always remaining on top, which implies a layer slip underneath and possibly the existence of screw dislocations.

  19. Advances in Natural Quasicrystals and Quasicrystal Tilings

    NASA Astrophysics Data System (ADS)

    Lin, Chaney C.

    The first part of this dissertation reports recent progress on natural quasicrystals. We present new evidence from a fragment of the quasicrystal-bearing CV3 carbonaceous chondritic meteorite Khatyrka that shows cross-cutting relationships and redox reaction between Al-Cu-bearing alloys and silicate phases. The new evidence establishes that the Al-Cu-bearing alloys (including quasicrystals) formed in outer space during a complex, multi-stage process. Some Al-bearing grains (including some quasicrystals) formed as a direct result of an impact in space a few 100 Ma. Most other Al-bearing grains (including quasicrystals) existed prior to the impact and thus formed in space at an earlier time. We also present the discovery of two new quasicrystals, including a second distinct Al-Cu-Fe icosahedral phase in Khatyrka--the first quasicrystal found in nature prior to discovery in the lab--and a synthetic Al-Fe-Cu-Cr-Ni icosahedral phase--the first quasicrystal to be synthesized in a laboratory shock experiment. In the second part of this dissertation, we explore how different local isomorphism (LI) classes of quasicrystals vary in their structural and physical properties. We examine the continuum of LI classes of pentagonal quasicrystal tilings obtained by direct projection from a five-dimensional hypercubic lattice. Our initial focus is on hyperuniformity, the suppression of long-wavelength density fluctuations relative to typical structurally disordered systems. We study how the degree of hyperuniformity depends on LI class. The results show that the degree of hyperuniformity is dominantly determined by the local distribution of vertex environments, and also exhibits a non-negligible dependence on the restorability. Among the pentagonal quasicrystal tilings, the Penrose tiling is the most hyperuniform. The difference in the degree of hyperuniformity is expected to affect physical characteristics, such as transport properties. We then turn to a study of photonic

  20. Array-comparative genomic hybridization profiling of immunohistochemical subgroups of diffuse large B-cell lymphoma shows distinct genomic alterations

    PubMed Central

    Guo, Ying; Takeuchi, Ichiro; Karnan, Sivasundaram; Miyata, Tomoko; Ohshima, Koichi; Seto, Masao

    2014-01-01

    Diffuse large B-cell lymphoma (DLBCL) displays striking heterogeneity at the clinical, genetic and molecular levels. Subtypes include germinal center B-cell-like (GCB) DLBCL and activated B-cell-like (ABC) DLBCL, according to microarray analysis, and germinal center type or non-germinal center type by immunohistochemistry. Although some reports have described genomic aberrations based upon microarray classification system, genomic aberrations based upon immunohistochemical classifications have rarely been reported. The present study aimed to ascertain the relationship between genomic aberrations and subtypes identified by immunohistochemistry, and to study the pathogenetic character of Chinese DLBCL. We conducted immunohistochemistry using antibodies against CD10, BCL6 and MUM1 in 59 samples of DLBCL from Chinese patients, and then performed microarray-based comparative genomic hybridization for each case. Characteristic genomic differences were found between GCB and non-GCB DLBCL from the array data. The GCB type was characterized by more gains at 7q (7q22.1, P < 0.05) and losses at 16q (P ≤ 0.05), while the non-GCB type was characterized by gains at 11q24.3 and 3q13.2 (P < 0.05). We found completely different mutations in BCL6+ and BCL6− non-GCB type DLBCL, whereby the BCL6− group had a higher number of gains at 1q and a loss at 14q32.13 (P ≤ 0.005), while the BCL6+ group showed a higher number of gains at 14q23.1 (P = 0.15) and losses at 6q (P = 0.07). The BCL6− group had a higher frequency of genomic imbalances compared to the BCL6+ group. In conclusion, the BCL6+ and BCL6− non-GCB type of DLBCL appear to have different mechanisms of pathogenesis. PMID:24843885

  1. Array-comparative genomic hybridization profiling of immunohistochemical subgroups of diffuse large B-cell lymphoma shows distinct genomic alterations.

    PubMed

    Guo, Ying; Takeuchi, Ichiro; Karnan, Sivasundaram; Miyata, Tomoko; Ohshima, Koichi; Seto, Masao

    2014-04-01

    Diffuse large B-cell lymphoma (DLBCL) displays striking heterogeneity at the clinical, genetic and molecular levels. Subtypes include germinal center B-cell-like (GCB) DLBCL and activated B-cell-like (ABC) DLBCL, according to microarray analysis, and germinal center type or non-germinal center type by immunohistochemistry. Although some reports have described genomic aberrations based upon microarray classification system, genomic aberrations based upon immunohistochemical classifications have rarely been reported. The present study aimed to ascertain the relationship between genomic aberrations and subtypes identified by immunohistochemistry, and to study the pathogenetic character of Chinese DLBCL. We conducted immunohistochemistry using antibodies against CD10, BCL6 and MUM1 in 59 samples of DLBCL from Chinese patients, and then performed microarray-based comparative genomic hybridization for each case. Characteristic genomic differences were found between GCB and non-GCB DLBCL from the array data. The GCB type was characterized by more gains at 7q (7q22.1, P < 0.05) and losses at 16q (P ≤ 0.05), while the non-GCB type was characterized by gains at 11q24.3 and 3q13.2 (P < 0.05). We found completely different mutations in BCL6+ and BCL6- non-GCB type DLBCL, whereby the BCL6- group had a higher number of gains at 1q and a loss at 14q32.13 (P ≤ 0.005), while the BCL6+ group showed a higher number of gains at 14q23.1 (P = 0.15) and losses at 6q (P = 0.07). The BCL6- group had a higher frequency of genomic imbalances compared to the BCL6+ group. In conclusion, the BCL6+ and BCL6- non-GCB type of DLBCL appear to have different mechanisms of pathogenesis.

  2. Array comparative genomic hybridization profiling analysis reveals deoxyribonucleic acid copy number variations associated with premature ovarian failure.

    PubMed

    Aboura, Azzedine; Dupas, Claire; Tachdjian, Gérard; Portnoï, Marie-France; Bourcigaux, Nathalie; Dewailly, Didier; Frydman, René; Fauser, Bart; Ronci-Chaix, Nathalie; Donadille, Bruno; Bouchard, Philippe; Christin-Maitre, Sophie

    2009-11-01

    Premature ovarian failure (POF) is defined by amenorrhea of at least 4- to 6-month duration, occurring before 40 yr of age, with two FSH levels in the postmenopausal range. Its etiology remains unknown in more than 80% of cases. Standard karyotypes, having a resolution of 5-10 Mb, have identified critical chromosomal regions, mainly located on the long arm of the X chromosome. Array comparative genomic hybridization (a-CGH) analysis is able to detect submicroscopic chromosomal rearrangements with a higher genomic resolution. We searched for copy number variations (CNVs), using a-CGH analysis with a resolution of approximately 0.7 Mb, in a cohort of patients with POF. We prospectively included 99 women. Our study included a conventional karyotype and DNA microarrays comprising 4500 bacterial artificial chromosome clones spread on the entire genome. Thirty-one CNVs have been observed, three on the X chromosome and 28 on autosomal chromosomes. Data have been compared to control populations obtained from the Database of Genomic Variants (http://projects.tcag.ca/variation). Eight statistically significantly different CNVs have been identified in chromosomal regions 1p21.1, 5p14.3, 5q13.2, 6p25.3, 14q32.33, 16p11.2, 17q12, and Xq28. We report the first study of CNV analysis in a large cohort of Caucasian POF patients. In the eight statistically significant CNVs we report, we found five genes involved in reproduction, thus representing potential candidate genes in POF. The current study along with emerging information regarding CNVs, as well as data on their potential association with human diseases, emphasizes the importance of assessing CNVs in cohorts of POF women.

  3. ALT-II armor tile design for upgraded TEXTOR operation

    SciTech Connect

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

    1994-08-01

    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.

  4. Photographing Shuttle Thermal Tiles in Space

    NASA Technical Reports Server (NTRS)

    2005-01-01

    Launched on July 26, 2005 from the Kennedy Space Center in Florida, STS-114 was classified as Logistics Flight 1. Among the Station-related activities of the mission were the delivery of new supplies and the replacement of one of the orbital outpost's Control Moment Gyroscopes (CMGs). STS-114 also carried the Raffaello Multi-Purpose Logistics Module and the External Stowage Platform-2. A major focus of the mission was the testing and evaluation of new Space Shuttle flight safety, which included new inspection and repair techniques. Upon its approach to the International Space Station (ISS), the Space Shuttle Discovery underwent a photography session in order to assess any damages that may have occurred during its launch and/or journey through Space. The mission's third and final Extra Vehicular Activity (EVA) included taking a close-up look and the repair of the damaged heat shield. Gap fillers were removed from between the orbiter's heat-shielding tiles located on the craft's underbelly. Never before had any repairs been done to an orbiter while still in space. This particular photo was taken by astronaut Stephen K. Robinson, STS-114 mission specialist, whose shadow is visible on the thermal protection tiles.

  5. Event Processing for Modular Gamma Cameras with Tiled Multi-Anode Photomultiplier Tubes

    PubMed Central

    Salçın, Esen; Furenlid, Lars R.

    2015-01-01

    Multi-anode photomultiplier tubes (MAPMTs) are good candidates as light sensors for a new generation of modular scintillation cameras for Single-photon emission computed tomography (SPECT) and Positron emission tomography (PET) applications. MAPMTs can provide improved intrinsic spatial resolution (<1mm) compared to arrays of larger individual PMTs due to their small anode sizes, and the increased number of channels also allows accurate estimation of depth-of-interaction (DOI). However, the area of a single MAPMT module is small for a modular gamma camera, so we are designing read-out electronics that will allow multiple individual MAPMT modules to be optically coupled to a single monolithic scintillator crystal. In order to allow such flexibility, the read-out electronics, which we refer to as the event processor, must be compact and adaptable. In combining arrays of MAPMTs, which may each have 64 to 1024 anodes per unit, issues need to be overcome with amplifying, digitizing, and recording potentially very large numbers of channels per gamma-ray event. In this study, we have investigated different event-processor strategies for gamma cameras with multiple MAPMTs that will employ maximum-likelihood (ML) methods for estimation of 3D spatial location, deposited energy and time of occurrence of events. We simulated anode signals for hypothetical gamma–camera geometries based on models of the stochastic processes inherent in scintillation cameras. The comparison between different triggering and read-out schemes was carried out by quantifying the information content in the anode signals via the Fisher Information Matrix (FIM). We observed that a decline in spatial resolution at the edges of the individual MAPMTs could be improved by the inclusion of neighboring MAPMT anode signals for events near the tiling boundaries. Thus in order to maintain spatial resolution uniformity throughout the modular camera face, we propose dividing an MAPMT’s array of anode signals

  6. An alternative method for the TileCal signal detection and amplitude estimation

    NASA Astrophysics Data System (ADS)

    Sotto-Maior Peralva, B.; ATLAS Collaboration

    2012-06-01

    The Tile Barrel Calorimeter (TileCal) is the central section of the hadronic calorimeter of ATLAS. It is a key detector for the reconstruction of hadrons, jets, taus and missing transverse energy and it assists the muon measurements due to a low signal-to-noise ratio. The energy deposited in each cell is read out by two electronic channels for redundancy and is estimated by reconstructing the amplitude of the digitized signal pulse sampled every 25 ns. This work presents an alternative approach for TileCal signal detection and amplitude estimation under low signal-to-noise ratio (SNR) conditions, exploring the applicability of a Matched Filter. The proposed method is compared to the Optimal Filter algorithm, that is currently being used at TileCal for energy reconstruction. The results for a simulated data set showed that for conditions where the signal pedestal could be considered stationary, the proposed method achieves a better SNR performance than the Optimal Filter technique.

  7. Large field-of-view tiled grating structures for X-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Schröter, Tobias J.; Koch, Frieder J.; Meyer, Pascal; Kunka, Danays; Meiser, Jan; Willer, Konstantin; Gromann, Lukas; Marco, Fabio D.; Herzen, Julia; Noel, Peter; Yaroshenko, Andre; Hofmann, Andreas; Pfeiffer, Franz; Mohr, Jürgen

    2017-01-01

    X-ray grating-based interferometry promises unique new diagnostic possibilities in medical imaging and materials analysis. To transfer this method from scientific laboratories or small-animal applications to clinical radiography applications, compact setups with a large field of view (FoV) are required. Currently the FoV is limited by the grating area, which is restricted due to the complex manufacturing process. One possibility to increase the FoV is tiling individual grating tiles to create one large area grating mounted on a carrier substrate. We investigate theoretically the accuracy needed for a tiling process in all degrees of freedom by applying a simulation approach. We show how the resulting precision requirements can be met using a custom-built frame for exact positioning. Precise alignment is achieved by comparing the fringe patterns of two neighboring grating tiles in a grating interferometer. With this method, the FoV can be extended to practically any desired length in one dimension. First results of a phase-contrast scanning setup with a full FoV of 384 mm × 24 mm show the suitability of this method.

  8. Study of the Pulse Shapes from the 3-in-1 Cards at ATLAS TileCal

    NASA Astrophysics Data System (ADS)

    Cheng, Y.; Dunford, M.; Kim, Y. K.

    2010-02-01

    The ATLAS Tile Calorimeter (TileCal) is designed to measure energy depositions in a single cell from 30 MeV to 2 TeV, and we expect to calibrate its response to 1-2%. We present studies of pulse shapes from the front-end electronics of the TileCal and infer their impact on minimum bias pile-up events, especially at high luminosity. High and low gain signals were obtained from both CERN and the University of Chicago test benches, using both the charge injection system and LED. In our studies, we quantify pulse-shapes and undershoot, measure card-to-card variations, and then compare these pulse shapes to the reference shapes used in ATLAS simulation. By running the TileCal pulse shape reconstruction using both the standard shapes in simulation and the shapes from test bench measurements, we are able to investigate the sensitivity of the reconstruction procedure to differences in pulse shape. )

  9. Drainage water management effects on tile discharge and water quality

    USDA-ARS?s Scientific Manuscript database

    Nitrogen (N) fluxes from tile drained watersheds have been implicated in water quality studies of the Mississippi River Basin, but the contribution of tile drains to N export in headwater watersheds is not well understood. The objective of this study was to ascertain seasonal and annual contribution...

  10. Future Armor Tiles MIL-STD-166O Tests.

    DTIC Science & Technology

    1997-02-01

    The U.S. Army Defense Ammunition Center (DAC), Validation Engineering Division, was tasked by DAC to conduct MIL- STD -1660 tests on armor tile...containers on a wooden pallet. This report contains test results with the armor tile containers on a wooden pallet meeting MIL- STD -1660, Design Criteria for Ammunition Unit Loads, requirements.

  11. Creative Tiling: A Story of 1000-and-1 Curves

    ERIC Educational Resources Information Center

    Al-Darwish, Nasir

    2012-01-01

    We describe a procedure that utilizes symmetric curves for building artistic tiles. One particular curve was found to mesh nicely with hundreds other curves, resulting in eye-catching tiling designs. The results of our work serve as a good example of using ideas from 2-D graphics and algorithms in a practical web-based application.

  12. Low-Density, Aerogel-Filled Thermal-Insulation Tiles

    NASA Technical Reports Server (NTRS)

    Santos, Maryann; Heng, Vann; Barney, Andrea; Oka, Kris; Droege, Michael

    2005-01-01

    Aerogel fillings have been investigated in a continuing effort to develop low-density thermal-insulation tiles that, relative to prior such tiles, have greater dimensional stability (especially less shrinkage), equal or lower thermal conductivity, and greater strength and durability. In preparation for laboratory tests of dimensional and thermal stability, prototypes of aerogel-filled versions of recently developed low-density tiles have been fabricated by impregnating such tiles to various depths with aerogel formations ranging in density from 1.5 to 5.6 lb/ft3 (about 53 to 200 kg/cu m). Results available at the time of reporting the information for this article showed that the thermal-insulation properties of the partially or fully aerogel- impregnated tiles were equivalent or superior to those of the corresponding non-impregnated tiles and that the partially impregnated tiles exhibited minimal (<1.5 percent) shrinkage after multiple exposures at a temperature of 2,300 F (1,260 C). Latest developments have shown that tiles containing aerogels at the higher end of the density range are stable after multiple exposures at the said temperature.

  13. New SWAT tile drain equations: Modifications, Calibration, Validation, and Application

    USDA-ARS?s Scientific Manuscript database

    Subsurface tile drainage is a commonly used agricultural practice to enhance crop yield in poorly drained but highly productive soils in many other regions of the world. However, the presence of subsurface tile drainage systems also expedites the transport of nitrate-nitrogen (NO3-N) and other chemi...

  14. Highly Symmetric and Congruently Tiled Meshes for Shells and Domes

    PubMed Central

    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

  15. 81. MORAVIAN POTTERY AND TILE WORKS, VIEW FROM THE SOUTHWEST. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    81. MORAVIAN POTTERY AND TILE WORKS, VIEW FROM THE SOUTHWEST. INDIAN HOUSE WING AT THE LEFT. SAME VIEW AS PA-107-2. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  16. 69. TILE WORKS UNDER CONSTRUCTION, 1912. SOURCE: FONTHILL MANUSCRIPT COLLECTION, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    69. TILE WORKS UNDER CONSTRUCTION, 1912. SOURCE: FONTHILL MANUSCRIPT COLLECTION, SPRUANCE LIBRARY, BUCKS COUNTY HISTORICAL SOCIETY (HEREAFTER SL/BCHS), UNCATALOGED GLASS PLATE NEGATIVE. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  17. Computerized Machine for Cutting Space Shuttle Thermal Tiles

    NASA Technical Reports Server (NTRS)

    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.

  18. Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

    PubMed Central

    2014-01-01

    Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy

  19. Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue.

    PubMed

    Kudesia, Rashmi; Li, Marilyn; Smith, Janice; Patel, Ankita; Williams, Zev

    2014-03-03

    Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on "rescue karyotyping", wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p=0.14) or gestational age at pregnancy loss (p=0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss.

  20. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples.

    PubMed

    Zhou, Qinghua; Wu, Shen-Yin; Amato, Katherine; DiAdamo, Autumn; Li, Peining

    2016-03-20

    Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomal trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples.

  1. Aneuploidy screening by array comparative genomic hybridization improves success rates of in vitro fertilization: A multicenter Indian study

    PubMed Central

    Kotdawala, Aditi; Patel, Deven; Herrero, Javier; Khajuria, Rajni; Mahajan, Nalini; Banker, Manish

    2016-01-01

    OBJECTIVE: To evaluate the usefulness of preimplantation genetic screening (PGS) using array comparative genomic hybridization (aCGH) in the Indian population. MATERIALS AND METHODS: This is a retrospective, multicenter study including 235 PGS cycles following intracytoplasmic sperm injection performed at six different infertility centers from September 2013 to June 2015. Patients were divided as per maternal age in several groups (<35, 35–36, 37–38, 39–40, and >40 years) and as per indication for undergoing PGS. Indications for performing PGS were recurrent miscarriage, repetitive implantation failure, severe male factor, previous trisomic pregnancy, and advanced maternal age (≥35). Day 3 embryo biopsy was performed and analyzed by aCGH followed by day 5 embryo transfer in the same cycle or the following cycle. Outcomes such as pregnancy rates (PRs)/transfer, implantation rates, miscarriage rates, percentage of abnormal embryos, and number of embryos with more than one aneuploidy and chaotic patterns were recorded for all the treated subjects based on different age and indication groups. RESULTS: aCGH helped in identifying aneuploid embryos, thus leading to consistent implantation (range: 33.3%–42.9%) and PRs per transfer (range: 31.8%–54.9%) that were obtained for all the indications in all the age groups, after performing PGS. CONCLUSION: Aneuploidy is one of the major factors which affect embryo implantation. aCGH can be successfully employed for screening of aneuploid embryos. When euploid embryos are transferred, an increase in PRs can be achieved irrespective of the age or the indication. PMID:28216909

  2. Enthalpy arrays

    PubMed Central

    Torres, Francisco E.; Kuhn, Peter; De Bruyker, Dirk; Bell, Alan G.; Wolkin, Michal V.; Peeters, Eric; Williamson, James R.; Anderson, Gregory B.; Schmitz, Gregory P.; Recht, Michael I.; Schweizer, Sandra; Scott, Lincoln G.; Ho, Jackson H.; Elrod, Scott A.; Schultz, Peter G.; Lerner, Richard A.; Bruce, Richard H.

    2004-01-01

    We report the fabrication of enthalpy arrays and their use to detect molecular interactions, including protein–ligand binding, enzymatic turnover, and mitochondrial respiration. Enthalpy arrays provide a universal assay methodology with no need for specific assay development such as fluorescent labeling or immobilization of reagents, which can adversely affect the interaction. Microscale technology enables the fabrication of 96-detector enthalpy arrays on large substrates. The reduction in scale results in large decreases in both the sample quantity and the measurement time compared with conventional microcalorimetry. We demonstrate the utility of the enthalpy arrays by showing measurements for two protein–ligand binding interactions (RNase A + cytidine 2′-monophosphate and streptavidin + biotin), phosphorylation of glucose by hexokinase, and respiration of mitochondria in the presence of 2,4-dinitrophenol uncoupler. PMID:15210951

  3. Effects of body formulation and firing temperature to properties of ceramic tile incorporated with electric arc furnace (EAF) slag waste

    NASA Astrophysics Data System (ADS)

    Sharif, Nurulakmal Mohd; Lim, Chi Yang; Teo, Pao Ter; Seman, Anasyida Abu

    2017-07-01

    Significant quantities of sludge and slag are generated as waste materials or by-products from steel industries. One of the by-products is Electric Arc Furnace (EAF) steel slag which consists of oxides such as CaO, Al2O3 and FeO. This makes it possible for slag to partially replace the raw materials in ceramic tile production. In our preliminary assessment of incorporating the EAF slag into ceramic tile, it was revealed that at fixed firing temperature of 1150°C, the tile of composition 40 wt.% EAF slag - 60 wt.% ball clay has comparable properties with commercial ceramic tile. Thus, this current study would focus on effects of body formulation (different weight percentages of K-feldspar and silica) and different firing temperatures to properties of EAF slag added ceramic tile. EAF slag from Southern Steel Berhad (SSB) was crushed into micron size (EAF slag content was 40 wt.%) and milled with ball clay, K-feldspar and silica before compacted and fired at 1125°C and 1150°C. The EAF slag added tile was characterized in terms of water absorption, apparent porosity, bulk density, modulus of rupture (MOR) and phase analysis via X-ray diffraction (XRD). The composition of 40 wt.% EAF slag - 30 wt.% ball clay - 10 wt.% K-feldspar - 20 wt.% silica (10F_20S), fired at 1150°C showed the lowest water absorption, apparent porosity and highest bulk density due to enhancement of densification process during firing. However, the same composition of ceramic tile (10F_20S) had the highest MOR at lower firing temperature of 1125°C, contributed by presence of the highest total amount of anorthite and wollastonite reinforcement crystalline phases (78.40 wt.%) in the tile. Overall, both the water absorption and MOR of all ceramic tiles surpassed the requirement regulated by MS ISO 13006:2014 Standard (Annex G: Dry-pressed ceramic tile with low water absorption, Eb ≤ 0.50 % and minimum MOR of 35 MPa).

  4. [First experiences with preimplantation genetic screening of chromosomal aberrations using oligonucleotide-based array comparative genomic hybridization].

    PubMed

    Kuglík, Petr; Smetana, Jan; Němcová, Darja; Vallová, Vladimíra; Mikulášová, Aneta; Gaillyová, Renata; Hubinka, Vít; Koudelka, Marek

    2015-01-01

    Preimplantation genetic diagnosis (PGD) is a complex approach for detecting genetic abnormalities in early-stage embryos using genetic or molecular cytogenetic methods. Recently, single cell genomic methods based on DNA microarrays have been used for PGD. In the presented paper, we discuss and demonstrate the possibility to detect copy number variation (CNVs) in trophectoderm cells biopsied from 5-day embryos using 60-mer oligonucleotide-based array-CGH with CytoSure 8 × 15K Aneuploidy Array. Whereas this microarray platform was originally designed for analysis of unamplified DNA derived from many cells, the new methods, developed for single-cell genomics, allow the application of oligo arrays technology in preimplanation genetic diagnosis. Preclinical validation of single cell array-CGH was made by analysis of 30 positive and negative controls. Validation process included whole genome amplification of DNA from 5-10 cells with normal karyotype and from samples with known aneuploidies and structural aberrations. Subsequently, we analyzed the whole genome profiles in 118 embryos; aneuploidies of chromosomes were observed in 26.7%; segmental imbalances were proved in 6.8% of embryos. Our first experience confirmed that this oligonucleotide-based array technique enables high-resolution preimplantation aneuploidy screening of all the 23 chromosome pairs and sensitive preimplantation diagnosis of segmental imbalances such as deletions, duplications and amplifications.

  5. Development of anti-slip sustainable tiles from agricultural waste

    NASA Astrophysics Data System (ADS)

    Zulkefli, Zainordin Firdaus; Zainol, Mohd Remy Rozainy Mohd Arif; Osman, Norhayati

    2017-04-01

    In general of 80% the human activities is located in the building. Buildings constructed should be in line with full functions and optimum safety features. Aspects to be emphasized is the slip on the floor of the building. The selection of tiles must have anti-slip characteristics and achieve standard strength stress. This study is conducted to develop anti-slip tiles modification using agricultural waste. The material used is agricultural waste such rice husks, palm fibre and saw dusk mixed into the clay and then baked at a temperature of 900-1185 C °. Agricultural waste mixture ratio is 5%, 10% and 15%. The samples of tiles are produced for experiments. The results of agricultural waste tiles show that the strength is higher than standard strength, the water absorption less than standard tiles and pendulum value test is exceeds 36.

  6. Edge exposure of poloidal divertor target plate tiles

    SciTech Connect

    Mohanti, R.B.; Gilligan, J.G.; Bourham, M.A.

    1996-12-01

    Exposure to near normal surfaces of poloidal divertor target plate tiles is a limiting feature of the power handling capability of the tiles. The problems associated with the design of poloidal divertor tiles, with beryllium chosen as the tile material, and possible methods of solving the problem are discussed. Thermal two- and three-dimensional analyses are carried out for the assessment of relative merits in performance due to modifications to the surface. The power handling capability (time to reach melting temperature of beryllium) of the target plate tiles is presented for unswept and swept plasma cases. Results have shown that sweeping the plasma improves the power handling capability by a factor of up to 10. 20 refs., 7 figs., 3 tabs.

  7. Comparative study of multimode CYTOP graded index and single-mode silica fibre Bragg grating array for the mode shape capturing of a free-free metal beam

    NASA Astrophysics Data System (ADS)

    Theodosiou, A.; Polis, M.; Lacraz, A.; Kalli, K.; Komodromos, M.; Stassis, A.

    2016-04-01

    The work described in this paper involved two different material fibre Bragg grating (FBG) arrays, investigating their performance as quasi-distributed sensors by capturing the vibrating response of a free-free metal beam close to its resonance frequencies. A six meter length of low-loss, gradient-index, multimode CYTOP fibre and of SMF-28 were used for the inscription of multiple FBG sensors using a femtosecond laser inscription method. The FBG arrays were multiplexed in the wavelength domain using a high-speed commercial demodulator, from which we recovered wavelengthand time-dependent displacement information. We compared the vibration response of the two arrays and using a novel computation algorithm we extract the first mode shape of the free-free metal beam that was exited at its first resonance frequency using a vibrating force.

  8. Clinical application of array-based comparative genomic hybridization for the identification of prognostically important genetic alterations in chronic lymphocytic leukemia.

    PubMed

    Higgins, Russell A; Gunn, Shelly R; Robetorye, Ryan S

    2008-01-01

    Genomic aberrations have increasingly gained attention as prognostic markers in B-cell chronic lymphocytic leukemia (CLL). Fluorescence in situ hybridization (FISH) has improved the detection rate of genomic alterations in CLL from approximately 50% using conventional cytogenetics to greater than 80%. More recently, array comparative genomic hybridization (CGH) has gained popularity as a clinical tool that can be applied to detect genomic gains and losses of prognostic importance in CLL. Array CGH and FISH are particularly useful in CLL because genomic gains and losses are key events with both biologic and prognostic significance, while balanced translocations have limited prognostic value. Although FISH has a higher technical sensitivity, it requires separate, targeted hybridizations for the detection of alterations at genomic loci of interest. Array CGH, on the other hand, has the ability to provide a genome-wide survey of genomic aberrations with a single hybridization reaction. Array CGH is expanding the known genomic regions of importance in CLL and allows these regions to be evaluated in the context of a genome-wide perspective. Ongoing clinical trials are evaluating the use of genomic aberrations as tools for risk-stratifying patients for therapy, thus increasing the need for reliable and high-yield methods to detect these genomic changes. In this review, we consider the use of array CGH as a clinical tool for the identification of genomic alterations with prognostic significance in CLL, and suggest ways to integrate this test into the clinical molecular diagnostic laboratory work flow.

  9. Molecular cytogenetic analysis of head and neck squamous cell carcinoma: By comparative genomic hybridization, spectral karyotyping, and expression array analysis.

    PubMed

    Squire, Jeremy A; Bayani, Jane; Luk, Catherine; Unwin, Lianne; Tokunaga, Jason; MacMillan, Christina; Irish, Jonathan; Brown, Dale; Gullane, Patrick; Kamel-Reid, Suzanne

    2002-09-01

    A combination of molecular cytogenetic and expression array analysis has been performed on head and neck squamous cell carcinoma (HNSCC) of the oral cavity and supraglottis. These studies were performed to identify consensus regions of chromosomal imbalance and structural rearrangement to determine whether genes located in these genomic regions are subject to alterations in gene expression. Such combinatorial studies may help to identify recurrent patterns of altered gene expression in the context of specific chromosomal changes. Comparative genomic hybridization (CGH) was used to identify net genomic imbalances and spectral karyotyping (SKY) to visualize the numerical and structural chromosomal changes in metaphase preparations. Expression microarray analysis of HNSCC cell lines and primary tongue tumors was also performed to identify genes that were commonly overexpressed or underexpressed compared with adjacent normal tissue. CGH detected gains at 3q (64%), 8q (45%) and 6q22-qter (45%) and losses at 18q22-qter (27%). SKY analysis of seven cell lines identified frequent structural rearrangement of the following chromosomal regions: 3q, 5p13-q11.2, 5q32-q34, 7p12-q11.2, 8p12-q12, 9p, 10p, 13p13-q12, 14q11.1-q11.2, 15p13-q11.2, 16p11.1-q11.1, 18q22-q23, and 22p13-q11.2. Consistent deregulation of interleukin 8, integrin alpha-6, c-MYC, epithelial discoidin domain receptor 1, and sterol regulatory element binding protein were apparent by expression analysis. Interestingly, some of these genes map to regions of genomic imbalance and chromosomal rearrangement as determined by our molecular cytogenetic analysis. In this small study, a combinatorial analysis using SKY, CGH, and microarray provides a model linking the changes in gene expression to changes in chromosomal dosage and structure. This approach has identified a subset of genetic changes that provide new opportunities for investigating the genetic basis of tumorigenesis in HNSCC. Copyright 2002 Wiley

  10. Eating in the absence of hunger in adolescents: intake after a large-array meal compared with that after a standardized meal123

    PubMed Central

    Tanofsky-Kraff, Marian; Zocca, Jaclyn M; Courville, Amber; Kozlosky, Merel; Columbo, Kelli M; Wolkoff, Laura E; Brady, Sheila M; Crocker, Melissa K; Ali, Asem H; Yanovski, Susan Z; Yanovski, Jack A

    2010-01-01

    Background: Eating in the absence of hunger (EAH) is typically assessed by measuring youths’ intake of palatable snack foods after a standard meal designed to reduce hunger. Because energy intake required to reach satiety varies among individuals, a standard meal may not ensure the absence of hunger among participants of all weight strata. Objective: The objective of this study was to compare adolescents’ EAH observed after access to a very large food array with EAH observed after a standardized meal. Design: Seventy-eight adolescents participated in a randomized crossover study during which EAH was measured as intake of palatable snacks after ad libitum access to a very large array of lunch-type foods (>10,000 kcal) and after a lunch meal standardized to provide 50% of the daily estimated energy requirements. Results: The adolescents consumed more energy and reported less hunger after the large-array meal than after the standardized meal (P values < 0.001). They consumed ≈70 kcal less EAH after the large-array meal than after the standardized meal (295 ± 18 compared with 365 ± 20 kcal; P < 0.001), but EAH intakes after the large-array meal and after the standardized meal were positively correlated (P values < 0.001). The body mass index z score and overweight were positively associated with EAH in both paradigms after age, sex, race, pubertal stage, and meal intake were controlled for (P values ≤ 0.05). Conclusion: EAH is observable and positively related to body weight regardless of whether youth eat in the absence of hunger from a very large-array meal or from a standardized meal. This trial was registered at clinicaltrials.gov as NCT00631644. PMID:20720255

  11. Initial Results from the BRAHMS Multiplicity Array

    NASA Astrophysics Data System (ADS)

    Ito, H.

    2000-10-01

    The BRAHMS Multiplicity Array is one of three systems used to characterize the centrality of RHIC collisions at the BRAHMS experiment. Together, these systems, which also include the Zero Degree Calorimeter (ZDC) and Beam-Beam Counter arrays, provide a global characterization of particle multiplicities, with the Multiplicity Array (-2.2<η<2.2) and Beam-Beam Arrays (3.2 <= |η|<= 4.3 ) sensitive to charged-particle multiplicity distributions over a large range of pseudorapidity η, and the ZDC measuring neutron distributions along the beam axis. The Multiplicity Array consists of an inner barrel of 24 modestly segmented Si Strip detectors and an outer barrel of 38 plastic scintillator tiles in a collinear arrangement about the beam axis. This talk will discuss some of the physics to be explored with the Multiplicity Array and present initial results obtained with the array during the first RHIC running period.

  12. A two-stage ceramic tile grout sealing process using a high power diode laser—II. Mechanical, chemical and physical properties

    NASA Astrophysics Data System (ADS)

    Lawrence, J.; Li, L.; Spencer, J. T.

    1998-04-01

    Ceramic tiles sealed using a portable 60 Wcw high power diode laser (HPDL) and a specially developed grout material having an impermeable enamel surface glaze have been tested in order to determine the mechanical, chemical and physical characteristics of the seals. The work showed that the generation of the enamel surface glaze resulted in a seal with improved mechanical and chemical properties over conventional epoxy tile grouts. Both epoxy tile grout and laser generated enamel seals were tested for compressive strength, surface roughness, wear, water permeability and acid/alkali resistance. The enamel seal showed clear improvements in strength, roughness and wear, whilst being impermeable to water, and resistant (up to 80% concentration) to nitric acid, sodium hydroxide and detergent acids. The bond strength and the rupture strength of the enamel seal were also investigated, revealing that the enamel adhered to the new grout and the ceramic tiles with an average bond strength of 45-60 MPa, whilst the rupture strength was comparable with the ceramic tiles themselves. The average surface roughness of the seals and the tiles was 0.36 and 0.06 μm, respectively, whilst for the conventional epoxy grout the average surface roughness when polished was 3.83 μm and in excess of 30 μm without polishing. Life assessment testing revealed that the enamel seals had an increase in actual wear life of 2.9 to 30.4 times over conventional epoxy tile grout, depending upon the corrosive environment.

  13. Tile-in-ONE: A web platform which integrates Tile Calorimeter data quality and calibration assessment

    NASA Astrophysics Data System (ADS)

    Sivolella, A.; Ferreira, F.; Maidantchik, C.; Solans, C.; Solodkov, A.; Burghgrave, B.; Smirnov, Y.

    2015-12-01

    The ATLAS Tile Calorimeter collaboration assesses the quality of calibration data in order to ensure its proper operation. A number of tasks is then performed by executing several tools and accessing web systems, which were independently developed to meet distinct collaboration's requirements and do not necessarily are connected with each other. Thus, to attend the collaboration needs, several programs are usually implemented without a global perspective of the detector, requiring basic software features. In addition, functionalities may overlap in their objectives and frequently replicate resources retrieval mechanisms. Tile-in-ONE is a designed and implemented platform that assembles various web systems used by the calorimeter community through a single framework and a standard technology. It provides an infrastructure to support the code implementation, avoiding duplication of work while integrating with an overall view of the detector status. Database connectors smooth the process of information access since developers do not need to be aware of where records are placed and how to extract them. Within the environment, a dashboard stands for a particular Tile operation aspect and gets together plug-ins, i.e. software components that add specific features to an existing application. A server contains the platform core, which represents the basic environment to deal with the configuration, manage user settings and load plug-ins at runtime. A web middleware assists users to develop their own plug-ins, perform tests and integrate them into the platform as a whole. Backends are employed to allow that any type of application is interpreted and displayed in a uniform way. This paper describes Tile-in-ONE web platform.

  14. Floor tile and mastic removal project report

    SciTech Connect

    Not Available

    1992-11-01

    A test program was developed and coordinated with State and Federal Regulators and carried out at Fort Sill, Oklahoma. This program was carefully designed to create the worst conditions in order to evaluate whether asbestos fibers are released when asbestos containing floor tile and mastic are removed. There were over 1,000 samples taken and analyzed during the execution of the program. The conclusions reached were based upon analysis of the critical samples using the Transmission Electron Microscope (TEM) technology. Additionally, the TEM procedures were used to evaluate personnel samples to determine whether those fibers found were asbestos or other materials. Most of the (TEM) samples were analyzed by the US Environmental Protection Agency (EPA) Risk Reduction Engineering Laboratory in Cincinnati, Ohio.

  15. Condensate oscillations in a Penrose tiling lattice

    NASA Astrophysics Data System (ADS)

    Akdeniz, Z.; Vignolo, P.

    2017-07-01

    We study the dynamics of a Bose-Einstein condensate subject to a particular Penrose tiling lattice. In such a lattice, the potential energy at each site depends on the neighbour sites, accordingly to the model introduced by Sutherland [16]. The Bose-Einstein wavepacket, initially at rest at the lattice symmetry center, is released. We observe a very complex time-evolution that strongly depends on the symmetry center (two choices are possible), on the potential energy landscape dispersion, and on the interaction strength. The condensate-width oscillates at different frequencies and we can identify large-frequency reshaping oscillations and low-frequency rescaling oscillations. We discuss in which conditions these oscillations are spatially bounded, denoting a self-trapping dynamics.

  16. Tile-Compressed FITS Kernel for IRAF

    NASA Astrophysics Data System (ADS)

    Seaman, R.

    2011-07-01

    The Flexible Image Transport System (FITS) is a ubiquitously supported standard of the astronomical community. Similarly, the Image Reduction and Analysis Facility (IRAF), developed by the National Optical Astronomy Observatory, is a widely used astronomical data reduction package. IRAF supplies compatibility with FITS format data through numerous tools and interfaces. The most integrated of these is IRAF's FITS image kernel that provides access to FITS from any IRAF task that uses the basic IMIO interface. The original FITS kernel is a complex interface of purpose-built procedures that presents growing maintenance issues and lacks recent FITS innovations. A new FITS kernel is being developed at NOAO that is layered on the CFITSIO library from the NASA Goddard Space Flight Center. The simplified interface will minimize maintenance headaches as well as add important new features such as support for the FITS tile-compressed (fpack) format.

  17. [Respiratory viral diagnosis by using an automated system of multiplex PCR (FilmArray) compared to conventional methods].

    PubMed

    Marcone, Débora N; Carballal, Guadalupe; Ricarte, Carmen; Echavarria, Marcela

    2015-01-01

    Acute respiratory infections, which are commonly caused by viruses, are an important cause of morbidity and mortality in children. In Argentina, national surveillance programs for the detection of respiratory viruses are usually performed by using immunofluorescence (IF) assays, although it is well known that molecular methods are more sensitive. An automated multiplex PCR device, the FilmArray-Respiratory Panel (FilmArray-RP), can detect 17 viral and 3 bacterial pathogens in a closed system that requires only 5 min of hands-on time and 1h of instrumentation time. A total of 315 respiratory samples from children under 6 years of age suffering from acute respiratory infections, were studied by IF for 8 respiratory viruses and by RT-PCR for rhinoviruses. Later, these samples were tested by the FilmArray-RP. The positivity frequency obtained for the 9 viruses tested was 75% by IF/RT-PCR and 92% by the FilmArray-RP. The positive and negative percent agreement between both methods was 70.5% whereas the negative percent agreement was 99.6% (95% confidence interval:65.5-75.1 and 99.2-99.8 respectively). The FilmArray-RP allowed a higher positive diagnosis (97%) and detected other viruses such as coronavirus NL63, 229E, OC43, HKU1 (10%) and bocavirus (18%). In addition, this method identified multiple coinfections (39%) with 2, 3, 4 and up to 5 different viruses. At present, IF is still the most frequently used method in most Latin American countries for respiratory viruses diagnosis due to its low cost, its capability to process a high number of samples simultaneously and the fast determination of results for the most frequent viruses, which are available within 5h. However, the coming incorporation of molecular methods in routine procedures will significantly increase the diagnostic yield of these infections.

  18. High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative genomic hybridization.

    PubMed

    Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard; Zhang, Xiuqing; Niebuhr, Anita; Albertson, Donna; Yang, Huanming; Gray, Joe; Niebuhr, Erik; Bolund, Lars; Pinkel, Dan

    2005-02-01

    We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.

  19. High-resolution mapping of genotype-phenotype relationships in cridu chat syndrome using array comparative genomic hybridization

    SciTech Connect

    Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard; Zhang,Xiuqing; Niebuhr, Anita; Albertson, Donna; Yang, Huanming; Gray, Joe; Niebuhr, Erik; Bolund, Lars; Pinkel, Dan

    2007-07-03

    We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.

  20. Array comparative genomic hybridisation analysis of boys with X linked hypopituitarism identifies a 3.9 Mb duplicated critical region at Xq27 containing SOX3

    PubMed Central

    Solomon, N; Ross, S; Morgan, T; Belsky, J; Hol, F; Karnes, P; Hopwood, N; Myers, S; Tan, A; Warne, G; Forrest, S; Thomas, P

    2004-01-01

    Introduction: Array comparative genomic hybridisation (array CGH) is a powerful method that detects alteration of gene copy number with greater resolution and efficiency than traditional methods. However, its ability to detect disease causing duplications in constitutional genomic DNA has not been shown. We developed an array CGH assay for X linked hypopituitarism, which is associated with duplication of Xq26–q27. Methods: We generated custom BAC/PAC arrays that spanned the 7.3 Mb critical region at Xq26.1–q27.3, and used them to search for duplications in three previously uncharacterised families with X linked hypopituitarism. Results: Validation experiments clearly identified Xq26–q27 duplications that we had previously mapped by fluorescence in situ hybridisation. Array CGH analysis of novel XH families identified three different Xq26–q27 duplications, which together refine the critical region to a 3.9 Mb interval at Xq27.2–q27.3. Expression analysis of six orthologous mouse genes from this region revealed that the transcription factor Sox3 is expressed at 11.5 and 12.5 days after conception in the infundibulum of the developing pituitary and the presumptive hypothalamus. Discussion: Array CGH is a robust and sensitive method for identifying X chromosome duplications. The existence of different, overlapping Xq duplications in five kindreds indicates that X linked hypopituitarism is caused by increased gene dosage. Interestingly, all X linked hypopituitarism duplications contain SOX3. As mutation of this gene in human beings and mice results in hypopituitarism, we hypothesise that increased dosage of Sox3 causes perturbation of pituitary and hypothalamic development and may be the causative mechanism for X linked hypopituitarism. PMID:15342697

  1. Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA

    PubMed Central

    2013-01-01

    Background Array-CGH represents a comprehensive tool to discover genomic disease alterations that could potentially be applied to body fluids. In this report, we aimed at applying array-CGH to urinary samples to characterize bladder cancer. Methods Urinary DNA from bladder cancer patients and controls were hybridized on 44K oligonucleotide arrays. Validation analyses of identified regions and candidates included fluorescent in situ hybridization (FISH) and immunohistochemistry in an independent set of bladder tumors spotted on custom-made tissue arrays (n = 181). Results Quality control of array-CGH provided high reproducibility in dilution experiments and when comparing reference pools. The most frequent genomic alterations (minimal recurrent regions) among bladder cancer urinary specimens included gains at 1q and 5p, and losses at 10p and 11p. Supervised hierarchical clustering identified the gain at 1q23.3-q24.1 significantly correlated to stage (p = 0.011), and grade (p = 0.002). The amplification and overexpression of Prefoldin (PFND2), a selected candidate mapping to 1q23.3-q24.1, correlated to increasing stage and tumor grade by means of custom-designed and optimized FISH (p = 0.013 and p = 0.023, respectively), and immunohistochemistry (p ≤0.0005 and p = 0.011, respectively), in an independent set of bladder tumors included in tissue arrays. Moreover, PFND2 overexpression was significantly associated with poor disease-specific survival (p ≤0.0005). PFND2 was amplified and overexpressed in bladder tumors belonging to patients providing urinary specimens where 1q23.3q24.1 amplification was detected by array-CGH. Conclusions Genomic profiles of urinary DNA mirrowed bladder tumors. Molecular profiling of urinary DNA using array-CGH contributed to further characterize genomic alterations involved in bladder cancer progression. PFND2 was identified as a tumor stratification and clinical outcome prognostic biomarker for bladder cancer

  2. DNA tile based self-assembly: building complex nanoarchitectures.

    PubMed

    Lin, Chenxiang; Liu, Yan; Rinker, Sherri; Yan, Hao

    2006-08-11

    DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.

  3. 57. ORIGINAL TILE PRESS AND EXPERIMENTAL DENTAL KILN, SECOND FLOOR, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    57. ORIGINAL TILE PRESS AND EXPERIMENTAL DENTAL KILN, SECOND FLOOR, NORTH WING, HENRY MERCER USED THE KILN FOR HIS EARLIEST GLAZE TESTS. THE PRESS WAS DESIGNED TO BE USED WITH METAL CASED MOLDS. SINCE ONLY THE EARLIEST TILE DESIGNS ARE IN METAL CASES. THIS TECHNIQUE WAS PROBABLY DISCONTINUED. THIS PRESS WAS, THEREFORE, PROBABLY NOT USED EXTENSIVELY AT THIS SITE. THE UPPER PART OF GLAZE KILN No. 2 IS AT THE LEFT REAR. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  4. Affine reflection groups for tiling applications: Knot theory and DNA

    NASA Astrophysics Data System (ADS)

    Bodner, M.; Patera, J.; Peterson, M.

    2012-01-01

    We present in this paper some non-conventional applications of affine Weyl groups Waff of rank 2, the symmetry group of the tiling/lattice. We first develop and present the tools for applications requiring tilings of a real Euclidean plane {R}^2. We then elucidate the equivalence of these tilings with 2D projections of knots. The resulting mathematical structure provides a framework within which is encompassed recent work utilizing knot theory for modeling the structure and function of genetic molecules, specifically the action of particular enzymes in altering the topology of DNA in site-specific recombination.

  5. Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array

    SciTech Connect

    Van Essen, B; Panda, R; Wood, A; Ebeling, C; Hauck, S

    2010-12-01

    Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous

  6. Clinical and cytogenetic features of a patient with partial trisomy 8q and partial monosomy 13q delineated by array comparative genomic hybridization.

    PubMed

    Sohn, Young Bae; Yun, Jun No; Park, Sang-Jin; Park, Moon Sung; Kim, Sung Hwan; Lee, Jang Hoon

    2013-01-01

    Partial trisomy 8q is rare and has distinctive clinical features, including severe mental retardation, growth impairment, dysmorphic facial appearances, cleft palate, congenital heart disease, and urogenital anomalies. Partial monosomy 13q is a rare genetic disorder displaying a variety of phenotypic characteristics including mental retardation, dysmorphic facial features, and congenital anomalies. Here, we describe for the first time clinical observations and cytogenetic analysis of a patient with a concomitant occurrence of partial trisomy of 8q (8q21.3→qter) and partial monosomy 13q(13q34→qter). The patient was a female neonate with facial dysmorphia, agenesis of the corpus callosum, cleft palate, and congenital heart disease. G-band standard karyotype was 46,XX,add(13)(q34). To determine the origin of additional genomic gain in chromosome 13, array comparative genomic hybridization (CGH) was performed. Array CGH showed a 56.8 Mb sized gain on chromosome 8q and a 0.28 Mb sized loss on chromosome 13q. Therefore, the final karyotype of the patient was defined as 46,XX, der(13)t(8;13)(q21.3;q34). In conclusion, we described the clinical and cytogenetic analysis of the patient with concomitant occurrence of partial trisomy 8q and partial monosomy 13q delineated by array CGH. This report suggests that the array CGH would be a valuable diagnostic tool for identifying the origin of small additional genetic materials.

  7. Investigation of the diagnostic value of chromosome analysis and bacterial artificial chromosome-based array comparative genomic hybridization in prenatal diagnosis.

    PubMed

    Savli, Hakan; Keskin, Seda Eren; Cine, Naci

    2015-01-01

    To investigate the diagnostic value of bacterial artificial chromosome (BAC)-based array comparative genomic hybridization (CGH) and chromosome analysis in prenatal diagnosis. This study included the chromosome analysis and BAC-based array CGH analysis of 140 amniocentesis samples with prenatal diagnosis indications. Karyotype analysis showed trisomy 21 in 4 patients, trisomy 18 in 5 patients, monosomy X in 1 patient, and other anomalies in 3 patients. The BAC-based array CGH analysis showed 4 patients with trisomy 21, 4 patients with trisomy 18, and 1 patient with monosomy X as a numerical chromosome anomaly, while partial duplication was observed in chromosome 14 in 1 case as a structural anomaly. The array CGH is the most effective method available to complement cases where chromosome analysis, a gold standard in prenatal diagnosis, proves to be insufficient. Considering the inherent limitations of both methods, complementary features should be introduced in order to be able to give the most accurate data at the right time.

  8. Analyses of Genotypes and Phenotypes of Ten Chinese Patients with Wolf-Hirschhorn Syndrome by Multiplex Ligation-dependent Probe Amplification and Array Comparative Genomic Hybridization

    PubMed Central

    Yang, Wen-Xu; Pan, Hong; Li, Lin; Wu, Hai-Rong; Wang, Song-Tao; Bao, Xin-Hua; Jiang, Yu-Wu; Qi, Yu

    2016-01-01

    Background: Wolf-Hirschhorn syndrome (WHS) is a contiguous gene syndrome that is typically caused by a deletion of the distal portion of the short arm of chromosome 4. However, there are few reports about the features of Chinese WHS patients. This study aimed to characterize the clinical and molecular cytogenetic features of Chinese WHS patients using the combination of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array CGH). Methods: Clinical information was collected from ten patients with WHS. Genomic DNA was extracted from the peripheral blood of the patients. The deletions were analyzed by MLPA and array CGH. Results: All patients exhibited the core clinical symptoms of WHS, including severe growth delay, a Greek warrior helmet facial appearance, differing degrees of intellectual disability, and epilepsy or electroencephalogram anomalies. The 4p deletions ranged from 2.62 Mb to 17.25 Mb in size and included LETM1, WHSC1, and FGFR3. Conclusions: The combined use of MLPA and array CGH is an effective and specific means to diagnose WHS and allows for the precise identification of the breakpoints and sizes of deletions. The deletion of genes in the WHS candidate region is closely correlated with the core WHS phenotype. PMID:26960370

  9. Modeling water flow in a tile drainage network in glacial clayey tills in an agricultural catchment

    NASA Astrophysics Data System (ADS)

    De Schepper, G.; Therrien, R.; Refsgaard, J.

    2013-12-01

    required grid discretization for accurate simulate of flow in the drain, as well as provide reference results for additional scenarios. For example, because representing drains as discrete features in the model requires a very fine mesh discretization, the size of the domain that can be simulated can be limited. We are therefore testing an alternate approach where the tile drainage network and surrounding porous medium are represented by a dual-continuum formulation and compared to the reference model. Comparisons are made for a series of simulations with different initial conditions and boundary conditions, such as different precipitation events. The required discretization for the dual continuum model is also assessed. Obtaining a valid representation of the drain network with a dual continuum model will reduce the computational requirements compared to discrete drain models. Simulation results should lead us to the definition and validation of satisfactory simplifications and required aspects for future models at larger scale (catchment scale) containing complex and dense tile drainage networks.

  10. Surface runoff and subsurface tile drain losses of neonicotinoids and companion herbicides at edge-of-field.

    PubMed

    Chrétien, François; Giroux, Isabelle; Thériault, Georges; Gagnon, Patrick; Corriveau, Julie

    2017-05-01

    With their application as seed coatings, the use of neonicotinoid insecticides increased dramatically during the last decade. They are now frequently detected in aquatic ecosystems at concentrations susceptible to harm aquatic invertebrates at individual and population levels. This study intent was to document surface runoff and subsurface tile drain losses of two common neonicotinoids (thiamethoxam and clothianidin) compared to those of companion herbicides (atrazine, glyphosate, S-metolachlor and mesotrione) at the edge of a 22.5-ha field under a corn-soybean rotation. A total of 14 surface runoff and tile drain discharge events were sampled over two years. Events and annual unit mass losses were computed using flow-weighted concentrations and total surface runoff and tile drain flow volumes. Detection frequencies close to 100% in edge-of-field surface runoff and tile drain water samples were observed for thiamethoxam and clothianidin even though only thiamethoxam had been applied in the first year. In 2014, thiamethoxam median concentrations in surface runoff and tile drain samples were respectively 0.46 and 0.16 μg/L, while respective maximum concentrations of 2.20 and 0.44 μg/L were measured in surface runoff and tile drain samples during the first post-seeding storm event. For clothianidin, median concentrations in surface runoff and tile drain samples were 0.02 and 0.01, μg/L, and respective maximum concentrations were 0.07 μg/L and 0.05 μg/L. Surface runoff and tile drain discharge were key transport mechanisms with similar contributions of 53 and 47% of measured mass losses, respectively. Even if thiamethoxam was applied at a relatively low rate and had a low mass exportation value (0.3%), the relative toxicity was one to two orders of magnitude higher than those of the other chemicals applied in 2014 and 2015. Companion herbicides, except glyphosate in tile drains, exceeded their water quality guideline during one sampling campaign after

  11. Array tomography: semiautomated image alignment.

    PubMed

    Micheva, Kristina D; O'Rourke, Nancy; Busse, Brad; Smith, Stephen J

    2010-11-01

    Array tomography is a volumetric microscopy method based on physical serial sectioning. Ultrathin sections of a plastic-embedded tissue are cut using an ultramicrotome, bonded in an ordered array to a glass coverslip, stained as desired, and imaged. The resulting two-dimensional image tiles can then be reconstructed computationally into three-dimensional volume images for visualization and quantitative analysis. The minimal thickness of individual sections permits high-quality rapid staining and imaging, whereas the array format allows reliable and convenient section handling, staining, and automated imaging. Also, the physical stability of the arrays permits images to be acquired and registered from repeated cycles of staining, imaging, and stain elution, as well as from imaging using multiple modalities (e.g., fluorescence and electron microscopy). Array tomography makes it possible to visualize and quantify previously inaccessible features of tissue structure and molecular architecture. However, careful preparation of the tissue is essential for successful array tomography; these steps can be time-consuming and require some practice to perfect. Successful array tomography requires that the captured images be properly stacked and aligned, and the software to achieve these ends is freely available. This protocol describes the construction of volumetric image stacks from images of fluorescently labeled arrays for three-dimensional image visualization, analysis, and archiving.

  12. Thermal modeling of a metallic thermal protection tile for entry vehicles

    NASA Technical Reports Server (NTRS)

    Wiese, M. R.

    1986-01-01

    The thermal Energy Flow Simulation (TEFS) computer program was developed to simulate transient heat transfer through composite solids and predict interfacial temperatures. The program and its usage are described. A simulation of the thermal response of a new thermal protection tile design for the Space Shuttle Orbiter is presented and graphically compared with actual data. An example is also provided which shows the program's usage as a design tool for theoretical models.

  13. South front, west part, showing wrought iron gates and tiling ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South front, west part, showing wrought iron gates and tiling at the former main entrance. - San Bernardino Valley College, Life Science Building, 701 South Mount Vernon Avenue, San Bernardino, San Bernardino County, CA

  14. 24. DETAIL VIEW OF TILE GAUGE IN INTERMEDIATE LOCK WALL, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. DETAIL VIEW OF TILE GAUGE IN INTERMEDIATE LOCK WALL, LOOKING NORTHEAST. NOTE STEEL WALL ARMOR EMBEDDED IN CONCRETE. - Upper Mississippi River 9-Foot Channel Project, Lock & Dam 26, Alton, Madison County, IL

  15. 25. CAFETERIA Note remains of tile floor in foreground. Food ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    25. CAFETERIA Note remains of tile floor in foreground. Food cooked on the stove was served to workers in the eating area to the left of the counter (off picture). - Hovden Cannery, 886 Cannery Row, Monterey, Monterey County, CA

  16. Integrator Based Readout in Tile Calorimeter of the ATLAS Experiment

    NASA Astrophysics Data System (ADS)

    González Parra, Garoé; ATLAS Collaboration

    TileCal is the Barrel hadronic calorimeter of the ATLAS experiment at LHC/CERN. To equalize the response of individual TileCal cells with a precision better than 1% and to monitor the response of each cell over time, a calibration and monitoring system based on a Cs137 radioactive source driven through the calorimeter volume by liquid flow has been implemented. This calibration system relies on a dedicated readout chain based on slow integrators that read currents from the TileCal photomultipliers integrating over milliseconds during the calibration runs. Moreover, during the LHC collisions the TileCal integrator based readout provides the signal coming from inelastic proton-proton collisions at low momentum transfer. This is used to monitor in ATLAS the instantaneous luminosity as well as the response of all calorimeter cells during data-taking.

  17. VIEW OF COMPASS ROSE TILE INLAY IN FLOOR OF LOBBY, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF COMPASS ROSE TILE INLAY IN FLOOR OF LOBBY, BUILDING 1, LOOKING SOUTHEAST - Roosevelt Base, Administration & Brig Building, Bounded by Nevada & Colorado Streets, Reeves & Richardson Avenues, Long Beach, Los Angeles County, CA

  18. Interference Heating to Cavities Between Simulated RSI Tiles

    NASA Technical Reports Server (NTRS)

    Johnson, C. B.

    1973-01-01

    Test results for full scale simulated surface insulation tiles on both the tunnel wall and in the free stream, for in-line and staggered tile orientations, are summarized as follows: (1) The staggered tile orientation has heating on the forward face which is a factor of 4.5 times higher than the heating to the forward face of the in-line tile orientation; (2) the longitudinal gap heating was the highest for the 0.3175 cm gap and the lowest for the 0.1587 cm gap; and (3) there was an order of magnitude decrease in the heating on the forward face of a spanwise gap when the gap size was decreased from 0.3175 cm to 0.1587 cm.

  19. 45. Everett, Weinreb, photographer DETAIL, CEMENT TILE PATTERN FROM RECEPTION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    45. Everett, Weinreb, photographer DETAIL, CEMENT TILE PATTERN FROM RECEPTION HALL LOOKING EAST ACROSS ARRIVAL LOBBY FLOOR - Los Angeles Union Passenger Terminal, Tracks & Shed, 800 North Alameda Street, Los Angeles, Los Angeles County, CA

  20. 44. Everett Weinreb, photographer DETAIL, CEMENT TILE PATTERN, FROM LOGGIA ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    44. Everett Weinreb, photographer DETAIL, CEMENT TILE PATTERN, FROM LOGGIA LOOKING EAST ACROSS RECEPTION HALL - Los Angeles Union Passenger Terminal, Tracks & Shed, 800 North Alameda Street, Los Angeles, Los Angeles County, CA

  1. Measurement of Tritium Surface Distribution on TFTR Bumper Limiter Tiles

    SciTech Connect

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

    2004-06-28

    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.

  2. Remote handling system development of armor tile replacement for FER

    SciTech Connect

    Adachi, J.; Yoshizawa, S.; Nakano, Y.

    1994-12-31

    A number of armor tiles are attached to the first wall of the Fusion Experimental Reactor (FER) in order to protect the first wall against severe heat/particle loads from plasma during its operation. Although the armor tiles are made of heat-resisting materials such as graphite, they are eroded and damaged due to the loads and thus they are categorized into scheduled maintenance component. A remote handling system is required to replace a large number of tiles rapidly in the highly activated circumstance and has to be capable for adjusting a manipulator`s motion taking into account a thermal deformation of the first wall and/or a positioning error of a manipulator for the remote handling system. For this purpose, a remote handling system of the armor tile replacement with a visual feedback control has been fabricated and this paper describes an experimental system and the performance test results.

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

    PubMed

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

    2007-10-15

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

  4. ATLAS Tile Calorimeter performance with Run 1 data

    NASA Astrophysics Data System (ADS)

    Cerdá Alberich, L.

    2016-07-01

    The performance of the central hadronic calorimeter, TileCal, in the ATLAS Experiment at the Large Hadron Collider is studied using cosmic-ray muons and the large sample of proton-proton collisions acquired during the Run 1 of LHC (2010-2012). Results are presented for the precision of the absolute energy scale and timing, noise characterization, and time-stability of the detector. The results show that the Tile Calorimeter performance is within the design requirements of the detector.

  5. Ceramic tile grout removal & sealing using high power lasers

    SciTech Connect

    Lawrence, J.; Li, L.; Spencer, J.T.

    1996-12-31

    Work has been conducted using a Nd:YAG laser, a CO{sub 2} laser and a high power diode laser (HPDL) in order to determine the feasibility of removing contaminated tile grout from the void between adjoining vitrified ceramic tiles, and to seal the void permanently with a material having an impermeable surface glaze. Reported on in the paper are; the basic process phenomena, the process effectiveness, suitable vitrifiable material development, a heat affect study and a morphological and compositional analysis.

  6. On the Minimum Weight Steiner Triangular Tiling problem

    SciTech Connect

    Doddi, S.; Zhu, B.

    1995-04-01

    In this paper, we introduce the Minimum Weight Steiner Triangular Tiling problem, which is a generalization of the Minimum Weight Steiner Triangulation. Contrary to the conjecture of Eppstein that the Minimum Weight Steiner Triangulation of a convex polygon has the property that the Steiner points all lie on the boundary of the polygon [Epp94], we show that the Steiner points of a Minimum Weight Steiner Triangular Tiling could lie in the interior of a convex polygon.

  7. 56. ORIGINAL MOLDS. THE MORAVIAN POTTERY AND TILE WORKS HAS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    56. ORIGINAL MOLDS. THE MORAVIAN POTTERY AND TILE WORKS HAS APPROXIMATELY 6,000 PLASTER MOLDS OF VARIOUS TYPES, INCLUDING THE DEEP CAVITY MOLDS IN THE CENTER OF THE PHOTOGRAPH. THESE MOLDS PRODUCED ALLEGORICAL FIGURES TO BE INSTALLED AROUND THE CORNICES OF PUBLIC SCHOOLS. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  8. No inherent glassiness in a Penrose tiling quasicrystal

    SciTech Connect

    Strandburg, K.J.; Dressel, P.R.

    1988-11-01

    Consideration of the structure of the Penrose pattern has led to speculation that a system with a Penrose tiling ground state might be subject to inherent glassy behavior. Monte Carol simulations show, using a simple model of the energetics, that there is no inherent glassiness in the Penrose tiling. Thermodynamic quantities measured are completely reversible, displaying no observable hysterisis, and the system may be easily cooled from a highly disordered configuration into its lowest energy state. 11 refs., 7 figs.

  9. Next-Generation Microshutter Arrays for Large-Format Imaging and Spectroscopy

    NASA Technical Reports Server (NTRS)

    Moseley, Samuel; Kutyrev, Alexander; Brown, Ari; Li, Mary

    2012-01-01

    A next-generation microshutter array, LArge Microshutter Array (LAMA), was developed as a multi-object field selector. LAMA consists of small-scaled microshutter arrays that can be combined to form large-scale microshutter array mosaics. Microshutter actuation is accomplished via electrostatic attraction between the shutter and a counter electrode, and 2D addressing can be accomplished by applying an electrostatic potential between a row of shutters and a column, orthogonal to the row, of counter electrodes. Microelectromechanical system (MEMS) technology is used to fabricate the microshutter arrays. The main feature of the microshutter device is to use a set of standard surface micromachining processes for device fabrication. Electrostatic actuation is used to eliminate the need for macromechanical magnet actuating components. A simplified electrostatic actuation with no macro components (e.g. moving magnets) required for actuation and latching of the shutters will make the microshutter arrays robust and less prone to mechanical failure. Smaller-size individual arrays will help to increase the yield and thus reduce the cost and improve robustness of the fabrication process. Reducing the size of the individual shutter array to about one square inch and building the large-scale mosaics by tiling these smaller-size arrays would further help to reduce the cost of the device due to the higher yield of smaller devices. The LAMA development is based on prior experience acquired while developing microshutter arrays for the James Webb Space Telescope (JWST), but it will have different features. The LAMA modular design permits large-format mosaicking to cover a field of view at least 50 times larger than JWST MSA. The LAMA electrostatic, instead of magnetic, actuation enables operation cycles at least 100 times faster and a mass significantly smaller compared to JWST MSA. Also, standard surface micromachining technology will simplify the fabrication process, increasing

  10. DNAzyme-Controlled Cleavage of Dimer and Trimer Origami Tiles.

    PubMed

    Wu, Na; Willner, Itamar

    2016-04-13

    Dimers of origami tiles are bridged by the Pb(2+)-dependent DNAzyme sequence and its substrate or by the histidine-dependent DNAzyme sequence and its substrate to yield the dimers T1-T2 and T3-T4, respectively. The dimers are cleaved to monomer tiles in the presence of Pb(2+)-ions or histidine as triggers. Similarly, trimers of origami tiles are constructed by bridging the tiles with the Pb(2+)-ion-dependent DNAzyme sequence and the histidine-dependent DNAzyme sequence and their substrates yielding the trimer T1-T5-T4. In the presence of Pb(2+)-ions and/or histidine as triggers, the programmed cleavage of trimer proceeds. Using Pb(2+) or histidine as trigger cleaves the trimer to yield T5-T4 and T1 or the dimer T1-T5 and T4, respectively. In the presence of Pb(2+)-ions and histidine as triggers, the cleavage products are the monomer tiles T1, T5, and T4. The different cleavage products are identified by labeling the tiles with 0, 1, or 2 streptavidin labels and AFM imaging.

  11. Diatoms as an indicator for tile drainage flow in a German lowland catchment

    NASA Astrophysics Data System (ADS)

    Wu, Naicheng; Faber, Claas; Ulrich, Uta; Schmalz, Britta; Fohrer, Nicola

    2014-05-01

    The separation of flow components within a model simulation is of great importance for a successful implementation of management measures. Tracers are commonly used to identify and assess runoff-generating processes and to detect sources of stream flow components within a target catchment. Diatoms could be an ideal tracer due to their diverse preferences to different aquatic habitats (van Dam et al. 1994, Pfister et al. 2009). As a part of a DFG (Deutsche Forschungsgemeinschaft) project, we collected diatom samples of 9 sites (4 tile drainage, and 5 river sites) weekly or biweekly from March to July 2013 in a German lowland catchment (the Kielstau catchment). First results showed that diatom species Achnanthes lanceolata, Fragilaria biceps and Navicula ingapirca dominated in tile drainage flow with relative abundances of 22.2%, 21.5% and 10.9%, respectively. For river sites, the most abundant species was Navicula cryptocephala (20.5%), followed by Fragilaria biceps (12.9%), Cyclotella meneghiniana (9.5%) and Achnanthes lanceolata (9.3%). Compared with river sites, tile drainage flow had lower diatom density, biomass, species richness and percentage of Aquatic/Riparian diatoms (AqRi%). However, the proportion of Riparian diatoms (RiZo%) increased at tile drainage flow. Indicator value method (IndVal) revealed that the two water types were characterized by different indicator species. Fifteen taxa (e.g. Cocconeis placentula, Cyclotella meneghiniana, Navicula cryptocephala and Fragilaria biceps) were significant indicators for river sites. Achnanthes lanceolata, Achnanthes minutissima and Navicula ingapirca were significant indicators for tile drainage flow. These results highlight the suitability of diatoms as an indicator for tile drainage flow. Spatial and temporal variations of diatom community should be considered in future surveys. Keywords: Diatoms, Flow components, Indicator value method, Tracer References: Pfister, L., J. J. McDonnell, S. Wrede, D. Hl

  12. Improved Titanium Billet Inspection Sensitivity through Optimized Phased Array Design, Part II: Experimental Validation and Comparative Study with Multizone

    SciTech Connect

    Hassan, W.; Vensel, F.; Knowles, B.

    2006-03-06

    The inspection of critical rotating components of aircraft engines has made important advances over the last decade. The development of Phased Array (PA) inspection capability for billet and forging materials used in the manufacturing of critical engine rotating components has been a priority for Honeywell Aerospace. The demonstration of improved PA inspection system sensitivity over what is currently used at the inspection houses is a critical step in the development of this technology and its introduction to the supply base as a production inspection. As described in Part I (in these proceedings), a new phased array transducer was designed and manufactured for optimal inspection of eight inch diameter Ti-6Al-4V billets. After confirming that the transducer was manufactured in accordance with the design specifications a validation study was conducted to assess the sensitivity improvement of the PAI over the current capability of Multi-zone (MZ) inspection. The results of this study confirm the significant ({approx_equal} 6 dB in FBH number sign sensitivity) improvement of the PAI sensitivity over that of MZI.

  13. Tiling solutions for optimal biological sensing

    NASA Astrophysics Data System (ADS)

    Walczak, Aleksandra M.

    2015-10-01

    Biological systems, from cells to organisms, must respond to the ever-changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically stochastic, many-body and often self-organized nature of the processes that control their sensing and response and limited resources. Despite a wide range of scales and functions that can be observed in the living world, some common principles that govern the behavior of biological systems emerge. Here I review two examples of very different biological problems: information transmission in gene regulatory networks and diversity of adaptive immune receptor repertoires that protect us from pathogens. I discuss the trade-offs that physical laws impose on these systems and show that the optimal designs of both immune repertoires and gene regulatory networks display similar discrete tiling structures. These solutions rely on locally non-overlapping placements of the responding elements (genes and receptors) that, overall, cover space nearly uniformly.

  14. Orbiter thermal pressure drop characteristics for shuttle orbiter thermal protection system components: High density tile, low density tile, densified low density tile, and strain isolation pad

    NASA Technical Reports Server (NTRS)

    Lawing, P. L.; Nystrom, D. M.

    1980-01-01

    Pressure drop tests were conducted on available samples of low and high density tile, densified low density tile, and strain isolation pads. The results are presented in terms of pressure drop, material thickness and volume flow rate. Although the test apparatus was only capable of a small part of the range of conditions to be encountered in a Shuttle Orbiter flight, the data serve to determine the type of flow characteristics to be expected for each material type tested; the measured quantities also should serve as input for initial venting and flow through analysis.

  15. Dissolved organic carbon in runoff and tile-drain water under corn and forage fertilized with hog manure.

    PubMed

    Royer, Isabelle; Angers, Denis A; Chantigny, Martin H; Simard, Régis R; Cluis, Daniel

    2007-01-01

    Dissolved organic carbon (DOC) export from soils can play a significant role in soil C cycling and in nutrient and pollutant transport. However, information about DOC losses from agricultural soils as influenced by management practices is scarce. We compared the effects of mineral fertilizer (MF) and liquid hog manure (LHM) applications on the concentration and molecular size of DOC released in runoff and tile-drain water under corn (Zea mays L.) and forage cropping systems. Runoff and tile-drain water samples were collected during a 2-mo period (October to December 1998) and DOC concentration was measured. Characterization of DOC was performed by tangential ultrafiltration with nominal cut-offs at 3 and 100 kDa. Mean concentration of DOC in runoff water (12.7 mg DOC L(-1)) was higher than in tile-drain water (6.5 mg DOC L(-1)). Incorporation of corn residues increased the DOC concentration by 6- to 17-fold in surface runoff, but this effect was short-lived. In runoff water, the relative size of the DOC molecules increased when corn residues and LHM were applied probably due to partial microbial breakdown of these organic materials and to a faster decomposition or preferential adsorption of the small molecules. The DOC concentration in tile-drain water was slightly higher under forage (7.5 mg DOC L(-1)) than under corn (5.4 mg DOC L(-1)) even though the application rates of LHM were higher in corn plots. We suggest that preferential flow facilitated the migration of DOC to tile drains in forage plots. In conclusion, incorporation of corn residues and LHM increased the concentration of DOC and the relative size of the molecules in surface runoff water, whereas DOC in tile-drain water was mostly influenced by the cropping system with relatively more DOC and larger molecules under forage than corn.

  16. Torsional Buckling Tests of a Simulated Solar Array

    NASA Technical Reports Server (NTRS)

    Thornton, E. A.

    1996-01-01

    Spacecraft solar arrays are typically large structures supported by long, thin deployable booms. As such, they may be particularly susceptible to abnormal structural behavior induced by mechanical and thermal loading. One example is the Hubble Space Telescope solar arrays which consist of two split tubes fit one inside the other called BiSTEMs. The original solar arrays on the Hubble Space Telescope were found to be severely twisted following deployment and later telemetry data showed the arrays were vibrating during daylight to night and night to daylight transition. The solar array twist however can force the BiSTEM booms to change in cross-section and cause tile solar arrays to react unpredictably to future loading. The solar arrays were redesigned to correct for tile vibration, however, upon redeployment they again twisted. To assess the influence of boom cross-sectional configuration, experiments were conducted on two types of booms, (1)booms with closed cross-sections, and (2) booms with open cross-sections. Both models were subjected to compressive loading and imposed tip deflections. An existing analytical model by Chung and Thornton was used to define the individual load ranges for each model solar array configuration. The load range for the model solar array using closed cross-section booms was 0-120 Newtons and 0-160 Newtons for the model solar array using open cross-section booms. The results indicate the model solar array with closed cross-section booms buckled only in flexure. However, the results of the experiment with open cross-section booms indicate the model solar array buckled only in torsion and with imposed tip deflections the cross section can degrade by rotation of the inner relative to the outer STEM. For tile Hubble Space Telescope solar arrays the results of these experiments indicate the twisting resulted from the initial mechanical loading of the open cross-section booms.

  17. Phase change material in floor tiles for thermal energy storage

    NASA Astrophysics Data System (ADS)

    Lee, Amy Sarah

    Traditional passive solar systems have relied on sensible heat storage for energy savings. Recent research has investigated taking advantage of latent heat storage for additional energy savings. This is accomplished by the incorporation of phase change material into building materials used in traditional passive applications. Trombe walls, ceilings and floors can all be enhanced with phase change materials. This research introduces a new flooring material that incorporates a phase change material ready for commercial manufacture. An agglomerate floor tile containing 20% by mass of encapsulated octadecane has been manufactured. Flexural and compressive strength of 7.4 MPa and 24.5 MPa respectively, were measured for the tile. Peak melting transition temperature was determined to be 27.2°C with a latent heat of 33.9 J/g of tile. Structural and thermal performance of the tile surpassed that of a typical ceramic tile. Each tile was composed of quartz, resin and phase change material. Statistical modeling was performed to analyze the response of flexural and compressive strength on varying amounts of quartz, resin and phase change material. Resulting polynomials described the effect of adding phase change material into the tile. With as little as 10% by mass of phase change material, the strength was reduced to less than 50% of tile without phase change material. It was determined that the maximum phase change material content to attain structural integrity greater than ceramic tile was 20% by mass. The statistical analysis used for this research was based on mixture experiments. A procedure was developed to simplify the selection of data points used in the fit of the polynomials to describe the response of flexural and compressive strengths. Analysis of energy savings using this floor tile containing 20% by mass of phase change material was performed as an addendum to this research. A known static simulation method, SLR (solar load ratio), was adapted to include

  18. ALT-II armor tile design for upgraded TEXTOR operation

    SciTech Connect

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

    1994-12-31

    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.

  19. Detection of genomic imbalances in microdissected Hodgkin and Reed-Sternberg cells of classical Hodgkin's lymphoma by array-based comparative genomic hybridization.

    PubMed

    Hartmann, Sylvia; Martin-Subero, José I; Gesk, Stefan; Hüsken, Julia; Giefing, Maciej; Nagel, Inga; Riemke, Jennifer; Chott, Andreas; Klapper, Wolfram; Parrens, Marie; Merlio, Jean-Philippe; Küppers, Ralf; Bräuninger, Andreas; Siebert, Reiner; Hansmann, Martin-Leo

    2008-09-01

    Cytogenetic analysis of classical Hodgkin's lymphoma is limited by the low content of the neoplastic Hodgkin-Reed-Sternberg cells in the affected tissues. However, available cytogenetic data point to an extreme karyotype complexity. To obtain insights into chromosomal imbalances in classical Hodgkin's lymphoma, we applied array-based comparative genomic hybridization (array comparative genomic hybridization) using DNA from microdissected Hodgkin-Reed-Sternberg cells. To avoid biases introduced by DNA amplification for array comparative genomic hybridization, cHL cases rich in Hodgkin-Reed-Sternberg cells were selected. DNA obtained from approximately 100,000 microdissected Hodgkin-Reed-Sternberg cells of each of ten classical Hodgkin's lymphoma cases was hybridized onto commercial 105 K oligonucleotide comparative genomic hybridization microarrays. Selected imbalances were confirmed by interphase cytogenetics and quantitative polymerase chain reaction analysis and further studied in an independent series of classical Hodgkin's lymphoma. Gains identified in at least five cHL affected 2p12-16, 5q15-23, 6p22, 8q13, 8q24, 9p21-24, 9q34, 12q13-14, 17q12, 19p13, 19q13 and 20q11 whereas losses recurrent in at least five cases involved Xp21, 6q23-24 and 13q22. Copy number changes of selected genes and a small deletion (156 kb) of the CDKN2B (p15) gene were confirmed by interphase cytogenetics and polymerase chain reaction analysis, respectively. Several gained regions included genes constitutively expressed in cHL. Among these, gains of STAT6 (12q13), NOTCH1 (9q34) and JUNB (19p13) were present in additional cHL with the usual low Hodgkin-Reed-Sternberg cell content. The present study demonstrates that array comparative genomic hybridization of microdissected Hodgkin-Reed-Sternberg cells is suitable for identifying and characterizing chromosomal imbalances. Regions affected by genomic changes in Hodgkin-Reed-Sternberg cells recurrently include genes constitutively

  20. Characterizing phosphorus dynamics in tile-drained agricultural fields of eastern Wisconsin

    NASA Astrophysics Data System (ADS)

    Madison, Allison M.; Ruark, Matthew D.; Stuntebeck, Todd D.; Komiskey, Matthew J.; Good, Lara W.; Drummy, Nancy; Cooley, Eric T.

    2014-11-01

    Artificial subsurface drainage provides an avenue for the rapid transfer of phosphorus (P) from agricultural fields to surface waters. This is of particular interest in eastern Wisconsin, where there is a concentrated population of dairy farms and high clay content soils prone to macropore development. Through collaboration with private landowners, surface and tile drainage was measured and analyzed for dissolved reactive P (DRP) and total P (TP) losses at four field sites in eastern Wisconsin between 2005 and 2009. These sites, which received frequent manure applications, represent a range of crop management practices which include: two chisel plowed corn fields (CP1, CP2), a no-till corn-soybean field (NT), and a grazed pasture (GP). Subsurface drainage was the dominant pathway of water loss at each site accounting for 66-96% of total water discharge. Average annual flow-weighted (FW) TP concentrations were 0.88, 0.57, 0.21, and 1.32 mg L-1 for sites CP1, CP2, NT, and GP, respectively. Low TP concentrations at the NT site were due to tile drain interception of groundwater flow where large volumes of tile drainage water diluted the FW-TP concentrations. Subsurface pathways contributed between 17% and 41% of the TP loss across sites. On a drainage event basis, total drainage explained between 36% and 72% of the event DRP loads across CP1, CP2, and GP; there was no relationship between event drainflow and event DRP load at the NT site. Manure applications did not consistently increase P concentrations in drainflow, but annual FW-P concentrations were greater in years receiving manure applications compared to years without manure application. Based on these field measures, P losses from tile drainage must be integrated into field level P budgets and P loss calculations on heavily manured soils, while also acknowledging the unique drainage patterns observed in eastern Wisconsin.

  1. Elastic-plastic-creep analysis of brazed carbon-carbon/OFHC divertor tile concepts for TPX

    SciTech Connect

    Chin, E.; Reis, E.E.

    1995-12-31

    The 7.5 MW/m{sup 2} heat flux requirements for the TPX divertor necessitate the use of high conductivity carbon-carbon (C-C) tiles that are brazed to annealed copper (OFHC) coolant tubes. Significant residual stresses are developed in the C-C tiles during the braze process due to large differences in the thermal expansion coefficients between these materials. Analyses which account for only the elastic-plastic strains developed in the OFHC tube may not accurately characterize the behavior of the tube during brazing. The elevated temperature creep behavior of the copper coolant tubes intuitively should reduce the calculated residual stresses in the C-C tiles. Two divertor tile concepts, the monoblock and the archblock, were analyzed for residual stress using 2-D finite element analysis for elastic-plastic-creep behavior of the OFHC tube during an assumed braze cooldown cycle. The results show that the inclusion of elevated temperature creep effects decrease the calculated residual stresses by only about 10% when compared to those analyses in which only elastic-plastic behavior of the OFHC is accounted for. The primary reason that creep effects at higher temperatures are not more significant is due to the low yield stress and nearly flat-top stress-strain curve of annealed OFHC. Since high temperature creep plays less of a role in the residual stress levels than previously thought, future scoping studies can be done in an elastic-plastic analysis with confidence that the stresses will be within approximately 10% of an elastic-plastic-creep analysis.

  2. Performance of the ATLAS Tile Hadronic Calorimeter at LHC in Run 1 and planned upgrades

    NASA Astrophysics Data System (ADS)

    Solovyanov, O.

    2014-10-01

    The Tile Calorimeter (TileCal) is the central section of the ATLAS hadronic calorimeter at the Large Hadron Collider, a key detector for the measurements of hadrons, jets, tau leptons and missing transverse energy. Scintillation light produced in the tiles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). The resulting electronic signals from approximately 10000 PMTs are digitized before being transferred to off-detector data-acquisition systems. The data quality procedures used during the LHC data-taking and the evolution of the detector status are explained in the presentation. The energy and the time reconstruction performance of the digitized signals is presented and the noise behaviour and its improvement during the detector consolidation in maintenance periods are shown. A set of calibration systems allow monitoring and equalization of the calorimeter channels responses via signal sources that act at every stage of the signal path, from scintillation light to digitized signal. These partially overlapping systems are described in detail, their individual performance is discussed as well as the comparative results from measurements of the evolution of the calorimeter response with time during the full LHC data-taking period. The TileCal upgrade aims at replacing the majority of the on- and off-detector electronics so that all calorimeter signals will be 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. For the off-detector electronics a special pre-processor board is being developed, which will take care of the initial trigger processing, while the main data are temporarily stored in the pipeline and de-randomiser memories.

  3. Characterizing phosphorus dynamics in tile-drained agricultural fieldsof eastern Wisconsin

    USGS Publications Warehouse

    Madison, Allison; Ruark, Matthew; Stuntebeck, Todd D.; Komiskey, Matthew J.; Good, Laura W; Drummy, Nancy; Cooley, Eric

    2014-01-01

    Artificial subsurface drainage provides an avenue for the rapid transfer of phosphorus (P) from agricultural fields to surface waters. This is of particular interest in eastern Wisconsin, where there is a concentrated population of dairy farms and high clay content soils prone to macropore development. Through collaboration with private landowners, surface and tile drainage was measured and analyzed for dissolved reactive P (DRP) and total P (TP) losses at four field sites in eastern Wisconsin between 2005 and 2009. These sites, which received frequent manure applications, represent a range of crop management practices which include: two chisel plowed corn fields (CP1, CP2), a no-till corn–soybean field (NT), and a grazed pasture (GP). Subsurface drainage was the dominant pathway of water loss at each site accounting for 66–96% of total water discharge. Average annual flow-weighted (FW) TP concentrations were 0.88, 0.57, 0.21, and 1.32 mg L−1 for sites CP1, CP2, NT, and GP, respectively. Low TP concentrations at the NT site were due to tile drain interception of groundwater flow where large volumes of tile drainage water diluted the FW-TP concentrations. Subsurface pathways contributed between 17% and 41% of the TP loss across sites. On a drainage event basis, total drainage explained between 36% and 72% of the event DRP loads across CP1, CP2, and GP; there was no relationship between event drainflow and event DRP load at the NT site. Manure applications did not consistently increase P concentrations in drainflow, but annual FW-P concentrations were greater in years receiving manure applications compared to years without manure application. Based on these field measures, P losses from tile drainage must be integrated into field level P budgets and P loss calculations on heavily manured soils, while also acknowledging the unique drainage patterns observed in eastern Wisconsin.

  4. Numerical simulation of armor capability of AI2O3 and SiC armor tiles

    NASA Astrophysics Data System (ADS)

    Rashid, T.; Aleem, M. A.; Akbar, S.; Rauf, A.; Shuaib, M.

    2016-08-01

    Alumina and Silicon Carbide armor plates have been tested numerically against 7.62x51 (mm x mm) armor piercing (AP) projectiles. A 2-D problem with axial symmetry has been designedand the simulations were carried out using commercial software ANSYS AUTODYN. Experiments were modeled for Alumina (99.5%), Alumina (99.7%) and SiC with a range of tile thicknesses (5, 10, 15 and 20 mm). The projectile was chosen as 7.62 x 51AP bullet (initial velocity 810 m/sec)with two different core materials Steel 4340 and WC, however, casing material was copper for both cores. SiC showed better defense against AP bullet as compared to Al2O3. The residual velocity and momentum of the bullet were found to decrease with increasing tile thickness. SiC tiles with thickness 15mm and 20 mm successfully sustained penetration against steel 4340 and WC core bullets, respectively. However none of the Alumina targets succeeded in stopping the bullet.

  5. Parametric Weight Comparison of Advanced Metallic, Ceramic Tile, and Ceramic Blanket Thermal Protection Systems

    NASA Technical Reports Server (NTRS)

    Myers, David E.; Martin, Carl J.; Blosser, Max L.

    2000-01-01

    A parametric weight assessment of advanced metallic panel, ceramic blanket, and ceramic tile thermal protection systems (TPS) was conducted using an implicit, one-dimensional (I-D) finite element sizing code. This sizing code contained models to account for coatings fasteners, adhesives, and strain isolation pads. Atmospheric entry heating profiles for two vehicles, the Access to Space (ATS) vehicle and a proposed Reusable Launch Vehicle (RLV), were used to ensure that the trends were not unique to a certain trajectory. Ten TPS concepts were compared for a range of applied heat loads and substructural heat capacities to identify general trends. This study found the blanket TPS concepts have the lightest weights over the majority of their applicable ranges, and current technology ceramic tiles and metallic TPS concepts have similar weights. A proposed, state-of-the-art metallic system which uses a higher temperature alloy and efficient multilayer insulation was predicted to be significantly lighter than the ceramic tile stems and approaches blanket TPS weights for higher integrated heat loads.

  6. Application of Hilbert-Huang Transform for Improved Defect Detection in Terahertz NDE of Shuttle Tiles

    NASA Technical Reports Server (NTRS)

    Anastasi, Robert F.; Madaras, Eric I.

    2005-01-01

    Terahertz NDE is being examined as a method to inspect the adhesive bond-line of Space Shuttle tiles for defects. Terahertz signals are generated and detected, using optical excitation of biased semiconductors with femtosecond laser pulses. Shuttle tile samples were manufactured with defects that included repair regions unbond regions, and other conditions that occur in Shuttle structures. These samples were inspected with a commercial terahertz NDE system that scanned a tile and generated a data set of RF signals. The signals were post processed to generate C-scan type images that are typically seen in ultrasonic NDE. To improve defect visualization the Hilbert-Huang Transform, a transform that decomposes a signal into oscillating components called intrinsic mode functions, was applied to test signals identified as being in and out of the defect regions and then on a complete data set. As expected with this transform, the results showed that the decomposed low-order modes correspond to signal noise while the high-order modes correspond to low frequency oscillations in the signal and mid-order modes correspond to local signal oscillations. The local oscillations compare well with various reflection interfaces and the defect locations in the original signal.

  7. Dominant controls on pesticide transport from tile to catchment scale: Lessons from a minimalist model

    NASA Astrophysics Data System (ADS)

    Zanardo, S.; Basu, N. B.; Botter, G.; Rinaldo, A.; Rao, P. S. C.

    2012-04-01

    This paper proposes a minimalist modeling approach for characterizing pesticide concentrations in runoff from agricultural catchments across spatial scales. The model proposed is of an intermediate level of complexity between traditional chromatographic separation models and the more complex dual-domain models. Parsimony in the model is achieved by assuming stationarity of catchment travel time distributions and by coupling a dual-domain source zone model that describes near-surface pesticide dynamics with the mass response function (MRF) approach, which describes catchment-scale solute transport. The model is evaluated by comparing predicted atrazine concentrations with measured values over a 5 yr period at two spatial scales (tile drain: 3-5 ha; river station: 69 km2) within an intensively managed agricultural catchment in Illinois, United States. Pesticide dynamics within the source zone provided the strongest control on leaching. Two parameters were calibrated at the tile scale, Γ, which describes partitioning in the dual-domain surficial source zone, and ke, which describes the mass transfer rate constant between the two domains. The initial peak of concentration was found to be sensitive to Γ, while the later peaks were sensitive to ke. The calibrated parameters at the tile stations were used to predict atrazine dynamics at the river station. Prediction errors are examined and related to the lack of detailed information about anthropogenic forcings across scales (e.g., land-use or soil/crop management practices).

  8. Towards Optimal Filtering on ARM for ATLAS Tile Calorimeter Front-End Processing

    NASA Astrophysics Data System (ADS)

    Cox, Mitchell A.

    2015-10-01

    The Large Hadron Collider at CERN generates enormous amounts of raw data which presents a serious computing challenge. After planned upgrades in 2022, the data output from the ATLAS Tile Calorimeter will increase by 200 times to over 40 Tb/s. Advanced and characteristically expensive Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs) are currently used to process this quantity of data. It is proposed that a cost- effective, high data throughput Processing Unit (PU) can be developed by using several ARM System on Chips in a cluster configuration to allow aggregated processing performance and data throughput while maintaining minimal software design difficulty for the end-user. ARM is a cost effective and energy efficient alternative CPU architecture to the long established x86 architecture. This PU could be used for a variety of high-level algorithms on the high data throughput raw data. An Optimal Filtering algorithm has been implemented in C++ and several ARM platforms have been tested. Optimal Filtering is currently used in the ATLAS Tile Calorimeter front-end for basic energy reconstruction and is currently implemented on DSPs.

  9. Initial Tile Temperature and Heat Flux Measurements in NSTX

    NASA Astrophysics Data System (ADS)

    Maingi, Rajesh; Kugel, Henry; Roquemore, Lane; Lasnier, Charles; Johnson, Dave

    1999-11-01

    Due to their compact nature, spherical tori are projected to experience higher peak heat flux than conventional aspect ratio tokamaks of comparable heating power. For NSTX, it has been predicted[1,2] that the peak heat flux in double-null divertor configuration could reach between 10-15 MW/m2, and single-null operation would result in even higher peak heat flux. To test these predictions and support physics operations, two infrared television cameras (Inframetrics 525) have been installed on NSTX to monitor real-time tile heating and surface heat flux. The data are analyzed in real-time with a frame grabber (IMAXX) and software, and these data are also archived on videotape for future analysis. The first set of measurements will focus on thermal emission from the RF antenna, the center stack, and divertor regions. Initial data and comparison with the earlier predictions will be presented. 1 R.Maingi, et. al., "Estimates of Scrape-Off Layer and Divertor Parameters in NSTX", Proc. 1996 Int’l Workshop on the Spherical Torus, Abingdon, U.K., Dec. 4-6, 1996. 2 R. Maingi, et. al., "2-D Edge Plasma Transport Calculations for NSTX", Proc. 1997 Int’l Workshop on the Spherical Torus, St. Petersburg, Russia, Sept. 3-5, 1997.

  10. Comparative study of fourteen alkaloids from Uncaria rhynchophylla hooks and leaves using HPLC-diode array detection-atmospheric pressure chemical ionization/MS method.

    PubMed

    Qu, Jialin; Gong, Tianxing; Ma, Bin; Zhang, Lin; Kano, Yoshihiro; Yuan, Dan

    2012-01-01

    The purpose of the study is to compare alkaloid profile of Uncaria rhynchophylla hooks and leaves. Ten oxindole alkaloids and four glycosidic indole alkaloids were identified using HPLC-diode array detection (DAD) or LC-atmospheric pressure chemical ionization (APCI)-MS method, and a HPLC-UV method for simultaneous quantification of major alkaloids was validated. The hooks are characterized by high levels of four oxindole alkaloids rhynchophylline (R), isorhynchophylline (IR), corynoxeine (C) and isocorynoxeine (IC), while the leaves contained high level of two glycosidic indole alkaloids vincoside lactam (VL) and strictosidine (S). The presented methods have proven its usefulness in chemical characterization of U. rhynchophylla hooks and leaves.

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

    SciTech Connect

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

    2009-05-15

    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.

  12. Adaptively Optimized Combination (AOC) of Phased-Array MR Spectroscopy Data in the Presence of Correlated Noise: Compared with Noise-Decorrelated or Whitened Methods.

    PubMed

    Wu, Minjie; Fang, Liang; Ray, Charles E; Kumar, Anand; Yang, Shaolin

    2017-09-01

    A method for adaptively optimized combination (AOC) of MR spectroscopic data from a coil array was recently introduced. The superior performance of the AOC method is evident when compared with the methods that assume uncorrelated noise between coil elements. However, it is unclear whether the AOC method represents the most optimal combination in the presence of correlated noise, when compared with the noise-decorrelated or whitened methods that specifically tackle the correlated noise between coil elements. A new, unified theoretical framework was developed to illustrate the relationship between the AOC method and three noise-decorrelated or whitened methods, namely, noise-decorrelated combination (nd-comb), whitened singular value decomposition (WSVD), and improved WSVD (WSVD+Apod). Simulation-based comparisons and in vivo human brain experiments on a 3 Tesla (T) MRI scanner were performed using an 8-channel phased-array head coil. Compared with the noise-decorrelated or whitened methods, the AOC method consistently yielded the best combination in terms of the robustness against noise and maintaining the combined spectrum from distortion, and the superior performance was most evident at a low signal-to-noise ratio (SNR). The AOC method represents the theoretical optimal combination in the presence of correlated noise between coil elements, whereas the three noise-decorrelated or whitened methods are asymptotically optimal. Magn Reson Med 78:848-859, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  13. Comprehensive meiotic segregation analysis of a 4-breakpoint t(1;3;6) complex chromosome rearrangement using single sperm array comparative genomic hybridization and FISH.

    PubMed

    Hornak, Miroslav; Vozdova, Miluse; Musilova, Petra; Prinosilova, Petra; Oracova, Eva; Linkova, Vlasta; Vesela, Katerina; Rubes, Jiri

    2014-10-01

    Complex chromosomal rearrangements (CCR) represent rare structural chromosome abnormalities frequently associated with infertility. In this study, meiotic segregation in spermatozoa of an infertile normospermic carrier of a 4-breakpoint t(1;3;6) CCR was analysed. A newly developed array comparative genomic hybridization protocol was used, and all chromosomes in 50 single sperm cells were simultaneously examined. Three-colour FISH was used to analyse chromosome segregation in 1557 other single sperm cells. It was also used to measure an interchromosomal effect; sperm chromatin structure assay was used to measure chromatin integrity. A high-frequency of unbalanced spermatozoa (84%) was observed, mostly arising from the 3:3 symmetrical segregation mode. Array comparative genomic hybridization was used to detect additional aneuploidies in two out of 50 spermatozoa (4%) in chromosomes not involved in the complex chromosome rearrangement. Significantly increased rates of diploidy and XY disomy were found in the CCR carrier compared with the control group (P < 0.001). Defective condensation of sperm chromatin was also found in 22.7% of spermatozoa by sperm chromatin structure assay. The results indicate that the infertility in the man with CCR and normal spermatozoa was caused by a production of chromosomally unbalanced, XY disomic and diploid spermatozoa and spermatozoa with defective chromatin condensation.

  14. Calibration of the Tile Hadronic Calorimeter of ATLAS at LHC

    NASA Astrophysics Data System (ADS)

    Boumediene, Djamel; ATLAS Collaboration

    2015-02-01

    The Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment. The TileCal provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses iron plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by means of wavelength shifting fibers to photomultiplier tubes (PMTs). The TileCal readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read by two PMTs. A brief description of the individual calibration systems (Cs radioactive source, laser, charge injection, minimum bias) is provided. Their combination allows to calibrate each part of the data acquisition chain (optical part, photomultiplier, readout electronics) and to monitor its stability to better than 1%. The procedure for setting and preserving the electromagnetic energy scale during Run 1 data taking is discussed. The issues of linearity and stability of the response, as well as the timing adjustment are also shown.

  15. Thermodynamically optimal whole-genome tiling microarray design and validation.

    PubMed

    Cho, Hyejin; Chou, Hui-Hsien

    2016-06-13

    Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.

  16. Microwave versus conventional sintering of silicon carbide tiles

    SciTech Connect

    Kass, M.D.; Caughman, J.B.O.; Forrester, S.C.; Akerman, A.

    1997-05-07

    Silicon carbide is being evaluated as an armor material because of its lightweight, high-hardness, and excellent armor efficiency. However, one of the problems associated with silicon carbide is the high cost associated with achieving fully dense tiles. Full density requires either hot pressing and sintering or reaction bonding. Past efforts have shown that hot pressed tiles have a higher armor efficiency than those produced by reaction bonded sintering. An earlier stuy showed that the acoustic properties of fully-dense silicon carbide tiles were enhanced through the use of post-sintered microwave heat treatments. One of the least expensive forming techniques is to isostatically press-and-sinter. In this study, the authors have used microwave energy to densify silicon carbide green bodies. Microwave sintering has been demonstrated to be a very quick way to sinter ceramics such as alumina to exceptionally high densities. Previous work has shown that microwave post treatment of fully-dense reaction bonded silicon carbide tiles significantly improves the acoustic properties of the tiles. These properties include Poisson`s ratio, Young`s modulus, shear modulus, and bulk modulus.

  17. Investigation of registration algorithms for the automatic tile processing system

    NASA Technical Reports Server (NTRS)

    Tamir, Dan E.

    1995-01-01

    The Robotic Tile Inspection System (RTPS), under development in NASA-KSC, is expected to automate the processes of post-flight re-water-proofing and the process of inspection of the Shuttle heat absorbing tiles. An important task of the robot vision sub-system is to register the 'real-world' coordinates with the coordinates of the robot model of the Shuttle tiles. The model coordinates relate to a tile data-base and pre-flight tile-images. In the registration process, current (post-flight) images are aligned with pre-flight images to detect the rotation and translation displacement required for the coordinate systems rectification. The research activities performed this summer included study and evaluation of the registration algorithm that is currently implemented by the RTPS, as well as, investigation of the utility of other registration algorithms. It has been found that the current algorithm is not robust enough. This algorithm has a success rate of less than 80% and is, therefore, not suitable for complying with the requirements of the RTPS. Modifications to the current algorithm has been developed and tested. These modifications can improve the performance of the registration algorithm in a significant way. However, this improvement is not sufficient to satisfy system requirements. A new algorithm for registration has been developed and tested. This algorithm presented very high degree of robustness with success rate of 96%.

  18. Thermal desorption analysis of beryllium tile pieces from JET

    NASA Astrophysics Data System (ADS)

    Macaulay-Newcombe, R. G.; Thompson, D. A.; Coad, J. P.

    1998-10-01

    Pieces of beryllium tile exposed to a D-D plasma in JET have been studied by thermal desorption spectroscopy. These tiles have a thick layer of redeposited Be-C-O with considerable hydrogen and deuterium present. The samples were heated at a constant rate of 2°C/min, from 100°C to 900°C. Desorption peaks occurred in the range of 140-480°C. There was no significant desorption at temperatures above 600°C. The amount of deuterium detected varied from a low of 8 × 10 21/m 2 to a high of 2.1 × 10 23/m 2. In one case, the amount of deuterium in a tile piece was seven times greater than the amount in a neighboring tile piece. Some of the tile pieces in the plasma-exposed region showed surface melting. Despite this, the deuterium yield from one of these pieces is >10 23/m 2.

  19. Analysis of Thick Sandwich Shells with Embedded Ceramic Tiles

    NASA Technical Reports Server (NTRS)

    Davila, Carlos G.; Smith, C.; Lumban-Tobing, F.

    1996-01-01

    The Composite Armored Vehicle (CAV) is an advanced technology demonstrator of an all-composite ground combat vehicle. The CAV upper hull is made of a tough light-weight S2-glass/epoxy laminate with embedded ceramic tiles that serve as armor. The tiles are bonded to a rubber mat with a carefully selected, highly viscoelastic adhesive. The integration of armor and structure offers an efficient combination of ballistic protection and structural performance. The analysis of this anisotropic construction, with its inherent discontinuous and periodic nature, however, poses several challenges. The present paper describes a shell-based 'element-layering' technique that properly accounts for these effects and for the concentrated transverse shear flexibility in the rubber mat. One of the most important advantages of the element-layering technique over advanced higher-order elements is that it is based on conventional elements. This advantage allows the models to be portable to other structural analysis codes, a prerequisite in a program that involves the computational facilities of several manufacturers and government laboratories. The element-layering technique was implemented into an auto-layering program that automatically transforms a conventional shell model into a multi-layered model. The effects of tile layer homogenization, tile placement patterns, and tile gap size on the analysis results are described.

  20. Interlaced Particle Systems and Tilings of the Aztec Diamond

    NASA Astrophysics Data System (ADS)

    Fleming, Benjamin J.; Forrester, Peter J.

    2011-02-01

    Motivated by the problem of domino tilings of the Aztec diamond, a weighted particle system is defined on N lines, with line j containing j particles. The particles are restricted to lattice points from 0 to N, and particles on successive lines are subject to an interlacing constraint. It is shown that this particle system is exactly solvable, to the extent that not only can the partition function be computed exactly, but so too can the marginal distributions. These results in turn are used to give new derivations within the particle picture of a number of known fundamental properties of the tiling problem, for example that the number of distinct configurations is 2 N( N+1)/2, and that there is a limit to the GUE minor process, which we show at the level of the joint PDFs. It is shown too that the study of tilings of the half Aztec diamond—not known from earlier literature—also leads to an interlaced particle system, now with successive lines 2 n-1 and 2 n ( n=1,…, N/2-1) having n particles. Its exact solution allows for an analysis of the half Aztec diamond tilings analogous to that given for the Aztec diamond tilings.

  1. Characterization of ceramic roof tile wastes as pozzolanic admixture.

    PubMed

    Lavat, Araceli E; Trezza, Monica A; Poggi, Mónica

    2009-05-01

    The aim of this work is to study the recycling of tile wastes in the manufacture of blended cements. Cracked or broken ceramic bodies are not accepted as commercial products and, therefore, the unsold waste of the ceramic industry becomes an environment problem. The use of powdered roof tile in cement production, as pozzolanic addition, is reported. The wastes were classified as nonglazed, natural and black glazed tiles. The mineralogy of the powders was controlled by SEM-EDX microscopy, XRD analysis and FTIR spectroscopy. Particle size was checked by laser granulometry. Once the materials were fully characterized, pozzolanic lime consumption tests and Fratini tests were carried out. Different formulations of cement-tile blends were prepared by incorporation of up to 30% weight ratios of recycled waste. The compressive strength of the resulting specimens was measured. The evolution of hydration of the cement-tile blends was analyzed by XRD and FTIR techniques. Vibrational spectroscopy presented accurate evidence of pozzolanic activity. The results of the investigation confirmed the potential use of these waste materials to produce pozzolanic cement.

  2. Distortion, Orientation, and Translation Corrections of Tiled EMCCD Detectors for the New Solid State X-ray Image Intensifier (SSXII).

    PubMed

    Hamwi, Hidab; Lee, Joseph W; Hoffmann, Kenneth R; Rudin, Stephen; Verevkin, Aleksandr

    2008-01-01

    We report on the technology of imaging corrections for a new solid state x-ray image intensifier (SSXII) with enhanced resolution and fluoroscopic imaging capabilities, made of a mosaic of modules (tiled-array) each consisting of CsI(Tl) phosphor coupled using a fiber-optic taper or minifier to an electron multiplier charge coupled device (EMCCD). Generating high quality images using this EMCCD tiled-array system requires the determination and correction of the individual EMCCD sub-images with respect to relative rotations and translations as well as optical distortions due to the fiber optic tapers. The image corrections procedure is based on comparison of resulting (distorted) images with the known square pattern of a wire mesh phantom. The mesh crossing point positions in each sub-image are automatically identified. With the crossing points identified, the mapping between distorted and an undistorted array is determined. For each pixel in a distorted sub-image, the corresponding location in the corrected sub-image is calculated using bilinear interpolation. For the rotation corrections between sub-images, the orientation of the vectors between respective mesh crossing points in the various sub-images are determined and each sub-image is appropriately rotated with the pixel values again determined using bilinear interpolation. Image translation corrections are performed using reference structures at known locations. According to our estimations, the distortion corrections are accurate to within 1%; the rotations are determined to within 0.1 degree, and translation corrections are accurate to well within 1 pixel. This technology will provide the basis for generating single composite images from tiled-image configurations of the SSXII regardless of how many modules are used to form the images.

  3. Cross-Correlation for Automated Stitching of Two-Dimensional Multi-Tile Electron Backscatter Diffraction Data (Preprint)

    DTIC Science & Technology

    2012-08-01

    270 350x 650 (25, 26) 2 20 Ni-15Al- 5Cr+C,B,Zr 187 x 187 500x 44 ( 4 , 11) 0.5 40 A. Coarse grain, single phase α- titanium The coarse grained... titanium alloy serves as an instructive example because, as evident in Figure 4 (a), only one triple point and one grain boundary appear in the search...wpafb.af.mil Figure 4 . Crystal orientation maps for the first (left) and second (current) tiles of (a) coarse grained α- Titanium , (b) a 2x2 array of a

  4. Surface-assisted large-scale ordering of DNA origami tiles.

    PubMed

    Aghebat Rafat, Ali; Pirzer, Tobias; Scheible, Max B; Kostina, Anna; Simmel, Friedrich C

    2014-07-14

    The arrangement of DNA-based nanostructures into extended higher order assemblies is an important step towards their utilization as functional molecular materials. We herein demonstrate that by electrostatically controlling the adhesion and mobility of DNA origami structures on mica surfaces by the simple addition of monovalent cations, large ordered 2D arrays of origami tiles can be generated. The lattices can be formed either by close-packing of symmetric, non-interacting DNA origami structures, or by utilizing blunt-end stacking interactions between the origami units. The resulting crystalline lattices can be readily utilized as templates for the ordered arrangement of proteins. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Solare Cell Roof Tile And Method Of Forming Same

    DOEpatents

    Hanoka, Jack I.; Real, Markus

    1999-11-16

    A solar cell roof tile includes a front support layer, a transparent encapsulant layer, a plurality of interconnected solar cells and a backskin layer. The front support layer is formed of light transmitting material and has first and second surfaces. The transparent encapsulant layer is disposed adjacent the second surface of the front support layer. The interconnected solar cells has a first surface disposed adjacent the transparent encapsulant layer. The backskin layer has a first surface disposed adjacent a second surface of the interconnected solar cells, wherein a portion of the backskin layer wraps around and contacts the first surface of the front support layer to form the border region. A portion of the border region has an extended width. The solar cell roof tile may have stand-offs disposed on the extended width border region for providing vertical spacing with respect to an adjacent solar cell roof tile.

  6. Flutter Analysis of the Shuttle Tile Overlay Repair Concept

    NASA Technical Reports Server (NTRS)

    Bey, Kim S.; Scott, Robert C.; Bartels, Robert E.; Waters, William A.; Chen, Roger

    2007-01-01

    The Space Shuttle tile overlay repair concept, developed at the NASA Johnson Space Center, is designed for on-orbit installation over an area of damaged tile to permit safe re-entry. The thin flexible plate is placed over the damaged area and secured to tile at discreet points around its perimeter. A series of flutter analyses were performed to determine if the onset of flutter met the required safety margins. Normal vibration modes of the panel, obtained from a simplified structural analysis of the installed concept, were combined with a series of aerodynamic analyses of increasing levels of fidelity in terms of modeling the flow physics to determine the onset of flutter. Results from these analyses indicate that it is unlikely that the overlay installed at body point 1800 will flutter during re-entry.

  7. Fly ash of mineral coal as ceramic tiles raw material.

    PubMed

    Zimmer, A; Bergmann, C P

    2007-01-01

    The aim of this work was to evaluate the use of mineral coal fly ash as a raw material in the production of ceramic tiles. The samples of fly ash came from Capivari de Baixo, a city situated in the Brazilian Federal State of Santa Catarina. The fly ash and the raw materials were characterized regarding their physical chemical properties, and, based on these results; batches containing fly ash and typical raw materials for ceramic tiles were prepared. The fly ash content in the batches varied between 20 and 80 wt%. Specimens were molded using a uniaxial hydraulic press and were fired. All batches containing ash up to 60 wt% present adequate properties to be classified as several kinds of products in the ISO 13006 standard () regarding its different absorption groups (pressed). The results obtained indicate that fly ash, when mixed with traditional raw materials, has the necessary requirements to be used as a raw material for production of ceramic tiles.

  8. Monte Carlo estimation of the number of tatami tilings

    NASA Astrophysics Data System (ADS)

    Kimura, Kenji; Higuchi, Saburo

    2016-04-01

    Motivated by the way Japanese tatami mats are placed on the floor, we consider domino tilings with a constraint and estimate the number of such tilings of plane regions. We map the system onto a monomer-dimer model with a novel local interaction on the dual lattice. We make use of a variant of the Hamiltonian replica exchange Monte Carlo method where data for ferromagnetic and anti-ferromagnetic models are combined to make a single family of histograms. The properties of the density of states is studied beyond exact enumeration and combinatorial methods. The logarithm of the number of the tilings is linear in the boundary length of the region for all the regions studied.

  9. [Genomic abnormalities in children with mental retardation and autism: the use of comparative genomic hybridization in situ (HRCGH) and molecular karyotyping with DNA-microchips (array CGH)].

    PubMed

    Vorsanova, S G; Iurov, I Iu; Kurinnaia, O S; Voinova, V Iu; Iurov, Iu B

    2013-01-01

    Genomic abnormalities occur with high frequency in children with mental retardation and autistic spectrum disorders (ADS). Molecular karyotyping using DNA microarrays is a new technology for diagnosis of genomic and chromosomal abnormalities in autism implemented in the fields of biological psychiatry and medical genetics. We carried out a comparative analysis of the frequency and spectrum of genome abnormalities in children with mental retardation and autism of unknown etiology using high-resolution comparative genomic methods for hybridization (HRCGH) and molecular karyotyping (array CGH). In a study of 100 children with autism, learning difficulties and congenital malformations by HRCGH, we identified genomic rearrangements in 46% of cases. Using array CGH we examined 50 children with autism. In 44 cases out of 50 (88%), different genomic abnormalities and genomic variations (CNV - copy number variations) were identified. Unbalanced genomic rearrangements, including deletions and duplications, were found in 23 cases out of 44 (52%). These data suggest that genomic abnormalities which are not detectable by common methods of chromosome analysis are often discovered by molecular cytogenetic techniques in children autism spectrum disorders. In addition, 54 children with idiopathic mental retardation and congenital malformations (31 boys and 23 girls) without autism spectrum disorders were examined using molecular karyotyping and microarray containing an increased number of DNA samples for genomic loci of chromosome X. Deletions and duplications affecting different regions of the chromosome X were detected in 11 out of 54 children (20.4%).

  10. Effect of acid vapor etching on morphological and opto-electric properties of flat silicon and silicon nanowire arrays: A comparative study

    NASA Astrophysics Data System (ADS)

    Amri, Chohdi; Ouertani, Rachid; Hamdi, Abderrahmen; Ezzaouia, Hatem

    2016-03-01

    In this paper, we report a comparative study between porous silicon (pSi) and porous silicon nanowires (pSiNWs). Acid Vapor Etching (AVE) treatment has been used to perform porous structure on flat Si and SiNWs array substrates respectively. SiNW structure is prepared by the widely used Silver catalyzed etching method. SEM and TEM images show that AVE treatment induces porous structure in the whole Si wafer and the SiNW sidewall. Comparatively to pSi, pSiNWs exhibit a low reflectivity in the whole spectral range which decreases with etching duration. However, the reflectivity of pSi changes with porous layer thickness. Both pSi and pSiNWs exhibit a significant PL peak situated at 2 eV. PL peaks are attributed to the quantum confinement effect in the silicon nanocrystallites (SiNCs). We discussed the significant enhancement in the peak intensities and a shift toward lower energy displayed in Raman spectra for both pSi and pSiNWs. We reported a correlative study of the AVE treatment effect on the minority carrier life time of flat silicon and SiNW arrays with the passivation effect of chemical induced silicon oxides highlighted by FTIR spectra.

  11. A three-step workflow procedure for the interpretation of array-based comparative genome hybridization results in patients with idiopathic mental retardation and congenital anomalies.

    PubMed

    Poot, Martin; Hochstenbach, Ron

    2010-08-01

    One of the aims of clinical genetics is to identify gene mutations or genomic rearrangements that may underlie complex presentations of phenotypic features, such as multiple congenital malformations and mental retardation. During the decade after publication of the first article on array-based comparative genome hybridization, this technique has supplemented karyotyping as the prime genome-wide screening method in patients with idiopathic multiple congenital malformations and mental retardation. The use of this novel, discovery-based, approach has dramatically increased the detection rate of genomic imbalances. Array-based comparative genome hybridization detects copy number changes in the genome of patients and healthy subjects, some of which may represent phenotypically neutral copy number variations. This prompts the need for properly distinguishing between those copy number changes that may contribute to the clinical phenotype amid a pool of neutral copy number variations. We briefly review the characteristics of copy number changes in relation to their clinical relevance. Second, we discuss several published workflow schemes to identify copy number changes putatively contributing to the phenotype, and third, we propose a three-step procedure aiming to rapidly evaluate copy number changes on a case-by-case basis as to their potential contribution to the phenotype of patients with idiopathic multiple congenital malformations and mental retardation. This workflow is gene-centered and should aid in identification of disease-related candidate genes and in estimating the recurrence risk for the disorder in the family.

  12. PHASE CHANGE MATERIALS IN FLOOR TILES FOR THERMAL ENERGY STORAGE

    SciTech Connect

    Douglas C. Hittle

    2002-10-01

    Passive solar systems integrated into residential structures significantly reduce heating energy consumption. Taking advantage of latent heat storage has further increased energy savings. This is accomplished by the incorporation of phase change materials into building materials used in passive applications. Trombe walls, ceilings and floors can all be enhanced with phase change materials. Increasing the thermal storage of floor tile by the addition of encapsulated paraffin wax is the proposed topic of research. Latent heat storage of a phase change material (PCM) is obtained during a change in phase. Typical materials use the latent heat released when the material changes from a liquid to a solid. Paraffin wax and salt hydrates are examples of such materials. Other PCMs that have been recently investigated undergo a phase transition from one solid form to another. During this process they will release heat. These are known as solid-state phase change materials. All have large latent heats, which makes them ideal for passive solar applications. Easy incorporation into various building materials is must for these materials. This proposal will address the advantages and disadvantages of using these materials in floor tile. Prototype tile will be made from a mixture of quartz, binder and phase change material. The thermal and structural properties of the prototype tiles will be tested fully. It is expected that with the addition of the phase change material the structural properties will be compromised to some extent. The ratio of phase change material in the tile will have to be varied to determine the best mixture to provide significant thermal storage, while maintaining structural properties that meet the industry standards for floor tile.

  13. Implications of tiling for performance and design flow

    NASA Astrophysics Data System (ADS)

    Demircan, Ertugrul; Tian, Ruiqi; Grobman, Warren D.

    2002-07-01

    In this paper, we discuss rule-based and model-based tiling methodologies for interconnect layers and their implications for design flows and performance. The addition of these 'dummy' tiling metal features modifies the final physical design and reduces the variation of back-end process parameters. This is a newly developing area of design flow and its importance is increasing with each succeeding semiconductor generation. Along with this development new methodologies and tools need to be introduced to handle time placement post-physical design, as well as efficient methods for representing the resulting large amount of dat. Additionally, the inclusion of tiles may introduce performance-degrading parasitic effects. The situation is complicated by the order of the elements of the design flow: parasitics characterization requires knowledge about the placement of dummy metal times, which takes place after physical design. In this study, we co pare the advantages of having uniform interconnect characteristics to the performance degradation caused by the additional layout parasitics. We also discuss several possible scenarios for the modification of design flows to account for these effects the thereby recover timing and power targets closure. These scenarios depend for their success on the very different length scales of polish and electromagnetic effects. Finally, an analysis of correlations in the parameters that define design corners leads to the new conclusion that the negative effect of increased parasitic loading due to tiling is not as sever as a simple analysis would suggest. This result is due to the fact that the tiling parasitic loading is somewhat compensated for by the improved planarity resulting from tiling, which tightens the process variation-induced spread of metal electrical parameters.

  14. Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in Arabidopsis thaliana with Tiling Microarray

    PubMed Central

    Leviatan, Noam; Alkan, Noam; Leshkowitz, Dena; Fluhr, Robert

    2013-01-01

    Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression. PMID:23776682

  15. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.

    PubMed

    Leviatan, Noam; Alkan, Noam; Leshkowitz, Dena; Fluhr, Robert

    2013-01-01

    Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.

  16. Automated Absorber Attachment for X-ray Microcalorimeter Arrays

    NASA Technical Reports Server (NTRS)

    Moseley, S.; Allen, Christine; Kilbourne, Caroline; Miller, Timothy M.; Costen, Nick; Schulte, Eric; Moseley, Samuel J.

    2007-01-01

    Our goal is to develop a method for the automated attachment of large numbers of absorber tiles to large format detector arrays. This development includes the fabrication of high quality, closely spaced HgTe absorber tiles that are properly positioned for pick-and-place by our FC150 flip chip bonder. The FC150 also transfers the appropriate minute amount of epoxy to the detectors for permanent attachment of the absorbers. The success of this development will replace an arduous, risky and highly manual task with a reliable, high-precision automated process.

  17. High-Performance Tiled WMS and KML Web Server

    NASA Technical Reports Server (NTRS)

    Plesea, Lucian

    2007-01-01

    This software is an Apache 2.0 module implementing a high-performance map server to support interactive map viewers and virtual planet client software. It can be used in applications that require access to very-high-resolution geolocated images, such as GIS, virtual planet applications, and flight simulators. It serves Web Map Service (WMS) requests that comply with a given request grid from an existing tile dataset. It also generates the KML super-overlay configuration files required to access the WMS image tiles.

  18. Evaluation of bioenergy crop growth and the impacts of bioenergy crops on streamflow, tile drain flow and nutrient losses in an extensively tile-drained watershed using SWAT.

    PubMed

    Guo, Tian; Cibin, Raj; Chaubey, Indrajeet; Gitau, Margaret; Arnold, Jeffrey G; Srinivasan, Raghavan; Kiniry, James R; Engel, Bernard A

    2017-09-19

    Large quantities of biofuel production are expected from bioenergy crops at a national scale to meet US biofuel goals. It is important to study biomass production of bioenergy crops and the impacts of these crops on water quantity and quality to identify environment-friendly and productive biofeedstock systems. SWAT2012 with a new tile drainage routine and improved perennial grass and tree growth simulation was used to model long-term annual biomass yields, streamflow, tile flow, sediment load, and nutrient losses under various bioenergy scenarios in an extensively agricultural watershed in the Midwestern US. Simulated results from bioenergy crop scenarios were compared with those from the baseline. The results showed that simulated annual crop yields were similar to observed county level values for corn and soybeans, and were reasonable for Miscanthus, switchgrass and hybrid poplar. Removal of 38% of corn stover (3.74Mg/ha/yr) with Miscanthus production on highly erodible areas and marginal land (17.49Mg/ha/yr) provided the highest biofeedstock production (279,000Mg/yr). Streamflow, tile flow, erosion and nutrient losses were reduced under bioenergy crop scenarios of bioenergy crops on highly erodible areas and marginal land. Corn stover removal did not result in significant water quality changes. The increase in sediment and nutrient losses under corn stover removal could be offset with the combination of other bioenergy crops. Potential areas for bioenergy crop production when meeting the criteria above were small (10.88km(2)), thus the ability to produce biomass and improve water quality was not substantial. The study showed that corn stover removal with bioenergy crops both on highly erodible areas and marginal land could provide more biofuel production relative to the baseline, and was beneficial to water quality at the watershed scale, providing guidance for further research on evaluation of bioenergy crop scenarios in a typical extensively tile

  19. Proximal 10q duplication in a child with severe central hypotonia characterized by array-comparative genomic hybridization: A case report and review of the literature

    PubMed Central

    MANOLAKOS, EMMANOUIL; VETRO, ANNALISA; GARAS, ANTONIOS; THOMAIDIS, LORETTA; KEFALAS, KONSTANTINOS; KITSOS, GEORGE; ZIEGLER, MONIKA; LIEHR, THOMAS; ZUFFARDI, ORSETTA; PAPOULIDIS, IOANNIS

    2014-01-01

    Proximal 10q duplication is a well-defined but rare genetic syndrome. Duplication of proximal segments of the long arm of chromosome 10 results in a pattern of malformations, which are distinct from those of the more common distal 10q trisomy syndrome. The present study describes the case of a boy with phenotypic abnormalities (severe central hypotonia, mild ataxia, moderate developmental delay and mild dysmorphic features), due to duplication of chromosome region, 10q11.21→q11.22, which was characterized by the array-comparative genomic hybridization (CGH) technique. The phenotypic findings were compared with those in eight additional similar published cases. Major similarities have emerged, suggesting a likely minimal critical region. However, only detailed characterization of additional cases may provide firm conclusions. PMID:24669257

  20. Tony Rollins fashions a new tile for the Space Shuttle orbiter

    NASA Technical Reports Server (NTRS)

    1998-01-01

    In the Tile Fabrication Shop, Tony Rollins, with United Space Alliance, holds down a curtain while making a test sample of tile on a block 5-axis computerized numerical control milling machine. About 70 percent of a Space Shuttle orbiter's external surface is shielded from heat by a network of more than 24,000 tiles formed from a silica fiber compound. They are known as High-Temperature Reusable Surface Insulation (HRSI) tiles and Low-Temperature Reusable Surface Insulation (LRSI) tiles. Most HRSI tiles are 6 inches square, but may be as large as 12 inches in some areas, and 1 to 5 inches thick. LRSI tiles are generally 8 inches square, ranging from 0.2- to 1-inch thick. More advanced materials such as Flexible Insulation Blankets have replaced tiles on some upper surfaces of the orbiter.

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

    NASA Technical Reports Server (NTRS)

    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

  2. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization.

    PubMed

    Singchat, Worapong; Hitakomate, Ekarat; Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology.

  3. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization

    PubMed Central

    Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  4. Carcinoma ex-pleomorphic adenoma derived from recurrent pleomorphic adenoma shows important difference by array CGH compared to recurrent pleomorphic adenoma without malignant transformation.

    PubMed

    Mariano, Fernanda Viviane; Giovanetti, Karina; Saccomani, Luis Fernando Vidal; Del Negro, André; Kowalski, Luiz Paulo; Krepischi, Ana Cristina Victorino; Altemani, Albina

    A key step of cancer development is the progressive accumulation of genomic changes resulting in disruption of several biological mechanisms. Carcinoma ex-pleomorphic adenoma (CXPA) is an aggressive neoplasm that arises from a pleomorphic adenoma. CXPA derived from a recurrent PA (RPA) has been rarely reported, and the genomic changes associated with these tumors have not yet been studied. We analyzed CXPA from RPAs and RPAs without malignant transformation using array-comparative genomic hybridization (array-CGH) to identify somatic copy number alterations and affected genes. DNA samples extracted from FFPE tumors were submitted to array-CGH investigation, and data was analyzed by Nexus Copy Number Discovery Edition v.7. No somatic copy number alterations were found in RPAs without malignant transformation. As for CXPA from RPA, although genomic profiles were unique for each case, we detected some chromosomal regions that appear to be preferentially affected by copy number alterations. The first case of CXPA-RPA (frankly invasive myoepithelial carcinoma) showed copy number alterations affecting 1p36.33p13, 5p and chromosomes 3 and 8. The second case of CXPA-RPA (frankly invasive epithelial-myoepithelial carcinoma) showed several alterations at chromosomes 3, 8, and 16, with two amplifications at 8p12p11.21 and 12q14.3q21.2. The third case of CXPA-RPA (minimally invasive epithelial-myoepithelial carcinoma) exhibited amplifications at 12q13.3q14.1, 12q14.3, and 12q15. The occurrence of gains at chromosomes 3 and 8 and genomic amplifications at 8p and 12q, mainly those encompassing the HMGA2, MDM2, WIF1, WHSC1L1, LIRG3, CDK4 in CXAP from RPA can be a significant promotional factor in malignant transformation. Copyright © 2016 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  5. Modeling Subsurface Storm and Tile Drain Systems in GSSHA with SUPERLINK

    DTIC Science & Technology

    2014-09-01

    capable of representing flow through a pipe network with inputs typical for an urban storm drain network or an agricultural tile drainage system...greater than zero is input for the materials surrounding any pipe in the network, then tile drainage will be computed, and the GRID_PIPE file must...tile drain pipes , as shown in Figure 5. The drainage to tile from ground water under this common condition can be calculated with one of two optional

  6. Bulk Universality for Random Lozenge Tilings Near Straight Boundaries and for Tensor Products

    NASA Astrophysics Data System (ADS)

    Gorin, Vadim

    2017-08-01

    We prove that the asymptotic of the bulk local statistics in models of random lozenge tilings is universal in the vicinity of straight boundaries of the tiled domains. The result applies to uniformly random lozenge tilings of large polygonal domains on triangular lattice and to the probability measures describing the decomposition in Gelfand-Tsetlin bases of tensor products of representations of unitary groups. In a weaker form our theorem also applies to random domino tilings.

  7. Identification of genetic alterations in pancreatic cancer by the combined use of tissue microdissection and array-based comparative genomic hybridisation

    PubMed Central

    Harada, T; Baril, P; Gangeswaran, R; Kelly, G; Chelala, C; Bhakta, V; Caulee, K; Mahon, P C; Lemoine, N R

    2007-01-01

    Pancreatic ductal adenocarcinoma (PDAC) is characterised pathologically by a marked desmoplastic stromal reaction that significantly reduces the sensitivity and specificity of cytogenetic analysis. To identify genetic alterations that reflect the characteristics of the tumour in vivo, we screened a total of 23 microdissected PDAC tissue samples using array-based comparative genomic hybridisation (array CGH) with 1 Mb resolution. Highly stringent statistical analysis enabled us to define the regions of nonrandom genomic changes. We detected a total of 41 contiguous regions (>3.0 Mb) of copy number changes, such as a genetic gain at 7p22.2–p15.1 (26.0 Mb) and losses at 17p13.3–p11.2 (13.6 Mb), 18q21.2–q22.1 (12.0 Mb), 18q22.3–q23 (7.1 Mb) and 18q12.3–q21.2 (6.9 Mb). To validate our array CGH results, fluorescence in situ hybridisation was performed using four probes from those regions, showing that these genetic alterations were observed in 37–68% of a separate sample set of 19 PDAC cases. In particular, deletion of the SEC11L3 gene (18q21.32) was detected at a very high frequency (13 out of 19 cases; 68%) and in situ RNA hybridisation for this gene demonstrated a significant correlation between deletion and expression levels. It was further confirmed by reverse transcription–PCR that SEC11L3 mRNA was downregulated in 16 out of 16 PDAC tissues (100%). In conclusion, the combination of tissue microdissection and array CGH provided a valid data set that represents in vivo genetic changes in PDAC. Our results raise the possibility that the SEC11L3 gene may play a role as a tumour suppressor in this disease. PMID:17242705

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

    PubMed

    Lo, Fang-Yi; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching

    2012-06-12

    Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

  9. Using a Multijunction Microfluidic Device to Inject Substrate inot an Array of Preformed Plugs Without Cross-Contamination: Comparing Theory and Experiments

    SciTech Connect

    Liang, L.; Boedicker, J; Ismagilov, R

    2007-01-01

    In this paper we describe a multijunction microfluidic device for the injection of a substrate into an array of preformed plugs carried by an immiscible fluid in a microchannel. The device uses multiple junctions to inject substrate into preformed plugs without synchronization of the flow of substrate and the array of preformed plugs of reagent, which reduces cross-contamination of the plugs, eliminates formation of small droplets of substrate, and allows a greater range of injection ratios compared to that of a single T-junction. The device was based on a previously developed physical model for transport that was here adapted to describe injection and experimentally verified. After characterization, the device was applied to two biochemical assays, including evaluation of the enzymatic activity of thrombin and determination of the coagulation time of human blood plasma, which both provided reliable results. The reduction of cross-contamination and greater range of injection ratios achieved by this device may improve the processes that involve addition and titration of reagents into plugs, such as high-throughput screening of protein crystallization conditions.

  10. Magnetic arrays

    DOEpatents

    Trumper, D.L.; Kim, W.; Williams, M.E.

    1997-05-20

    Electromagnet arrays are disclosed which can provide selected field patterns in either two or three dimensions, and in particular, which can provide single-sided field patterns in two or three dimensions. These features are achieved by providing arrays which have current densities that vary in the windings both parallel to the array and in the direction of array thickness. 12 figs.

  11. Magnetic arrays

    SciTech Connect

    Trumper, David L.; Kim, Won-jong; Williams, Mark E.

    1997-05-20

    Electromagnet arrays which can provide selected field patterns in either two or three dimensions, and in particular, which can provide single-sided field patterns in two or three dimensions. These features are achieved by providing arrays which have current densities that vary in the windings both parallel to the array and in the direction of array thickness.

  12. Analog pixel array detectors.

    PubMed

    Ercan, A; Tate, M W; Gruner, S M

    2006-03-01

    X-ray pixel array detectors (PADs) are generally thought of as either digital photon counters (DPADs) or X-ray analog-integrating pixel array detectors (APADs). Experiences with APADs, which are especially well suited for X-ray imaging experiments where transient or high instantaneous flux events must be recorded, are reported. The design, characterization and experimental applications of several APAD designs developed at Cornell University are discussed. The simplest design is a ;flash' architecture, wherein successive integrated X-ray images, as short as several hundred nanoseconds in duration, are stored in the detector chips for later off-chip digitization. Radiography experiments using a prototype flash APAD are summarized. Another design has been implemented that combines flash capability with the ability to continuously stream X-ray images at slower (e.g. milliseconds) rates. Progress is described towards radiation-hardened APADs that can be tiled to cover a large area. A mixed-mode PAD, design by combining many of the attractive features of both APADs and DPADs, is also described.

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

    EPA Science Inventory

    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...

  14. 40 CFR 427.70 - Applicability; description of the asbestos floor tile subcategory.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... asbestos floor tile subcategory. 427.70 Section 427.70 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Asbestos Floor Tile Subcategory § 427.70 Applicability; description of the asbestos floor tile...

  15. 40 CFR 427.70 - Applicability; description of the asbestos floor tile subcategory.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... asbestos floor tile subcategory. 427.70 Section 427.70 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) EFFLUENT GUIDELINES AND STANDARDS ASBESTOS MANUFACTURING POINT SOURCE CATEGORY Asbestos Floor Tile Subcategory § 427.70 Applicability; description of the asbestos floor tile subcategory...

  16. Divertor sheath power studies in DIII-D using fixed Langmuir probes and three-dimensional modeling of tile heat flows

    NASA Astrophysics Data System (ADS)

    Donovan, D.; Nygren, R.; Buchenauer, D.; Watkins, J.; Rudakov, D.; Leonard, A.; Wong, C. P. C.; Makowski, M.

    2014-04-01

    Experimental results are presented from the three-Langmuir probe (LP) diagnostic head of the divertor material evaluation system (DiMES) on DIII-D that confirm the size of the projected current collection area of the LPs, which is essential for properly measuring ion saturation current density (Jsat) and the sheath power transmission factor (SPTF). Also using the 3-LP DiMES head, the hypothesis that collisional effects on plasma density occurring in the magnetic sheath of the tile are responsible for a lower than expected SPTF is tested and deemed not to have a significant impact on the SPTF. Three-dimensional thermal modeling of wall tiles is presented that accounts for lateral heat conduction, temperature dependence of tile material properties and radiative heat loss from the tile surface. This modeling was developed to be used in the analysis of temperature profiles of the divertor embedded thermocouple (TC) array to obtain more accurate interpretations of TC temperature profiles to infer divertor surface heat flux than have previously been accomplished using more basic one-dimensional methods.

  17. Nitrogen, phosphorus, and bacteria tile and groundwater quality following direct injection of dewatered municipal biosolids into soil.

    PubMed

    Gottschall, N; Edwards, M; Topp, E; Bolton, P; Payne, M; Curnoe, W E; Coelho, B Ball; Lapen, D R

    2009-01-01

    Application of municipal biosolids (sewage) to agricultural land is a common practice to improve soil physical quality and fertility. The chosen method of land application can have a strong impact on the extent of adjacent water contamination by nutrients and bacteria. Dewatered municipal biosolids (DMB) were applied to silt-clay loam experimental field plots in Ontario, Canada using two application methods: (i) surface spreading followed by shallow incorporation (SS) and (ii) a newly developed implement that directly injects DMB into the topsoil (DI). The objective of this study was to compare N, P, and bacteria quality of tile drainage and shallow groundwater associated with each land application technique. There were no significant differences (P > 0.05) in N, P, and bacteria tile mass loads among the application treatments for time periods <100 d postapplication, when the greatest peak loads and peak tile water concentrations were observed. Both land application treatments caused groundwater Escherichia coli contamination to at least 1.2 m depth below surface after the first postapplication rainfall event, and NO(3)-N contamination to at least 2.0 m depth below surface. The DI treatment did, however, have significantly (P < 0.05) higher tile mass loads of total Kjeldahl N (TKN), total phosphorus (TP), E. coli, Enterococci, and Clostridium perfringens relative to the SS treatment for time periods >100 d postapplication. Nevertheless, relative to tile effluent data collected <100 d postapplication (no application treatment differences), peak loads, and concentrations during this time were, overall, considerably lower for both treatments. This finding, along with no significant differences in N, P, and bacteria groundwater concentrations among the application treatments, and that the direct injection technique could potentially reduce vector attraction problems and odor, suggests that the direct injection technique should be considered a dewatered municipal

  18. Task 4 supporting technology. Part 1: Detailed test plan for leading edge tile development. Leading edge material development and testing

    NASA Technical Reports Server (NTRS)

    Hogenson, P. A.; Staszak, Paul; Hinkle, Karrie

    1995-01-01

    This task develops two alternative candidate tile materials for leading edge applications: coated alumina enhanced thermal barrier (AETB) tile and silicone impregnated reusable ceramic ablator (SIRCA) tile. Upon reentry of the X-33/RLV space vehicle, the leading edges experience the highest heating rates and temperatures. The wing leading edge and nose cap experience peak temperatures in the range 2000 to 2700 F. Replacing reinforced carbon-carbon (RCC) with tile-based thermal protection system (TPS) materials is the primary objective. Weight, complexity, coating impact damage, and repairability are among the problems that this tile technology development addresses. The following subtasks will be performed in this development effort: tile coating development; SIRCA tile development; robustness testing of tiles; tile repair development; tile operations/processing; tile leading edge configuration; and life cycle testing.

  19. EVALUATION OF FUNGAL GROWTH (PENICILLIUM GLABRUM) ON A CEILING TILE

    EPA Science Inventory

    The paper gives results of a study employing static chambers to study the impact of different equilibrium relative humidities (RHs) and moisture conditions on the ability of a new ceiling tile to support fungal growth. Amplification of the mold, Penicillium glabrum, occurred at R...

  20. EVALUATION OF FUNGAL GROWTH (PENICILLIUM GLABRUM) ON A CEILING TILE

    EPA Science Inventory

    The paper gives results of a study employing static chambers to study the impact of different equilibrium relative humidities (RHs) and moisture conditions on the ability of a new ceiling tile to support fungal growth. Amplification of the mold, Penicillium glabrum, occurred at R...