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Sample records for high copy arrays

  1. A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer.

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    Li, Ming; Wen, Yalu; Fu, Wenjiang

    2014-01-01

    Cumulative evidence has shown that structural variations, due to insertions, deletions, and inversions of DNA, may contribute considerably to the development of complex human diseases, such as breast cancer. High-throughput genotyping technologies, such as Affymetrix high density single-nucleotide polymorphism (SNP) arrays, have produced large amounts of genetic data for genome-wide SNP genotype calling and copy number estimation. Meanwhile, there is a great need for accurate and efficient statistical methods to detect copy number variants. In this article, we introduce a hidden-Markov-model (HMM)-based method, referred to as the PICR-CNV, for copy number inference. The proposed method first estimates copy number abundance for each single SNP on a single array based on the raw fluorescence values, and then standardizes the estimated copy number abundance to achieve equal footing among multiple arrays. This method requires no between-array normalization, and thus, maintains data integrity and independence of samples among individual subjects. In addition to our efforts to apply new statistical technology to raw fluorescence values, the HMM has been applied to the standardized copy number abundance in order to reduce experimental noise. Through simulations, we show our refined method is able to infer copy number variants accurately. Application of the proposed method to a breast cancer dataset helps to identify genomic regions significantly associated with the disease.

  2. Genome-wide copy number profiling using high-density SNP array in chickens.

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    Yi, G; Qu, L; Chen, S; Xu, G; Yang, N

    2015-04-01

    Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome-wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high-density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high-density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high-density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens. © 2015 Stichting International Foundation for Animal Genetics.

  3. High-resolution copy number arrays in cancer and the problem of normal genome copy number variation.

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    Gorringe, Kylie L; Campbell, Ian G

    2008-11-01

    High-resolution techniques for analysis of genome copy number (CN) enable the analysis of complex cancer somatic genetics. However, the analysis of these data is difficult, and failure to consider a number of issues in depth may result in false leads or unnecessary rejection of true positives. First, segmental duplications may falsely generate CN breakpoints in aneuploid samples. Second, even when tumor data were each normalized to matching lymphocyte DNA, we still observed copy number polymorphisms masquerading as somatic alterations due to allelic imbalance. We investigated a number of different solutions and determined that evaluating matching normal DNA, or at least using locally derived normal baseline data, were preferable to relying on current online databases because of poor cross-platform compatibility and the likelihood of excluding genuine small somatic alterations.

  4. DNA copy number changes in high-grade malignant peripheral nerve sheath tumors by array CGH

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    Bjerkehagen Bodil

    2008-06-01

    Full Text Available Abstract Background Malignant peripheral nerve sheath tumors (MPNSTs are rare and highly aggressive soft tissue tumors showing complex chromosomal aberrations. In order to identify recurrent chromosomal regions of gain and loss, and thereby novel gene targets of potential importance for MPNST development and/or progression, we have analyzed DNA copy number changes in seven high-grade MPNSTs using microarray-based comparative genomic hybridization (array CGH. Results Considerable more gains than losses were observed, and the most frequent minimal recurrent regions of gain included 1q24.1-q24.2, 1q24.3-q25.1, 8p23.1-p12, 9q34.11-q34.13 and 17q23.2-q25.3, all gained in five of seven samples. The 17q23.2-q25.3 region was gained in all five patients with poor outcome and not in the two patients with disease-free survival. cDNA microarray analysis and quantitative real-time reverse transcription PCR were used to investigate expression of genes located within these regions. The gene lysyl oxidase-like 2 (LOXL2 was identified as a candidate target for the 8p23.1-p12 gain. Within 17q, the genes topoisomerase II-α (TOP2A, ets variant gene 4 (E1A enhancer binding protein, E1AF (ETV4 and baculoviral IAP repeat-containing 5 (survivin (BIRC5 showed increased expression in all samples compared to two benign tumors. Increased expression of these genes has previously been associated with poor survival in other malignancies, and for TOP2A, in MPNSTs as well. In addition, we have analyzed the expression of five micro RNAs located within the 17q23.2-q25.3 region, but none of them showed high expression levels compared to the benign tumors. Conclusion Our study shows the potential of using DNA copy number changes obtained by array CGH to predict the prognosis of MPNST patients. Although no clear correlations between the expression level and patient outcome were observed, the genes TOP2A, ETV4 and BIRC5 are interesting candidate targets for the 17q gain associated

  5. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

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    Park, Hansoo; Kim, Jong-Il; Ju, Young Seok; Gokcumen, Omer; Mills, Ryan E; Kim, Sheehyun; Lee, Seungbok; Suh, Dongwhan; Hong, Dongwan; Kang, Hyunseok Peter; Yoo, Yun Joo; Shin, Jong-Yeon; Kim, Hyun-Jin; Yavartanoo, Maryam; Chang, Young Wha; Ha, Jung-Sook; Chong, Wilson; Hwang, Ga-Ram; Darvishi, Katayoon; Kim, Hyeran; Yang, Song Ju; Yang, Kap-Seok; Kim, Hyungtae; Hurles, Matthew E; Scherer, Stephen W; Carter, Nigel P; Tyler-Smith, Chris; Lee, Charles; Seo, Jeong-Sun

    2010-05-01

    Copy number variants (CNVs) account for the majority of human genomic diversity in terms of base coverage. Here, we have developed and applied a new method to combine high-resolution array comparative genomic hybridization (CGH) data with whole-genome DNA sequencing data to obtain a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations (Korean, Chinese and Japanese) were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes. Whole-genome sequencing data from a reference genome (NA10851, with 28.3x coverage) and two Asian genomes (AK1, with 27.8x coverage and AK2, with 32.0x coverage) were used to transform the relative copy number information obtained from array CGH experiments into absolute copy number values. We discovered 5,177 CNVs, of which 3,547 were putative Asian-specific CNVs. These common CNVs in Asian populations will be a useful resource for subsequent genetic studies in these populations, and the new method of calling absolute CNVs will be essential for applying CNV data to personalized medicine.

  6. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

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    Rajini R Haraksingh

    Full Text Available Accurate and efficient genome-wide detection of copy number variants (CNVs is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH, Single Nucleotide Polymorphism (SNP genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications.

  7. Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds.

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    Jiying Wang

    Full Text Available Copy number variations (CNVs are important forms of genomic variation, and have attracted extensive attentions in humans as well as domestic animals. In the study, using a custom-designed 2.1 M array comparative genomic hybridization (aCGH, genome-wide CNVs were identified among 12 individuals from diverse pig breeds, including one Asian wild population, six Chinese indigenous breeds and two modern commercial breeds (Yorkshire and Landrace, with one individual of the other modern commercial breed, Duroc, as the reference. A total of 1,344 CNV regions (CNVRs were identified, covering 47.79 Mb (∼1.70% of the pig genome. The length of these CNVRs ranged from 3.37 Kb to 1,319.0 Kb with a mean of 35.56 Kb and a median of 11.11 Kb. Compared with similar studies reported, most of the CNVRs (74.18% were firstly identified in present study. In order to confirm these CNVRs, 21 CNVRs were randomly chosen to be validated by quantitative real time PCR (qPCR and a high rate (85.71% of confirmation was obtained. Functional annotation of CNVRs suggested that the identified CNVRs have important function, and may play an important role in phenotypic and production traits difference among various breeds. Our results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.

  8. High copy arrays containing a sequence upstream of mec-3 alter cell migration and axonal morphology in C. elegans

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    Patchen Brandi

    2001-01-01

    Full Text Available Abstract Background The Caenorhabditis elegans gene mec-3 encodes a LIM-homeodomain protein that is a master regulator of touch receptor neuron genes. Two of the touch neurons, the ALM neurons, are generated in the anterior of the animal and then migrate to near the middle of the animal. In animals transformed with a sequence upstream of mec-3, the ALM touch receptor neurons failed to migrate to their normal positions and sometimes migrated in the wrong direction, and the PLM touch receptor neurons showed axonal defects. Here we characterize this effect and identify the sequence causing the cell migration and axonal defects. Results The ALM migration defect did not result from RNA interference (RNAi, nonspecific effects of carrying a transgenic array, expression of GFP, or the marker gene used to make the transformants. Instead, the ALM migration defect resulted from transgenic arrays containing many copies of a specific 104 bp DNA sequence. Transgenic arrays containing this sequence did not affect all cell migrations. Conclusions The mec-3 upstream sequence appeared to be sequestering (titrating out a specific DNA-binding factor that is required for the ALMs to migrate correctly. Because titration of this factor could reverse the direction of ALM migrations, it may be part of a program that specifies both the direction and extent of ALM migrations. mec-3 is a master regulator of touch receptor neuron genes, so the factor or factors that bind this sequence may also be involved in specifying the fate of touch receptor neurons.

  9. Major copy proportion analysis of tumor samples using SNP arrays

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    Li Cheng

    2008-04-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput genotyping of up to 900,000 human SNPs and have been used widely in linkage and cancer genomics studies. We have previously used Hidden Markov Models (HMM to analyze SNP array data for inferring copy numbers and loss-of-heterozygosity (LOH from paired normal and tumor samples and unpaired tumor samples. Results We proposed and implemented major copy proportion (MCP analysis of oligonucleotide SNP array data. A HMM was constructed to infer unobserved MCP states from observed allele-specific signals through emission and transition distributions. We used 10 K, 100 K and 250 K SNP array datasets to compare MCP analysis with LOH and copy number analysis, and showed that MCP performs better than LOH analysis for allelic-imbalanced chromosome regions and normal contaminated samples. The major and minor copy alleles can also be inferred from allelic-imbalanced regions by MCP analysis. Conclusion MCP extends tumor LOH analysis to allelic imbalance analysis and supplies complementary information to total copy numbers. MCP analysis of mixing normal and tumor samples suggests the utility of MCP analysis of normal-contaminated tumor samples. The described analysis and visualization methods are readily available in the user-friendly dChip software.

  10. High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues.

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    van Essen, Hendrik F; Ylstra, Bauke

    2012-01-01

    We describe protocols to acquire high-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissues for the use in array comparative genome hybridization (CGH). Formalin fixation combined with paraffin embedding is routine procedure for solid malignancies in the diagnostic practice of the pathologist. As a consequence, large archives of FFPE tissues are available in pathology institutes across the globe. This archival material is for many research questions an invaluable resource, with long-term clinical follow-up and survival data available. FFPE is, thus, highly attractive for large genomics studies, including experiments requiring samples for test/learning and validation. Most larger array CGH studies have, therefore, made use of FFPE material and show that CNAs have tumor- and tissue-specific traits (Chin et al. Cancer Cell 10: 529-541, 2006; Fridlyand et al. BMC Cancer 6: 96, 2006; Weiss et al. Oncogene 22: 1872-1879, 2003; Jong et al. Oncogene 26: 1499-1506, 2007). The protocols described are tailored to array CGH of FFPE solid malignancies: from sectioning FFPE blocks to specific cynosures for pathological revisions of sections, DNA isolation, quality testing, and amplification. The protocols are technical in character and elaborate up to the labeling of isolated DNA while further processes and interpretation and data analysis are beyond the scope.

  11. Characteristics of Highly Polymorphic Segmental Copy-Number Variations Observed in Japanese by BAC-Array-CGH

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    Takahashi, Norio; Satoh, Yasunari; Sasaki, Keiko; Shimoichi, Yuko; Sugita, Keiko; Katayama, Hiroaki

    2011-01-01

    Segmental copy-number variations (CNVs) may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH). We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals. PMID:21197411

  12. A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data

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    Ian Roberts

    2012-01-01

    Full Text Available Reliable identification of copy number aberrations (CNA from comparative genomic hybridization data would be improved by the availability of a generalised method for processing large datasets. To this end, we developed swatCGH, a data analysis framework and region detection heuristic for computational grids. swatCGH analyses sequentially displaced (sliding windows of neighbouring probes and applies adaptive thresholds of varying stringency to identify the 10% of each chromosome that contains the most frequently occurring CNAs. We used the method to analyse a published dataset, comparing data preprocessed using four different DNA segmentation algorithms, and two methods for prioritising the detected CNAs. The consolidated list of the most commonly detected aberrations confirmed the value of swatCGH as a simplified high-throughput method for identifying biologically significant CNA regions of interest.

  13. A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data

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    Roberts, Ian; Carter, Stephanie A.; Scarpini, Cinzia G.; Karagavriilidou, Konstantina; Barna, Jenny C. J.; Calleja, Mark; Coleman, Nicholas

    2012-01-01

    Reliable identification of copy number aberrations (CNA) from comparative genomic hybridization data would be improved by the availability of a generalised method for processing large datasets. To this end, we developed swatCGH, a data analysis framework and region detection heuristic for computational grids. swatCGH analyses sequentially displaced (sliding) windows of neighbouring probes and applies adaptive thresholds of varying stringency to identify the 10% of each chromosome that contains the most frequently occurring CNAs. We used the method to analyse a published dataset, comparing data preprocessed using four different DNA segmentation algorithms, and two methods for prioritising the detected CNAs. The consolidated list of the most commonly detected aberrations confirmed the value of swatCGH as a simplified high-throughput method for identifying biologically significant CNA regions of interest. PMID:23008709

  14. Characteristics of Highly Polymorphic Segmental Copy-Number Variations Observed in Japanese by BAC-Array-CGH

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    Norio Takahashi

    2011-01-01

    Full Text Available Segmental copy-number variations (CNVs may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH. We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals.

  15. A multilevel model to address batch effects in copy number estimation using SNP arrays.

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    Scharpf, Robert B; Ruczinski, Ingo; Carvalho, Benilton; Doan, Betty; Chakravarti, Aravinda; Irizarry, Rafael A

    2011-01-01

    Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of base pairs in the genome. Genomewide association studies (GWAS) may simultaneously screen for copy number phenotype and single nucleotide polymorphism (SNP) phenotype associations as part of the analytic strategy. However, genomewide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post hoc quality control procedures to exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of biallelic genotype calls from experimental data to estimate batch-specific and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in the quantile-normalized intensities, while the latter illustrates the robustness of our approach to a data set in which approximately 27% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R

  16. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.

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    Veltman, J.A.; Fridlyand, J.; Pejavar, S.; Olshen, A.B.; Korkola, J.E.; Vries, S. de; Carroll, P.; Kuo, W.L.; Pinkel, D.; Albertson, D.; Cordon-Cardo, C.; Jain, A.N.; Waldman, F.M.

    2003-01-01

    Genome-wide copy number profiles were characterized in 41 primary bladder tumors using array-based comparative genomic hybridization (array CGH). In addition to previously identified alterations in large chromosomal regions, alterations were identified in many small genomic regions, some with high-l

  17. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

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    Chadwick Brian P

    2010-11-01

    Full Text Available Abstract Background Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized. Results Here we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain. Conclusions Our results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome.

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

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    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.

  19. Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

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    Bejjani Bassem A

    2010-06-01

    Full Text Available Abstract Background Microarray-based comparative genomic hybridization (aCGH is a powerful diagnostic tool for the detection of DNA copy number gains and losses associated with chromosome abnormalities, many of which are below the resolution of conventional chromosome analysis. It has been presumed that whole-genome oligonucleotide (oligo arrays identify more clinically significant copy-number abnormalities than whole-genome bacterial artificial chromosome (BAC arrays, yet this has not been systematically studied in a clinical diagnostic setting. Results To determine the difference in detection rate between similarly designed BAC and oligo arrays, we developed whole-genome BAC and oligonucleotide microarrays and validated them in a side-by-side comparison of 466 consecutive clinical specimens submitted to our laboratory for aCGH. Of the 466 cases studied, 67 (14.3% had a copy-number imbalance of potential clinical significance detectable by the whole-genome BAC array, and 73 (15.6% had a copy-number imbalance of potential clinical significance detectable by the whole-genome oligo array. However, because both platforms identified copy number variants of unclear clinical significance, we designed a systematic method for the interpretation of copy number alterations and tested an additional 3,443 cases by BAC array and 3,096 cases by oligo array. Of those cases tested on the BAC array, 17.6% were found to have a copy-number abnormality of potential clinical significance, whereas the detection rate increased to 22.5% for the cases tested by oligo array. In addition, we validated the oligo array for detection of mosaicism and found that it could routinely detect mosaicism at levels of 30% and greater. Conclusions Although BAC arrays have faster turnaround times, the increased detection rate of oligo arrays makes them attractive for clinical cytogenetic testing.

  20. Detection of genomic copy number changes in patients with idiopathic mental retardation by high-resolution X-array-CGH: important role for increased gene dosage of XLMR genes.

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    Froyen, Guy; Van Esch, Hilde; Bauters, Marijke; Hollanders, Karen; Frints, Suzanna G M; Vermeesch, Joris R; Devriendt, Koen; Fryns, Jean-Pierre; Marynen, Peter

    2007-10-01

    A tiling X-chromosome-specific genomic array with a theoretical resolution of 80 kb was developed to screen patients with idiopathic mental retardation (MR) for submicroscopic copy number differences. Four patients with aberrations previously detected at lower resolution were first analyzed. This facilitated delineation of the location and extent of the aberration at high resolution and subsequently, more precise genotype-phenotype analyses. A cohort of 108 patients was screened, 57 of which were suspected of X-linked mental retardation (XLMR), 26 were probands of brother pairs, and 25 were sporadic cases. A total of 15 copy number changes in 14 patients (13%) were detected, which included two deletions and 13 duplications ranging from 0.1 to 2.7 Mb. The aberrations are associated with the phenotype in five patients (4.6%), based on the following criteria: de novo aberration; involvement of a known or candidate X-linked nonsyndromic(syndromic) MR (MRX(S)) gene; segregation with the disease in the family; absence in control individuals; and skewed X-inactivation in carrier females. These include deletions that contain the MRX(S) genes CDKL5, OPHN1, and CASK, and duplications harboring CDKL5, NXF5, MECP2, and GDI1. In addition, seven imbalances were apparent novel polymorphic regions because they do not fulfill the proposed criteria. Taken together, our data strongly suggest that not only deletions but also duplications on the X chromosome contribute to the phenotype more often than expected, supporting the increased gene dosage mechanism for deregulation of normal cognitive development.

  1. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization

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    Abernathy, J.; Li, X.; Jia, X.; Chou, W.; Lamont, S.J.; Crooijmans, R.P.M.A.; Zhou, H.

    2014-01-01

    Copy number variation refers to regions along chromosomes that harbor a type of structural variation, such as duplications or deletions. Copy number variants (CNVs) play a role in many important traits as well as in genetic diversity. Previous analyses of chickens using array comparative genomic hyb

  2. DNA copy number aberrations in breast cancer by array comparative genomic hybridization

    DEFF Research Database (Denmark)

    Li, J.; Wang, K.; Li, S.;

    2009-01-01

    Array comparative genomic hybridization (CGH) has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome CGH arrays. A number of h...

  3. Copy Number Variation Analysis by Array Analysis of Single Cells Following Whole Genome Amplification.

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    Dimitriadou, Eftychia; Zamani Esteki, Masoud; Vermeesch, Joris Robert

    2015-01-01

    Whole genome amplification is required to ensure the availability of sufficient material for copy number variation analysis of a genome deriving from an individual cell. Here, we describe the protocols we use for copy number variation analysis of non-fixed single cells by array-based approaches following single-cell isolation and whole genome amplification. We are focusing on two alternative protocols, an isothermal and a PCR-based whole genome amplification method, followed by either comparative genome hybridization (aCGH) or SNP array analysis, respectively.

  4. Detection of clinically relevant exonic copy-number changes by array CGH.

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    Boone, Philip M; Bacino, Carlos A; Shaw, Chad A; Eng, Patricia A; Hixson, Patricia M; Pursley, Amber N; Kang, Sung-Hae L; Yang, Yaping; Wiszniewska, Joanna; Nowakowska, Beata A; del Gaudio, Daniela; Xia, Zhilian; Simpson-Patel, Gayle; Immken, LaDonna L; Gibson, James B; Tsai, Anne C-H; Bowers, Jennifer A; Reimschisel, Tyler E; Schaaf, Christian P; Potocki, Lorraine; Scaglia, Fernando; Gambin, Tomasz; Sykulski, Maciej; Bartnik, Magdalena; Derwinska, Katarzyna; Wisniowiecka-Kowalnik, Barbara; Lalani, Seema R; Probst, Frank J; Bi, Weimin; Beaudet, Arthur L; Patel, Ankita; Lupski, James R; Cheung, Sau Wai; Stankiewicz, Pawel

    2010-12-01

    Array comparative genomic hybridization (aCGH) is a powerful tool for the molecular elucidation and diagnosis of disorders resulting from genomic copy-number variation (CNV). However, intragenic deletions or duplications--those including genomic intervals of a size smaller than a gene--have remained beyond the detection limit of most clinical aCGH analyses. Increasing array probe number improves genomic resolution, although higher cost may limit implementation, and enhanced detection of benign CNV can confound clinical interpretation. We designed an array with exonic coverage of selected disease and candidate genes and used it clinically to identify losses or gains throughout the genome involving at least one exon and as small as several hundred base pairs in size. In some patients, the detected copy-number change occurs within a gene known to be causative of the observed clinical phenotype, demonstrating the ability of this array to detect clinically relevant CNVs with subkilobase resolution. In summary, we demonstrate the utility of a custom-designed, exon-targeted oligonucleotide array to detect intragenic copy-number changes in patients with various clinical phenotypes.

  5. A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

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    Torring Niels

    2007-11-01

    Full Text Available Abstract Background Affymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlying events leading to cancer. Genomic copy-numbers are today routinely derived from SNP array data, but the proposed algorithms for this task most often disregard the genotype information available from germline cells in paired germline-tumour samples. Including this information may deepen our understanding of the "true" biological situation e.g. by enabling analysis of allele specific copy-numbers. Here we rely on matched germline-tumour samples and have developed a Hidden Markov Model (HMM to estimate allelic copy-number changes in tumour cells. Further with this approach we are able to estimate the proportion of normal cells in the tumour (mixture proportion. Results We show that our method is able to recover the underlying copy-number changes in simulated data sets with high accuracy (above 97.71%. Moreover, although the known copy-numbers could be well recovered in simulated cancer samples with more than 70% cancer cells (and less than 30% normal cells, we demonstrate that including the mixture proportion in the HMM increases the accuracy of the method. Finally, the method is tested on HapMap samples and on bladder and prostate cancer samples. Conclusion The HMM method developed here uses the genotype calls of germline DNA and the allelic SNP intensities from the tumour DNA to estimate allelic copy-numbers (including changes in the tumour. It differentiates between different events like uniparental disomy and allelic imbalances. Moreover, the HMM can estimate the mixture proportion, and thus inform about the purity of the tumour sample.

  6. SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR.

    Science.gov (United States)

    Stabley, Deborah L; Harris, Ashlee W; Holbrook, Jennifer; Chubbs, Nicholas J; Lozo, Kevin W; Crawford, Thomas O; Swoboda, Kathryn J; Funanage, Vicky L; Wang, Wenlan; Mackenzie, William; Scavina, Mena; Sol-Church, Katia; Butchbach, Matthew E R

    2015-07-01

    Proximal spinal muscular atrophy (SMA) is an early-onset motor neuron disease characterized by loss of α-motor neurons and associated muscle atrophy. SMA is caused by deletion or other disabling mutation of survival motor neuron 1 (SMN1). In the human genome, a large duplication of the SMN-containing region gives rise to a second copy of this gene (SMN2) that is distinguishable by a single nucleotide change in exon 7. Within the SMA population, there is substantial variation in SMN2 copy number; in general, those individuals with SMA who have a high SMN2 copy number have a milder disease. Because SMN2 functions as a disease modifier, its accurate copy number determination may have clinical relevance. In this study, we describe the development of an assay to assess SMN1 and SMN2 copy numbers in DNA samples using an array-based digital PCR (dPCR) system. This dPCR assay can accurately and reliably measure the number of SMN1 and SMN2 copies in DNA samples. In a cohort of SMA patient-derived cell lines, the assay confirmed a strong inverse correlation between SMN2 copy number and disease severity. Array dPCR is a practical technique to determine, accurately and reliably, SMN1 and SMN2 copy numbers from SMA samples.

  7. Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones.

    Science.gov (United States)

    Wild, Jadwiga; Hradecna, Zdenka; Szybalski, Waclaw

    2002-09-01

    The widely used, very-low-copy BAC (bacterial artificial chromosome) vectors are the mainstay of present genomic research. The principal advantage of BACs is the high stability of inserted clones, but an important disadvantage is the low yield of DNA, both for vectors alone and when carrying genomic inserts. We describe here a novel class of single-copy/high-copy (SC/HC) pBAC/oriV vectors that retain all the advantages of low-copy BAC vectors, but are endowed with a conditional and tightly controlled oriV/TrfA amplification system that allows: (1) a yield of ~100 copies of the vector per host cell when conditionally induced with L-arabinose, and (2) analogous DNA amplification (only upon induction and with copy number depending on the insert size) of pBAC/oriV clones carrying >100-kb inserts. Amplifiable clones and libraries facilitate high-throughput DNA sequencing and other applications requiring HC plasmid DNA. To turn on DNA amplification, which is driven by the oriV origin of replication, we used copy-up mutations in the gene trfA whose expression was very tightly controlled by the araC-P(araBAD) promoter/regulator system. This system is inducible by L-arabinose, and could be further regulated by glucose and fucose. Amplification of DNA upon induction with L-arabinose and its modulation by glucose are robust and reliable. Furthermore, we discovered that addition of 0.2% D-glucose to the growth medium helped toward the objective of obtaining a real SC state for all BAC systems, thus enhancing the stability of their maintenance, which became equivalent to cloning into the host chromosome

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

    Directory of Open Access Journals (Sweden)

    Siggberg Linda

    2012-09-01

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

  9. SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas.

    Directory of Open Access Journals (Sweden)

    Ahmed Idbaih

    Full Text Available Anaplastic oligodendrogliomas (AOD are rare glial tumors in adults with relative homogeneous clinical, radiological and histological features at the time of diagnosis but dramatically various clinical courses. Studies have identified several molecular abnormalities with clinical or biological relevance to AOD (e.g. t(1;19(q10;p10, IDH1, IDH2, CIC and FUBP1 mutations.To better characterize the clinical and biological behavior of this tumor type, the creation of a national multicentric network, named "Prise en charge des OLigodendrogliomes Anaplasiques (POLA," has been supported by the Institut National du Cancer (InCA. Newly diagnosed and centrally validated AOD patients and their related biological material (tumor and blood samples were prospectively included in the POLA clinical database and tissue bank, respectively.At the molecular level, we have conducted a high-resolution single nucleotide polymorphism array analysis, which included 83 patients. Despite a careful central pathological review, AOD have been found to exhibit heterogeneous genomic features. A total of 82% of the tumors exhibited a 1p/19q-co-deletion, while 18% harbor a distinct chromosome pattern. Novel focal abnormalities, including homozygously deleted, amplified and disrupted regions, have been identified. Recurring copy neutral losses of heterozygosity (CNLOH inducing the modulation of gene expression have also been discovered. CNLOH in the CDKN2A locus was associated with protein silencing in 1/3 of the cases. In addition, FUBP1 homozygous deletion was detected in one case suggesting a putative tumor suppressor role of FUBP1 in AOD.Our study showed that the genomic and pathological analyses of AOD are synergistic in detecting relevant clinical and biological subgroups of AOD.

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

    Directory of Open Access Journals (Sweden)

    Chan Alan

    2006-06-01

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

  11. Identification of genome-wide copy number variations among diverse pig breeds by array CGH

    Directory of Open Access Journals (Sweden)

    Li Yan

    2012-12-01

    Full Text Available Abstract Background Recent studies have shown that copy number variation (CNV in mammalian genomes contributes to phenotypic diversity, including health and disease status. In domestic pigs, CNV has been catalogued by several reports, but the extent of CNV and the phenotypic effects are far from clear. The goal of this study was to identify CNV regions (CNVRs in pigs based on array comparative genome hybridization (aCGH. Results Here a custom-made tiling oligo-nucleotide array was used with a median probe spacing of 2506 bp for screening 12 pigs including 3 Chinese native pigs (one Chinese Erhualian, one Tongcheng and one Yangxin pig, 5 European pigs (one Large White, one Pietrain, one White Duroc and two Landrace pigs, 2 synthetic pigs (Chinese new line DIV pigs and 2 crossbred pigs (Landrace × DIV pigs with a Duroc pig as the reference. Two hundred and fifty-nine CNVRs across chromosomes 1–18 and X were identified, with an average size of 65.07 kb and a median size of 98.74 kb, covering 16.85 Mb or 0.74% of the whole genome. Concerning copy number status, 93 (35.91% CNVRs were called as gains, 140 (54.05% were called as losses and the remaining 26 (10.04% were called as both gains and losses. Of all detected CNVRs, 171 (66.02% and 34 (13.13% CNVRs directly overlapped with Sus scrofa duplicated sequences and pig QTLs, respectively. The CNVRs encompassed 372 full length Ensembl transcripts. Two CNVRs identified by aCGH were validated using real-time quantitative PCR (qPCR. Conclusions Using 720 K array CGH (aCGH we described a map of porcine CNVs which facilitated the identification of structural variations for important phenotypes and the assessment of the genetic diversity of pigs.

  12. Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model

    Directory of Open Access Journals (Sweden)

    Gerstein Mark B

    2010-10-01

    Full Text Available Abstract Background Copy number variants (CNVs have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH and newly developed read-depth approach through ultrahigh throughput genomic sequencing both provide rapid, robust, and comprehensive methods to identify CNVs on a whole-genome scale. Results We developed a Bayesian statistical analysis algorithm for the detection of CNVs from both types of genomic data. The algorithm can analyze such data obtained from PCR-based bacterial artificial chromosome arrays, high-density oligonucleotide arrays, and more recently developed high-throughput DNA sequencing. Treating parameters--e.g., the number of CNVs, the position of each CNV, and the data noise level--that define the underlying data generating process as random variables, our approach derives the posterior distribution of the genomic CNV structure given the observed data. Sampling from the posterior distribution using a Markov chain Monte Carlo method, we get not only best estimates for these unknown parameters but also Bayesian credible intervals for the estimates. We illustrate the characteristics of our algorithm by applying it to both synthetic and experimental data sets in comparison to other segmentation algorithms. Conclusions In particular, the synthetic data comparison shows that our method is more sensitive than other approaches at low false positive rates. Furthermore, given its Bayesian origin, our method can also be seen as a technique to refine CNVs identified by fast point-estimate methods and also as a framework to integrate array-CGH and sequencing data with other CNV-related biological knowledge, all through informative priors.

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

    Science.gov (United States)

    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.

  14. A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array.

    Science.gov (United States)

    Kiiski, Kirsi; Lehtokari, Vilma-Lotta; Löytynoja, Ari; Ahlstén, Liina; Laitila, Jenni; Wallgren-Pettersson, Carina; Pelin, Katarina

    2016-04-01

    Recently, new large variants have been identified in the nebulin gene (NEB) causing nemaline myopathy (NM). NM constitutes a heterogeneous group of disorders among the congenital myopathies, and disease-causing variants in NEB are a main cause of the recessively inherited form of NM. NEB consists of 183 exons and it includes homologous sequences such as a 32-kb triplicate region (TRI), where eight exons are repeated three times (exons 82-89, 90-97, 98-105). In human, the normal copy number of NEB TRI is six (three copies in each allele). Recently, we described a custom NM-CGH microarray designed to detect copy number variations (CNVs) in the known NM genes. The array has now been updated to include all the currently known 10 NM genes. The NM-CGH array is superior in detecting CNVs, especially of the NEB TRI, that is not included in the exome capture kits. To date, we have studied 266 samples from 196 NM families using the NM-CGH microarray, and identified a novel recurrent NEB TRI variation in 13% (26/196) of the families and in 10% of the controls (6/60). An analysis of the breakpoints revealed adjacent repeat elements, which are known to predispose for rearrangements such as CNVs. The control CNV samples deviate only one copy from the normal six copies, whereas the NM samples include CNVs of up to four additional copies. Based on this study, NEB seems to tolerate deviations of one TRI copy, whereas addition of two or more copies might be pathogenic.

  15. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms

    DEFF Research Database (Denmark)

    Gunnarsson, R.; Staaf, J.; Jansson, M.;

    2008-01-01

    Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K...... detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation...

  16. Genome-wide detection of copy number variations among diverse horse breeds by array CGH.

    Science.gov (United States)

    Wang, Wei; Wang, Shenyuan; Hou, Chenglin; Xing, Yanping; Cao, Junwei; Wu, Kaifeng; Liu, Chunxia; Zhang, Dong; Zhang, Li; Zhang, Yanru; Zhou, Huanmin

    2014-01-01

    Recent studies have found that copy number variations (CNVs) are widespread in human and animal genomes. CNVs are a significant source of genetic variation, and have been shown to be associated with phenotypic diversity. However, the effect of CNVs on genetic variation in horses is not well understood. In the present study, CNVs in 6 different breeds of mare horses, Mongolia horse, Abaga horse, Hequ horse and Kazakh horse (all plateau breeds) and Debao pony and Thoroughbred, were determined using aCGH. In total, seven hundred CNVs were identified ranging in size from 6.1 Kb to 0.57 Mb across all autosomes, with an average size of 43.08 Kb and a median size of 15.11 Kb. By merging overlapping CNVs, we found a total of three hundred and fifty-three CNV regions (CNVRs). The length of the CNVRs ranged from 6.1 Kb to 1.45 Mb with average and median sizes of 38.49 Kb and 13.1 Kb. Collectively, 13.59 Mb of copy number variation was identified among the horses investigated and accounted for approximately 0.61% of the horse genome sequence. Five hundred and eighteen annotated genes were affected by CNVs, which corresponded to about 2.26% of all horse genes. Through the gene ontology (GO), genetic pathway analysis and comparison of CNV genes among different breeds, we found evidence that CNVs involving 7 genes may be related to the adaptation to severe environment of these plateau horses. This study is the first report of copy number variations in Chinese horses, which indicates that CNVs are ubiquitous in the horse genome and influence many biological processes of the horse. These results will be helpful not only in mapping the horse whole-genome CNVs, but also to further research for the adaption to the high altitude severe environment for plateau horses.

  17. Precise ERBB2 copy number assessment in breast cancer by means of molecular inversion probe array analysis.

    Science.gov (United States)

    Christgen, Matthias; van Luttikhuizen, Jana L; Raap, Mieke; Braubach, Peter; Schmidt, Lars; Jonigk, Danny; Feuerhake, Friedrich; Lehmann, Ulrich; Schlegelberger, Brigitte; Kreipe, Hans H; Steinemann, Doris

    2016-12-13

    HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott). Following macrodissection of invasive breast cancer tissue and DNA extraction, ERBB2 copy number was also determined by molecular inversion probe array analysis (MIP, OncoScan, Affymetrix) and next generation sequencing combined with normalized amplicon coverage analysis (NGS/NAC, AmpliSeq, Ion Torrent). ERBB2 copy number values obtained by MIP or NGS/NAC were tightly correlated with ERBB2 copy number values obtained by conventional FISH (rs = 0.940 and rs = 0.894, P copy number detection and should be considered as an ancillary method for clinical HER2 testing.

  18. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

    NARCIS (Netherlands)

    Hehir-Kwa, J.Y.; Egmont-Peterson, M.; Janssen, I.M.; Smeets, D.F.C.M.; Geurts van Kessel, A.H.M.; Veltman, J.A.

    2007-01-01

    Recently, comparative genomic hybridization onto bacterial artificial chromosome (BAC) arrays (array-based comparative genomic hybridization) has proved to be successful for the detection of submicroscopic DNA copy-number variations in health and disease. Technological improvements to achieve a high

  19. High voltage load resistor array

    Energy Technology Data Exchange (ETDEWEB)

    Lehmann, Monty Ray [Smithfield, VA

    2005-01-18

    A high voltage resistor comprising an array of a plurality of parallel electrically connected resistor elements each containing a resistive solution, attached at each end thereof to an end plate, and about the circumference of each of the end plates, a corona reduction ring. Each of the resistor elements comprises an insulating tube having an electrode inserted into each end thereof and held in position by one or more hose clamps about the outer periphery of the insulating tube. According to a preferred embodiment, the electrode is fabricated from stainless steel and has a mushroom shape at one end, that inserted into the tube, and a flat end for engagement with the end plates that provides connection of the resistor array and with a load.

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

    Directory of Open Access Journals (Sweden)

    Martínez F

    2007-11-01

    Full Text Available Abstract 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.

  1. Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.

    Science.gov (United States)

    Hostetter, Galen; Kim, Su Young; Savage, Stephanie; Gooden, Gerald C; Barrett, Michael; Zhang, Jian; Alla, Lalitamba; Watanabe, April; Einspahr, Janine; Prasad, Anil; Nickoloff, Brian J; Carpten, John; Trent, Jeffrey; Alberts, David; Bittner, Michael

    2010-01-01

    Genomic technologies, such as array comparative genomic hybridization (aCGH), increasingly offer definitive gene dosage profiles in clinical samples. Historically, copy number profiling was limited to large fresh-frozen tumors where intact DNA could be readily extracted. Genomic analyses of pre-neoplastic tumors and diagnostic biopsies are often limited to DNA processed by formalin-fixation and paraffin-embedding (FFPE). We present specialized protocols for DNA extraction and processing from FFPE tissues utilizing DNase processing to generate randomly fragmented DNA. The protocols are applied to FFPE clinical samples of varied tumor types, from multiple institutions and of varied block age. Direct comparative analyses with regression coefficient were calculated on split-sample (portion fresh/portion FFPE) of colorectal tumor samples. We show equal detection of a homozygous loss of SMAD4 at the exon-level in the SW480 cell line and gene-specific alterations in the split tumor samples. aCGH application to a set of archival FFPE samples of skin squamous cell carcinomas detected a novel hemizygous deletion in INPP5A on 10q26.3. Finally we present data on derivative of log ratio, a particular sensitive detector of measurement variance, for 216 sequential hybridizations to assess protocol reliability over a wide range of FFPE samples.

  2. Significance of genome-wide analysis of copy number alterations and UPD in myelodysplastic syndromes using combined CGH - SNP arrays.

    Science.gov (United States)

    Ahmad, Ausaf; Iqbal, M Anwar

    2012-01-01

    Genetic information is an extremely valuable data source in characterizing the personal nature of cancer. Chromosome instability is a hallmark of most cancer cells. Chromosomal abnormalities are correlated with poor prognosis, disease classification, risk stratification, and treatment selection. Copy number alterations (CNAs) are an important molecular signature in cancer initiation, development, and progression. Recent application of whole-genome tools to characterize normal and cancer genomes provides the powerful molecular cytogenetic means to enumerate the multiple somatic, genetic and epigenetic alterations that occur in cancer. Combined array comparative genomic hybridization (aCGH) with single nucleotide polymorphism (SNP) array is a useful technique allowing detection of CNAs and loss of heterozygosity (LOH) or uni-parental disomy (UPD) together in a single experiment. It also provides allelic information on deletions, duplications, and amplifications. UPD can result in an abnormal phenotype when the chromosomes involved are imprinted. Myelodysplastic syndromes (MDS) are the most common clonal stem cell hematologic malignancy characterized by ineffective hematopoiesis, which leads to rapid progression into acute myeloid leukemia. UPD that occurs without concurrent changes in the gene copy number is a common chromosomal defect in hematologic malignancies, especially in MDS. Approximately 40-50% of MDS patients do not have karyotypic abnormalities that are detectable using classical metaphase cytogenetic techniques (MC) because of inherent limitations of MC, low resolution and the requirement of having dividing cells. In this review, we highlight advances in the clinical application of microarray technology in MDS and discuss the clinical potential of microarray.

  3. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms

    DEFF Research Database (Denmark)

    2008-01-01

    Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K...... of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis using dChip revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping...

  4. High density arrays of micromirrors

    Energy Technology Data Exchange (ETDEWEB)

    Folta, J. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Decker, J. Y. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kolman, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lee, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Brase, J. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    1999-02-01

    We established and achieved our goal to (1) fabricate and evaluate test structures based on the micromirror design optimized for maskless lithography applications, (2) perform system analysis and code development for the maskless lithography concept, and (3) identify specifications for micromirror arrays (MMAs) for LLNL's adaptive optics (AO) applications and conceptualize new devices.

  5. Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation

    Directory of Open Access Journals (Sweden)

    Aldred Micheala A

    2007-07-01

    Full Text Available Abstract Background The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In particular, a SNP site can no longer always be accurately assigned one of three genotypes in an individual. In the presence of copy number variability, the individual may theoretically harbor any number of copies of each of the two SNP alleles. Results To address this issue, we have developed a method to infer a "generalized genotype" from raw SNP microarray data. Here we apply our approach to data from 48 individuals and uncover thousands of aberrant SNPs, most in regions that were previously unreported as copy number variants. We show that our allele-specific copy numbers follow Mendelian inheritance patterns that would be obscured in the absence of SNP allele information. The interplay between duplication and point mutation in our data shed light on the relative frequencies of these events in human history, showing that at least some of the duplication events were recurrent. Conclusion This new multi-allelic view of SNPs has a complicated role in disease association studies, and further work will be necessary in order to accurately assess its importance. Software to perform generalized genotyping from SNP array data is freely available online 1.

  6. Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arrays.

    Directory of Open Access Journals (Sweden)

    Rani E George

    Full Text Available BACKGROUND: Neuroblastomas are characterized by chromosomal alterations with biological and clinical significance. We analyzed paired blood and primary tumor samples from 22 children with high-risk neuroblastoma for loss of heterozygosity (LOH and DNA copy number change using the Affymetrix 10K single nucleotide polymorphism (SNP array. FINDINGS: Multiple areas of LOH and copy number gain were seen. The most commonly observed area of LOH was on chromosome arm 11q (15/22 samples; 68%. Chromosome 11q LOH was highly associated with occurrence of chromosome 3p LOH: 9 of the 15 samples with 11q LOH had concomitant 3p LOH (P = 0.016. Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss, indicating hemizygous deletion within these regions. The one exception was on chromosome 11p, where LOH in all four cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Gain of copy number was most frequently observed on chromosome arm 17q (21/22 samples; 95% and was associated with allelic imbalance in six samples. Amplification of MYCN was also noted, and also amplification of a second gene, ALK, in a single case. CONCLUSIONS: This analysis demonstrates the power of SNP arrays for high-resolution determination of LOH and DNA copy number change in neuroblastoma, a tumor in which specific allelic changes drive clinical outcome and selection of therapy.

  7. Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays.

    Directory of Open Access Journals (Sweden)

    Jiying Wang

    Full Text Available Copy number variations (CNVs are important forms of genetic variation complementary to SNPs, and can be considered as promising markers for some phenotypic and economically important traits or diseases susceptibility in domestic animals. In the present study, we performed a genome-wide CNV identification in 14 individuals selected from diverse populations, including six types of Chinese indigenous breeds, one Asian wild boar population, as well as three modern commercial foreign breeds. We identified 63 CNVRs in total, which covered 9.98 Mb of polymorphic sequence and corresponded to 0.36% of the genome sequence. The length of these CNVRs ranged from 3.20 to 827.21 kb, with an average of 158.37 kb and a median of 97.85 kb. Functional annotation revealed these identified CNVR have important molecular function, and may play an important role in exploring the genetic basis of phenotypic variability and disease susceptibility among pigs. Additionally, to confirm these potential CNVRs, we performed qPCR for 12 randomly selected CNVRs and 8 of them (66.67% were confirmed successfully. CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.

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

    Science.gov (United States)

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

    2014-06-01

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

  9. High resolution measurement of DUF1220 domain copy number from whole genome sequence data.

    Science.gov (United States)

    Astling, David P; Heft, Ilea E; Jones, Kenneth L; Sikela, James M

    2017-08-14

    DUF1220 protein domains found primarily in Neuroblastoma BreakPoint Family (NBPF) genes show the greatest human lineage-specific increase in copy number of any coding region in the genome. There are 302 haploid copies of DUF1220 in hg38 (~160 of which are human-specific) and the majority of these can be divided into 6 different subtypes (referred to as clades). Copy number changes of specific DUF1220 clades have been associated in a dose-dependent manner with brain size variation (both evolutionarily and within the human population), cognitive aptitude, autism severity, and schizophrenia severity. However, no published methods can directly measure copies of DUF1220 with high accuracy and no method can distinguish between domains within a clade. Here we describe a novel method for measuring copies of DUF1220 domains and the NBPF genes in which they are found from whole genome sequence data. We have characterized the effect that various sequencing and alignment parameters and strategies have on the accuracy and precision of the method and defined the parameters that lead to optimal DUF1220 copy number measurement and resolution. We show that copy number estimates obtained using our read depth approach are highly correlated with those generated by ddPCR for three representative DUF1220 clades. By simulation, we demonstrate that our method provides sufficient resolution to analyze DUF1220 copy number variation at three levels: (1) DUF1220 clade copy number within individual genes and groups of genes (gene-specific clade groups) (2) genome wide DUF1220 clade copies and (3) gene copy number for DUF1220-encoding genes. To our knowledge, this is the first method to accurately measure copies of all six DUF1220 clades and the first method to provide gene specific resolution of these clades. This allows one to discriminate among the ~300 haploid human DUF1220 copies to an extent not possible with any other method. The result is a greatly enhanced capability to analyze the

  10. Genome arrays for the detection of copy number variations in idiopathic mental retardation, idiopathic generalized epilepsy and neuropsychiatric disorders: lessons for diagnostic workflow and research.

    Science.gov (United States)

    Hochstenbach, R; Buizer-Voskamp, J E; Vorstman, J A S; Ophoff, R A

    2011-01-01

    We review the contributions and limitations of genome-wide array-based identification of copy number variants (CNVs) in the clinical diagnostic evaluation of patients with mental retardation (MR) and other brain-related disorders. In unselected MR referrals a causative genomic gain or loss is detected in 14-18% of cases. Usually, such CNVs arise de novo, are not found in healthy subjects, and have a major impact on the phenotype by altering the dosage of multiple genes. This high diagnostic yield justifies array-based segmental aneuploidy screening as the initial genetic test in these patients. This also pertains to patients with autism (expected yield about 5-10% in nonsyndromic and 10-20% in syndromic patients) and schizophrenia (at least 5% yield). CNV studies in idiopathic generalized epilepsy, attention-deficit hyperactivity disorder, major depressive disorder and Tourette syndrome indicate that patients have, on average, a larger CNV burden as compared to controls. Collectively, the CNV studies suggest that a wide spectrum of disease-susceptibility variants exists, most of which are rare (<0.1%) and of variable and usually small effect. Notwithstanding, a rare CNV can have a major impact on the phenotype. Exome sequencing in MR and autism patients revealed de novo mutations in protein coding genes in 60 and 20% of cases, respectively. Therefore, it is likely that arrays will be supplanted by next-generation sequencing methods as the initial and perhaps ultimate diagnostic tool in patients with brain-related disorders, revealing both CNVs and mutations in a single test. Copyright © 2011 S. Karger AG, Basel.

  11. High speed adaptive liquid microlens array

    NARCIS (Netherlands)

    Murade, C.U.; van den Ende, Henricus T.M.; Mugele, Friedrich Gunther

    2012-01-01

    Liquid microlenses are attractive for adaptive optics because they offer the potential for both high speed actuation and parallelization into large arrays. Yet, in conventional designs, resonances of the liquid and the complexity of driving mechanisms and/or the device architecture have hampered a

  12. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

    NARCIS (Netherlands)

    Hehir-Kwa, J.Y.; Egmont-Peterson, M.; Janssen, I.M.; Smeets, D.F.C.M.; Geurts van Kessel, A.H.M.; Veltman, J.A.

    2007-01-01

    Recently, comparative genomic hybridization onto bacterial artificial chromosome (BAC) arrays (array-based comparative genomic hybridization) has proved to be successful for the detection of submicroscopic DNA copy-number variations in health and disease. Technological improvements to achieve a

  13. Peer—to—Peer Computing for secure High Performance Data Copying

    Institute of Scientific and Technical Information of China (English)

    AndrewHanushevsky; ArtemTrunov; 等

    2001-01-01

    The BaBar Copy Program(bbcp) is an excellent representative of peer-to-peer(P2P) computing.It is also a pioneering application of its type in the p2p arena.Built upon the foundation of its predecessor,Secure Fast Copy(sfctp),bbcp incorporates significant improvements performance and usability,As with sfcp,bbcp usec ssh for authentication;providing an elegant and simple working model-if you can ssh to a location, you can copy files to or from that location.To fully support this notion,bbcp transparently supports 3rd party copy operations.The program also incorporates several mechanism to deal with firewall security;the bane of P2P computing,To achieve high performance in a wide area network,bbcp allows a user to independently specily,the number of parallel network streams,tcp window size,and the file I/O blocking factor.Using these parameters data is pipelined from source to target to provide a uniform traffic pattern that maximizes router efficiency.For improved recoveralbiltiy,bbcp also keeps track of copy operations so that an operation can be restarted from the point of failure at a later time;minimizing the amount of network traffic in the event of a copy failure,Here,we preset the bbcp architecture,it's various features,and the reasons for their inclusion.

  14. Array comparative genomic hybridization profiling analysis reveals deoxyribonucleic acid copy number variations associated with premature ovarian failure.

    Science.gov (United States)

    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.

  15. Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles.

    Science.gov (United States)

    Mc Sherry, E A; Mc Goldrick, A; Kay, E W; Hopkins, A M; Gallagher, W M; Dervan, P A

    2007-11-01

    Formalin-fixed paraffin-embedded (FFPE) archival clinical specimens are invaluable in discovery of prognostic and therapeutic targets for diseases such as cancer. However, the suitability of FFPE-derived genetic material for array-based comparative genomic hybridization (array-CGH) studies is underexplored. In this study, genetic profiles of matched FFPE and fresh-frozen specimens were examined to investigate DNA integrity differences between these sample types and determine the impact this may have on genetic profiles. Genomic DNA was extracted from three patient-matched FFPE and fresh-frozen clinical tissue samples. T47D breast cancer control cells were also grown in culture and processed to yield a fresh T47D sample, a fresh-frozen T47D sample and a FFPE T47D sample. DNA was extracted from all the samples; array-CGH conducted and genetic profiles of matched samples were then compared. A loss of high molecular weight DNA was observed in the FFPE clinical tissues and FFPE T47D samples. A dramatic increase in absolute number of genetic alterations was observed in all FFPE tissues relative to matched fresh-frozen counterparts. In future, alternative fixation and tissue-processing procedures, and/or new DNA extraction and CGH profiling protocols, may be implemented, enabling identification of changes involved in disease progression using stored clinical specimens.

  16. An all-statistics, high-speed algorithm for the analysis of copy number variation in genomes.

    Science.gov (United States)

    Chen, Chih-Hao; Lee, Hsing-Chung; Ling, Qingdong; Chen, Hsiao-Rong; Ko, Yi-An; Tsou, Tsong-Shan; Wang, Sun-Chong; Wu, Li-Ching; Lee, H C

    2011-07-01

    Detection of copy number variation (CNV) in DNA has recently become an important method for understanding the pathogenesis of cancer. While existing algorithms for extracting CNV from microarray data have worked reasonably well, the trend towards ever larger sample sizes and higher resolution microarrays has vastly increased the challenges they face. Here, we present Segmentation analysis of DNA (SAD), a clustering algorithm constructed with a strategy in which all operational decisions are based on simple and rigorous applications of statistical principles, measurement theory and precise mathematical relations. Compared with existing packages, SAD is simpler in formulation, more user friendly, much faster and less thirsty for memory, offers higher accuracy and supplies quantitative statistics for its predictions. Unique among such algorithms, SAD's running time scales linearly with array size; on a typical modern notebook, it completes high-quality CNV analyses for a 250 thousand-probe array in ∼1 s and a 1.8 million-probe array in ∼8 s.

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

    Directory of Open Access Journals (Sweden)

    Zadeh Soheila

    2010-07-01

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

  18. High-Resolution Analysis of Gene Copy Number Alterations in Human Prostate Cancer Using CGH on cDNA Microarrays: Impact of Copy Number on Gene Expression

    Directory of Open Access Journals (Sweden)

    Maija Wolf

    2004-05-01

    Full Text Available Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied high-resolution comparative genomic hybridization (CGH on cDNA microarrays for analysis of prostate cancer cell lines. CGH microarrays identified most of the alterations detected by classical chromosomal CGH, as well as a number of previously unreported alterations. Specific recurrent regions of gain (28 and loss (18 were found, their boundaries defined with sub-megabasepair accuracy. The most common changes included copy number decreases at 13% and gains at iq and 5p. Refined mapping identified several sites, such as at 13q (33-44, 49-51, 74-76 Mbp from the p-telomere, which matched with minimal regions of loss seen in extensive loss of heterozygosity mapping studies of large numbers of tumors. Previously unreported recurrent changes were found at 2p, 2q, 3p, 17q (losses, at 3q, 5p, 6p (gains. Integration of genomic and transcriptomic data revealed the role of individual candidate target genes for genomic alterations as well as a highly significant (P < .0001 overall association between copy number levels and the percentage of differentially expressed genes. Across the genome, the overall impact of copy number on gene expression levels was, to a large extent, attributable to low-level gains and losses of copy number, corresponding to common deletions and gains of often large chromosomal regions.

  19. Column Grid Array Rework for High Reliability

    Science.gov (United States)

    Mehta, Atul C.; Bodie, Charles C.

    2008-01-01

    Due to requirements for reduced size and weight, use of grid array packages in space applications has become common place. To meet the requirement of high reliability and high number of I/Os, ceramic column grid array packages (CCGA) were selected for major electronic components used in next MARS Rover mission (specifically high density Field Programmable Gate Arrays). ABSTRACT The probability of removal and replacement of these devices on the actual flight printed wiring board assemblies is deemed to be very high because of last minute discoveries in final test which will dictate changes in the firmware. The questions and challenges presented to the manufacturing organizations engaged in the production of high reliability electronic assemblies are, Is the reliability of the PWBA adversely affected by rework (removal and replacement) of the CGA package? and How many times can we rework the same board without destroying a pad or degrading the lifetime of the assembly? To answer these questions, the most complex printed wiring board assembly used by the project was chosen to be used as the test vehicle, the PWB was modified to provide a daisy chain pattern, and a number of bare PWB s were acquired to this modified design. Non-functional 624 pin CGA packages with internal daisy chained matching the pattern on the PWB were procured. The combination of the modified PWB and the daisy chained packages enables continuity measurements of every soldered contact during subsequent testing and thermal cycling. Several test vehicles boards were assembled, reworked and then thermal cycled to assess the reliability of the solder joints and board material including pads and traces near the CGA. The details of rework process and results of thermal cycling are presented in this paper.

  20. Construction of thiostrepton-inducible, high-copy-number expression vectors for use in Streptomyces spp.

    NARCIS (Netherlands)

    Takano, Eriko; White, Janet; Thompson, Charles J.; Bibb, Mervyn J.

    1995-01-01

    A high-copy-number plasmid expression vector (pIJ6021) was constructed that contains a thiostrepton-inducible promoter, PtipA, from Streptomyces lividans 66. The promoter and ribosome-binding site of tipA lie immediately upstream from a multiple cloning site (MCS) which begins with a NdeI site (5'-C

  1. Targeted array comparative genomic hybridization--a new diagnostic tool for the detection of large copy number variations in nemaline myopathy-causing genes.

    Science.gov (United States)

    Kiiski, K; Laari, L; Lehtokari, V-L; Lunkka-Hytönen, M; Angelini, C; Petty, R; Hackman, P; Wallgren-Pettersson, C; Pelin, K

    2013-01-01

    Nemaline myopathy (NM) constitutes a heterogeneous group of congenital myopathies. Mutations in the nebulin gene (NEB) are the main cause of recessively inherited NM. NEB is one of the most largest genes in human. To date, 68 NEB mutations, mainly small deletions or point mutations have been published. The only large mutation characterized is the 2.5 kb deletion of exon 55 in the Ashkenazi Jewish population. To investigate any copy number variations in this enormous gene, we designed a novel custom comparative genomic hybridization microarray, NM-CGH, targeted towards the seven known genes causative for NM. During the validation of the NM-CGH array we identified two novel deletions in two different families. The first is the largest deletion characterized in NEB to date, (∼53 kb) encompassing 24 exons. The second deletion (1 kb) covers two exons. In both families, the copy number change was the second mutation to be characterized and shown to have been inherited from one of the healthy carrier parents. In addition to these novel mutations, copy number variation was identified in four samples in three families in the triplicate region of NEB. We conclude that this method appears promising for the detection of copy number variations in NEB. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Copy-Number Variations Observed in a Japanese Population by BAC Array CGH: Summary of Relatively Rare CNVs

    Directory of Open Access Journals (Sweden)

    Yasunari Satoh

    2012-01-01

    Full Text Available Copy-number variations (CNVs may contribute to genetic variation in humans. Reports regarding existence and characteristics of CNVs in a large apparently healthy Japanese cohort are quite limited. We report the data from a screening of 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC aCGH. In a previous paper, we summarized the data by focusing on highly polymorphic CNVs (in ≥5.0 % of the individuals. However, rare variations have recently received attention from scientists who espouse a hypothesis called “common disease and rare variants.” Here, we report CNVs identified in fewer than 10 individuals in our study population. We found a total of 126 CNVs at 52 different BAC regions in the genome. The CNVs observed at 27 of the 52 BAC-regions were found in only one unrelated individual. The majority of CNVs found in this study were not identified in the Japanese who were examined in the other studies. Family studies were conducted, and the results demonstrated that the CNVs were inherited from one parent in the families.

  3. A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements.

    Directory of Open Access Journals (Sweden)

    Jason E Chan

    2011-05-01

    Full Text Available Ty elements are high copy number, dispersed repeated sequences in the Saccharomyces cerevisiae genome known to mediate gross chromosomal rearrangements (GCRs. Here we found that introduction of Ty912, a previously identified Ty1 element, onto the non-essential terminal region of the left arm of chromosome V led to a 380-fold increase in the rate of accumulating GCRs in a wild-type strain. A survey of 48 different mutations identified those that either increased or decreased the rate of Ty-mediated GCRs and demonstrated that suppression of Ty-mediated GCRs differs from that of both low copy repeat sequence- and single copy sequence-mediated GCRs. The majority of the Ty912-mediated GCRs observed were monocentric nonreciprocal translocations mediated by RAD52-dependent homologous recombination (HR between Ty912 and a Ty element on another chromosome arm. The remaining Ty912-mediated GCRs appeared to involve Ty912-mediated formation of unstable dicentric translocation chromosomes that were resolved by one or more Ty-mediated breakage-fusion-bridge cycles. Overall, the results demonstrate that the Ty912-mediated GCR assay is an excellent model for understanding mechanisms and pathways that suppress genome rearrangements mediated by high copy number repeat sequences, as well as the mechanisms by which such rearrangements occur.

  4. High copy number of mitochondrial DNA predicts poor prognosis in patients with advanced stage colon cancer.

    Science.gov (United States)

    Wang, Yun; He, Shuixiang; Zhu, Xingmei; Qiao, Wei; Zhang, Juan

    2016-12-23

    The aim of this investigation was to determine whether alterations in mitochondrial DNA (mtDNA) copy number in colon cancer were associated with clinicopathological parameters and postsurgical outcome. By quantitative real-time PCR assay, the mtDNA copy number was detected in a cohort of colon cancer and matched adjacent colon tissues (n = 162). The majority of patients had higher mtDNA content in colon cancer tissues than matched adjacent colon tissues. Moreover, high mtDNA content in tumor tissues was associated with larger tumor size, higher serum CEA level, advanced TNM stage, vascular emboli, and liver metastases. Further survival curve analysis showed that high mtDNA content was related to the worst survival in patients with colon cancer at advanced TNM stage. High mtDNA content is a potential effective factor of poor prognosis in patients with advanced stage colon cancer.

  5. Array-based comparative genomic hybridization analysis reveals chromosomal copy number aberrations associated with clinical outcome in canine diffuse large B-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Arianna Aricò

    Full Text Available Canine Diffuse Large B-cell Lymphoma (cDLBCL is an aggressive cancer with variable clinical response. Despite recent attempts by gene expression profiling to identify the dog as a potential animal model for human DLBCL, this tumor remains biologically heterogeneous with no prognostic biomarkers to predict prognosis. The aim of this work was to identify copy number aberrations (CNAs by high-resolution array comparative genomic hybridization (aCGH in 12 dogs with newly diagnosed DLBCL. In a subset of these dogs, the genetic profiles at the end of therapy and at relapse were also assessed. In primary DLBCLs, 90 different genomic imbalances were counted, consisting of 46 gains and 44 losses. Two gains in chr13 were significantly correlated with clinical stage. In addition, specific regions of gains and losses were significantly associated to duration of remission. In primary DLBCLs, individual variability was found, however 14 recurrent CNAs (>30% were identified. Losses involving IGK, IGL and IGH were always found, and gains along the length of chr13 and chr31 were often observed (>41%. In these segments, MYC, LDHB, HSF1, KIT and PDGFRα are annotated. At the end of therapy, dogs in remission showed four new CNAs, whereas three new CNAs were observed in dogs at relapse compared with the previous profiles. One ex novo CNA, involving TCR, was present in dogs in remission after therapy, possibly induced by the autologous vaccine. Overall, aCGH identified small CNAs associated with outcome, which, along with future expression studies, may reveal target genes relevant to cDLBCL.

  6. Quadruplex MAPH: improvement of throughput in high-resolution copy number screening

    Directory of Open Access Journals (Sweden)

    Walker Susan

    2009-09-01

    Full Text Available Abstract Background Copy number variation (CNV in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way. Results Multiplex Amplifiable Probe Hybridisation (MAPH is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH" that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC samples. Conclusion QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms.

  7. A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP array

    Directory of Open Access Journals (Sweden)

    Bailey Dione K

    2007-05-01

    Full Text Available Abstract Background DNA copy number aberration (CNA is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH, the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required. Results We have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step. Conclusion Using simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data.

  8. Acoustic trapping with a high frequency linear phased array

    OpenAIRE

    Zheng, Fan; Ying LI; Hsu, Hsiu-Sheng; Liu, Changgeng; Tat Chiu, Chi; Lee, Changyang; Ham Kim, Hyung; Shung, K. Kirk

    2012-01-01

    A high frequency ultrasonic phased array is shown to be capable of trapping and translating microparticles precisely and efficiently, made possible due to the fact that the acoustic beam produced by a phased array can be both focused and steered. Acoustic manipulation of microparticles by a phased array is advantageous over a single element transducer since there is no mechanical movement required for the array. Experimental results show that 45 μm diameter polystyrene microspheres can be eas...

  9. Novel high- and low-copy stable cosmids for use in Agrobacterium and Rhizobium.

    Science.gov (United States)

    Gallie, D R; Novak, S; Kado, C I

    1985-09-01

    Presented are a set of cosmids based on the unit copy Agrobacterium plasmid, pTAR, and the high-copy-number mutant plasmid, pUCD500, of pTiC58. The addition of a par function derived from pTAR to the vectors allowed them to be stably maintained throughout the cell population in the absence of selective pressure. These vectors, designed for Agrobacterium and Rhizobium, also work in Escherichia coli. The vectors can be cotransferred to Rhizobiaceae from E. coli with the helper plasmid, pRK2013. The pTiC58 origin containing vectors, pUCD1000 and pUCD1001 were found to be incompatible with a 250-kb plasmid harbored by R. meliloti RM102Z1. RM102Z1(pUCD1000) was still capable of nodulating roots in alfalfa.

  10. Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification.

    Science.gov (United States)

    Stokes, Angela; Drozdov, Ignat; Guerra, Eliete; Ouzounis, Christos A; Warnakulasuriya, Saman; Gleeson, Michael J; McGurk, Mark; Tavassoli, Mahvash; Odell, Edward W

    2011-01-01

    The requirement for large amounts of good quality DNA for whole-genome applications prohibits their use for small, laser capture micro-dissected (LCM), and/or rare clinical samples, which are also often formalin-fixed and paraffin-embedded (FFPE). Whole-genome amplification of DNA from these samples could, potentially, overcome these limitations. However, little is known about the artefacts introduced by amplification of FFPE-derived DNA with regard to genotyping, and subsequent copy number and loss of heterozygosity (LOH) analyses. Using a ligation adaptor amplification method, we present data from a total of 22 Affymetrix SNP 6.0 experiments, using matched paired amplified and non-amplified DNA from 10 LCM FFPE normal and dysplastic oral epithelial tissues, and an internal method control. An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples, and concordance was a promising 82.4%. Paired analysis for copy number, LOH, and both combined, showed that copy number changes were reduced in amplified DNA, but were 99.5% concordant when detected, amplifications were the changes most likely to be 'missed', only 30% of non-amplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined ∼50% of gene changes detected in the unamplified DNA were also detected in the amplified DNA and within these changes, 86.5% were concordant for both copy number and LOH status. However, there are also changes introduced as ∼20% of changes in the amplified DNA are not detected in the non-amplified DNA. An integrative network biology approach revealed that changes in amplified DNA of dysplastic oral epithelium localize to topologically critical regions of the human protein-protein interaction network, suggesting their functional implication in the pathobiology of this disease. Taken together, our results support the use of amplification of FFPE-derived DNA, provided sufficient samples are used to increase power

  11. High-Performance, Multi-Node File Copies and Checksums for Clustered File Systems

    Science.gov (United States)

    Kolano, Paul Z.; Ciotti, Robert B.

    2012-01-01

    Modern parallel file systems achieve high performance using a variety of techniques, such as striping files across multiple disks to increase aggregate I/O bandwidth and spreading disks across multiple servers to increase aggregate interconnect bandwidth. To achieve peak performance from such systems, it is typically necessary to utilize multiple concurrent readers/writers from multiple systems to overcome various singlesystem limitations, such as number of processors and network bandwidth. The standard cp and md5sum tools of GNU coreutils found on every modern Unix/Linux system, however, utilize a single execution thread on a single CPU core of a single system, and hence cannot take full advantage of the increased performance of clustered file systems. Mcp and msum are drop-in replacements for the standard cp and md5sum programs that utilize multiple types of parallelism and other optimizations to achieve maximum copy and checksum performance on clustered file systems. Multi-threading is used to ensure that nodes are kept as busy as possible. Read/write parallelism allows individual operations of a single copy to be overlapped using asynchronous I/O. Multinode cooperation allows different nodes to take part in the same copy/checksum. Split-file processing allows multiple threads to operate concurrently on the same file. Finally, hash trees allow inherently serial checksums to be performed in parallel. Mcp and msum provide significant performance improvements over standard cp and md5sum using multiple types of parallelism and other optimizations. The total speed-ups from all improvements are significant. Mcp improves cp performance over 27x, msum improves md5sum performance almost 19x, and the combination of mcp and msum improves verified copies via cp and md5sum by almost 22x. These improvements come in the form of drop-in replacements for cp and md5sum, so are easily used and are available for download as open source software at http://mutil.sourceforge.net.

  12. Acoustic trapping with a high frequency linear phased array.

    Science.gov (United States)

    Zheng, Fan; Li, Ying; Hsu, Hsiu-Sheng; Liu, Changgeng; Tat Chiu, Chi; Lee, Changyang; Ham Kim, Hyung; Shung, K Kirk

    2012-11-19

    A high frequency ultrasonic phased array is shown to be capable of trapping and translating microparticles precisely and efficiently, made possible due to the fact that the acoustic beam produced by a phased array can be both focused and steered. Acoustic manipulation of microparticles by a phased array is advantageous over a single element transducer since there is no mechanical movement required for the array. Experimental results show that 45 μm diameter polystyrene microspheres can be easily and accurately trapped and moved to desired positions by a 64-element 26 MHz phased array.

  13. High performance compound semiconductor SPAD arrays

    Science.gov (United States)

    Harmon, Eric S.; Naydenkov, Mikhail; Bowling, Jared

    2016-05-01

    Aggregated compound semiconductor single photon avalanche diode (SPAD) arrays are emerging as a viable alternative to the silicon photomultiplier (SiPM). Compound semiconductors have the potential to surpass SiPM performance, potentially achieving orders of magnitude lower dark count rates and improved radiation hardness. New planar processing techniques have been developed to enable compound semiconductor SPAD devices to be produced with pixel pitches of 11 - 25 microns, with thousands of SPADs per array.

  14. Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization

    Institute of Scientific and Technical Information of China (English)

    LIAO Can; FU Fang; YANG Xin; SUN Yi-min; LI Dong-zhi

    2011-01-01

    Background Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis.Methods Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction.Results All the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene.Conclusions The results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

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

    Directory of Open Access Journals (Sweden)

    Goldstein Alisa M

    2006-11-01

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

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

    Science.gov (United States)

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

    2011-03-01

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

  17. Piezoresistive Probe Array for High Throughput Applications

    NARCIS (Netherlands)

    Gaitas, A.; French, P.

    2011-01-01

    Microcantilevers are used in a number of applications including atomic-force microscopy (AFM). In this work, piezoresistive deflection-sensing elements are integrated onto micromachined cantilevers to increase sensitivity, and reduce complexity and cost. An array of probes with 5 nm gold ultrathin f

  18. Research of High Sensitivity Uncooled Infrared Detector Array

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Pingchuan [Huazhong University of Science and Technology, Wuhan 430074 (China); Zhang, Bo, E-mail: redmoon123456@126.com, E-mail: lhzyzb@126.com [Luohe Vocational Technology College, Luohe 462002 (China)

    2011-02-01

    The infrared thermal imaging technology has been widely used in military and civilian fields and the field of the infrared detection and infrared thermal imaging technology has been of concern for a long time. On infrared thermal imaging, its core components for the infrared focal plane arrays, how to develop a high sensitivity of the multi-focal plane infrared detector is a key issue. Although the Common focal plane array of quantum has high sensitivity, but it requires low temperature cooling work environment and led to complexity and high cost, difficult to compact. Conventional uncooled infrared focal plane array is contrast to the quantum focal plane arrays. Therefore, this article preceded by the uncooled infrared detector array to improve the wide temperature sensitivity in examining the feasibility PMN composite film, materials composition, structure design and preparation process technology.

  19. High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

    Science.gov (United States)

    Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

    2012-01-01

    Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

  20. High quality genomic copy number data from archival formalin-fixed paraffin-embedded leiomyosarcoma: optimisation of universal linkage system labelling.

    Science.gov (United States)

    Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

    2012-01-01

    Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment.

  1. High quality genomic copy number data from archival formalin-fixed paraffin-embedded leiomyosarcoma: optimisation of universal linkage system labelling.

    Directory of Open Access Journals (Sweden)

    Abdulazeez Salawu

    Full Text Available Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels. Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment.

  2. High Power Fiber Bundle Array Coupled LDA Module

    Institute of Scientific and Technical Information of China (English)

    QU Zhou; LIU Yang; ZHAO Chong-guang; WANG Ji; YIN Hong-he; WANG Li-jun

    2006-01-01

    An optical fiber bundle array coupling module with high output power is presented in this paper. The device integrated the coupling technique of the high power laser diode array (LDA) and the micro-ball lenses fiber array. This module can efficiently couple the output laser of the LDA into 19 fibers array with micro-ball lens endsurface. The difference of the couple efficiency between the flat-end fiber and micro-ball-end fiber is discussed.The micro-ball lenses fiber array made of 19 fibers have the same fiber core diameter of 200 μm, and then the endsurfaces of 19 fibers are fused to 19 micro-ball lenses. The micro-ball lenses fiber array are fixed precisely in the neighborhood on the V-grooves, and the fiber array has the same arrange period with the semiconductor laser units of LDA. This configuration of micro-ball lens fiber array can greatly reduce the divergence of the laser beam from all directions, and a very efficient laser beam homogenizer and shaper are obtained. Finally, high output power of 30.1 W of the fiber coupled LDA is achieved, and the maximal coupling efficiency is >83% with the numeral aperture (NA) of 0.16.

  3. Affordable High Performance Electromagnetically Clean Solar Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose an Electromagnetically Clean Solar Array (ECSA) with enhanced performance, in Watts/kg and Watts/m2, using flight proven, high efficiency solar cells. For...

  4. Modular Ultra-High Power Solar Array Architecture Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Deployable Space Systems, Inc. (DSS) will focus the proposed SBIR program on the development of a new highly-modularized and extremely-scalable solar array that...

  5. Identification of rare recurrent copy number variants in high-risk autism families and their prevalence in a large ASD population.

    Directory of Open Access Journals (Sweden)

    Nori Matsunami

    Full Text Available Structural variation is thought to play a major etiological role in the development of autism spectrum disorders (ASDs, and numerous studies documenting the relevance of copy number variants (CNVs in ASD have been published since 2006. To determine if large ASD families harbor high-impact CNVs that may have broader impact in the general ASD population, we used the Affymetrix genome-wide human SNP array 6.0 to identify 153 putative autism-specific CNVs present in 55 individuals with ASD from 9 multiplex ASD pedigrees. To evaluate the actual prevalence of these CNVs as well as 185 CNVs reportedly associated with ASD from published studies many of which are insufficiently powered, we designed a custom Illumina array and used it to interrogate these CNVs in 3,000 ASD cases and 6,000 controls. Additional single nucleotide variants (SNVs on the array identified 25 CNVs that we did not detect in our family studies at the standard SNP array resolution. After molecular validation, our results demonstrated that 15 CNVs identified in high-risk ASD families also were found in two or more ASD cases with odds ratios greater than 2.0, strengthening their support as ASD risk variants. In addition, of the 25 CNVs identified using SNV probes on our custom array, 9 also had odds ratios greater than 2.0, suggesting that these CNVs also are ASD risk variants. Eighteen of the validated CNVs have not been reported previously in individuals with ASD and three have only been observed once. Finally, we confirmed the association of 31 of 185 published ASD-associated CNVs in our dataset with odds ratios greater than 2.0, suggesting they may be of clinical relevance in the evaluation of children with ASDs. Taken together, these data provide strong support for the existence and application of high-impact CNVs in the clinical genetic evaluation of children with ASD.

  6. Telescoping Solar Array Concept for Achieving High Packaging Efficiency

    Science.gov (United States)

    Mikulas, Martin; Pappa, Richard; Warren, Jay; Rose, Geoff

    2015-01-01

    Lightweight, high-efficiency solar arrays are required for future deep space missions using high-power Solar Electric Propulsion (SEP). Structural performance metrics for state-of-the art 30-50 kW flexible blanket arrays recently demonstrated in ground tests are approximately 40 kW/cu m packaging efficiency, 150 W/kg specific power, 0.1 Hz deployed stiffness, and 0.2 g deployed strength. Much larger arrays with up to a megawatt or more of power and improved packaging and specific power are of interest to mission planners for minimizing launch and life cycle costs of Mars exploration. A new concept referred to as the Compact Telescoping Array (CTA) with 60 kW/cu m packaging efficiency at 1 MW of power is described herein. Performance metrics as a function of array size and corresponding power level are derived analytically and validated by finite element analysis. Feasible CTA packaging and deployment approaches are also described. The CTA was developed, in part, to serve as a NASA reference solar array concept against which other proposed designs of 50-1000 kW arrays for future high-power SEP missions could be compared.

  7. High Glucose-Induced Oxidative Stress Increases the Copy Number of Mitochondrial DNA in Human Mesangial Cells

    Directory of Open Access Journals (Sweden)

    Ghada Al-Kafaji

    2013-01-01

    Full Text Available Oxidative damage to mitochondrial DNA (mtDNA has been linked to the pathogenicity of diabetic nephropathy. We tested the hypothesis that mtDNA copy number may be increased in human mesangial cells in response to high glucose-induced reactive oxygen species (ROS to compensate for damaged mtDNA. The effect of manganese superoxide dismutase mimetic (MnTBAP on glucose-induced mtDNA copy number was also examined. The copy number of mtDNA was determined by real-time PCR in human mesangial cells cultured in 5 mM glucose, 25 mM glucose, and mannitol (osmotic control, as well as in cells cultured in 25 mM glucose in the presence and absence of 200 μM MnTBAP. Intracellular ROS was assessed by confocal microscopy and flow cytometry in human mesangial cells. The copy number of mtDNA was significantly increased when human mesangial cells were incubated with 25 mM glucose compared to 5 mM glucose and mannitol. In addition, 25 mM glucose rapidly generated ROS in the cells, which was not detected in 5 mM glucose. Furthermore, mtDNA copy number was significantly decreased and maintained to normal following treatment of cells with 25 mM glucose and MnTBAP compared to 25 mM glucose alone. Inclusion of MnTBAP during 25 mM glucose incubation inhibited mitochondrial superoxide in human mesangial cells. Increased mtDNA copy number in human mesangial cells by high glucose could contribute to increased mitochondrial superoxide, and prevention of mtDNA copy number could have potential in retarding the development of diabetic nephropathy.

  8. Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays

    Directory of Open Access Journals (Sweden)

    Malloff Chad A

    2004-01-01

    Full Text Available Abstract Background The recent development of array based comparative genomic hybridization (CGH technology provides improved resolution for detection of genomic DNA copy number alterations. In array CGH, generating spotting solution is a multi-step process where bacterial artificial chromosome (BAC clones are converted to replenishable PCR amplified fragments pools (AFP for use as spotting solution in a microarray format on glass substrate. With completion of the human and mouse genome sequencing, large BAC clone sets providing complete genome coverage are available for construction of whole genome BAC arrays. Currently, Southern hybridization, fluorescent in-situ hybridization (FISH, and BAC end sequencing methods are commonly used to identify the initial BAC clone but not the end product used for spotting arrays. The AFP sequencing technique described in this study is a novel method designed to verify the identity of array spotting solution in a high throughput manner. Results We show here that Southern hybridization, FISH, and AFP sequencing can be used to verify the identity of final spotting solutions using less than 10% of the AFP product. Single pass AFP sequencing identified over half of the 960 AFPs analyzed. Moreover, using two vector primers approximately 90% of the AFP spotting solutions can be identified. Conclusions In this feasibility study we demonstrate that current methods for identifying initial BAC clones can be adapted to verify the identity of AFP spotting solutions used in printing arrays. Of these methods, AFP sequencing proves to be the most efficient for large scale identification of spotting solution in a high throughput manner.

  9. GaN Nanowire Arrays for High-Output Nanogenerators

    KAUST Repository

    Huang, Chi-Te

    2010-04-07

    Three-fold symmetrically distributed GaN nanowire (NW) arrays have been epitaxially grown on GaN/sapphire substrates. The GaN NW possesses a triangular cross section enclosed by (0001), (2112), and (2112) planes, and the angle between the GaN NW and the substrate surface is ∼62°. The GaN NW arrays produce negative output voltage pulses when scanned by a conductive atomic force microscope in contact mode. The average of piezoelectric output voltage was about -20 mV, while 5-10% of the NWs had piezoelectric output voltages exceeding -(0.15-0.35) V. The GaN NW arrays are highly stable and highly tolerate to moisture in the atmosphere. The GaN NW arrays demonstrate an outstanding potential to be utilized for piezoelectric energy generation with a performance probably better than that of ZnO NWs. © 2010 American Chemical Society.

  10. Photolithographic Approaches for Fabricating Highly Ordered Nanopatterned Arrays

    Directory of Open Access Journals (Sweden)

    Li Xiaoru

    2008-01-01

    Full Text Available Abstract In this work, we report that large area metal nanowire and polymer nanotube arrays were successfully patterned by photolithographic approach using anodic aluminum oxide (AAO templates. Nanowires were produced by electrochemical deposition, and nanotubes by solution-wetting. The highly ordered patterns of nanowire and nanotube arrays were observed using scanning electron microscopy (SEM and found to stand free on the substrate. The method is expected to play an important role in the application of microdevices in the future.

  11. Temperature-Modulated Array High-Performance Liquid Chromatography

    OpenAIRE

    Premstaller, Andreas; Xiao, Wenzhong; Oberacher, Herbert; O'Keefe, Matthew; Stern, David; Willis, Thomas; Huber, Christian G.; Peter J. Oefner

    2001-01-01

    Using novel monolithic poly(styrene-divinylbenzene) capillary columns with an internal diameter of 0.2 mm, we demonstrate for the first time the feasibility of constructing high-performance liquid chromatography arrays for the detection of mutations by heteroduplex analysis under partially denaturing conditions. In one embodiment, such an array can be used to analyze one sample simultaneously at different temperatures to maximize the detection of mutations in DNA fragments containing multiple...

  12. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  13. Finite difference programs and array processors. [High-speed floating point processing by coupling host computer to programable array processor

    Energy Technology Data Exchange (ETDEWEB)

    Rudy, T.E.

    1977-08-01

    An alternative to maxi computers for high-speed floating-point processing capabilities is the coupling of a host computer to a programable array processor. This paper compares the performance of two finite difference programs on various computers and their expected performance on commercially available array processors. The significance of balancing array processor computation, host-array processor control traffic, and data transfer operations is emphasized. 3 figures, 1 table.

  14. Low profile conformal antenna arrays on high impedance substrate

    CERN Document Server

    Singh, Hema; Jha, Rakesh Mohan

    2016-01-01

    This book presents electromagnetic (EM) design and analysis of dipole antenna array over high impedance substrate (HIS). HIS is a preferred substrate for low-profile antenna design, owing to its unique boundary conditions. Such substrates permit radiating elements to be printed on them without any disturbance in the radiation characteristics. Moreover HIS provides improved impedance matching, enhanced bandwidth, and increased broadside directivity owing to total reflection from the reactive surface and high input impedance. This book considers different configurations of HIS for array design on planar and non-planar high-impedance surfaces. Results are presented for cylindrical dipole, printed dipole, and folded dipole over single- and double-layered square-patch-based HIS and dogbone-based HIS. The performance of antenna arrays is analyzed in terms of performance parameters such as return loss and radiation pattern. The design presented shows acceptable return loss and mainlobe gain of radiation pattern. Thi...

  15. High-Temperature Gas Sensor Array (Electronic Nose) Demonstrated

    Science.gov (United States)

    Hunter, Gary W.

    2002-01-01

    The ability to measure emissions from aeronautic engines and in commercial applications such as automotive emission control and chemical process monitoring is a necessary first step if one is going to actively control those emissions. One single sensor will not give all the information necessary to determine the chemical composition of a high-temperature, harsh environment. Rather, an array of gas sensor arrays--in effect, a high-temperature electronic "nose"--is necessary to characterize the chemical constituents of a diverse, high-temperature environment, such as an emissions stream. The signals produced by this nose could be analyzed to determine the constituents of the emission stream. Although commercial electronic noses for near-room temperature applications exist, they often depend significantly on lower temperature materials or only one sensor type. A separate development effort necessary for a high-temperature electronic nose is being undertaken by the NASA Glenn Research Center, Case Western Reserve University, Ohio State University, and Makel Engineering, Inc. The sensors are specially designed for hightemperature environments. A first-generation high-temperature electronic nose has been demonstrated on a modified automotive engine. This nose sensor array was composed of sensors designed for hightemperature environments fabricated using microelectromechanical-systems- (MEMS-) based technology. The array included a tin-oxide-based sensor doped for nitrogen oxide (NOx) sensitivity, a SiC-based hydrocarbon (CxHy) sensor, and an oxygen sensor (O2). These sensors operate on different principles--resistor, diode, and electrochemical cell, respectively--and each sensor has very different responses to the individual gases in the environment. A picture showing the sensor head for the array is shown in the photograph on the left and the sensors installed in the engine are shown in the photograph on the right. Electronics are interfaced with the sensors for

  16. High-density SNP arrays improve detection of HER2 amplification and polyploidy in breast tumors

    DEFF Research Database (Denmark)

    Hansen, Thomas V. O.; Vikesaa, Jonas; Buhl, Sine S

    2015-01-01

    ) arrays can provide additional diagnostic power to assess HER2 gene status. METHODS: DNA from 65 breast tumor samples previously diagnosed by HER2 IHC and FISH analysis were blinded and examined for HER2 copy number variation employing SNP array analysis. RESULTS: SNP array analysis identified 24 (37......%) samples with selective amplification or imbalance of the HER2 region in the q-arm of chromosome 17. In contrast, only 15 (23%) tumors were found to have HER2 amplification by IHC and FISH analysis. In total, there was a discrepancy in 19 (29%) samples between SNP array and IHC/FISH analysis. In 12...

  17. The Telescope Array Ultra High Energy Cosmic Ray Obsrevatory

    Science.gov (United States)

    Matthews, John

    2016-07-01

    The Telescope Array measures the properties of ultra high energy cosmic ray induced extensive air showers. We do this using a variety of techniques including an array of scintillator detectors to sample the footprint of the air shower when it reaches the Earth's surface and telescopes to measure the fluorescence and Cerenkov light of the air shower. From this we determine the energy spectrum and chemical composition of the primary particles. We also search for sources of cosmic rays and anisotropy. We have found evidence of a possible source of ultra high energy cosmic rays in the northern sky. The experiment and its most recent measurements will be discussed.

  18. Original Copies

    DEFF Research Database (Denmark)

    Sørensen, Tim Flohr

    2013-01-01

    of similarity by looking at artefactual similarity as the results of prototyping and as a production of simulacra. In this light, the concept of copying turns out to be more than simply a matter of trying to imitate an exotic or prestigious original, and it fundamentally raises the question how different a copy...

  19. Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin.

    Science.gov (United States)

    Guelker, Megan; Stagg, Loren; Wittung-Stafshede, Pernilla; Shamoo, Yousif

    2009-06-01

    The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3(1)21 and P4(3), at 2.5 and 2.0 A resolution, respectively. Structure determination in space group P3(1)21 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3(1)21 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P4(3), which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3(1)21 crystal form. During the early stages of refinement, application of the appropriate twin law, (-h, -k, l), was required to converge to reasonable R-factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition.

  20. Impact of Solar Array Designs on High Voltage Operations

    Science.gov (United States)

    Brandhorst, Henry W., Jr.; Ferguson, Dale; Piszczor, Mike; ONeill, Mark

    2006-01-01

    As power levels of advanced spacecraft climb above 25 kW, higher solar array operating voltages become attractive. Even in today s satellites, operating spacecraft buses at 100 V and above has led to arcing in GEO communications satellites, so the issue of spacecraft charging and solar array arcing remains a design problem. In addition, micrometeoroid impacts on all of these arrays can also lead to arcing if the spacecraft is at an elevated potential. For example, tests on space station hardware disclosed arcing at 75V on anodized A1 structures that were struck with hypervelocity particles in Low Earth Orbit (LEO) plasmas. Thus an understanding of these effects is necessary to design reliable high voltage solar arrays of the future, especially in light of the Vision for Space Exploration of NASA. In the future, large GEO communication satellites, lunar bases, solar electric propulsion missions, high power communication systems around Mars can lead to power levels well above 100 kW. As noted above, it will be essential to increase operating voltages of the solar arrays well above 80 V to keep the mass of cabling needed to carry the high currents to an acceptable level. Thus, the purpose of this paper is to discuss various solar array approaches, to discuss the results of testing them at high voltages, in the presence of simulated space plasma and under hypervelocity impact. Three different types of arrays will be considered. One will be a planar array using thin film cells, the second will use planar single or multijunction cells and the last will use the Stretched Lens Array (SLA - 8-fold concentration). Each of these has different approaches for protection from the space environment. The thin film cell based arrays have minimal covering due to their inherent radiation tolerance, conventional GaAs and multijunction cells have the traditional cerium-doped microsheet glasses (of appropriate thickness) that are usually attached with Dow Corning DC 93-500 silicone

  1. High-power phase locking of a fiber amplifier array

    Science.gov (United States)

    Shay, T. M.; Baker, J. T.; Sanchez, A. D.; Robin, C. A.; Vergien, C. L.; Zeringue, C.; Gallant, D.; Lu, Chunte A.; Pulford, Benjamin; Bronder, T. J.; Lucero, Arthur

    2009-02-01

    We report high power phase locked fiber amplifier array using the Self-Synchronous Locking of Optical Coherence by Single-detector Electronic-frequency Tagging technique. We report the first experimental results for a five element amplifier array with a total locked power of more than 725-W. We will report on experimental measurements of the phase fluctuations versus time when the control loop is closed. The rms phase error was measured to be λ/60. Recent results will be reported. To the best of the authors' knowledge this is the highest fiber laser power to be coherently combined.

  2. High-level expression of Proteinase K from Tritirachium album Limber in Pichia pastoris using multi-copy expression strains.

    Science.gov (United States)

    Yang, Hu; Zhai, Chao; Yu, Xianhong; Li, Zhezhe; Tang, Wei; Liu, Yunyun; Ma, Xiaojian; Zhong, Xing; Li, Guolong; Wu, Di; Ma, Lixin

    2016-06-01

    Proteinase K is widely used in scientific research and industries. This report was aimed to achieve high-level expression of proteinase K using Pichia pastoris GS115 as the host strain. The coding sequence of a variant of proteinase K that has higher activity than the wild type protein was chosen and optimized based on the codon usage preference of P. pastoris. The novel open reading frame was synthesized and a series of multi-copy expression vectors were constructed based on the pHBM905BDM plasmid, allowing for the tandem integration of multiple copies of the target gene into the genome of P. pastoris with a single recombination. These strains were used to study the correlation between the gene copy number and the expression level of proteinase K. The results of quantitative polymerase chain reaction (qPCR) indicated that the tandem expression cassettes were integrated into the host genome stably. Meanwhile, the results of qPCR and enzyme activity assays indicated that the mRNA and protein expression levels of the target gene increased as the gene copy number increased. Moreover, the effect of gene dosage on the expression level of the recombinant protein was more obvious using high-density fermentation. The maximum expression level and enzyme activity of proteinase K, which were obtained from the recombinant yeast strain bearing 5 copies of the target gene after an 84-h induction, were approximately 8.069 mg/mL and 108,295 U/mL, respectively. The recombinant proteinase was purified and characterized. The optimum pH and temperature for the activity of this protease were approximately pH 11 and 55 °C, respectively.

  3. Ka-band MMIC microstrip array for high rate communications

    Science.gov (United States)

    Lee, R. Q.; Raquet, C. A.; Tolleson, J. B.; Sanzgiri, S. M.

    1991-01-01

    In a recent technology assessment of alternative communication systems for the space exploration initiative (SEI), Ka-band (18 to 40 GHz) communication technology was identified to meet the mission requirements of telecommunication, navigation, and information management. Compared to the lower frequency bands, Ka-band antennas offer higher gain and broader bandwidths; thus, they are more suitable for high data rate communications. Over the years, NASA has played an important role in monolithic microwave integrated circuit (MMIC) phased array technology development, and currently, has an ongoing contract with Texas Instrument (TI) to develop a modular Ka-band MMIC microstrip subarray (NAS3-25718). The TI contract emphasizes MMIC integration technology development and stipulates using existing MMIC devices to minimize the array development cost. The objective of this paper is to present array component technologies and integration techniques used to construct the subarray modules.

  4. Plasma Interaction with International Space Station High Voltage Solar Arrays

    Science.gov (United States)

    Heard, John W.

    2002-01-01

    The International Space Station (ISS) is presently being assembled in low-earth orbit (LEO) operating high voltage solar arrays (-160 V max, -140 V typical with respect to the ambient atmosphere). At the station's present altitude, there exists substantial ambient plasma that can interact with the solar arrays. The biasing of an object to an electric potential immersed in plasma creates a plasma "sheath" or non-equilibrium plasma around the object to mask out the electric fields. A positively biased object can collect electrons from the plasma sheath and the sheath will draw a current from the surrounding plasma. This parasitic current can enter the solar cells and effectively "short out" the potential across the cells, reducing the power that can be generated by the panels. Predictions of collected current based on previous high voltage experiments (SAMPIE (Solar Array Module Plasma Interactions Experiment), PASP+ (Photovoltaic Array Space Power) were on the order of amperes of current. However, present measurements of parasitic current are on the order of several milliamperes, and the current collection mainly occurs during an "eclipse exit" event, i.e., when the space station comes out of darkness. This collection also has a time scale, t approx. 1000 s, that is much slower than any known plasma interaction time scales. The reason for the discrepancy between predictions and present electron collection is not understood and is under investigation by the PCU (Plasma Contactor Unit) "Tiger" team. This paper will examine the potential structure within and around the solar arrays, and the possible causes and reasons for the electron collection of the array.

  5. The source of high signal cooperativity in bacterial chemosensory arrays.

    Science.gov (United States)

    Piñas, Germán E; Frank, Vered; Vaknin, Ady; Parkinson, John S

    2016-03-22

    The Escherichia coli chemosensory system consists of large arrays of transmembrane chemoreceptors associated with a dedicated histidine kinase, CheA, and a linker protein, CheW, that couples CheA activity to receptor control. The kinase activity responses to receptor ligand occupancy changes can be highly cooperative, reflecting allosteric coupling of multiple CheA and receptor molecules. Recent structural and functional studies have led to a working model in which receptor core complexes, the minimal units of signaling, are linked into hexagonal arrays through a unique interface 2 interaction between CheW and the P5 domain of CheA. To test this array model, we constructed and characterized CheA and CheW mutants with amino acid replacements at key interface 2 residues. The mutant proteins proved defective in interface 2-specific in vivo cross-linking assays, and formed signaling complexes that were dispersed around the cell membrane rather than clustered at the cell poles as in wild type chemosensory arrays. Interface 2 mutants down-regulated CheA activity in response to attractant stimuli in vivo, but with much less cooperativity than the wild type. Moreover, mutant cells containing fluorophore-tagged receptors exhibited greater basal anisotropy that changed rapidly in response to attractant stimuli, consistent with facile changes in loosely packed receptors. We conclude that interface 2 lesions disrupt important network connections between core complexes, preventing receptors from operating in large, allosteric teams. This work confirms the critical role of interface 2 in organizing the chemosensory array, in directing the clustered array to the cell poles, and in producing its highly cooperative signaling properties.

  6. High Density Planar High Temperature Superconducting Josephson Junctions Arrays

    Science.gov (United States)

    2006-09-01

    TIT,) 3 dependance . At lower temperatures it follows a (1 - T/T,)2 depen- dance ........ ................................... 57 4.7 Shapiro steps in...70 4.23 Dependance of the critical current for a ten junction array on mi- crowave power ..................................... 71 4.24 Resistance vs...GHz microwave radiation. (b) Microwave power dependance of the critical current and 1st-order Shapiro step. 76 5.2 (a) Single junction critical current

  7. Design and operation of a portable scanner for high performance microchip capillary array electrophoresis.

    Science.gov (United States)

    Scherer, James R; Liu, Peng; Mathies, Richard A

    2010-11-01

    We have developed a compact, laser-induced fluorescence detection scanner, the multichannel capillary array electrophoresis portable scanner (McCAEPs) as a platform for electrophoretic detection and control of high-throughput, integrated microfluidic devices for genetic and other analyses. The instrument contains a confocal optical system with a rotary objective for detecting four different fluorescence signals, a pneumatic system consisting of two pressure/vacuum pumps and 28 individual addressable solenoid valves for control of on-chip microvalves and micropumps, four Polymerase Chain Reaction (PCR) temperature control systems, and four high voltage power supplies for electrophoresis. The detection limit of the instrument is ~20 pM for on-chip capillary electrophoresis of fluorescein dyes. To demonstrate the system performance for forensic short tandem repeat (STR) analysis, two experiments were conducted: (i) electrophoretic separation and detection of STR samples on a 96-lane microfabricated capillary array electrophoresis microchip. Fully resolved PowerPlex(®) 16 STR profiles amplified from 1 ng of 9947A female standard DNA were successfully obtained; (ii) nine-plex STR amplification, sample injection, separation, and fluorescence detection of 100-copy 9948 male standard DNA in a single integrated PCR- capillary electrophoresis microchip. These results demonstrate that the McCAEPs can be used as a versatile control and detection instrument that operates integrated microfluidic devices for high-performance forensic human identification.

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

    Science.gov (United States)

    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.

  9. Achieving ultra-high temperatures with a resistive emitter array

    Science.gov (United States)

    Danielson, Tom; Franks, Greg; Holmes, Nicholas; LaVeigne, Joe; Matis, Greg; McHugh, Steve; Norton, Dennis; Vengel, Tony; Lannon, John; Goodwin, Scott

    2016-05-01

    The rapid development of very-large format infrared detector arrays has challenged the IR scene projector community to also develop larger-format infrared emitter arrays to support the testing of systems incorporating these detectors. In addition to larger formats, many scene projector users require much higher simulated temperatures than can be generated with current technology in order to fully evaluate the performance of their systems and associated processing algorithms. Under the Ultra High Temperature (UHT) development program, Santa Barbara Infrared Inc. (SBIR) is developing a new infrared scene projector architecture capable of producing both very large format (>1024 x 1024) resistive emitter arrays and improved emitter pixel technology capable of simulating very high apparent temperatures. During earlier phases of the program, SBIR demonstrated materials with MWIR apparent temperatures in excess of 1400 K. New emitter materials have subsequently been selected to produce pixels that achieve even higher apparent temperatures. Test results from pixels fabricated using the new material set will be presented and discussed. A 'scalable' Read In Integrated Circuit (RIIC) is also being developed under the same UHT program to drive the high temperature pixels. This RIIC will utilize through-silicon via (TSV) and Quilt Packaging (QP) technologies to allow seamless tiling of multiple chips to fabricate very large arrays, and thus overcome the yield limitations inherent in large-scale integrated circuits. Results of design verification testing of the completed RIIC will be presented and discussed.

  10. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae

    Directory of Open Access Journals (Sweden)

    Kevin Weitemier

    2015-01-01

    Full Text Available Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%. Most nrDNA positions (91% were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming.

  11. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)

    Science.gov (United States)

    Straub, Shannon C.K.; Fishbein, Mark; Liston, Aaron

    2015-01-01

    Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming). PMID:25653903

  12. Solar Array at Very High Temperatures: Ground Tests

    Science.gov (United States)

    Vayner, Boris

    2016-01-01

    Solar array design for any spacecraft is determined by the orbit parameters. For example, operational voltage for spacecraft in Low Earth Orbit (LEO) is limited by significant differential charging due to interactions with low temperature plasma. In order to avoid arcing in LEO, solar array is designed to generate electrical power at comparatively low voltages (below 100 volts) or to operate at higher voltages with encapsulation of all suspected discharge locations. In Geosynchronous Orbit (GEO) differential charging is caused by energetic electrons that produce differential potential between the coverglass and the conductive spacecraft body in a kilovolt range. In such a case, the weakly conductive layer over coverglass, indium tin oxide (ITO) is one of the possible measures to eliminate dangerous discharges on array surface. Temperature variations for solar arrays in both orbits are measured and documented within the range of minus150 degrees Centigrade to plus 1100 degrees Centigrade. This wide interval of operational temperatures is regularly reproduced in ground tests with radiative heating and cooling inside a shroud with flowing liquid nitrogen. The requirements to solar array design and tests turn out to be more complicated when planned trajectory crosses these two orbits and goes closer to the Sun. The conductive layer over coverglass causes a sharp increase in parasitic current collected from LEO plasma, high temperature may cause cracks in encapsulating (Room Temperature Vulcanizing (RTV) material; radiative heating of a coupon in vacuum chamber becomes practically impossible above 1500 degrees Centigrade; conductivities of glass and adhesive go up with temperature that decrease array efficiency; and mechanical stresses grow up to critical magnitudes. A few test arrangements and respective results are presented in current paper. Coupons were tested against arcing in simulated LEO and GEO environments under elevated temperatures up to 2000 degrees

  13. Custom CGH array profiling of copy number variations (CNVs on chromosome 6p21.32 (HLA locus in patients with venous malformations associated with multiple sclerosis

    Directory of Open Access Journals (Sweden)

    Salvi Fabrizio

    2010-04-01

    Full Text Available Abstract Background Multiple sclerosis (MS is a complex disorder thought to result from an interaction between environmental and genetic predisposing factors which have not yet been characterised, although it is known to be associated with the HLA region on 6p21.32. Recently, a picture of chronic cerebrospinal venous insufficiency (CCSVI, consequent to stenosing venous malformation of the main extra-cranial outflow routes (VM, has been described in patients affected with MS, introducing an additional phenotype with possible pathogenic significance. Methods In order to explore the presence of copy number variations (CNVs within the HLA locus, a custom CGH array was designed to cover 7 Mb of the HLA locus region (6,899,999 bp; chr6:29,900,001-36,800,000. Genomic DNA of the 15 patients with CCSVI/VM and MS was hybridised in duplicate. Results In total, 322 CNVs, of which 225 were extragenic and 97 intragenic, were identified in 15 patients. 234 known polymorphic CNVs were detected, the majority of these being situated in non-coding or extragenic regions. The overall number of CNVs (both extra- and intragenic showed a robust and significant correlation with the number of stenosing VMs (Spearman: r = 0.6590, p = 0.0104; linear regression analysis r = 0.6577, p = 0.0106. The region we analysed contains 211 known genes. By using pathway analysis focused on angiogenesis and venous development, MS, and immunity, we tentatively highlight several genes as possible susceptibility factor candidates involved in this peculiar phenotype. Conclusions The CNVs contained in the HLA locus region in patients with the novel phenotype of CCSVI/VM and MS were mapped in detail, demonstrating a significant correlation between the number of known CNVs found in the HLA region and the number of CCSVI-VMs identified in patients. Pathway analysis revealed common routes of interaction of several of the genes involved in angiogenesis and immunity contained within this region

  14. High-frequency ultrasonic arrays for ocular imaging

    Science.gov (United States)

    Jaeger, M. D.; Kline-Schoder, R. J.; Douville, G. M.; Gagne, J. R.; Morrison, K. T.; Audette, W. E.; Kynor, D. B.

    2007-03-01

    High-resolution ultrasound imaging of the anterior portion of the eye has been shown to provide important information for sizing of intraocular lens implants, diagnosis of pathological conditions, and creation of detailed maps of corneal topography to guide refractive surgery. Current ultrasound imaging systems rely on mechanical scanning of a single acoustic element over the surface of the eye to create the three-dimensional information needed by clinicians. This mechanical scanning process is time-consuming and subject to errors caused by eye movement during the scanning period. This paper describes development of linear ultrasound imaging arrays intended to increase the speed of image acquisition and reduce problems associated with ocular motion. The arrays consist of a linear arrangement of high-frequency transducer elements designed to operate in the 50 - 75 MHz frequency range. The arrays are produced using single-crystal lithium niobate piezoelectric material, thin film electrodes, and epoxy-based acoustic layers. The array elements have been used to image steel test structures and bovine cornea.

  15. Development of high frequency annular array ultrasound transducers

    Science.gov (United States)

    Gottlieb, Emanuel John

    The advantage of ultrasonic annular arrays over conventional single element transducers has been in the ability to transmit focus at multiple points throughout the depth of field, as well as receive dynamic focus. Today, annular, linear and multidimensional array imaging systems are not commercially available at frequencies greater than 20 MHz. The fabrication technology used to develop a high frequency (>50 MHz) annular array transducer is presented. A 9 mum P(VDF-TrFE) film was bonded to gold annuli electrodes on the top layer of a two sided polyimide flexible circuit. Each annulus was separated by a 30 mum kerf and had several electroplated micro vias that connected to electrode traces on the bottom side of the polyimide flexible circuit. The array's performance was evaluated by measuring the electrical impedance, pulse echo response and crosstalk measurement for each element in the array. In order to improve device sensitivity each element was electrically matched to an impedance magnitude of 50 O and 0° phase at resonance. The average round trip insertion loss measured for the array and compensated for diffraction effects was -33.5 dB. The measured average center frequency and bandwidth of an element was 55 MHz and 47 respectively. The measured crosstalk between adjacent elements remained below -29 dB at the center frequency in water. A vertical wire phantom was imaged using a single focus transmit beamformer and dynamic focusing receive beamformer. This image showed a significant improvement in lateral resolution over a range of 9 mm after the dynamic focusing receive algorithm was applied. These results correlated well with predictions from a Field II simulation. After beamforming the minimum lateral resolution (-6 dB) was 108 mum at the focus. Preliminary ultrasound B-mode images of the rabbit eye using this transducer were shown in conjunction with a multi-channel digital beamformer. A feasibility study of designing and fabricating tunable copolymer

  16. Highly Uniform Epitaxial ZnO Nanorod Arrays for Nanopiezotronics

    Directory of Open Access Journals (Sweden)

    Nagata T

    2009-01-01

    Full Text Available Abstract Highly uniform and c-axis-aligned ZnO nanorod arrays were fabricated in predefined patterns by a low temperature homoepitaxial aqueous chemical method. The nucleation seed patterns were realized in polymer and in metal thin films, resulting in, all-ZnO and bottom-contacted structures, respectively. Both of them show excellent geometrical uniformity: the cross-sectional uniformity according to the scanning electron micrographs across the array is lower than 2%. The diameter of the hexagonal prism-shaped nanorods can be set in the range of 90–170 nm while their typical length achievable is 0.5–2.3 μm. The effect of the surface polarity was also examined, however, no significant difference was found between the arrays grown on Zn-terminated and on O-terminated face of the ZnO single crystal. The transmission electron microscopy observation revealed the single crystalline nature of the nanorods. The current–voltage characteristics taken on an individual nanorod contacted by a Au-coated atomic force microscope tip reflected Schottky-type behavior. The geometrical uniformity, the designable pattern, and the electrical properties make the presented nanorod arrays ideal candidates to be used in ZnO-based DC nanogenerator and in next-generation integrated piezoelectric nano-electromechanical systems (NEMS.

  17. Stacked Polymer nanofiber array for high-performance supercapacitors

    Science.gov (United States)

    Wang, Shiren; Qiu, Jenny

    2015-03-01

    The vertically aligned polyaniline (PANI) nanowires arrays and monolayer graphene sheets were layer-by-layered deposited to specific substrate for tailored structures. Driven by external voltage, aniline molecules and graphene oxide were alternatively assembled for hierarchical porous three-dimensional nanostructures while graphene oxide was in-situ reduced to graphene during the assembly process. As-produced stacked arrays were used as the electrodes of an ultra-capacitor, and an unusual electrochemical behavior was discovered. The capacitance increases as the stack of nanowire arrays increases, resulting in high energy density and high power density at same time. Further analysis found that the distinctive electrochemical behavior originates from the electrode/electrolyte interactions and the dependence on the diffusion and charge transferring process. The specific energy density was as high as 137 Wh/Kg while power density is in excess of 2000 W/Kg. This work pointed a simple pathway to tailor polymer structure and electrochemistry for robust design of high-performance ultra-capacitor at a limited lateral size. National Science Foundation.

  18. Are there any more ovarian tumor suppressor genes? A new perspective using ultra high-resolution copy number and loss of heterozygosity analysis.

    Science.gov (United States)

    Gorringe, Kylie L; Ramakrishna, Manasa; Williams, Louise H; Sridhar, Anita; Boyle, Samantha E; Bearfoot, Jennifer L; Li, Jason; Anglesio, Michael S; Campbell, Ian G

    2009-10-01

    Ovarian cancer is characterized by complex genetic alterations, including copy number loss and copy number-neutral loss of heterozygosity (LOH). These alterations are assumed to represent the "second hit" of the underlying tumor suppressor gene (TSG), however, relative to the number of LOH hotspots reported, few ovarian TSGs have been identified. We conducted a high-resolution LOH analysis using SNP arrays (500K and SNP6.0) of 106 primary ovarian tumors of various histological subtypes together with matching normal DNA. LOH was detected in at least 35% of samples on chromosomes 17, 19p, 22q, Xp, 13q, 8p, 6q, 4q, 5q, 1p, 16q, and 9q with a median minimal region of overlap of only 300 kb. Subtype-specific differences in LOH frequency were noted, particularly for mucinous cases. We also identified 192 somatic homozygous deletions (HDs). Recurrent HDs targeted known TSGs such as CDKN2A (eight samples), RB1 (five samples), and PTEN (three samples). Additional recurrent HDs targeted 16 candidate TSGs near minimal regions of LOH on chromosomes 17, 13, 8p, 5q, and X. Given the importance of HDs in inactivating known genes, these candidates are highly likely to be ovarian TSGs. Our data suggest that the poor success of previous LOH studies was due to the inability of previous technology to resolve complex genomic alterations and distinguish true LOH from allelic imbalance. This study shows that recurrent regions of LOH and HD frequently align with known TSGs suggesting that LOH analysis remains a valid approach to discovering new candidates.

  19. EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

    Directory of Open Access Journals (Sweden)

    Zhu Yuelin

    2008-01-01

    Full Text Available Abstract Background Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand. Results EzArray is a web-based Affymetrix expression array data management and analysis system for researchers who need to organize microarray data efficiently and get data analyzed instantly. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures. EzArray performs data preprocessing and detection of differentially expressed genes with statistical methods. All analysis procedures are optimized and highly automated so that even novice users with limited pre-knowledge of microarray data analysis can complete initial analysis quickly. Since all input files, analysis parameters, and executed scripts can be downloaded, EzArray provides maximum reproducibility for each analysis. In addition, EzArray integrates with Gene Expression Omnibus (GEO and allows instantaneous re-analysis of published array data. Conclusion EzArray is a novel Affymetrix expression array data analysis and sharing system. EzArray provides easy-to-use tools for re-analyzing published microarray data and will help both novice and experienced users perform initial analysis of their microarray data from the location of data storage. We believe EzArray will be a useful system for facilities with microarray services and laboratories with multiple members involved in microarray data analysis. EzArray is freely available from http://www.ezarray.com/.

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

    OpenAIRE

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

    2005-01-01

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

  1. The high granularity and large solid angle detection array EXPADES

    Energy Technology Data Exchange (ETDEWEB)

    Strano, E., E-mail: estrano@pd.infn.it [Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, I-35131 Padova (Italy); INFN – Sezione di Padova, Via Marzolo 8, I-35131 Padova (Italy); Anastasio, A. [INFN – Sezione di Napoli, Via Cintia, I-80126 Napoli (Italy); Bettini, M. [INFN – Sezione di Padova, Via Marzolo 8, I-35131 Padova (Italy); Boiano, A. [INFN – Sezione di Napoli, Via Cintia, I-80126 Napoli (Italy); Boiano, C. [INFN – Sezione di Milano, Via Celoria 16, I-20133 Milano (Italy); Cassese, C. [INFN – Sezione di Napoli, Via Cintia, I-80126 Napoli (Italy); Castellani, L.; Corti, D. [INFN – Sezione di Padova, Via Marzolo 8, I-35131 Padova (Italy); Di Meo, P. [INFN – Sezione di Napoli, Via Cintia, I-80126 Napoli (Italy); Galet, G. [Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, I-35131 Padova (Italy); Glodariu, T. [NIPNE, Str. Reactorului No. 30, P.O. Box MG-6, Bucharest-Magurele (Romania); Grebosz, J. [IFJ PAN, ul. Radzikowskiego 152, 31-342 Kraków (Poland); Guglielmetti, A. [Dipartimento di Fisica, Università di Milano, Via Celoria 16, I-20133 Milano (Italy); INFN – Sezione di Milano, Via Celoria 16, I-20133 Milano (Italy); La Commara, M. [Dipartimento di Scienze Fisiche, Università di Napoli, Via Cintia, I-80126 Napoli (Italy); INFN – Sezione di Napoli, Via Cintia, I-80126 Napoli (Italy); Manea, C. [INFN – Sezione di Padova, Via Marzolo 8, I-35131 Padova (Italy); Mazzocco, M.; Molini, P. [Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, I-35131 Padova (Italy); INFN – Sezione di Padova, Via Marzolo 8, I-35131 Padova (Italy); Nicoletto, M. [INFN – Sezione di Padova, Via Marzolo 8, I-35131 Padova (Italy); and others

    2013-12-15

    Highlights: • We realized a detection array for Exotic Radioactive Ion Beams. • High granularity (32 × 32 pixels 2 × 2 mm wide for 8 telescopes). • High solid angle (8 telescopes 64 × 64 mm wide in a cylindrical configuration covering up to 2.6 sr). • We tested each component of the array by both alpha particles and in-beam environment. • We measured the angular distribution for {sup 17}O elastic scattering on a {sup 58}Ni target. -- Abstract: The EXPADES (EXotic PArticle DEtection System) detector array consists of 16 Double Side Silicon Strip Detectors (DSSSD) with active areas of 64 × 64 mm{sup 2}, arranged in 8 ΔE (40/50 μm)–E (300 μm) telescopes. All detector faces are segmented into 32 × 2-mm wide strips, ensuring a 2 × 2 mm{sup 2} pixel configuration. Eight ionization chambers can be alternatively used as ΔE stages or, if needed, as an additional third layer for more complex triple telescopes. The signals from silicon ΔE layers and from ionization chambers are read by standard electronics, while innovative 32-channel ASIC chips are employed for the readout of the E stages. The results of off-line tests with alpha sources and from the first in-beam experiment with a {sup 17}O beam are presented.

  2. Magnetic probe array with high sensitivity for fluctuating field.

    Science.gov (United States)

    Kanamaru, Yuki; Gota, Hiroshi; Fujimoto, Kayoko; Ikeyama, Taeko; Asai, Tomohiko; Takahashi, Tsutomu; Nogi, Yasuyuki

    2007-03-01

    A magnetic probe array is constructed to measure precisely the spatial structure of a small fluctuating field included in a strong confinement field that varies with time. To exclude the effect of the confinement field, the magnetic probes consisting of figure-eight-wound coils are prepared. The spatial structure of the fluctuating field is obtained from a Fourier analysis of the probe signal. It is found that the probe array is more sensitive to the fluctuating field with a high mode number than that with a low mode number. An experimental demonstration of the present method is attempted using a field-reversed configuration plasma, where the fluctuating field with 0.1% of the confinement field is successfully detected.

  3. Novel recurrent chromosomal aberrations detected in clonal plasma cells of light chain amyloidosis patients show potential adverse prognostic effect: first results from a genome-wide copy number array analysis.

    Science.gov (United States)

    Granzow, Martin; Hegenbart, Ute; Hinderhofer, Katrin; Hose, Dirk; Seckinger, Anja; Bochtler, Tilmann; Hemminki, Kari; Goldschmidt, Hartmut; Schönland, Stefan O; Jauch, Anna

    2017-07-01

    Immunoglobulin light chain (AL) amyloidosis is a rare plasma cell dyscrasia characterized by the deposition of abnormal amyloid fibrils in multiple organs, thus impairing their function. In the largest cohort studied up to now of 118 CD138-purified plasma cell samples from previously untreated immunoglobulin light chain amyloidosis patients, we assessed in parallel copy number alterations using high-density copy number arrays and interphase fluorescence in situ hybridization (iFISH). We used fluorescence in situ hybridization probes for the IgH translocations t(11;14), t(4;14), and t(14;16) or any other IgH rearrangement as well as numerical aberrations of the chromosome loci 1q21, 8p21, 5p15/5q35, 11q22.3 or 11q23, 13q14, 15q22, 17p13, and 19q13. Recurrent gains included chromosomes 1q (36%), 9 (24%), 11q (24%), as well as 19 (15%). Recurrent losses affected chromosome 13 (29% monosomy) and partial losses of 14q (19%), 16q (14%) and 13q (12%), respectively. In 88% of patients with translocation t(11;14), the hallmark chromosomal aberration in AL amyloidosis, a concomitant gain of 11q22.3/11q23 detected by iFISH was part of the unbalanced translocation der(14)t(11;14)(q13;q32) with the breakpoint in the CCND1/MYEOV gene region. Partial loss of chromosome regions 14q and 16q were significantly associated to gain 1q. Gain 1q21 detected by iFISH almost always resulted from a gain of the long arm of chromosome 1 and not from trisomy 1, whereas deletions on chromosome 1p were rarely found. Overall and event-free survival analysis found a potential adverse prognostic effect of concomitant gain 1q and deletion 14q as well as of deletion 1p. In conclusion, in the first whole genome report of clonal plasma cells in AL amyloidosis, novel aberrations and hitherto unknown potential adverse prognostic effects were uncovered. Copyright© 2017 Ferrata Storti Foundation.

  4. Sub-array patterns of spherical-section phased array for high intensity focused ultrasound surgery

    Institute of Scientific and Technical Information of China (English)

    WANG Xiaodong; WANG Xufei; LU Mingzhu; WAN Mingxi

    2005-01-01

    The sub-array field patterns of spherical-section phased array were implemented for noninvasive ultrasound surgery of liver-tumor. The sub-array approach included field calculation, pseudo-inverse method and genetic algorithm. The sub-arrays uncovered by ribs according to scanned images normally emitted ultrasound. The results from different sub-arrays demonstrated quite satisfied acoustic performances, which included qualified focus size and intensity level for ultrasound surgery with single-focus and multi-foci patterns. Moreover, the patterns could decrease power accumulation on the ribs, and avoid damaging normal tissues. Thus the sub-array method provides a promising tool for phased array ultrasound propagating through strong obstacles like human rib cage, and it may broaden the therapeutic area, make the surgery safer and more flexible.

  5. Highly tunable plasmonic nanoring arrays for nanoparticle manipulation and detection

    Science.gov (United States)

    Sergides, M.; Truong, V. G.; Chormaic, S. Nic

    2016-09-01

    The advancement of trapping and detection of nano-objects at very low laser powers in the near-infra-red region (NIR) is crucial for many applications. Singular visible-light nano-optics based on abrupt phase changes have recently demonstrated a significant improvement in molecule detection. Here, we propose and demonstrate tunable plasmonic nanodevices, which can improve both the trapping field enhancement and detection of nano-objects using singular phase drops in the NIR range. The plasmonic nanostructures, which consist of gaps with dimensions 50 nm × 50 nm connecting nanorings in arrays is discussed. These gaps act as individual detection and trapping sites. The tunability of the system is evident from extinction and reflection spectra while increasing the aperture size in the arrays. Additionally, in the region where the plasmonic nano-array exhibits topologically-protected, near-zero reflection behaviour, the phase displays a rapid change. Our experimental data predict that, using this abrupt phase changes, one can improve the detection sensitivity by 10 times compared to the extinction spectra method. We finally report experimental evidence of 100 nm polystyrene beads trapping using low incident power on these devices. The overall design demonstrates strong capability as an optical, label-free, non-destructive tool for single molecule manipulation where low trapping intensity, minimal photo bleaching and high sensitivity is required.

  6. Anti-Viral Antibody Profiling by High Density Protein Arrays

    Science.gov (United States)

    Bian, Xiaofang; Wiktor, Peter; Kahn, Peter; Brunner, Al; Khela, Amritpal; Karthikeyan, Kailash; Barker, Kristi; Yu, Xiaobo; Magee, Mitch; Wasserfall, Clive H.; Gibson, David; Rooney, Madeleine E; Qiu, Ji; LaBaer, Joshua

    2015-01-01

    Viral infections elicit anti-viral antibodies and have been associated with various chronic diseases. Detection of these antibodies can facilitate diagnosis, treatment of infection and understanding of the mechanisms of virus associated diseases. In this work, we assayed anti-viral antibodies using a novel high density-nucleic acid programmable protein array (HD-NAPPA) platform. Individual viral proteins were expressed in situ directly from plasmids encoding proteins in an array of microscopic reaction chambers. Quality of protein display and serum response was assured by comparing intra- and inter- array correlation within or between printing batches with average correlation coefficients of 0.91 and 0.96, respectively. HD-NAPPA showed higher signal to background (S/B) ratio compared with standard NAPPA on planar glass slides and ELISA. Antibody responses to 761 antigens from 25 different viruses were profiled among patients with juvenile idiopathic arthritis (JIA) and type 1 diabetes (T1D). Common as well as unique antibody reactivity patterns were detected between patients and healthy controls. We believe HD-viral-NAPPA will enable the study of host-pathogen interactions at unprecedented dimensions and elucidate the role of pathogen infections in disease development. PMID:25758251

  7. High-performance flexible supercapacitor based on porous array electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Shieh, Jen-Yu; Tsai, Sung-Ying; Li, Bo-Yan [Institute of Electro-Optical and Materials Science, National Formosa University, 64 Wenhua Road, Huwei, Yunlin 63208, Taiwan (China); Yu, Hsin Her, E-mail: hhyu@nfu.edu.tw [Department of Biotechnology, National Formosa University, 64 Wenhua Road, Huwei, Yunlin 63208, Taiwan (China)

    2017-07-01

    In this study, an array of polystyrene (PS) spheres was synthesized by a dispersion-polymerization technique as a template onto which a porous polydimethylsiloxane (PDMS) microarray structure was fabricated by soft lithography. A conducting layer was coated on the surface of the microarray after a suspension of multi-walled carbon nanotubes (MWCNTs) mixed with graphene (G) had been poured into the porous array. A PDMS-based porous supercapacitor was assembled by sandwiching a separator between two porous electrodes filled with a H{sub 3}PO{sub 4}/polyvinyl alcohol (PVA) gel electrolyte. The specific capacitance, electrochemical properties, and cycle stability of the porous electrode supercapacitors were explored. The porous PDMS-electrode-based supercapacitor exhibited high specific capacitance and good cycle stability, indicating its enormous potential for future applications in wearable and portable electronic products. - Highlights: • Porous electrode was prepared using an array of polystyrene spheres as template. • The porous electrodes provided increased contact area with the electrolyte. • A gel electrolyte averted problems with leakage and poor interfacial contact. • A larger separator pore size effectively reduced the internal resistance, iR{sub drop}. • Porous PDMS supercapacitor showed superior flexibility and cycling stability.

  8. Highly-compliant, conformal and stretchable microelectrode arrays

    Institute of Scientific and Technical Information of China (English)

    Zhang Hongzhi; Xie Lei; Yu Mei; Liu Zhiyuan; Li Yuchun; Yu Zhe

    2013-01-01

    Most biological tissues are supple and elastic,While current electronic devices fabricated by semiconductors and metals are usually stiff and brittle.As a result,implanted electronic devices can irritate and damage surrounding tissues,causing immune reaction and scarring.In this work,we develop stretchable microelectrode arrays,with the development of a novel soft lithography technology,which are designed and fabricated with a polymer/stretchable metal/polymer sandwich structure.With the great deformability of stretch,compression,bend and twisting,while preserving electrical property,this technology overcomes the fundamental mismatch of mechanical properties between biological tissues and electronic devices,and provides highly-compliant,conformal and stretchable bio-electronic interfaces.Here we also describe the following three applications of the stretchable electrode arrays:a.monitoring intracranial electroencephalography (EEG); b.stimulating peripheral nerves to drive muscles; c.monitoring epicardial electrocardiography (ECG).Stretchable microelectrode arrays create a promising field in biomedical applications for its better modulus match with biological tissues and robust mechanical and electrical properties.They allow for construction of electronic integrated circuits spread over on complex and dynamic curved surfaces,providing a much friendlier bio-electronic interface for diagnosis,treatment and intelligent bio-control.

  9. High-throughput quantitative analysis with cell growth kinetic curves for low copy number mutant cells.

    Science.gov (United States)

    Xing, James Z; Gabos, Stephan; Huang, Biao; Pan, Tianhong; Huang, Min; Chen, Jie

    2012-10-01

    The mutation rate in cells induced by environmental genotoxic hazards is very low and difficult to detect using traditional cell counting assays. The established genetic toxicity tests currently recognized by regulatory authorities, such as conventional Ames and hypoxanthine guanine phosphoribosyl-transferase (HPRT) assays, are not well suited for higher-throughput screening as they require large amounts of test compounds and are very time consuming. In this study, we developed a novel cell-based assay for quantitative analysis of low numbers of cell copies with HPRT mutation induced by an environmental mutagen. The HPRT gene mutant cells induced by the mutagen were selected by 6-thioguanine (6-TG) and the cell's kinetic growth curve monitored by a real-time cell electronic sensor (RT-CES) system. When a threshold is set at a certain cell index (CI) level, samples with different initial mutant cell copies take different amounts of time in order for their growth (or CI accumulation) to cross this threshold. The more cells that are initially seeded in the test well, the faster the cell accumulation and therefore the shorter the time required to cross this threshold. Therefore, the culture time period required to cross the threshold of each sample corresponds to the original number of cells in the sample. A mutant cell growth time threshold (MT) value of each sample can be calculated to predict the number of original mutant cells. For mutagenesis determination, the RT-CES assay displayed an equal sensitivity (p > 0.05) and coefficients of variation values with good correlation to conventional HPRT mutagenic assays. Most importantly, the RT-CES mutation assay has a higher throughput than conventional cellular assays.

  10. Identification of cryptic microaberrations in osteosarcoma by high-definition oligonucleotide array comparative genomic hybridization.

    Science.gov (United States)

    Selvarajah, Shamini; Yoshimoto, Maisa; Maire, Georges; Paderova, Jana; Bayani, Jane; Squire, Jeremy A; Zielenska, Maria

    2007-11-01

    Osteosarcoma (OS) is an aggressive bone tumor characterized by complex abnormal karyotypes and a high level of genomic instability. Using high-resolution array comparative genomic hybridization (aCGH), a novel class of localized copy number variations called microaberrations has been detected. These genomic anomalies typically involve DNA imbalances affecting 700 kb to 1 Mb DNA, and are often associated with some type of genetic syndromes. Because the origin of instability in OS is poorly understood, we used aCGH to determine whether microaberrations were a characteristic of four OS cell lines: U-2 OS, HOS, MG-63, and SAOS-2. TP53 is mutated in SAOS-2, a line in which 17 microaberrations were found. In contrast, U-2 OS, which has a wild-type TP53, had only six such anomalies, the lowest incidence. A 500-kb microaberration within a region of gain at 5p15.33 in SAOS-2 was confirmed by fluorescence in situ hybridization. Significantly, this genomic location is close to the TERT gene, a region of gain in all four cell lines. To our knowledge, this is the first systematic analysis of the incidence of microaberrations in OS. The high levels of these anomalies detected suggest that the instability processes in OS that lead to a highly abnormal karyotypes may also be associated with acquisition of genomic microaberrations.

  11. Fast, High-Precision Readout Circuit for Detector Arrays

    Science.gov (United States)

    Rider, David M.; Hancock, Bruce R.; Key, Richard W.; Cunningham, Thomas J.; Wrigley, Chris J.; Seshadri, Suresh; Sander, Stanley P.; Blavier, Jean-Francois L.

    2013-01-01

    The GEO-CAPE mission described in NASA's Earth Science and Applications Decadal Survey requires high spatial, temporal, and spectral resolution measurements to monitor and characterize the rapidly changing chemistry of the troposphere over North and South Americas. High-frame-rate focal plane arrays (FPAs) with many pixels are needed to enable such measurements. A high-throughput digital detector readout integrated circuit (ROIC) that meets the GEO-CAPE FPA needs has been developed, fabricated, and tested. The ROIC is based on an innovative charge integrating, fast, high-precision analog-to-digital circuit that is built into each pixel. The 128×128-pixel ROIC digitizes all 16,384 pixels simultaneously at frame rates up to 16 kHz to provide a completely digital output on a single integrated circuit at an unprecedented rate of 262 million pixels per second. The approach eliminates the need for off focal plane electronics, greatly reducing volume, mass, and power compared to conventional FPA implementations. A focal plane based on this ROIC will require less than 2 W of power on a 1×1-cm integrated circuit. The ROIC is fabricated of silicon using CMOS technology. It is designed to be indium bump bonded to a variety of detector materials including silicon PIN diodes, indium antimonide (InSb), indium gallium arsenide (In- GaAs), and mercury cadmium telluride (HgCdTe) detector arrays to provide coverage over a broad spectral range in the infrared, visible, and ultraviolet spectral ranges.

  12. ICRF array module development and optimization for high power density

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, P.M.; Swain, D.W.

    1997-02-01

    This report describes the analysis and optimization of the proposed International Thermonuclear Experimental Reactor (ITER) Antenna Array for the ion cyclotron range of frequencies (ICRF). The objectives of this effort were to: (1) minimize the applied radiofrequency rf voltages occurring in vacuum by proper layout and shape of components, limit the component`s surface/volumes where the rf voltage is high; (2) study the effects of magnetic insulation, as applied to the current design; (3) provide electrical characteristics of the antenna for the development and analysis of tuning, arc detection/suppression, and systems for discriminating between arcs and edge-localized modes (ELMs); (4) maintain close interface with mechanical design.

  13. High-performance deployable structures for the support of high-concentration ratio solar array modules

    Science.gov (United States)

    Mobrem, M.

    1985-01-01

    A study conducted on high-performance deployable structures for the support of high-concentration ratio solar array modules is discussed. Serious consideration is being given to the use of high-concentration ratio solar array modules or applications such as space stations. These concentrator solar array designs offer the potential of reduced cost, reduced electrical complexity, higher power per unit area, and improved survivability. Arrays of concentrators, such as the miniaturized Cassegrainian concentrator modules, present a serious challenge to the structural design because their mass per unit area (5.7 kg/square meters) is higher than that of flexible solar array blankets, and the requirement for accurate orientation towards the Sun (plus or minus 0.5 degree) requires structures with improved accuracy potentials. In addition, use on a space station requires relatively high structural natural frequencies to avoid deleterious interactions with control systems and other large structural components. The objective here is to identify and evaluate conceptual designs of structures suitable for deploying and accurately supporting high-concentration ratio solar array modules.

  14. Compensated readout for high-density MOS-gated memristor crossbar array

    KAUST Repository

    Zidan, Mohammed A.

    2015-01-01

    Leakage current is one of the main challenges facing high-density MOS-gated memristor arrays. In this study, we show that leakage current ruins the memory readout process for high-density arrays, and analyze the tradeoff between the array density and its power consumption. We propose a novel readout technique and its underlying circuitry, which is able to compensate for the transistor leakage-current effect in the high-density gated memristor array.

  15. Template fabrication of highly ordered arrays of organic semiconductor nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Heckel, Christian; Ostendorp, Stefan; Lei, Yong; Wilde, Gerhard [Institut fuer Materialphysik, Muenster (Germany)

    2011-07-01

    Porous alumina membrane (PAM) is a widely used template for the fabrication of highly ordered arrays of one-dimensional (1D) nanostructures. The structural parameters of the PAMs are adjustable, including the pore diameter and spacing, and the thickness of the membranes. And thus the structures of the 1D nanomaterials prepared using PAMs can be controlled. On the other hand, the investigation of organic semiconductors opens a new field of applications in computer technology like twistable displays or printing integrated circuits. In the current work, these two technologies are combined by depositing organic n-type semiconductors into the pores of PAMs using different synthesizing processes such as molecular evaporation and solution-phase self-assembly. As a result, highly ordered arrays of organic semiconducting wires are obtained within the pores with a diameter of about 50 nm, which indicates that it is possible to fill the pores with organic materials.The properties of these ''filled'' membranes are characterized by measuring the electrical properties of several nanowires pooled together and also of single nanowires by AFM-based methods.

  16. High-resolution ionization detector and array of such detectors

    Energy Technology Data Exchange (ETDEWEB)

    McGregor, Douglas S. (Ypsilanti, MI); Rojeski, Ronald A. (Pleasanton, CA)

    2001-01-16

    A high-resolution ionization detector and an array of such detectors are described which utilize a reference pattern of conductive or semiconductive material to form interaction, pervious and measurement regions in an ionization substrate of, for example, CdZnTe material. The ionization detector is a room temperature semiconductor radiation detector. Various geometries of such a detector and an array of such detectors produce room temperature operated gamma ray spectrometers with relatively high resolution. For example, a 1 cm.sup.3 detector is capable of measuring .sup.137 Cs 662 keV gamma rays with room temperature energy resolution approaching 2% at FWHM. Two major types of such detectors include a parallel strip semiconductor Frisch grid detector and the geometrically weighted trapezoid prism semiconductor Frisch grid detector. The geometrically weighted detector records room temperature (24.degree. C.) energy resolutions of 2.68% FWHM for .sup.137 Cs 662 keV gamma rays and 2.45% FWHM for .sup.60 Co 1.332 MeV gamma rays. The detectors perform well without any electronic pulse rejection, correction or compensation techniques. The devices operate at room temperature with simple commercially available NIM bin electronics and do not require special preamplifiers or cooling stages for good spectroscopic results.

  17. Experimental study on high-voltage solar array sustained arc discharge induced by high charging

    Institute of Scientific and Technical Information of China (English)

    LI Kai; XIE ErQing; WANG Li; LIU YanXia; YANG Yang; SUN YanZheng; CUI XinYu; MAI ShengLi

    2007-01-01

    It has been reported that sustained arc discharge induced by electrostatic discharge (ESD) could cause permanent damage to high-power and high-voltage solar array of spacecrafts. The paper focuses on ESD simulating experiments on Si and GaAs samples, and induces sustained arc discharge. The physical mechanism of sustained arc discharge is discussed by comparing the charging/discharging phenomena between Si and GaAs samples. The experiments show that sustained arc discharge can produce a permanent short-circuit channel between solar cell strings through which the solar array's photovoltaic power may flow out sustainedly. The analyses show that sustained arc discharge strongly depends on solar array structure, solar array operating voltage, ESD characteristics and cell materials.

  18. Application of high resolution SNP arrays in patients with congenital oral clefts in south China

    Indian Academy of Sciences (India)

    TING-YING LEI; HONG-TAO WANG; FAN LI; YING-QIU CUI; FANG FU; RU LI; CAN LIAO

    2016-12-01

    Chromosome microarray analysis (CMA) has proven to be a powerful tool in postnatal patients with intellectual disabilities. However, the diagnostic capability of CMA in patients with congenital oral clefts remain mysterious. Here, we present ourclinical experience in implementing whole-genome high-resolution SNP arrays to investigate 33 patients with syndromic and nonsyndromic oral clefts in whom standard karyotyping analyses showed normal karyotypes. We aim to identify the genomic aetiology and candidate genes in patients with congenital oral clefts. CMA revealed copy number variants (CNVs) in every patient, which ranged from 2 to 9 per sample. The size of detected CNVs varied from 100 to 3.2 Mb. In 33 patients, we identified six clinically significant CNVs. The incidence of clinically significant CNVs was 18.2% (6/33). Three of these six CNVs were detected in patients with nonsyndromic clefts, including one who presented with isolated cleft lip with cleft palate (CLP) and two with cleft palate only (CPO). The remaining three CNVs were detected in patients with syndromic clefts. However, no CNV was detected in patients with cleft lip only (CLO). The six clinically significant CNVs were as follows: 8p23.1 microduplication (198 kb); 10q22.2-q22.3 microdeletion (1766 kb); 18q12.3 microduplication (638 kb); 20p12.1 microdeletion (184 kb); 6q26 microdeletion (389 kb); and 22q11.21-q11.23 microdeletion (3163 kb). In addition, two novel candidate genes for oral clefts, KAT6B and MACROD2, were putatively identified. We also found a CNV of unknown clinical significance witha detection rate of 3.0% (1/33). Our results further support the notion that CNVs significantly contributed to the genetic aetiology of oral clefts and emphasize the efficacy of whole-genome high-resolution SNP arrays to detect novel candidate genes in patients with syndromic and nonsyndromic clefts.

  19. High Gain and High Directive of Antenna Arrays Utilizing Dielectric Layer on Bismuth Titanate Ceramics

    Directory of Open Access Journals (Sweden)

    F. H. Wee

    2012-01-01

    Full Text Available A high gain and high directive microstrip patch array antenna formed from dielectric layer stacked on bismuth titanate (BiT ceramics have been investigated, fabricated, and measured. The antennas are designed and constructed with a combination of two-, four-, and six-BiT elements in an array form application on microwave substrate. For gain and directivity enhancement, a layer of dielectric was stacked on the BiT antenna array. We measured the gain and directivity of BiT array antennas with and without the dielectric layer and found that the gain of BiT array antenna with the dielectric layer was enhanced by about 1.4 dBi of directivity and 1.3 dB of gain over the one without the dielectric layer at 2.3 GHz. The impedance bandwidth of the BiT array antenna both with and without the dielectric layer is about 500 MHz and 350 MHz, respectively, which is suitable for the application of the WiMAX 2.3 GHz system. The utilization of BiT ceramics that covers about 90% of antenna led to high radiation efficiency, and small-size antennas were produced. In order to validate the proposed design, theoretical and measured results are provided and discussed.

  20. High efficiency micro solar cells integrated with lens array

    Science.gov (United States)

    Fidaner, Onur; Suarez, Ferran A.; Wiemer, Michael; Sabnis, Vijit A.; Asano, Tetsuya; Itou, Akihiro; Inoue, Daijiro; Hayashi, Nobuhiko; Arase, Hidekazu; Matsushita, Akio; Nakagawa, Tohru

    2014-03-01

    We demonstrate high efficiency triple junction solar cells with submillimeter dimensions in an all-back-contact architecture. 550 × 550 μm2 cells flash at 41.3% efficiency under the air mass 1.5 direct normal spectrum at 50 W/cm2 at 25 °C. Compared to standard size production cells, the micro cells have reduced performance at 1-sun due to perimeter recombination, but the performance gap closes at higher concentrations. Micro cells integrated with lens arrays were tested on-sun with an efficiency of 34.7%. All-back-contact architecture and submillimeter dimensions are advantageous for module integration and heat dissipation, allowing for high-performance, compact, lightweight, and cost-effective concentrated photovoltaic modules.

  1. Reverse Phase Protein Arrays for High-throughput Toxicity Screening

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    High-throughput screening is extensively applied for identification of drug targets and drug discovery and recently it found entry into toxicity testing. Reverse phase protein arrays (RPPAs) are used widespread for quantification of protein markers. We reasoned that RPPAs also can be utilized...... beneficially in automated high-throughput toxicity testing. An advantage of using RPPAs is that, in addition to the baseline toxicity readout, they allow testing of multiple markers of toxicity, such as inflammatory responses, which do not necessarily cumulate in cell death. We used transfection of si...... a robotic screening platform. Furthermore, we automated sample tracking and data analysis by developing a bundled bioinformatics tool named “MIRACLE”. Automation and RPPA-based viability/toxicity readouts enable rapid testing of large sample numbers, while granting the possibility for flexible consecutive...

  2. High Density Nano-Electrode Array for Radiation Detection

    Energy Technology Data Exchange (ETDEWEB)

    Mano Misra

    2010-05-07

    Bulk single crystals of Cd1-xZnxTe (x=0.04 to x=0.2) compound semiconductor is used for room temperature radiation detection. The production of large volume of Cd1-xZnxTe with low defect density is expensive. As a result there is a growing research interest in the production of nanostructured compound semiconductors such as Cd1-xZnxTe in an electrochemical route. In this investigation, Cd1-xZnxTe ternary compound semiconductor, referred as CZT, was electrodeposited in the form of nanowires onto a TiO2 nanotubular template from propylene carbonate as the non-aqueous electrolyte, using a pulse-reverse electrodeposition process at 130 ºC. The template acted as a support in growing ordered nanowire of CZT which acts as a one dimensional conductor. Cyclic Voltammogram (CV) studies were conducted in determining the potentials for the growth of nanowires of uniform stoichiometry. The morphologies and composition of CZT were characterized by using SEM, TEM and XRD. The STEM mapping carried out on the nanowires showed the uniform distribution of Cd, Zn and Te elements. TEM image showed that the nanowires were polycrystalline in nature. The Mott-Schottky analysis carried on the nanowires showed that the nanowires were a p-type semiconductor. The carrier density, band gap and resistivity of the Cd0.9Zn0.1Te nanowires were 4.29x1013 cm-3, 1.56 eV and 2.76x1011Ω-cm respectively. The high resistivity was attributed to the presence of deep defect states such as cadmium vacancies or Te antisites which were created by the anodic cycle of the pulse-reverse electrodeposition process. Stacks of series connected CZT nanowire arrays were tested with different bias potentials. The background current was in the order of tens of picoamperes. When exposed to radiation source Amerecium-241 (60 KeV, 4 μCi), the stacked CZT nanowires arrays showed sensing behavior. The sensitivity of the nanowire arrays increased as the number of stacks increased. The preliminary results indicate that the

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

    OpenAIRE

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

    2006-01-01

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

  4. DNM1DN: a new class of paralogous genomic segments (duplicons) with highly conserved copies on chromosomes Y and 15.

    Science.gov (United States)

    Makrinou, E; Fox, M; Wolfe, J; Cameron, J; Taylor, K; Edwards, Y H

    2004-03-01

    Screening a testis cDNA selection library for Y-linked genes yielded 79 cDNAs. Of these, 9 matched the 3' region of the dynamin 1 gene (DNM1) on chromosome 9q34 with >90% identity. Fluoresence in situ hybridisation and PCR amplification were used to localise a large number of DNM1-like sequences to human chromosomes 15 and Y. PCR amplification of overlapping Y-linked YACs allowed a more accurate mapping of the Y-linked DNM1-like cDNAs to a euchromatic locus in close proximity to heterochromatin at Yq11.23. A search of the genome database identified 64 highly homologous copies of the DNM1 fragment. Most of these copies were localised to chromosomes 15 and Y, but others mapped to chromosomes 5, 8, 10, 12, 19 and 22. These sequences exhibit all the major features of a duplicon and have been designated DNM1DN (DNM1 duplicon). Evolutionary studies using fluorescence in situ hybridisation indicate that transposition of the DNM1DN sequence to chromosome 15 took place earlier in primate evolution than the transposition to the Y chromosome. The translocation to the Y took place at a time following the divergence of a common ancestor from gorilla, approximately 4-7 million years ago.

  5. Dendritic Heterojunction Nanowire Arrays for High-Performance Supercapacitors

    Science.gov (United States)

    Zou, Rujia; Zhang, Zhenyu; Yuen, Muk Fung; Hu, Junqing; Lee, Chun-Sing; Zhang, Wenjun

    2015-01-01

    Herein, we designed and synthesized for the first time a series of 3D dendritic heterojunction arrays on Ni foam substrates, with NiCo2S4 nanowires as cores and NiCo2O4, NiO, Co3O4, and MnO2 nanowires as branches, and studied systematically their electrochemical performance in comparison with their counterparts in core/shell structure. Attributed to the following reasons: (1) both core and branch are pseudocapacitively active materials, (2) the special dendritic structure with considerable inter-nanowire space enables easy access of electrolyte to the core and branch surfaces, and (3) the highly conductive NiCo2S4 nanowire cores provide ``superhighways'' for charge transition, NiCo2S4-cored dendritic heterojunction electrodes synergistically lead to ultrahigh specific capacitance, good rate capability, and excellent cycling life. These results of core/branch dentritic heterojunction arrays is universially superior to their core/shell conterparts, thus this is a significant improvement of overall electrochemical performance.

  6. Crystallographic alignment of high-density gallium nitride nanowire arrays.

    Science.gov (United States)

    Kuykendall, Tevye; Pauzauskie, Peter J; Zhang, Yanfeng; Goldberger, Joshua; Sirbuly, Donald; Denlinger, Jonathan; Yang, Peidong

    2004-08-01

    Single-crystalline, one-dimensional semiconductor nanostructures are considered to be one of the critical building blocks for nanoscale optoelectronics. Elucidation of the vapour-liquid-solid growth mechanism has already enabled precise control over nanowire position and size, yet to date, no reports have demonstrated the ability to choose from different crystallographic growth directions of a nanowire array. Control over the nanowire growth direction is extremely desirable, in that anisotropic parameters such as thermal and electrical conductivity, index of refraction, piezoelectric polarization, and bandgap may be used to tune the physical properties of nanowires made from a given material. Here we demonstrate the use of metal-organic chemical vapour deposition (MOCVD) and appropriate substrate selection to control the crystallographic growth directions of high-density arrays of gallium nitride nanowires with distinct geometric and physical properties. Epitaxial growth of wurtzite gallium nitride on (100) gamma-LiAlO(2) and (111) MgO single-crystal substrates resulted in the selective growth of nanowires in the orthogonal [1\\[Evec]0] and [001] directions, exhibiting triangular and hexagonal cross-sections and drastically different optical emission. The MOCVD process is entirely compatible with the current GaN thin-film technology, which would lead to easy scale-up and device integration.

  7. Coherent beam combining architectures for high power tapered laser arrays

    Science.gov (United States)

    Schimmel, G.; Janicot, S.; Hanna, M.; Decker, J.; Crump, P.; Erbert, G.; Witte, U.; Traub, M.; Georges, P.; Lucas-Leclin, G.

    2017-02-01

    Coherent beam combining (CBC) aims at increasing the spatial brightness of lasers. It consists in maintaining a constant phase relationship between different emitters, in order to combine them constructively in one single beam. We have investigated the CBC of an array of five individually-addressable high-power tapered laser diodes at λ = 976 nm, in two architectures: the first one utilizes the self-organization of the lasers in an interferometric extended-cavity, which ensures their mutual coherence; the second one relies on the injection of the emitters by a single-frequency laser diode. In both cases, the coherent combining of the phase-locked beams is ensured on the front side of the array by a transmission diffractive grating with 98% efficiency. The passive phase-locking of the laser bar is obtained up to 5 A (per emitter). An optimization algorithm is implemented to find the proper currents in the five ridge sections that ensured the maximum combined power on the front side. Under these conditions we achieve a maximum combined power of 7.5 W. In the active MOPA configuration, we can increase the currents in the tapered sections up to 6 A and get a combined power of 11.5 W, corresponding to a combining efficiency of 76%. It is limited by the beam quality of the tapered emitters and by fast phase fluctuations between emitters. Still, these results confirm the potential of CBC approaches with tapered lasers to provide a high-power and high-brightness beam, and compare with the current state-of-the-art with laser diodes.

  8. High-spin research with HERA (High Energy-Resolution Array)

    Energy Technology Data Exchange (ETDEWEB)

    Diamond, R.M.

    1987-06-01

    The topic of this report is high spin research with the High Energy Resolution Array (HERA) at Lawrence Berkeley Laboratory. This is a 21 Ge detector system, the first with bismuth germanate (BGO) Compton suppression. The array is described briefly and some of the results obtained during the past year using this detector facility are discussed. Two types of studies are described: observation of superdeformation in the light Nd isotopes, and rotational damping at high spin and excitation energy in the continuum gamma ray spectrum.

  9. High-throughput single-cell analysis of low copy number β-galactosidase by a laboratory-built high-sensitivity flow cytometer.

    Science.gov (United States)

    Yang, Lingling; Huang, Tianxun; Zhu, Shaobin; Zhou, Yingxing; Jiang, Yunbin; Wang, Shuo; Chen, Yuqing; Wu, Lina; Yan, Xiaomei

    2013-10-15

    Single-cell analysis is vital in providing insights into the heterogeneity in molecular content and phenotypic characteristics of complex or clonal cell populations. As many essential proteins and most transcription factors are produced at a low copy number, analytical tools with superior sensitivity to enable the analysis of low abundance proteins in single cells are in high demand. β-galactosidase (β-gal) has been the standard cellular reporter for gene expression in both prokaryotic and eukaryotic cells. Here we report the development of a high-throughput method for the single-cell analysis of low copy number β-gal proteins using a laboratory-built high-sensitivity flow cytometer (HSFCM). Upon fluorescence staining with a fluorogenic substrate, quantitative measurements of the basal and near-basal expression of β-gal in single Escherichia coli BL21(DE3) cells were demonstrated. Statistical distribution can be determined quickly by analyzing thousands of individual cells in 1-2min, which reveals the heterogeneous expression pattern that is otherwise masked by the ensemble analysis. Combined with the quantitative fluorometric assay and the rapid bacterial enumeration by HSFCM, the β-gal expression distribution profile could be converted from arbitrary fluorescence units to protein copy numbers per cell. The sensitivity and speed of the HSFCM offers great capability in quantitative analysis of low abundance proteins in single cells, which would help gaining a deeper insight into the heterogeneity and fundamental biological processes in microbial populations.

  10. High Efficient Universal Buck Boost Solar Array Regulator SAR Module

    Science.gov (United States)

    Kimmelmann, Stefan; Knorr, Wolfgang

    2014-08-01

    The high efficient universal Buck Boost Solar Array Regulator (SAR) module concept is applicable for a wide range of input and output voltages. The single point failure tolerant SAR module contains 3 power converters for the transfer of the SAR power to the battery dominated power bus. The converters are operating parallel in a 2 out of 3 redundancy and are driven by two different controllers. The output power of one module can be adjusted up to 1KW depending on the requirements. The maximum power point tracker (MPPT) is placed on a separate small printed circuit board and can be used if no external tracker signal is delivered. Depending on the mode and load conditions an efficiency of more than 97% is achievable. The stable control performance is achieved by implementing the magnetic current sense detection. The sensed power coil current is used in Buck and Boost control mode.

  11. High-resolution displacement sensor using squid array amplifier

    Science.gov (United States)

    Chui, T.; Penanen, K.; Barmatz, M.; Paik, H.

    Improvement in the measurement of displacement has profound implications for gravitational physics. Examples of high-impact projects that can benefit from a better displacement sensor are: detection of gravitational waves, test of the equivalence principle, search for the postulated ?axion? particle, and test of the inverse square law of gravity. We describe the concept of a new displacement sensor that makes use of a recent development in the Superconducting Quantum Interference Device (SQUID) technology. The SQUID array amplifier, invented by Welty and Martinis (IEEE Trans. Appl. Superconductivity 3, 2605, 1993), has about the same noise as a conventional SQUID; however, it can work at a much higher frequency of up to 5 MHz. We explain how the higher bandwidth can be translated into higher resolution using a bridge-balancing scheme that can simultaneously balance out both the carrier signal at the bridge output and the electrostatic force acting on the test mass.

  12. High-resolution imaging methods in array signal processing

    DEFF Research Database (Denmark)

    Xenaki, Angeliki

    The purpose of this study is to develop methods in array signal processing which achieve accurate signal reconstruction from limited observations resulting in high-resolution imaging. The focus is on underwater acoustic applications and sonar signal processing both in active (transmit and receive...... in active sonar signal processing for detection and imaging of submerged oil contamination in sea water from a deep-water oil leak. The submerged oil _eld is modeled as a uid medium exhibiting spatial perturbations in the acoustic parameters from their mean ambient values which cause weak scattering......) and passive (only receive) mode. The study addresses the limitations of existing methods and shows that, in many cases, the proposed methods overcome these limitations and outperform traditional methods for acoustic imaging. The project comprises two parts; The first part deals with computational methods...

  13. High speed, high power one-dimensional beam steering from a 6-element optical phased array.

    Science.gov (United States)

    Huang, W Ronny; Montoya, Juan; Kansky, Jan E; Redmond, Shawn M; Turner, George W; Sanchez-Rubio, Antonio

    2012-07-30

    Beam steering at high speed and high power is demonstrated from a 6-element optical phased array using coherent beam combining (CBC) techniques. The steering speed, defined as the inverse of the time to required to sweep the beam across the steering range, is 40 MHz and the total power is 396 mW. The measured central lobe FWHM width is 565 μrad. High on-axis intensity is maintained periodically by phase-locking the array via a stochastic-parallel-gradient-descent (SPGD) algorithm. A master-oscillator-power-amplifier (MOPA) configuration is used where the amplifier array elements are semiconductor slab-coupled-optical-waveguide-amplifiers (SCOWAs). The beam steering is achieved by LiNbO(3) phase modulators; the phase-locking occurs by current adjustment of the SCOWAs. The system can be readily scaled to GHz steering speed and multiwatt-class output.

  14. Exploration of highly accelerated magnetic resonance elastography using high-density array coils

    Science.gov (United States)

    Bosshard, John C.; Yallapragada, Naresh; McDougall, Mary P.

    2017-01-01

    Background Magnetic resonance elastography (MRE) measures tissue mechanical properties by applying a shear wave and capturing its propagation using magnetic resonance imaging (MRI). By using high density array coils, MRE images are acquired using single echo acquisition (SEA) and at high resolutions with significantly reduced scan times. Methods Sixty-four channel uniplanar and 32×32 channel biplanar receive arrays are used to acquire MRE wave image sets from agar samples containing regions of varying stiffness. A mechanical actuator triggered by a stepped delay time introduces vibrations into the sample while a motion sensitizing gradient encodes micrometer displacements into the phase. SEA imaging is used to acquire each temporal offset in a single echo, while multiple echoes from the same array are employed for highly accelerated imaging at high resolutions. Additionally, stiffness variations as a function of temperature are studied by using a localized heat source above the sample. A custom insertable gradient coil is employed for phase compensation of SEA imaging with the biplanar array to allow imaging of multiple slices. Results SEA MRE images show a mechanical shear wave propagating into and across agar samples. A set of 720 images was obtained in 720 echoes, plus a single reference scan for both harmonic and transient MRE. A set of 2,950 wave image frames was acquired from pairs of SEA images captured during heating, showing the change in mechanical wavelength with the change in agar properties. A set of 240 frames was acquired from two slices simultaneously using the biplanar array, with phase images processed into displacement maps. Combining the narrow sensitivity patterns and SNR advantage of the SEA array coil geometry allowed acquisition of a data set with a resolution of 156 µm × 125 µm × 1,000 µm in only 64 echoes, demonstrating high resolution and high acceleration factors. Conclusions MRE using high-density arrays offers the unique ability

  15. Alternative Optimizations of X-ray TES Arrays: Soft X-rays, High Count Rates, and Mixed-Pixel Arrays

    Science.gov (United States)

    Kilbourne, C. A.; Bandler, S. R.; Brown, A.-D.; Chervenak, J. A.; Figueroa-Feliciano, E.; Finkbeiner, F. M.; Iyomoto, N.; Kelley, R. L.; Porter, F. S.; Smith, S. J.

    2007-01-01

    We are developing arrays of superconducting transition-edge sensors (TES) for imaging spectroscopy telescopes such as the XMS on Constellation-X. While our primary focus has been on arrays that meet the XMS requirements (of which, foremost, is an energy resolution of 2.5 eV at 6 keV and a bandpass from approx. 0.3 keV to 12 keV), we have also investigated other optimizations that might be used to extend the XMS capabilities. In one of these optimizations, improved resolution below 1 keV is achieved by reducing the heat capacity. Such pixels can be based on our XMS-style TES's with the separate absorbers omitted. These pixels can added to an array with broadband response either as a separate array or interspersed, depending on other factors that include telescope design and science requirements. In one version of this approach, we have designed and fabricated a composite array of low-energy and broad-band pixels to provide high spectral resolving power over a broader energy bandpass than could be obtained with a single TES design. The array consists of alternating pixels with and without overhanging absorbers. To explore optimizations for higher count rates, we are also optimizing the design and operating temperature of pixels that are coupled to a solid substrate. We will present the performance of these variations and discuss other optimizations that could be used to enhance the XMS or enable other astrophysics experiments.

  16. Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis

    Directory of Open Access Journals (Sweden)

    Zhengyu eJiang

    2012-12-01

    Full Text Available Recent high-throughput transcript discoveries have yielded a growing recognition of long intergenic non-coding RNAs (lincRNAs, a class of arbitrarily defined transcripts (>200 nt that are primarily produced from the intergenic space. LincRNAs have been increasingly acknowledged for their expressional dynamics and likely functional associations with cancers. However, differential gene dosage of lincRNA genes between cancer genomes is less studied. By using the high-density Human Omni5-Quad BeadChips (Illumina, we investigated genomic copy number aberrations in a set of seven tumor-normal paired primary human mammary epithelial cells (HMECs established from patients with invasive ductal carcinoma. This Beadchip platform includes a total of 2,435,915 SNP loci dispersed at an average interval of ~700 nt throughout the intergenic region of the human genome. We mapped annotated or putative lincRNA genes to a subset of 332,539 SNP loci, which were included in our analysis for lincRNA-associated copy number variations (CNV. We have identified 122 lincRNAs, which were affected by somatic CNV with overlapped aberrations ranging from 0.14% to 100% in length. LincRNA-associated aberrations were detected predominantly with copy number losses and preferential clustering to the ends of chromosomes. Interestingly, lincRNA genes appear to be much less susceptible to CNV in comparison to both protein-coding and intergenic regions (CNV affected segments in percentage: 1.8%, 37.5% and 60.6%, respectively. In summary, our study established a novel approach utilizing high-resolution SNP array to identify lincRNA candidates, which could functionally link to tumorigenesis, and provide new strategies for the diagnosis and treatment of breast cancer.

  17. Experimental study on high-voltage solar array sustained arc discharge induced by high charging

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    It has been reported that sustained arc discharge induced by electrostatic discharge (ESD) could cause permanent damage to high-power and high-voltage solar array of spacecrafts. The paper focuses on ESD simulating experiments on Si and GaAs samples, and induces sustained arc discharge. The physical mechanism of sustained arc discharge is discussed by comparing the charging/discharging phenomena between Si and GaAs samples. The experiments show that sustained arc discharge can produce a permanent short-circuit channel between solar cell strings through which the solar array’s photovoltaic power may flow out sustainedly. The analyses show that sustained arc discharge strongly depends on solar array structure, solar array operating voltage, ESD characteristics and cell materials.

  18. High-Directivity Antenna Array Based on Artificial Electromagnetic Metamaterials with Low Refractive Index

    Directory of Open Access Journals (Sweden)

    Zhigang Xiao

    2015-01-01

    Full Text Available Planar metamaterials (MTMs with low refractive index are proposed as a cover in a high-gain patch antenna array configuration. This MTMs array antenna has the following features: the number of array elements significantly decreases compared with the conventional array; the elements spacing is larger than a wave length by far; the feeding network is simpler. MTMs are made of two layers of periodic square metallic grids and placed above the feeding array. With the same aperture size, the directivity of MTMs-cover antenna array is higher than the conventional antenna array. The simulation results show that an array of 2 × 2 patch elements integrated with MTMs yields about 26 dB of directivity which is higher than that of conventional 8 × 8 patch array. Furthermore, on the condition of the same aperture size, an array patch with 4 × 4 elements integrated with the MTMs-cover has an equivalent gain compared with the conventional patch array with 16 × 16 array elements. Obviously, the former has a simpler feeding network and higher aperture efficiency. The experimental work has verified that the 2 × 2 array case and the measured results have good agreement with the simulation.

  19. High-power laser arrays with 100% fill factor emission facet

    Science.gov (United States)

    Yanson, Dan A.; McDougall, Stewart D.; Qiu, Bocang; Loyo-Maldonado, Valentin; Bacchin, Gianluca; Robertson, Stephen; Bon, Sébastien; Marsh, John H.

    2008-02-01

    Novel types of laser diode array with a 100% filling factor at the emission facet are reported. The arrays utilize both parallel and tapered cavity emitters that are connected via a common Laterally Unconfined Non-Absorbing Mirror (LUNAM) defined with quantum-well intermixing technology at 808 nm wavelength. Two LUNAM array types are considered: incoherent (weakly coupled) and coherent (diffraction coupled). Incoherent LUNAM arrays benefit from a reduced power density at the facet, improving reliability, and a near-uniform intensity distribution across the array aperture. Stacked laser diode arrays built with LUNAM bars deliver 950 W power under QCW operation with monolithically integrated LUNAM Talbot cavity. The devices produce a single-lobed horizontal far-field pattern over a limited current range with <10% slope efficiency penalty compared to an uncoupled case. The LUNAM arrays are promising candidates for high-power, high-brightness and high-reliability operation.

  20. High-throughput sequencing and copy number variation detection using formalin fixed embedded tissue in metastatic gastric cancer.

    Directory of Open Access Journals (Sweden)

    Seokhwi Kim

    Full Text Available In the era of targeted therapy, mutation profiling of cancer is a crucial aspect of making therapeutic decisions. To characterize cancer at a molecular level, the use of formalin-fixed paraffin-embedded tissue is important. We tested the Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay in 89 formalin-fixed paraffin-embedded gastric cancer samples to determine whether they are applicable in archival clinical samples for personalized targeted therapies. We validated the results with Sanger sequencing, real-time quantitative PCR, fluorescence in situ hybridization and immunohistochemistry. Frequently detected somatic mutations included TP53 (28.17%, APC (10.1%, PIK3CA (5.6%, KRAS (4.5%, SMO (3.4%, STK11 (3.4%, CDKN2A (3.4% and SMAD4 (3.4%. Amplifications of HER2, CCNE1, MYC, KRAS and EGFR genes were observed in 8 (8.9%, 4 (4.5%, 2 (2.2%, 1 (1.1% and 1 (1.1% cases, respectively. In the cases with amplification, fluorescence in situ hybridization for HER2 verified gene amplification and immunohistochemistry for HER2, EGFR and CCNE1 verified the overexpression of proteins in tumor cells. In conclusion, we successfully performed semiconductor-based sequencing and nCounter copy number variation analyses in formalin-fixed paraffin-embedded gastric cancer samples. High-throughput screening in archival clinical samples enables faster, more accurate and cost-effective detection of hotspot mutations or amplification in genes.

  1. TALE nickase mediates high efficient targeted transgene integration at the human multi-copy ribosomal DNA locus.

    Science.gov (United States)

    Wu, Yong; Gao, Tieli; Wang, Xiaolin; Hu, Youjin; Hu, Xuyun; Hu, Zhiqing; Pang, Jialun; Li, Zhuo; Xue, Jinfeng; Feng, Mai; Wu, Lingqian; Liang, Desheng

    2014-03-28

    Although targeted gene addition could be stimulated strikingly by a DNA double strand break (DSB) created by either zinc finger nucleases (ZFNs) or TALE nucleases (TALENs), the DSBs are really mutagenic and toxic to human cells. As a compromised solution, DNA single-strand break (SSB) or nick has been reported to mediate high efficient gene addition but with marked reduction of random mutagenesis. We previously demonstrated effective targeted gene addition at the human multicopy ribosomal DNA (rDNA) locus, a genomic safe harbor for the transgene with therapeutic potential. To improve the transgene integration efficiency by using TALENs while lowering the cytotoxicity of DSBs, we created both TALENs and TALE nickases (TALENickases) targeting this multicopy locus. A targeting vector which could integrate a GFP cassette at the rDNA locus was constructed and co-transfected with TALENs or TALENickases. Although the fraction of GFP positive cells using TALENs was greater than that using TALENickases during the first few days after transfection, it reduced to a level less than that using TALENickases after continuous culture. Our findings showed that the TALENickases were more effective than their TALEN counterparts at the multi-copy rDNA locus, though earlier studies using ZFNs and ZFNickases targeting the single-copy loci showed the reverse. Besides, TALENickases mediated the targeted integration of a 5.4 kb fragment at a frequency of up to 0.62% in HT1080 cells after drug selection, suggesting their potential application in targeted gene modification not being limited at the rDNA locus.

  2. A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection.

    Science.gov (United States)

    Hung, Tran Quang; Chin, Wai Hoe; Sun, Yi; Wolff, Anders; Bang, Dang Duong

    2017-04-15

    Solid-phase PCR (SP-PCR) has become increasingly popular for molecular diagnosis and there have been a few attempts to incorporate SP-PCR into lab-on-a-chip (LOC) devices. However, their applicability for on-line diagnosis is hindered by the lack of sensitive and portable on-chip optical detection technology. In this paper, we addressed this challenge by combining the SP-PCR with super critical angle fluorescence (SAF) microlens array embedded in a microchip. We fabricated miniaturized SAF microlens array as part of a microfluidic chamber in thermoplastic material and performed multiplexed SP-PCR directly on top of the SAF microlens array. Attribute to the high fluorescence collection efficiency of the SAF microlens array, the SP-PCR assay on the LOC platform demonstrated a high sensitivity of 1.6 copies/µL, comparable to off-chip detection using conventional laser scanner. The combination of SP-PCR and SAF microlens array allows for on-chip highly sensitive and multiplexed pathogen detection with low-cost and compact optical components. The LOC platform would be widely used as a high-throughput biosensor to analyze food, clinical and environmental samples.

  3. High density penetrating electrode arrays for autonomic nerves.

    Science.gov (United States)

    Burns, John; Yee-Hsee Hsieh; Mueller, Andrew; Chevallier, Juliette; Sriram, T S; Lewis, Stephen J; Chew, Daniel; Achyuta, Anil; Fiering, Jason

    2016-08-01

    Electrode arrays for recording and stimulation in the central nervous system have enabled numerous advances in basic science and therapeutic strategies. In particular, micro-fabricated arrays with precision size and spacing offer the benefit of accessing single neurons and permit mapping of neuronal function. Similar advances are envisioned toward understanding the autonomic nervous system and developing therapies based on its modulation, but appropriate electrode arrays are lacking. Here, we present for the first time, a multi-channel electrode array suitable for penetration of peripheral nerves having diameters as small as 0.1mm, and demonstrate performance in vivo. These arrays have the potential to access multiple discrete nerve fibers in small nerves. We fabricated and characterized five-channel arrays and obtained preliminary recordings of activity when penetrating rat carotid sinus nerve. The electrodes were constructed using hybrid microfabrication processes. The individual electrode shafts are as small as 0.01mm in diameter and at its tip each has a defined site that is addressable via a standard electronic connector. In addition to acute in vivo results, we evaluate the device by electrochemical impedance spectroscopy. Having established the fabrication method, our next steps are to incorporate the arrays into an implantable configuration for chronic studies, and here we further describe concepts for such a device.

  4. Fabrication of high thermal conductivity arrays of carbon nanotubes and their composites

    Science.gov (United States)

    Geohegan, David B [Knoxville, TN; Ivanov, Ilya N [Knoxville, TN; Puretzky, Alexander A [Knoxville, TN

    2010-07-27

    Methods and apparatus are described for fabrication of high thermal conductivity arrays of carbon nanotubes and their composites. A composition includes a vertically aligned nanotube array including a plurality of nanotubes characterized by a property across substantially all of the vertically aligned nanotube array. A method includes depositing a vertically aligned nanotube array that includes a plurality of nanotubes; and controlling a deposition rate of the vertically aligned nanotubes array as a function of an in situ monitored property of the plurality of nanotubes.

  5. See Also:physica status solidi (b)physica status solidi (c)Copyright © 2004 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimGet Sample CopyFree Online Trial -->Recommend to Your LibrarianSave Title to My ProfileSet E-Mail Alert language="javascript">var homepagelinks = new Array(new Array("Journal Home","/cgi-bin/jhome/40000761",""),new Array("Issues","/cgi-bin/jtoc/40000761/",""),new Array("Early View","/cgi-bin/jeview/40000761/",""),new Array("News","/cgi-bin/jabout/40000761/news/index.html",""),new Array("Reviews","/cgi-bin/jabout/40000761/reviews.html",""),new Array("Read Cover Story","/cgi-bin/jabout/40000761/cover/2231/current.html","e"),new Array("","","s"),new Array("Product Information","/cgi-bin/jabout/40000761/2231_info.html",""),new Array("Editorial Board","/cgi-bin/jabout/40000761/edbd.html",""),new Array("For Authors","/cgi-bin/jabout/40000761/authors.html",""),new Array("For Referees","/cgi-bin/jabout/40000761/refserv.html",""),new Array("Subscribe","http://jws-edcv.wiley.com/jcatalog/JournalsCatalogOrder/JournalOrder?PRINT_ISSN=0031-8965",""),new Array("Contact","/cgi-bin/jabout/40000761/contact.html",""),new Array("Online Submission","http://www.manuscriptxpress.org/osm/",""),new Array("","","x"));writeJournalLinks("", "40000761");border="0" cellspacing="0" cellpadding="0" align="right"> Previous Issue | Next Issue >Volume 201, Issue14 (November 2004)Articles in the Current Issue:Rapid Research NoteHighly (001)-textured WS2-x films prepared by reactive radio frequency magnetron sputtering

    Science.gov (United States)

    Ellmer, K.; Mientus, R.; Seeger, S.; Weiß, V.

    2004-11-01

    Highly (001)-oriented WS2-x films were grown onto oxidized silicon substrates by reactive magnetron sputtering from a metallic tungsten target in argon-hydrogen sulfide mixtures. The best films with respect to the van-der-Waals orientation, i.e. with the (001) planes parallel to the substrate surface, were grown by excitation of the plasma with radio frequency of 27.12 MHz. These films exhibit the largest grains and the lowest film strain. It is shown that this effect is not due to the lower deposition rate at this high excitation frequency. Instead it was found that the lower DC voltage at the sputtering target is advantageous for the film growth since the bombardment of the growing film by highly energetic particles is avoided by this type of plasma excitation.

  6. Birefringent Microlens Array for Ultra High Resolution HMDs Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Small Business Innovation Research Phase I project will be used to analyze, design, model, and test a birefringent microlens array for use in a new type of...

  7. A Compact High Energy Camera for the Cherenkov Telescope Array

    CERN Document Server

    Daniel, M K; Berge, D; Buckley, J; Chadwick, P M; Cotter, G; Funk, S; Greenshaw, T; Hidaka, N; Hinton, J; Lapington, J; Markoff, S; Moore, P; Nolan, S; Ohm, S; Okumura, A; Ross, D; Sapozhnikov, L; Schmoll, J; Sutcliffe, P; Sykes, J; Tajima, H; Varner, G S; Vandenbroucke, J; Vink, J; Williams, D

    2013-01-01

    The Compact High Energy Camera (CHEC) is a camera-development project involving UK, US, Japanese and Dutch institutes for the dual-mirror Small-Sized Telescopes (SST-2M) of the Cherenkov Telescope Array (CTA). Two CHEC prototypes, based on different photosensors are funded and will be assembled and tested in the UK over the next ~18 months. CHEC is designed to record flashes of Cherenkov light lasting from a few to a hundred nanoseconds, with typical RMS image width and length of ~0.2 x 1.0 degrees, and has a 9 degree field of view. The physical camera geometry is dictated by the telescope optics: a curved focal surface with radius of curvature 1m and diameter ~35cm is required. CHEC is designed to work with both the ASTRI and GATE SST-2M telescope structures and will include an internal LED flasher system for calibration. The first CHEC prototype will be based on multi-anode photomultipliers (MAPMs) and the second on silicon photomultipliers (SiPMs or MPPCs). The first prototype will soon be installed on the...

  8. High NA diffractive array illuminators and application in a multi-spot scanning microscope

    NARCIS (Netherlands)

    Hulsken, B.; Vossen, D.; Stallinga, S.

    2012-01-01

    Array illuminators generating spots with high NA at high efficiency are presented. They are designed via application of high-NA scalar optics methods, and implemented as periodic binary phase structures. These array illuminators are used in a multi-spot scanning microscope for scanning large sample

  9. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

    Directory of Open Access Journals (Sweden)

    Nick D.L. Owens

    2016-01-01

    Full Text Available Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that “temporal synexpression” predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.

  10. Array Tomography: High-Resolution Three-Dimensional Immunofluorescence

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Kristina D. Micheva, Nancy O’Rourke, Brad Busse and Stephen J. Smith Adapted from [*Imaging: A Laboratory Manual* ](http://www.cshlpress.com/link/imagingp.htm)(ed. Yuste). CSHL Press, Cold Spring Harbor, NY, USA, 2010. ### INTRODUCTION Array tomography, which is described in this article, 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 g...

  11. High frequency of rare copy number variants affecting functionally related genes in patients with structural brain malformations

    DEFF Research Database (Denmark)

    Kariminejad, Roxana; Lind-Thomsen, Allan; Tümer, Zeynep;

    2011-01-01

    ) to investigate copy number variants (CNVs) in a cohort of 169 patients with various structural brain malformations including lissencephaly, polymicrogyria, focal cortical dysplasia, and corpus callosum agenesis. The majority of the patients had intellectual disabilities (ID) and suffered from symptomatic...

  12. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

    Science.gov (United States)

    Liu, Sanzhen; Zheng, Jun; Migeon, Pierre; Ren, Jie; Hu, Ying; He, Cheng; Liu, Hongjun; Fu, Junjie; White, Frank F.; Toomajian, Christopher; Wang, Guoying

    2017-01-01

    The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement. PMID:28186206

  13. High-sensitivity high-throughput chip based biosensor array for multiplexed detection of heavy metals

    Science.gov (United States)

    Yan, Hai; Tang, Naimei; Jairo, Grace A.; Chakravarty, Swapnajit; Blake, Diane A.; Chen, Ray T.

    2016-03-01

    Heavy metal ions released into the environment from industrial processes lead to various health hazards. We propose an on-chip label-free detection approach that allows high-sensitivity and high-throughput detection of heavy metals. The sensing device consists of 2-dimensional photonic crystal microcavities that are combined by multimode interferometer to form a sensor array. We experimentally demonstrate the detection of cadmium-chelate conjugate with concentration as low as 5 parts-per-billion (ppb).

  14. New high fill-factor triangular micro-lens array fabrication method using UV proximity printing

    CERN Document Server

    Lin, T -H; Chao, C -K

    2008-01-01

    A simple and effective method to fabricate a high fill-factor triangular microlens array using the proximity printing in lithography process is reported. The technology utilizes the UV proximity printing by controlling a printing gap between the mask and substrate. The designed approximate triangle microlens array pattern can be fabricated the high fill-factor triangular microlens array in photoresist. It is due to the UV light diffraction to deflect away from the aperture edges and produce a certain exposure in photoresist material outside the aperture edges. This method can precisely control the geometric profile of high fill factor triangular microlens array. The experimental results showed that the triangular micro-lens array in photoresist could be formed automatically when the printing gap ranged from 240 micrometers to 840 micrometers. The gapless triangular microlens array will be used to increases of luminance for backlight module of liquid crystal displays.

  15. Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis

    DEFF Research Database (Denmark)

    Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A

    2017-01-01

    BACKGROUND: Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their d......BACKGROUND: Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account......, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. RESULTS: Fifty-seven CNAs and cnLOH were observed in the ameloblastomas and six CNAs in the AC. Seven of the CNAs were rare (six in UA and one in MA), four of them encompassing genes (gains of 7q11.21, 1q32......: Ameloblastomas show rare CNAs and cnLOH, presenting a specific genomic profile with no overlapping of the rare alterations among UA, MA, and AC. These genomic changes might play a role in tumor evolution and in BRAFV600E-negative tumors....

  16. A Series of Medium and High Copy Number Arabinose-Inducible Escherichia coli Expression Vectors Compatible with pBR322 and pACYC184

    OpenAIRE

    Chakravartty, Vandana; Cronan, John E.

    2015-01-01

    The original pBAD24 plasmid and the derived lower copy number (the pBAD322 series) expression vectors have been widely used in Escherichia coli, Salmonella enterica, and related bacteria. However, a flexible pBAD expression system has been available only in pMB1 (ColE1) vectors. We report a series of pBAD vectors that replicate using the origin of plasmid RSF1030 that are compatible with pMB1 (ColE1) and p15A (pACYC) vectors. Both high (≥pBAD24) and medium (~pBAD322) copy number plasmids enco...

  17. Highly Ordered TiO2 Macropore Arrays as Transparent Photocatalysts

    OpenAIRE

    Yuan Dong; Junfeng Chao; Zhong Xie; Xin Xu; Zhuoran Wang; Di Chen

    2012-01-01

    Highly ordered transparent TiO2 macropore arrays were synthesized via a simple glass-clamping method at room temperature. The as-synthesized TiO2 macropore arrays show high transmittance in the visible light region and can be used as transparent photocatalysts for degradation of organic dyes.

  18. A Broadband and High Gain Tapered Slot Antenna for W-Band Imaging Array Applications

    Directory of Open Access Journals (Sweden)

    Dong Sik Woo

    2014-01-01

    Full Text Available A broadband and high gain tapered slot antenna (TSA by utilizing a broadband microstrip- (MS- to-coplanar stripline (CPS balun has been developed for millimeter-wave imaging systems and sensors. This antenna exhibits ultrawideband performance for frequency ranges from 70 to over 110 GHz with the high antenna gain, low sidelobe levels, and narrow beamwidth. The validity of this antenna as imaging arrays is also demonstrated by analyzing mutual couplings and 4-element linear array. This antenna can be applied to mm-wave phased array, imaging array for plasma diagnostics applications.

  19. Radiation-hard/high-speed array-based optical engine

    Science.gov (United States)

    Gan, K. K.; Buchholz, P.; Heidbrink, S.; Kagan, H. P.; Kass, R. D.; Moore, J.; Smith, D. S.; Vogt, M.; Ziolkowski, M.

    2016-12-01

    We have designed and fabricated a compact array-based optical engine for transmitting data at 10 Gb/s. The device consists of a 4-channel ASIC driving a VCSEL (Vertical Cavity Surface Emitting Laser) array in an optical package. The ASIC is designed using only core transistors in a 65 nm CMOS process to enhance the radiation-hardness. The ASIC contains an 8-bit DAC to control the bias and modulation currents of the individual channels in the VCSEL array. The DAC settings are stored in SEU (single event upset) tolerant registers. Several devices were irradiated with 24 GeV/c protons and the performance of the devices is satisfactory after the irradiation.

  20. Virtual electrodes for high-density electrode arrays

    Energy Technology Data Exchange (ETDEWEB)

    Cela, Carlos Jose; Lazzi, Gianluca

    2017-05-23

    The present embodiments are directed to implantable electrode arrays having virtual electrodes. The virtual electrodes may improve the resolution of the implantable electrode array without the burden of corresponding complexity of electronic circuitry and wiring. In a particular embodiment, a virtual electrode may include one or more passive elements to help steer current to a specific location between the active electrodes. For example, a passive element may be a metalized layer on a substrate that is adjacent to, but not directly connected to an active electrode. In certain embodiments, an active electrode may be directly coupled to a power source via a conductive connection. Beneficially, the passive elements may help to increase the overall resolution of the implantable array by providing additional stimulation points without requiring additional wiring or driver circuitry for the passive elements.

  1. BAC TG-EMBED: one-step method for high-level, copy-number-dependent, position-independent transgene expression.

    Science.gov (United States)

    Bian, Qian; Belmont, Andrew S

    2010-06-01

    Chromosome position effects combined with transgene silencing of multi-copy plasmid insertions lead to highly variable and usually quite low expression levels of mini-genes integrated into mammalian chromosomes. Together, these effects greatly complicate obtaining high-level expression of therapeutic proteins in mammalian cells or reproducible expression of individual or multiple transgenes. Here, we report a simple, one-step procedure for obtaining high-level, reproducible mini-gene expression in mammalian cells. By inserting mini-genes at different locations within a BAC containing the DHFR housekeeping gene locus, we obtain copy-number-dependent, position-independent expression with chromosomal insertions of one to several hundred BAC copies. These multi-copy DHFR BAC insertions adopt similar large-scale chromatin conformations independent of their chromosome integration site, including insertions within centromeric heterochromatin. Prevention of chromosome position effects, therefore, may be the result of embedding the mini-gene within the BAC-specific large-scale chromatin structure. The expression of reporter mini-genes can be stably maintained during continuous, long-term culture in the presence of drug selection. Finally, we show that this method is extendable to reproducible, high-level expression of multiple mini-genes, providing improved expression of both single and multiple transgenes.

  2. Photonic Links for High-Performance Arraying of Antennas

    Science.gov (United States)

    Huang, Shouhua; Tjoelker, Robert

    2009-01-01

    An architecture for arraying microwave antennas in the next generation of NASA s Deep Space Network (DSN) involves the use of all photonic links between (1) the antennas in a given array and (2) a signal processing center. In this architecture, all affected parts at each antenna pedestal [except a front-end low-noise amplifier for the radio-frequency (RF) signal coming from the antenna and an optical transceiver to handle monitor and control (M/C) signals] would be passive optical parts

  3. Conductively cooled high-power high-brightness bars and fiber-coupled arrays

    Science.gov (United States)

    Zhou, Hailong; Mondry, Mark; Fouksman, Michael; Weiss, Eli; Anikitchev, Serguei; Kennedy, Keith; Li, Jun; Zucker, Erik; Rudy, Paul; Kongas, Jukka; Haapamaa, Jouko; Lehkonen, Sami

    2005-03-01

    Solid-state-laser and fiber laser pumping, reprographics, medical and materials processing applications require high power, high-brightness bars and fiber-coupled arrays. Conductively cooled laser diode bars allow customers to simplify system design and reduce operational size, weight, and costs. We present results on next generation high brightness, high reliability bars and fiber-coupled arrays at 790-830 nm, 940 nm and 980 nm wavelengths. By using novel epitaxial structures, we have demonstrated highly reliable 808 nm, 30% fill-factor conductively cooled bars operating at 60W CW mode, corresponding to a linear power density (LPD) of 20 mW/&mum. At 25°C, the bars have shown greater than 50% wall-plug-efficiency (WPE) when operating at 60W. Our novel approach has also reduced the fast-axis divergence FWHM from 31° to less than 24°. These bars have a 50% brightness improvement compared to our standard products with this geometry. At 980nm, we have demonstrated greater than 100W CW from 20% fill-factor conductively cooled bars, corresponding to a LPD of 50 mW/μm. At 25°C, the WPE for 976nm bars consistently peaks above 65% and remains greater than 60% at 100W. We coupled the beam output from those high-brightness bars into fiber-array-packages ("FAPs"), and we also achieved high-brightness and high-efficiency FAPs. We demonstrated 60W from a 600μm core-diameter fiber-bundle with a high WPE of 55%, and a low numerical aperture of 0.115. The brightness of such FAPs is four times higher than our standard high-power 40W FAP products at Coherent. Ongoing life test data suggests an extrapolated lifetime greater than 10,000 hours at 80W CW operating-condition based on 30%FF conductively cooled bar geometry.

  4. Low-copy episomal vector pFY20 and high-saturation coverage genomic libraries for the fission yeast Schizosaccharomyces pombe.

    Science.gov (United States)

    Wahls, Wayne P; Davidson, Mari K

    2008-09-01

    In fission yeast, as in many organisms, episomally replicating plasmid DNA molecules can be used for a wide variety of applications. However, replicating plasmids described previously are each propagated at a high copy number per cell. Plasmid fission yeast twenty (pFY20) contains the ura4(+) gene for positive and negative selection, an origin of replication (ars1) and a stability element (stb). Although this plasmid does not have a centromere, it is propagated with a copy number of about two plasmids per haploid genome equivalent and it is transmitted with relatively high fidelity in mitosis and meiosis. This low-copy vector is useful for screens and mutational studies where overexpression (e.g. from high copy plasmids) is undesirable. We therefore constructed multiple partial-digest, size-fractionated, fission yeast genomic DNA libraries in pFY20 and in the cloning vector pBluescript KS(+). These libraries have sufficient complexity (average of 2100 genome equivalents each) for saturation screening by complementation, plasmid shuffle or hybridization.

  5. High Resolution Processing with an Active Phased Array SAR

    NARCIS (Netherlands)

    Nijenboer, F.J.; Otten, M.P.G.

    1999-01-01

    The Dutch PHARUS system is a polarimetric active phased array SAR capable of performing advanced SAR modes. Advanced SAR modes that are being investigated are: spotlight SAR, sliding spotlight SAR, stepped frequency SAR and interferometric SAR. The flight experiments and automatic beam steering

  6. Cognitive MIMO Frequency Diverse Array Radar with High LPI Performance

    Directory of Open Access Journals (Sweden)

    Ling Huang

    2016-01-01

    Full Text Available Frequency diverse array (FDA has its unique advantage in realizing low probability of intercept (LPI technology for its dependent beam pattern. In this paper, we proposed a cognitive radar based on the frequency diverse array multiple-input multiple-output (MIMO. To implement LPI of FDA MIMO transmit signals, a scheme for array weighting design is proposed, which is to minimize the energy of the target location and maximize the energy of the receiver. This is based on the range dependent characteristics of the frequency diverse array transmit beam pattern. To realize the objective problem, the algorithm is proposed as follows: the second-order nonconvex optimization problem is converted into a convex problem and solved by the bisection method and convex optimization. To get the information of target, the FDA MIMO radar is proposed to estimate the target parameters. Simulation results show that the proposed approach is effective in decreasing the detection probability of radar with lossless detection performance of the receive signal.

  7. The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.

    Science.gov (United States)

    Nguyen, Hoang T; Merriman, Tony R; Black, Michael A

    2014-01-01

    Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN) at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralog ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust the results across multiple populations, in combination with a Bayesian normal mixture model to cluster segmentation scores into groups for individual CN counts. The performance of CNVrd2 was compared to that of two other read depth-based methods (CNVnator, cn.mops) at the CCL3L1 and DEFB103A loci. The highest concordance with the paralog ratio test method was observed for CNVrd2 (77.8/90.4% for CNVrd2, 36.7/4.8% for cn.mops and 7.2/1% for CNVnator at CCL3L1 and DEF103A). CNVrd2 is available as an R package as part of the Bioconductor project: http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html.

  8. The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data

    Directory of Open Access Journals (Sweden)

    Hoang eNguyen

    2014-08-01

    Full Text Available Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralogue ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust the results across multiple populations, in combination with a Bayesian normal mixture model to cluster segmentation scores into groups for individual CN counts. The performance of CNVrd2 was compared to that of two other read depth-based methods (CNVnator, cn.mops at the CCL3L1 and DEFB103A loci, and the highest concordance with the paralog ratio test method was observed for CNVrd2 (77.8%/90.4% for CNVrd2, 36.7%/4.8% for cn.mops and 7.2%/1% for CNVnator at CCL3L1 and DEF103A. CNVrd2 is available as an R package as part of the Bioconductor project: http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html.

  9. High-Sensitivity Phased Arrays for Radio Astronomy and Satellite Communications

    Science.gov (United States)

    Diao, Junming

    Radio astronomy is used to study stars, galaxies, black holes and gas clouds radiation at radio frequencies. Detecting extremely weak signals from deep space radio sources requires high sensitive feed system associated with large dish antennas. The key figure of merit is survey speed, or the time required to map a region of the sky to a given source flux density. Survey speed is proportional to the frequency bandwidth, the field of view or observable region of the sky, and the squared sensitivity, where sensitivity is related to reflector aperture efficiency and system noise temperature. Compared to the traditional single feed, phased array feeds with significantly expanded field of view are considered as the next generation feed for radio telescope. This dissertation outlines the design, analysis and measurement of high sensitivity L-band and mm-wave phased array feeds for the 100-meter Green Bank Telescope. Theoretical works for radio astronomy includes design guideline for high sensitivity phased array feed, fundamental frequency bandwidth limit, array antenna loss influenced by mutual coupling and beamformer coefficients and possibility of superdirectivity for radio telescopes and other antennas. These study are helpful to understand and guide the design of a phased array feed system. In the absence of dish antennas, sparse phased arrays with aperiodic structure have been developed for satellite communications. A compromise between the peak side lobe level, array element density, directivity and design complexity is studied. We have found that the array peak side lobe level can be reduced by enhancing the array element direction at the main lobe direction, increasing the array element density and enlarging the array size. A Poynting streamline approach develops to understand the properties of a receiving antenna and the mutual coupling effects between array elements. This method has been successfully used to generate effective area shape for many types of

  10. High Sensitivity Indium Phosphide Based Avalanche Photodiode Focal Plane Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — nLight has demonstrated highly-uniform APD arrays based on the highly sensitive InGaAs/InP material system. These results provide great promise for achieving the...

  11. Highly Integrated, Reconfigurable, Large-Area, Flexible Radar Antenna Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Highly-integrated, reconfigurable radar antenna arrays fabricated on flexible substrates offer high functionality in a portable package that can be rolled up and...

  12. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  13. Highly sensitive glucose biosensor based on Au-Ni coaxial nanorod array having high aspect ratio.

    Science.gov (United States)

    Hsu, Che-Wei; Wang, Gou-Jen

    2014-06-15

    An effective glucose biosensor requires a sufficient amount of GOx immobilizing on the electrode surface. An electrode of a 3D nanorod array, having a larger surface-to-volume ratio than a 2D nanostructure, can accommodate more GOx molecules to immobilize onto the surface of the nanorods. In this study, a highly sensitive Au-Ni coaxial nanorod array electrode fabricated through the integration of nano electroforming and immersion gold (IG) method for glucose detection was developed. The average diameter of the as-synthesized Ni nanorods and that of the Au-Ni nanorods were estimated to be 150 and 250 nm, respectively; both had a height of 30 μm. The aspect ratio was 120. Compared to that of a flat Au electrode, the effective sensing area was enhanced by 79.8 folds. Actual glucose detections demonstrated that the proposed Au-Ni coaxial nanorod array electrode could operate in a linear range of 27.5 μM-27.5mM with a detection limit of 5.5μM and a very high sensitivity of 769.6 μA mM(-1)cm(-2). Good selectivity of the proposed sensing device was verified by sequential injections of uric acid (UA) and ascorbic acid (AA). Long-term stability was examined through successive detections over a period of 30 days.

  14. Highly reproducible SERS arrays directly written by inkjet printing

    Science.gov (United States)

    Yang, Qiang; Deng, Mengmeng; Li, Huizeng; Li, Mingzhu; Zhang, Cong; Shen, Weizhi; Li, Yanan; Guo, Dan; Song, Yanlin

    2014-12-01

    SERS arrays with uniform gold nanoparticle distribution were fabricated by direct-writing with an inkjet printing method. Quantitative analysis based on Raman detection was achieved with a small standard statistical deviation of less than 4% for the reproducibility and less than 5% for the long-term stability for 12 weeks.SERS arrays with uniform gold nanoparticle distribution were fabricated by direct-writing with an inkjet printing method. Quantitative analysis based on Raman detection was achieved with a small standard statistical deviation of less than 4% for the reproducibility and less than 5% for the long-term stability for 12 weeks. Electronic supplementary information (ESI) available: Additional information on the experimental details, gold nanoparticle characterization, and theoretical calculation for the diameters of contact area of droplets on substrates with different contact angles. See DOI: 10.1039/c4nr04656k

  15. High-energy interactions in Kinetic Inductance Detectors arrays

    CERN Document Server

    D'Addabbo, A; Goupy, J; Benoit, A; Bourrion, O; Catalano, A; Macias-Perez, J F; Monfardini, A

    2015-01-01

    The impacts of Cosmic Rays on the detectors are a key problem for space-based missions. We are studying the effects of such interactions on arrays of Kinetic Inductance Detectors (KID), in order to adapt this technology for use on board of satellites. Before proposing a new technology such as the Kinetic Inductance Detectors for a space-based mission, the problem of the Cosmic Rays that hit the detectors during in-flight operation has to be studied in detail. We present here several tests carried out with KID exposed to radioactive sources, which we use to reproduce the physical interactions induced by primary Cosmic Rays, and we report the results obtained adopting different solutions in terms of substrate materials and array geometries. We conclude by outlining the main guidelines to follow for fabricating KID for space-based applications.

  16. Highly Directive Reflect Array Antenna Design for Wireless Power Transfer

    Science.gov (United States)

    2017-04-14

    Duttagupta, “A broadband reflect-array with combination of sub-wavelength phasing elements,” in Asia Pacific Microwave Conference ( IEEE - APMC) New Delhi...1] Bialkowski et al. IEEE Transactions on Antennas and Propagation, November 2008 [2] Rajagopalan et al., IEEE Antennas and Propagation Magazine...October 2012 [3] Yoon et al., IEEE Transactions on Antennas and Propagation, February 2015 [4] Yoon et al., Electronics Letters, April 2014 Funds

  17. Mate Choice Copying in Humans.

    Science.gov (United States)

    Waynforth, D

    2007-09-01

    There is substantial evidence that in human mate choice, females directly select males based on male display of both physical and behavioral traits. In non-humans, there is additionally a growing literature on indirect mate choice, such as choice through observing and subsequently copying the mating preferences of conspecifics (mate choice copying). Given that humans are a social species with a high degree of sharing information, long-term pair bonds, and high parental care, it is likely that human females could avoid substantial costs associated with directly searching for information about potential males by mate choice copying. The present study was a test of whether women perceived men to be more attractive when men were presented with a female date or consort than when they were presented alone, and whether the physical attractiveness of the female consort affected women's copying decisions. The results suggested that women's mate choice decision rule is to copy only if a man's female consort is physically attractive. Further analyses implied that copying may be a conditional female mating tactic aimed at solving the problem of informational constraints on assessing male suitability for long-term sexual relationships, and that lack of mate choice experience, measured as reported lifetime number of sex partners, is also an important determinant of copying.

  18. Update-in-Place Analysis for True Multidimensional Arrays

    Directory of Open Access Journals (Sweden)

    Steven M. Fitzgerald

    1996-01-01

    Full Text Available Applicative languages have been proposed for defining algorithms for parallel architectures because they are implicitly parallel and lack side effects. However, straightforward implementations of applicative-language compilers may induce large amounts of copying to preserve program semantics. The unnecessary copying of data can increase both the execution time and the memory requirements of an application. To eliminate the unnecessary copying of data, the Sisal compiler uses both build-in-place and update-in-place analyses. These optimizations remove unnecessary array copy operations through compile-time analysis. Both build-in-place and update-in-place are based on hierarchical ragged arrays, i.e., the vector-of-vectors array model. Although this array model is convenient for certain applications, many optimizations are precluded, e.g., vectorization. To compensate for this deficiency, new languages, such as Sisal 2.0, have extended array models that allow for both high-level array operations to be performed and efficient implementations to be devised. In this article, we introduce a new method to perform update-in-place analysis that is applicable to arrays stored either in hierarchical or in contiguous storage. Consequently, the array model that is appropriate for an application can be selected without the loss of performance. Moreover, our analysis is more amenable for distributed memory and large software systems.

  19. High burden of copy number alterations and c-MYC amplification in prostate cancer from BRCA2 germline mutation carriers

    NARCIS (Netherlands)

    Castro, E.; Jugurnauth-Little, S.; Karlsson, Q.; Al-Shahrour, F.; Pineiro-Yanez, E.; Van de Poll, F.; Leongamornlert, D.; Dadaev, T.; Govindasami, K.; Guy, M.; Eeles, R.; Kote-Jarai, Z.; Oosterwijk, J. C.

    2015-01-01

    Background: Germline BRCA2 mutations are associated with poorer outcome prostate cancer ( PCa) compared with sporadic tumours but this association remains to be characterised. In this study, we aim to assess if there is a signature set of copy number alterations ( CNA) that could aid to the identifi

  20. Scaling up Copy Detection

    OpenAIRE

    Li, Xian; Dong, Xin Luna; Lyons, Kenneth B.; Meng, Weiyi; Srivastava, Divesh

    2015-01-01

    Recent research shows that copying is prevalent for Deep-Web data and considering copying can significantly improve truth finding from conflicting values. However, existing copy detection techniques do not scale for large sizes and numbers of data sources, so truth finding can be slowed down by one to two orders of magnitude compared with the corresponding techniques that do not consider copying. In this paper, we study {\\em how to improve scalability of copy detection on structured data}. Ou...

  1. The NumPy array: a structure for efficient numerical computation

    CERN Document Server

    Van Der Walt, Stefan; Varoquaux, Gaël

    2011-01-01

    In the Python world, NumPy arrays are the standard representation for numerical data. Here, we show how these arrays enable efficient implementation of numerical computations in a high-level language. Overall, three techniques are applied to improve performance: vectorizing calculations, avoiding copying data in memory, and minimizing operation counts. We first present the NumPy array structure, then show how to use it for efficient computation, and finally how to share array data with other libraries.

  2. Arc arrays: studies of high resolution techniques for multibeam bathymetric applications

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.; Schenke, H.W.

    arrayof 15 degrees arc. The superiorityof the high resolution methods is seen by examining the patterns of the 15 degrees arc array under multiple source/interference conditions, i.e. the situation for rough terrain or artefactcreating conditions...

  3. TRUSSELATOR - On-Orbit Fabrication of High Performance Support Structures for Solar Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Trusselator technology will enable on-orbit fabrication of support structures for high-power solar arrays and large antennas, achieving order-of-magnitude...

  4. FDM-HAWK, A High Performance Compact Modular Solar Array Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Developing a next generation high performance solar array with significant reduction in size and weight will result in improved NASA mission capabilities at lower...

  5. High Resolution, Radiation Tolerant Focal Plane Array for Lunar And Deep Space Applications Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Aerius Photonics and its partners propose the development of a high resolution, radiation hardened 3-D FLASH Focal Plane Array (FPA), with performance expected to be...

  6. 2D SQIF arrays using 20 000 YBCO high R n Josephson junctions

    Science.gov (United States)

    Mitchell, E. E.; Hannam, K. E.; Lazar, J.; Leslie, K. E.; Lewis, C. J.; Grancea, A.; Keenan, S. T.; Lam, S. K. H.; Foley, C. P.

    2016-06-01

    Superconducting quantum interference filters (SQIFs) have been created using two dimensional arrays of YBCO step-edge Josephson junctions connected together in series and parallel configurations via superconducting loops with a range of loop areas and loop inductances. A SQIF response, as evidenced by a single large anti-peak at zero applied flux, is reported at 77 K for step-edge junction arrays with the junction number N = 1 000 up to 20 000. The SQIF sensitivity (slope of peak) increased linearly with N up to a maximum of 1530 V T-1. Array parameters related to geometry and average junction characteristics are investigated in order to understand and improve the SQIF performance in high temperature superconducting arrays. Initial investigations also focus on the effect of the SQUID inductance factor on the SQIF sensitivity by varying both the mean critical current and the mean inductance of the loops in the array. The RF response to a 30 MHz signal is demonstrated.

  7. Monolithic blue LED series arrays for high-voltage AC operation

    Energy Technology Data Exchange (ETDEWEB)

    Ao, Jin-Ping [Satellite Venture Business Laboratory, University of Tokushima, Tokushima 770-8506 (Japan); Sato, Hisao; Mizobuchi, Takashi; Morioka, Kenji; Kawano, Shunsuke; Muramoto, Yoshihiko; Sato, Daisuke; Sakai, Shiro [Nitride Semiconductor Co. Ltd., Naruto, Tokushima 771-0360 (Japan); Lee, Young-Bae; Ohno, Yasuo [Department of Electrical and Electronic Engineering, University of Tokushima, Tokushima 770-8506 (Japan)

    2002-12-16

    Design and fabrication of monolithic blue LED series arrays that can be operated under high ac voltage are described. Several LEDs, such as 3, 7, and 20, are connected in series and in parallel to meet ac operation. The chip size of a single device is 150 {mu}m x 120 {mu}m and the total size is 1.1 mm x 1 mm for a 40(20+20) LED array. Deep dry etching was performed as device isolation. Two-layer interconnection and air bridge are utilized to connect the devices in an array. The monolithic series array exhibit the expected operation function under dc and ac bias. The output power and forward voltage are almost proportional to LED numbers connected in series. On-wafer measurement shows that the output power is 40 mW for 40(20+20) LED array under ac 72 V. (Abstract Copyright [2002], Wiley Periodicals, Inc.)

  8. High Precision and High Yield Fabrication of Dense Nanoparticle Arrays onto DNA Origami at Statistically Independent Binding Sites †

    OpenAIRE

    Takabayashi, Sadao; Klein, William P.; Onodera, Craig; Rapp, Blake; Flores-Estrada, Juan; Lindau, Elias; Snowball, Lejmarc; Sam, Joseph Tyler; Padilla, Jennifer E.; Lee, Jeunghoon; Knowlton, William B.; Graugnard, Elton; Yurke, Bernard; Kuang, Wan; Hughes, William L.

    2014-01-01

    High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templa...

  9. High risk genetic factor in Chinese patients with idiopathic male infertility:deletion of DAZ gene copy on Y chromosome

    Institute of Scientific and Technical Information of China (English)

    杨元; 肖翠英; 张思仲; 张思孝; 黄明孔; 林立

    2004-01-01

    @@ Idiopathic azoospermia or oligozoospermia affects approximately 2%-4% of all married males. Recently studies have confirmed that the deletion of DAZ in AZFc region of Y chromosome may be one of the important genetic aetiologies of Caucasian male infertility. To determine the relationship between DAZ gene deletion and idiopathic male infertility in Chinese population, we analysed the DAZ gene copy number of AZFc region in patients with idiopathic azoospermia or oligozoospermia, as well as fertile Chinese men.

  10. Patterned growth of high aspect ratio silicon wire arrays at moderate temperature

    Science.gov (United States)

    Morin, Christine; Kohen, David; Tileli, Vasiliki; Faucherand, Pascal; Levis, Michel; Brioude, Arnaud; Salem, Bassem; Baron, Thierry; Perraud, Simon

    2011-04-01

    High aspect ratio silicon wire arrays with excellent pattern fidelity over wafer-scale area were grown by chemical vapor deposition at moderate temperature, using a gas mixture of silane and hydrogen chloride. An innovative two-step process was developed for in situ doping of silicon wires by diborane. This process led to high p-type doping levels, up to 10 18-10 19 cm -3, without degradation of the silicon wire array pattern fidelity.

  11. New multi-purpose high copy number vector with greater mitotic stability for diverse applications in fission yeast Schizosaccharomyces pombe.

    Science.gov (United States)

    Verma, Hemant Kumar; Singh, Jagmohan

    2012-11-01

    We have constructed a pUC19-based multipurpose ATG vector in Schizosaccharomyces pombe with higher copy number and mitotic stability possible with commonly used vectors. The vector, having an NdeI site in its polylinker to provide ATG site for expression, carries a greatly truncated version of URA3 gene, URA3m, of Saccharomyces cerevisiae as a selection marker. In addition, it contains the mat2P-right flank region (mat2P-RF) of S. pombe as an autonomous replicating sequence (ARS) and a polylinker with wider choice of restriction sites. While URA3m confers an increase in plasmid copy number up to 200 copies/cell, mat2P-RF imparts greater mitotic stability than the standard ars1 element of S. pombe. Finally, the vector also includes the transcription termination signal of the nmt1 gene (Tnmt1). This basic vector should serve as a versatile tool for studies of gene function in S. pombe.

  12. Unlikely Combination of Experiments With a Novel High-Voltage CIGS Photovoltaic Array: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    del Cueto, J. A.; Sekulic, B. R.

    2006-05-01

    A new high-voltage array comprising bipolar strings of copper indium gallium diselenide (CIGS) photovoltaic (PV) modules was inaugurated in 2005. It is equipped with a unique combination of tests, which likely have never before been deployed simultaneously within a single array: full current-voltage (I-V) traces, high-voltage leakage current measurements, and peak-power tracking or temporal stepped-bias profiling. The array nominally produces 1 kW power at 1 sun. The array's electrical characteristics are continuously monitored and controlled with a programmable electronic load interfaced to a data acquisition system (DAS), that also records solar and meteorological data. The modules are mounted with their frames electrically isolated from earth ground, in order to facilitate measurement of the leakage currents that arise between the high voltage bias developed in the series-connected cells and modules and their mounting frames. Because the DAS can perform stepped biasing of the array as a function of time, synchronous detection of the leakage current data with alternating bias is available. Leakage current data and their dependence on temperature and voltage are investigated. Array power data are analyzed across a wide range of varying illuminations and temperatures from the I-V traces. Array performance is also analyzed from an energy output perspective using peak-power tracking data.

  13. Electronic system for high power load control. [solar arrays

    Science.gov (United States)

    Miller, E. L. (Inventor)

    1980-01-01

    Parallel current paths are divided into two groups, with control devices in the current paths of one group each having a current limiting resistor, and the control devices in the other group each having no limiting resistor, so that when the control devices of the second group are turned fully on, a short circuit is achieved by the arrangement of parallel current paths. Separate but coordinated control signals are provided to turn on the control devices of the first group and increase their conduction toward saturation as a function of control input, and when fully on, or shortly before, to turn on the control devices of the second group and increase their conduction toward saturation as a function of the control input as that input continues to increase. Electronic means may be used to generate signals. The system may be used for 1-V characteristic measurements of solar arrays as well as for other load control purposes.

  14. High Altitude Infrasound Measurements using Balloon-Borne Arrays

    Science.gov (United States)

    Bowman, D. C.; Johnson, C. S.; Gupta, R. A.; Anderson, J.; Lees, J. M.; Drob, D. P.; Phillips, D.

    2015-12-01

    For the last fifty years, almost all infrasound sensors have been located on the Earth's surface. A few experiments consisting of microphones on poles and tethered aerostats comprise the remainder. Such surface and near-surface arrays likely do not capture the full diversity of acoustic signals in the atmosphere. Here, we describe results from a balloon mounted infrasound array that reached altitudes of up to 38 km (the middle stratosphere). The balloon drifted at the ambient wind speed, resulting in a near total reduction in wind noise. Signals consistent with tropospheric turbulence were detected. A spectral peak in the ocean microbarom range (0.12 - 0.35 Hz) was present on balloon-mounted sensors but not on static infrasound stations near the flight path. A strong 18 Hz signal, possibly related to building ventilation systems, was observed in the stratosphere. A wide variety of other narrow band acoustic signals of uncertain provenance were present throughout the flight, but were absent in simultaneous recordings from nearby ground stations. Similar phenomena were present in spectrograms from the last balloon infrasound campaign in the 1960s. Our results suggest that the infrasonic wave field in the stratosphere is very different from that which is readily detectable on surface stations. This has implications for modeling acoustic energy transfer between the lower and upper atmosphere as well as the detection of novel acoustic signals that never reach the ground. Our work provides valuable constraints on a proposed mission to detect earthquakes on Venus using balloon-borne infrasound sensors.

  15. Growth of high-density horizontally aligned SWNT arrays using Trojan catalysts.

    Science.gov (United States)

    Hu, Yue; Kang, Lixing; Zhao, Qiuchen; Zhong, Hua; Zhang, Shuchen; Yang, Liangwei; Wang, Zequn; Lin, Jingjing; Li, Qingwen; Zhang, Zhiyong; Peng, Lianmao; Liu, Zhongfan; Zhang, Jin

    2015-01-20

    Single-walled carbon nanotube (SWNT)-based electronics have been regarded as one of the most promising candidate technologies to replace or supplement silicon-based electronics in the future. These applications require high-density horizontally aligned SWNT arrays. During the past decade, significant efforts have been directed towards growth of high-density SWNT arrays. However, obtaining SWNT arrays with suitable density and quality still remains a big challenge. Herein, we develop a rational approach to grow SWNT arrays with ultra-high density using Trojan catalysts. The density can be as high as 130 SWNTs μm(-1). Field-effect transistors fabricated with our SWNT arrays exhibit a record drive current density of -467.09 μA μm(-1) and an on-conductance of 233.55 μS μm(-1). Radio frequency transistors fabricated on these samples exhibit high intrinsic fT and fMAX of 6.94 and 14.01 GHz, respectively. These results confirm our high-density SWNT arrays are strong candidates for applications in electronics.

  16. A high-copy T7 Escherichia coli expression vector for the production of recombinant proteins with a minimal N-terminal His-tagged fusion peptide

    Directory of Open Access Journals (Sweden)

    Ramos C.R.R.

    2004-01-01

    Full Text Available We report here the construction of a vector derived from pET3-His and pRSET plasmids for the expression and purification of recombinant proteins in Escherichia coli based on T7 phage RNA polymerase. The resulting pAE plasmid combined the advantages of both vectors: small size (pRSET, expression of a short 6XHis tag at N-terminus (pET3-His and a high copy number of plasmid (pRSET. The small size of the vector (2.8 kb and the high copy number/cell (200-250 copies facilitate the subcloning and sequencing procedures when compared to the pET system (pET3-His, 4.6 kb and 40-50 copies and also result in high level expression of recombinant proteins (20 mg purified protein/liter of culture. In addition, the vector pAE enables the expression of a fusion protein with a minimal amino-terminal hexa-histidine affinity tag (a tag of 9 amino acids using XhoI restriction enzyme for the 5'cloning site as in the case of pET3-His plasmid and in contrast to proteins expressed by pRSET plasmids (a tag of 36 amino acids using BamHI restriction enzyme for the 5'cloning site. Thus, although proteins expressed by pRSET plasmids also have a hexa-histidine tag, the fusion peptide is much longer and may represent a problem for some recombinant proteins.

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

    Science.gov (United States)

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

    2014-09-01

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

  18. High-Throughput Amplicon-Based Copy Number Detection of 11 Genes in Formalin-Fixed Paraffin-Embedded Ovarian Tumour Samples by MLPA-Seq.

    Science.gov (United States)

    Kondrashova, Olga; Love, Clare J; Lunke, Sebastian; Hsu, Arthur L; Waring, Paul M; Taylor, Graham R

    2015-01-01

    Whilst next generation sequencing can report point mutations in fixed tissue tumour samples reliably, the accurate determination of copy number is more challenging. The conventional Multiplex Ligation-dependent Probe Amplification (MLPA) assay is an effective tool for measurement of gene dosage, but is restricted to around 50 targets due to size resolution of the MLPA probes. By switching from a size-resolved format, to a sequence-resolved format we developed a scalable, high-throughput, quantitative assay. MLPA-seq is capable of detecting deletions, duplications, and amplifications in as little as 5ng of genomic DNA, including from formalin-fixed paraffin-embedded (FFPE) tumour samples. We show that this method can detect BRCA1, BRCA2, ERBB2 and CCNE1 copy number changes in DNA extracted from snap-frozen and FFPE tumour tissue, with 100% sensitivity and >99.5% specificity.

  19. Fiber-coupled high resolution infrared array spectrometer for the Kuiper Airborne Observatory

    Science.gov (United States)

    Glenar, D. A.; Reuter, D.; Mumma, M. J.; Chin, G.; Wiedemann, G.; Jennings, D.

    1990-01-01

    A novel cryogenic grating spectrometer (FCAS) is being designed for observations of volatiles in cometary and planetary atmospheres, and in newly forming planetary systems. The instrument features two-dimensional detector arrays coupled to a high-dispersion echelle by infrared fibers, and will achieve a spectral resolving power of about 40,000. The primary observational platform for this instrument will be the Kuiper Airborne Observatory, but it will also be configured for use at ground-based observatories. Initially, the spectrometer will use a 58 x 62, 1- to 5-micron InSb array. Larger-format IR arrays and arrays of different composition, will later be incorporated as they become available. The instrument will be used in two modes. The first uses a large format IR array in the spectral image plane for the customary one-dimensional spectral-one-dimensional spatial coverage. In the second mode, a massive, coherent bundle of infrared transmitting ZrF4 fibers will be installed after the dispersive element, to reformat the two-dimensional array into an elongated one-dimensional array for wide spectral coverage, allowing multiple lines to be measured in a single integration with high sensitivity. The overall instrument design is discussed, and the system sensitivity is estimated.

  20. A High-throughput Genomic Tool: Diversity Array Technology Complementary for Rice Genotyping

    Institute of Scientific and Technical Information of China (English)

    Yong Xie; Kenneth McNally; Cheng-Yun Li; Hei Leung; You-Yong Zhu

    2006-01-01

    Diversity array technology (DArTTM) was a genotyping tool characterized gel-independent and high throughput.The main purpose of present study is to validate DArT for rice (Oryza sativa L.)genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a generalpurpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc (Numerical taxonomy system for cluster and ordination analysis, v. 2.02j) software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple Sequence repeats genotyping outline and varieties' pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.

  1. Novel design of multicapillary arrays for high-throughput DNA sequencing.

    Science.gov (United States)

    Tsupryk, Andriy; Gorbovitski, Michael; Kabotyanski, Evgeni A; Gorfinkel, Vera

    2006-07-01

    A novel approach to design and optimize linear multicapillary arrays (LMCAs) for high-throughput DNA sequencing is proposed. A significant increase in the number of capillary lanes is obtained due to the use of composite insertions alternately placed between working capillaries of the array and a specific combination of refractive indices of the DNA separation matrix, capillary glass, the insertions and a medium which surrounds the capillary array. Theoretical and experimental studies showed that in conjunction with a dual-side laser illumination scheme, the proposed LMCA design allows a simultaneous uniform irradiation of as many as 550 working capillaries.

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

    Science.gov (United States)

    Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

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

  3. Quantum copying: A review

    Directory of Open Access Journals (Sweden)

    Mark Hillery

    2000-07-01

    Full Text Available Quantum information is stored in two-level quantum systems known as qubits. The no-cloning theorem states that the state of an unknown qubit cannot be copied. This is in contrast to classical information which can be copied. If one drops the requirement that the copies be perfect it is possible to design quantum copiers. This paper presents a short review of the theory of quantum copying.

  4. High taxonomic level fingerprint of the human intestinal microbiota by Ligase Detection Reaction - Universal Array approach

    Directory of Open Access Journals (Sweden)

    Vitali Beatrice

    2010-04-01

    Full Text Available Abstract Background Affecting the core functional microbiome, peculiar high level taxonomic unbalances of the human intestinal microbiota have been recently associated with specific diseases, such as obesity, inflammatory bowel diseases, and intestinal inflammation. Results In order to specifically monitor microbiota unbalances that impact human physiology, here we develop and validate an original DNA-microarray (HTF-Microbi.Array for the high taxonomic level fingerprint of the human intestinal microbiota. Based on the Ligase Detection Reaction-Universal Array (LDR-UA approach, the HTF-Microbi.Array enables specific detection and approximate relative quantification of 16S rRNAs from 30 phylogenetically related groups of the human intestinal microbiota. The HTF-Microbi.Array was used in a pilot study of the faecal microbiota of eight young adults. Cluster analysis revealed the good reproducibility of the high level taxonomic microbiota fingerprint obtained for each of the subject. Conclusion The HTF-Microbi.Array is a fast and sensitive tool for the high taxonomic level fingerprint of the human intestinal microbiota in terms of presence/absence of the principal groups. Moreover, analysis of the relative fluorescence intensity for each probe pair of our LDR-UA platform can provide estimation of the relative abundance of the microbial target groups within each samples. Focusing the phylogenetic resolution at division, order and cluster levels, the HTF-Microbi.Array is blind with respect to the inter-individual variability at the species level.

  5. Fabrication and structural characterization of highly ordered titania nanotube arrays

    Science.gov (United States)

    Shi, Hongtao; Ordonez, Rosita

    Titanium (Ti) dioxide nanotubes have drawn much attention in the past decade due to the fact that titania is an extremely versatile material with a variety of technological applications. Anodizing Ti in different electrolytes has proved to be quite successful so far in creating the nanotubes, however, their degree of order is still not nearly as good as nanoporous anodic alumina. In this work, we first deposit a thin layer of aluminum (Al) onto electropolished Ti substrates, using thermal evaporation. Such an Al layer is then anodized in 0.3 M oxalic acid, forming an ordered nanoporous alumina mask on top of Ti. Afterwards, the anodization of Ti is accomplished at 20 V in solutions containing 1 M NaH2PO4 and 0.5% HF or H2SO4, which results in the creation of ordered titania nanotube arrays. The inner pore diameter of the nanotubes can be tuned from ~50 nm to ~75 nm, depending on the anodization voltage applied to Al or Ti. X-ray diffractometry shows the as-grown titania nanotubes are amorphous. Samples annealed at different temperatures in ambient atmosphere will be also reported.

  6. Preparation of electrochemically active silicon nanotubes in highly ordered arrays

    Directory of Open Access Journals (Sweden)

    Tobias Grünzel

    2013-10-01

    Full Text Available Silicon as the negative electrode material of lithium ion batteries has a very large capacity, the exploitation of which is impeded by the volume changes taking place upon electrochemical cycling. A Si electrode displaying a controlled porosity could circumvent the difficulty. In this perspective, we present a preparative method that yields ordered arrays of electrochemically competent silicon nanotubes. The method is based on the atomic layer deposition of silicon dioxide onto the pore walls of an anodic alumina template, followed by a thermal reduction with lithium vapor. This thermal reduction is quantitative, homogeneous over macroscopic samples, and it yields amorphous silicon and lithium oxide, at the exclusion of any lithium silicides. The reaction is characterized by spectroscopic ellipsometry for thin silica films, and by nuclear magnetic resonance and X-ray photoelectron spectroscopy for nanoporous samples. After removal of the lithium oxide byproduct, the silicon nanotubes can be contacted electrically. In a lithium ion electrolyte, they then display the electrochemical waves also observed for other bulk or nanostructured silicon systems. The method established here paves the way for systematic investigations of how the electrochemical properties (capacity, charge/discharge rates, cyclability of nanoporous silicon negative lithium ion battery electrode materials depend on the geometry.

  7. Two-dimensional Josephson junction arrays coupled through a high-Q cavity

    DEFF Research Database (Denmark)

    Filatrella, G.; Pedersen, Niels Falsig; Wiesenfeld, K.

    2001-01-01

    the cavity. The highly resonant cavity induces synchronized behavior, which is qualitatively different than what is familiar from other studies on nonlinear oscillator arrays, for example the Kuramoto model. We also address the effects of disorder, as well as the role of detuning between the spontaneous...... emission frequency of the junctions and the cavity resonant frequency. We show with a simple argument that we can predict the scaling behavior of disorder with the size of the array. The consequences for the design of microwave oscillators in the Gigahertz region are discussed......The problem of disordered two-dimensional arrays of underdamped Josephson junctions is addressed. Our simulations show that when coupled to a high-Q cavity, the array exhibits synchronized behavior, and the power emitted can be considerably increased once enough junctions are activated to pump...

  8. High-resolution microcontact printing and transfer of massive arrays of microorganisms on planar and compartmentalized nanoporous aluminium oxide

    NARCIS (Netherlands)

    Ingham, C.J.; Bomer, J.; Sprenkels, A.; Berg, van der A.; Vos, de W.M.; Hylckama, van J.

    2010-01-01

    Handling microorganisms in high throughput and their deployment into miniaturized platforms presents significant challenges. Contact printing can be used to create dense arrays of viable microorganisms. Such "living arrays", potentially with multiple identical replicates, are useful in the selection

  9. High-resolution microcontact printing and transfer of massive arrays of microorganisms on planar and compartmentalized nanoporous aluminium oxide

    NARCIS (Netherlands)

    Ingham, Colin; Bomer, Johan; Sprenkels, Ad; Berg, van den Albert; Vos, de Willem; Hylckama Vlieg, van Johan

    2010-01-01

    Handling microorganisms in high throughput and their deployment into miniaturized platforms presents significant challenges. Contact printing can be used to create dense arrays of viable microorganisms. Such "living arrays'', potentially with multiple identical replicates, are useful in the selectio

  10. Degradation of Solar Array Components in a Combined UV/VUV High Temperature Test Environment

    Directory of Open Access Journals (Sweden)

    Nömayr Christel

    2017-01-01

    A design verification test under UV/VUV conditions of sun exposed materials and technologies on component level is presented which forms part of the overall verification and qualification of the solar array design of the MTM and MPO. The test concentrates on the self-contamination aspects and the resulting performance losses of the solar array under high intensity and elevated temperature environment representative for the photovoltaic assembly (PVA.

  11. HIGH-PRECISION DETERMINATION OF THE ANGULAR POSITION FOR POINT LIGHT SOURCE WITH CCD-ARRAYS

    Directory of Open Access Journals (Sweden)

    Y. G. Lebedko

    2015-05-01

    Full Text Available Subject of study. A method of angular position measuring for point light source in the system with CCD arrays is proposed by converting of angle – time – code in low light conditions and at high signal / noise ratio. Assessment of the method potential accuracy is given. It is determined by instrumental irremovable random errors of measurement in terms of optimal processing of incoming information with a single reading it with CCD – arrays. Method. This work introduces an optoelectronic system circuit with CCD arrays with stretched sensing elements and a point of reference for angular position measuring. In this case the arrays have images projections of both the reference point source and the target point source, which angular position is measured with high precision. From the CCD array output the signals arrive at an optimal (or apt linear filter, and then to the signal peak position detection circuit. The scheme provides minimum error due to the influence of noise. Pulse edges, corresponding to the signals maximum, make a time interval filled with high-frequency counting pulses. The number of pulses in this interval will correspond to the measured angular position of the target point source. Main results. Analysis of random errors has been carried out in terms of statistical decision theory. Analysis takes into account the spectral function of the signals defined by transfer functions of the optical system and a CCD array as an image analyzer. Research of measurement accuracy is carried out depending on the clock frequency of reading information from CCD arrays for different values of signal-to-noise ratio. It has been shown that even with a single readout with CCD array by the proposed opto-electronic circuit measuring error does not exceed 0.01 of the sensing element size. Practical significance. The results are usable in high-precision measuring opto-electronic systems of star sensors for determining the angular position of the low

  12. Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays

    OpenAIRE

    2008-01-01

    Chromosomal DNA is characterized by variation between individuals at the level of entire chromosomes (e.g., aneuploidy in which the chromosome copy number is altered), segmental changes (including insertions, deletions, inversions, and translocations), and changes to small genomic regions (including single nucleotide polymorphisms). A variety of alterations that occur in chromosomal DNA, many of which can be detected using high density single nucleotide polymorphism (SNP)...

  13. Exploring highly porous Co2P nanowire arrays for electrochemical energy storage

    Science.gov (United States)

    Chen, Minghua; Zhou, Weiwei; Qi, Meili; Yin, Jinghua; Xia, Xinhui; Chen, Qingguo

    2017-02-01

    Controllable synthesis of mesoporous conductive metal phosphide nanowire arrays is critical for developing highly-active electrodes of alkaline batteries. Herein we develop a simple combined strategy for rational synthesis of mesoporous Co2P nanowire arrays by hydrothermal-phosphorization method. Free-standing mesoporous Co2P nanowires consisting of interconnected nanoparticles of 10-20 nm grow vertically to the substrate forming arrays. High electrical conductivity and large porosity are obtained in the arrays architecture. When characterized as the cathode of high-rate alkaline batteries, the designed Co2P nanowire arrays are proven with good electrochemical performance with a large capacity (133 mAh g-1 at 1 A g-1), stable cycling life with a capacity retention of almost 100% after 5000 cycles at 10 A g-1 owing to the mesoporous nanowire structure with short ion/electron transport path. Our synthetic approach can be useful for construction of other porous metal phosphide arrays for energy storage and conversion.

  14. Development of high performance SWIR InGaAs focal plane array

    Science.gov (United States)

    Nagi, Richie; Bregman, Jeremy; Mizuno, Genki; Oduor, Patrick; Olah, Robert; Dutta, Achyut K.; Dhar, Nibir K.

    2015-05-01

    Banpil Photonics has developed a novel InGaAs based photodetector array for Short-Wave Infrared (SWIR) imaging, for the most demanding security, defense, and machine vision applications. These applications require low noise from both the detector and the readout integrated circuit arrays. In order to achieve high sensitivity, it is crucial to minimize the dark current generated by the photodiode array. This enables the sensor to function in extremely low light situations, which enables it to successfully exploit the benefits of the SWIR band. In addition to minimal dark current generation, it is essential to develop photodiode arrays with higher operating temperatures. This is critical for reducing the power consumption of the device, as less energy is spent in cooling down the focal plane array (in order to reduce the dark current). We at Banpil Photonics are designing, simulating, fabricating and testing SWIR InGaAs arrays, and have achieved low dark current density at room temperature. This paper describes Banpil's development of the photodetector array. We also highlight the fabrication technique used to reduce the amount of dark current generated by the photodiode array, in particular the surface leakage current. This technique involves the deposition of strongly negatively doped semiconductor material in the area between the pixels. This process reduces the number of dangling bonds present on the edges of each pixel, which prevents electrons from being swept across the surface of the pixels. This in turn drastically reduces the amount of surface leakage current at each pixel, which is a major contributor towards the total dark current. We present the optical and electrical characterization data, as well as the analysis that illustrates the dark current mechanisms. Also highlighted are the challenges and potential opportunities for further reduction of dark current, while maintaining other parameters of the photodiode array, such as size, weight, temperature

  15. High yield, single droplet electrode arrays for nanoscale printed electronics.

    Science.gov (United States)

    Caironi, Mario; Gili, Enrico; Sakanoue, Tomo; Cheng, Xiaoyang; Sirringhaus, Henning

    2010-03-23

    In this work we demonstrate two building blocks of a scalable manufacturing technology for nanoscale electronic devices based on direct-write printing: an architecture for high-yield printing of electrode gaps with 100 nm dimension and a low-temperature silver complex ink for integration of organic materials with high conductivity metal interconnects. We use single printed droplets that are made to dewet slowly from each other to allow reliable, high yield patterning even in the presence of certain surface defects.

  16. Wide bandwidth and high resolution planar filter array based on DBR-metasurface-DBR structures

    CERN Document Server

    Horie, Yu; Arbabi, Ehsan; Kamali, Seyedeh Mahsa; Faraon, Andrei

    2016-01-01

    We propose and experimentally demonstrate a planar array of optical bandpass filters composed of low loss dielectric metasurface layers sandwiched between two distributed Bragg reflectors (DBRs). The two DBRs form a Fabry-P\\'erot resonator whose center wavelength is controlled by the design of the transmissive metasurface layer which functions as a phase shifting element. We demonstrate an array of bandpass filters with spatially varying center wavelengths covering a wide range of operation wavelengths of 250 nm around {\\lambda} = 1550 nm ({\\Delta}{\\lambda}/{\\lambda} = 16%). The center wavelengths of each filter are independently controlled only by changing the in-plane geometry of the sandwiched metasurfaces, and the experimentally measured quality factors are larger than 700. The demonstrated filter array can be directly integrated on top of photodetector arrays to realize on-chip high-resolution spectrometers with free-space coupling.

  17. Highly efficient ultrathin-film amorphous silicon solar cells on top of imprinted periodic nanodot arrays

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Wensheng, E-mail: yws118@gmail.com; Gu, Min, E-mail: mgu@swin.edu.au [Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122 (Australia); Tao, Zhikuo [College of Electronic Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210023 (China); Ong, Thiam Min Brian [Plasma Sources and Application Center, NIE, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616 (Singapore); Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602 (Singapore)

    2015-03-02

    The addressing of the light absorption and conversion efficiency is critical to the ultrathin-film hydrogenated amorphous silicon (a-Si:H) solar cells. We systematically investigate ultrathin a-Si:H solar cells with a 100 nm absorber on top of imprinted hexagonal nanodot arrays. Experimental evidences are demonstrated for not only notable silver nanodot arrays but also lower-cost ITO and Al:ZnO nanodot arrays. The measured external quantum efficiency is explained by the simulation results. The J{sub sc} values are 12.1, 13.0, and 14.3 mA/cm{sup 2} and efficiencies are 6.6%, 7.5%, and 8.3% for ITO, Al:ZnO, and silver nanodot arrays, respectively. Simulated optical absorption distribution shows high light trapping within amorphous silicon layer.

  18. High speed vision processor with reconfigurable processing element array based on full-custom distributed memory

    Science.gov (United States)

    Chen, Zhe; Yang, Jie; Shi, Cong; Qin, Qi; Liu, Liyuan; Wu, Nanjian

    2016-04-01

    In this paper, a hybrid vision processor based on a compact full-custom distributed memory for near-sensor high-speed image processing is proposed. The proposed processor consists of a reconfigurable processing element (PE) array, a row processor (RP) array, and a dual-core microprocessor. The PE array includes two-dimensional processing elements with a compact full-custom distributed memory. It supports real-time reconfiguration between the PE array and the self-organized map (SOM) neural network. The vision processor is fabricated using a 0.18 µm CMOS technology. The circuit area of the distributed memory is reduced markedly into 1/3 of that of the conventional memory so that the circuit area of the vision processor is reduced by 44.2%. Experimental results demonstrate that the proposed design achieves correct functions.

  19. Study on Millimeter-Wave Vivaldi Rectenna and Arrays with High Conversion Efficiency

    Directory of Open Access Journals (Sweden)

    Guan-Nan Tan

    2016-01-01

    Full Text Available A novel Vivaldi rectenna operated at 35 GHz with high millimeter wave to direct current (MMW-to-DC conversion efficiency is presented and the arrays are investigated. The measured conversion efficiency is 51.6% at 35 GHz and the efficiency higher than 30% is from 33.2 GHz to 36.6 GHz when the input MMW power is 79.4 mW. The receiving Vivaldi antenna loaded with metamaterial units has a high gain of 10.4 dBi at 35 GHz. A SIW- (substrate integrated waveguide- to-microstrip transition is designed not only to integrate the antenna with the rectifying circuit directly but also to provide the DC bypass for the rectifying circuit. When the power density is 8.7 mW/cm2, the received MMW power of the antenna is 5.6 mW, and the maximum conversion efficiency of the rectenna element is 31.5%. The output DC voltage of the element is nearly the same as that of the parallel array and is about half of the series array. The DC power obtained by the 1 × 2 rectenna arrays is about two times as much as that of the element. The conversion efficiencies of the arrays are very close to that of the element. Large scale arrays could be expended for collecting more DC power.

  20. CCL3L1 copy number, HIV load, and immune reconstitution in sub-Saharan Africans

    Science.gov (United States)

    2013-01-01

    Background The role of copy number variation of the CCL3L1 gene, encoding MIP1α, in contributing to the host variation in susceptibility and response to HIV infection is controversial. Here we analyse a sub-Saharan African cohort from Tanzania and Ethiopia, two countries with a high prevalence of HIV-1 and a high co-morbidity of HIV with tuberculosis. Methods We use a form of quantitative PCR called the paralogue ratio test to determine CCL3L1 gene copy number in 1134 individuals and validate our copy number typing using array comparative genomic hybridisation and fiber-FISH. Results We find no significant association of CCL3L1 gene copy number with HIV load in antiretroviral-naïve patients prior to initiation of combination highly active anti-retroviral therapy. However, we find a significant association of low CCL3L1 gene copy number with improved immune reconstitution following initiation of highly active anti-retroviral therapy (p = 0.012), replicating a previous study. Conclusions Our work supports a role for CCL3L1 copy number in immune reconstitution following antiretroviral therapy in HIV, and suggests that the MIP1α -CCR5 axis might be targeted to aid immune reconstitution. PMID:24219137

  1. High power diode laser array development using completely indium free packaging technology with narrow spectrum

    Science.gov (United States)

    Hou, Dong; Wang, Jingwei; Gao, Lijun; Liang, Xuejie; Li, Xiaoning; Liu, Xingsheng

    2016-03-01

    The high power diode lasers have been widely used in many fields. In this work, a sophisticated high power and high performance horizontal array of diode laser stacks have been developed and fabricated with high duty cycle using hard solder bonding technology. CTE-matched submount and Gold Tin (AuSn) hard solder are used for bonding the diode laser bar to achieve the performances of anti-thermal fatigue, higher reliability and longer lifetime. This array consists of 30 bars with the expected optical output peak power of 6000W. By means of numerical simulation and analytical results, the diode laser bars are aligned on suitable positions along the water cooled cooler in order to achieve the uniform wavelength with narrow spectrum and accurate central wavelength. The performance of the horizontal array, such as output power, spectrum, thermal resistance, life time, etc., is characterized and analyzed.

  2. Patterning pallet arrays for cell selection based on high-resolution measurements of fluorescent biosensors.

    Science.gov (United States)

    Shadpour, Hamed; Zawistowski, Jon S; Herman, Annadele; Hahn, Klaus; Allbritton, Nancy L

    2011-06-24

    Pallet arrays enable cells to be separated while they remain adherent to a surface and provide a much greater range of cell selection criteria relative to that of current technologies. However there remains a need to further broaden cell selection criteria to include dynamic intracellular signaling events. To demonstrate the feasibility of measuring cellular protein behavior on the arrays using high resolution microscopy, the surfaces of individual pallets were modified to minimize the impact of scattered light at the pallet edges. The surfaces of the three-dimensional pallets on an array were patterned with a coating such as fibronectin using a customized stamping tool. Micropatterns of varying shape and size were printed in designated regions on the pallets in single or multiple steps to demonstrate the reliability and precision of patterning molecules on the pallet surface. Use of a fibronectin matrix stamped at the center of each pallet permitted the localization of H1299 and mouse embryonic fibroblast (MEF) cells to the pallet centers and away from the edges. Compared to pallet arrays with fibronectin coating the entire top surface, arrays with a central fibronectin pattern increased the percentage of cells localized to the pallet center by 3-4-fold. Localization of cells to the pallet center also enabled the physical separation of cells from optical artifacts created by the rough pallet side walls. To demonstrate the measurement of dynamic intracellular signaling on the arrays, fluorescence measurements of high spatial resolution were performed using a RhoA GTPase biosensor. This biosensor utilized fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) to measure localized RhoA activity in cellular ruffles at the cell periphery. These results demonstrated the ability to perform spatially resolved measurements of fluorescence-based sensors on the pallet arrays. Thus, the patterned pallet arrays

  3. Modular Ultra-High Power Solar Array Architecture Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Deployable Space Systems (DSS) will focus the proposed Phase 2 SBIR program on the hardware-based development and TRL advance of a highly-modularized and...

  4. High Count Rate Single Photon Counting Detector Array Project

    Data.gov (United States)

    National Aeronautics and Space Administration — An optical communications receiver requires efficient and high-rate photon-counting capability so that the information from every photon, received at the aperture,...

  5. A comprehensive zero-copy architecture for high performance distributed Data Acquisition over advanced network technologies for the CMS experiment

    CERN Document Server

    Bauer, Gerry; Branson, James; Bukowiec, Sebastian Czeslaw; Chaze, Olivier; Cittolin, Sergio; Coarasa, J. A; Deldicque, Christian; Dobson, Marc; Dupont, Aymeric; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, R; Hartl, Christian; Holzner, Andre Georg; Masetti, Lorenzo; Meijers, Franciscus; Meschi, Emilio; Mommsen, Remigius; Nunez-Barranco, C; O'Dell, Vivian; Orsini, Luciano; Paus, Christoph Maria Ernst; Petrucci, Andrea; Pieri, Marco; Polese, Giovanni; Racz, Attila; Raginel, Olivier; Sakulin, Hannes; Sani, Matteo; Schwick, Christoph; Spataru, Andrei Cristian; Stoeckli, Fabian; Sumorok, Konstanty

    2013-01-01

    This paper outlines a software architecture where zero-copy operations are used comprehensively at every processing point from the Application layer to the Physical layer. The proposed architecture is being used during feasibility studies on advanced networking technologies for the CMS experiment at CERN. The design relies on a homogeneous peer-to-peer message passing system, which is built around memory pool caches allowing efficient and deterministic latency handling of messages of any size through the different software layers. In this scheme portable distributed applications can be programmed to process input to output operations by mere pointer arithmetic and DMA operations only. The approach combined with the open fabric protocol stack (OFED) allows one to attain near wire-speed message transfer at application level. The architecture supports full portability of user applications by encapsulating the protocol details and network into modular peer transport services whereas a transparent replacement of t...

  6. Implementation of digital multiplexing for high resolution X-ray detector arrays.

    Science.gov (United States)

    Sharma, P; Swetadri Vasan, S N; Titus, A H; Cartwright, A N; Bednarek, D R; Rudin, S

    2012-01-01

    We describe and demonstrate for the first time the use of the novel Multiple Module Multiplexer (MMMIC) for a 2×2 array of new electron multiplying charge coupled device (EMCCD) based x-ray detectors. It is highly desirable for x-ray imaging systems to have larger fields of view (FOV) extensible in two directions yet to still be capable of doing high resolution imaging over regions-of-interest (ROI). The MMMIC achieves these goals by acquiring and multiplexing data from an array of imaging modules thereby enabling a larger FOV, and at the same time allowing high resolution ROI imaging through selection of a subset of modules in the array. MMMIC also supports different binning modes. This paper describes how a specific two stage configuration connecting three identical MMMICs is used to acquire and multiplex data from a 2×2 array of EMCCD based detectors. The first stage contains two MMMICs wherein each MMMIC is getting data from two EMCCD detectors. The multiplexed data from these MMMICs is then forwarded to the second stage MMMIC in the similar fashion. The second stage that has only one MMMIC gives the final 12 bit multiplexed data from four modules. This data is then sent over a high speed Camera Link interface to the image processing computer. X-ray images taken through the 2×2 array of EMCCD based detectors using this two stage configuration of MMMICs are shown successfully demonstrating the concept.

  7. Fabrication of nanopore and nanoparticle arrays with high aspect ratio AAO masks

    Science.gov (United States)

    Li, Z. P.; Xu, Z. M.; Qu, X. P.; Wang, S. B.; Peng, J.; Mei, L. H.

    2017-03-01

    How to use high aspect ratio anodic aluminum oxide (AAO) membranes as an etching and evaporation mask is one of the unsolved problems in the application of nanostructured arrays. Here we describe the versatile utilizations of the highly ordered AAO membranes with a high aspect ratio of more than 20 used as universal masks for the formation of various nanostructure arrays on various substrates. The result shows that the fabricated nanopore and nanoparticle arrays of substrates inherit the regularity of the AAO membranes completely. The flat AAO substrates and uneven AAO frontages were attached to the Si substrates respectively as an etching mask, which demonstrates that the two kinds of replication, positive and negative, represent the replication of the mirroring of Si substrates relative to the flat AAO substrates and uneven AAO frontages. Our work is a breakthrough for the broad research field of surface nano-masking.

  8. The nuclear spectroscopic telescope array (NuSTAR) high-energy X-ray mission

    DEFF Research Database (Denmark)

    Harrison, Fiona A.; Craig, William W.; Christensen, Finn Erland

    2013-01-01

    The Nuclear Spectroscopic Telescope Array (NuSTAR) mission, launched on 2012 June 13, is the first focusing high-energy X-ray telescope in orbit. NuSTAR operates in the band from 3 to 79 keV, extending the sensitivity of focusing far beyond the ~10 keV high-energy cutoff achieved by all previous X...

  9. PMN-PT single-crystal high-frequency kerfless phased array.

    Science.gov (United States)

    Chen, Ruimin; Cabrera-Munoz, Nestor E; Lam, Kwok Ho; Hsu, Hsiu-sheng; Zheng, Fan; Zhou, Qifa; Shung, K Kirk

    2014-06-01

    This paper reports the design, fabrication, and characterization of a miniature high-frequency kerfless phased array prepared from a PMN-PT single crystal for forward-looking intravascular or endoscopic imaging applications. After lapping down to around 40 μm, the PMN-PT material was utilized to fabricate 32-element kerfless phased arrays using micromachining techniques. The aperture size of the active area was only 1.0 × 1.0 mm. The measured results showed that the array had a center frequency of 40 MHz, a bandwidth of 34% at -6 dB with a polymer matching layer, and an insertion loss of 20 dB at the center frequency. Phantom images were acquired and compared with simulated images. The results suggest that the feasibility of developing a phased array mounted at the tip of a forward-looking intravascular catheter or endoscope. The fabricated array exhibits much higher sensitivity than PZT ceramic-based arrays and demonstrates that PMN-PT is well suited for this application.

  10. Multi-channel microstrip transceiver arrays using harmonics for high field MR imaging in humans.

    Science.gov (United States)

    Wu, Bing; Wang, Chunsheng; Lu, Jonathan; Pang, Yong; Nelson, Sarah J; Vigneron, Daniel B; Zhang, Xiaoliang

    2012-02-01

    Radio-frequency (RF) transceiver array design using primary and higher order harmonics for in vivo parallel magnetic resonance imaging imaging (MRI) and spectroscopic imaging is proposed. The improved electromagnetic decoupling performance, unique magnetic field distributions and high-frequency operation capabilities of higher-order harmonics of resonators would benefit transceiver arrays for parallel MRI, especially for ultrahigh field parallel MRI. To demonstrate this technique, microstrip transceiver arrays using first and second harmonic resonators were developed for human head parallel imaging at 7T. Phantom and human head images were acquired and evaluated using the GRAPPA reconstruction algorithm. The higher-order harmonic transceiver array design technique was also assessed numerically using FDTD simulation. Compared with regular primary-resonance transceiver designs, the proposed higher-order harmonic technique provided an improved g-factor and increased decoupling among resonant elements without using dedicated decoupling circuits, which would potentially lead to a better parallel imaging performance and ultimately faster and higher quality imaging. The proposed technique is particularly suitable for densely spaced transceiver array design where the increased mutual inductance among the elements becomes problematic. In addition, it also provides a simple approach to readily upgrade the channels of a conventional primary resonator microstrip array to a larger number for faster imaging.

  11. MNSs genotyping by MALDI-TOF MS shows high concordance with serology, allows gene copy number testing and reveals new St(a) alleles.

    Science.gov (United States)

    Meyer, Stefan; Vollmert, Caren; Trost, Nadine; Sigurdardottir, Sonja; Portmann, Claudia; Gottschalk, Jochen; Ries, Judith; Markovic, Alexander; Infanti, Laura; Buser, Andreas; Amar El Dusouqui, Soraya; Rigal, Emmanuel; Castelli, Damiano; Weingand, Bettina; Maier, Andreas; Mauvais, Simon M; Sarraj, Amira; Braisch, Monica C; Thierbach, Jutta; Hustinx, Hein; Frey, Beat M; Gassner, Christoph

    2016-08-01

    Results of genotyping with true high-throughput capability for MNSs antigens are underrepresented, probably because of technical issues, due to the high level of nucleotide sequence homology of the paralogous genes GYPA, GYPB and GYPE. Eight MNSs-specific single nucleotide polymorphisms (SNP) were detected using matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI-TOF MS) in 5800 serologically M/N and S/s pre-typed Swiss blood donors and 50 individuals of known or presumptive black African ethnicity. Comparison of serotype with genotype delivered concordance rates of 99·70% and 99·90% and accuracy of genotyping alone of 99·88% and 99·95%, for M/N and S/s, respectively. The area under the curve of peak signals was measured in intron 1 of the two highly homologous genes GYPB and GYPE and allowed for gene copy number variation estimates in all individuals investigated. Elevated GYPB:GYPE ratios accumulated in several carriers of two newly observed GYP*401 variants, termed type G and H, both encoding for the low incidence antigen St(a). In black Africans, reduced GYPB gene contents were proven in pre-typed S-s-U- phenotypes and could be reproduced in unknown specimens. Quantitative gene copy number estimates represented a highly attractive supplement to conventional genotyping, solely based on MNSs SNPs. © 2016 John Wiley & Sons Ltd.

  12. High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals

    DEFF Research Database (Denmark)

    Norskov, M.S.; Frikke-Schmidt, R.; Loft, S.;

    2009-01-01

    OBJECTIVES: Characteristic for the genes encoding glutathione S-transferase (GST) M1 and GSTT1 is a null allele, suggested to increase susceptibility to chronic diseases. We report an optimized method for the determination of copy number variation (CNV) in GST genes. DESIGN AND METHODS: Real...... to 100 ng. In a general population sample of 20,687 individuals the genotype frequencies were concordant with other methods used as standards. Throughput was 4600 genotypes per day at a reagent price of 0.5 euros per sample. CONCLUSIONS: This high-throughput, low cost method accurately determines CNV...

  13. Fabrication of high-aspect ratio SU-8 micropillar arrays

    DEFF Research Database (Denmark)

    Amato, Letizia; Keller, Stephan S.; Heiskanen, Arto

    2012-01-01

    SU-8 is the preferred photoresist for development and fabrication of high aspect ratio (HAR) three dimensional patterns. However, processing of SU-8 is a challenging task, especially when the film thickness as well as the aspect ratio is increasing and the size of the features is close to the res...

  14. High-resolution images of tremor migrations beneath the Olympic Peninsula from stacked array of arrays seismic data

    Science.gov (United States)

    Peng, Yajun; Rubin, Allan M.

    2016-02-01

    Episodic tremor and slip (ETS) in subduction zones is generally interpreted as the manifestation of shear slip near the base of earthquake-generating portion of the plate interface. Here we devise a new method of cross-correlating stacked Array of Arrays seismic data that provides greatly improved tremor locations, a proxy for the underlying slow slip, beneath the Olympic Peninsula. This increased resolution allows us to image many features of tremor that were not visible previously. We resolve the spatial transition between the rupture zones of the inter-ETS and major ETS episodes in 2010, suggesting stress redistribution by the former. Most tremor migrations propagated along the slowly advancing main tremor front during both the inter-ETS and the major ETS episodes, even though the main front of the former deviated strongly from its usual (along-dip) orientation. We find a distinct contrast between along-dip rupture extent of large-scale rapid tremor reversals (RTRs) to the south and that to the north in our study region that anticorrelates with the locations of inter-ETS events. These RTRs originate from the main front, similar to smaller-scale RTRs previously observed at high-resolution, and many start by propagating along the main front. This could be consistent with RTRs being triggered by a cascading failure of brittle asperities. After initiation, the RTRs repeatedly occupy the same source region, and the early repetitions appear not to be tidally driven. Their stress drop may come from continuing fault weakening processes within the tremor zone, or loading by aseismic slip in surrounding regions.

  15. Two-dimensional DOA Estimation with High Accuracy for MIMO Radar Using Cross Array

    Directory of Open Access Journals (Sweden)

    Liang Hao

    2016-06-01

    Full Text Available In this study, we investigate the estimation of the Two-Dimensional (2D Direction Of Arrival (DOA in monostatic multiple-input–multiple-output radar with cross array and propose a novel, highly accurate DOA estimation method based on unitary transformation. First, we design a new unitary matrix using the central symmetry of a cross array at transmit and receive sites. Then, the rotational invariance relationships of these arrays with long and short baselines can be transformed into a real-value field via unitary transformation. In addition, non-ambiguous and highly accurate 2D DOA estimations can be obtained using a unitary dual-resolution ESPRIT algorithm. Simulations show that the proposed method can estimate 2D highly accurate spatial angles using automatic pairing without incurring the expense of array aperture and peak searching. Compared with traditional unitary transformation, the steering vectors of transmit and receive arrays can be transformed into real-value fields via the unitary matrix and the transformation method of our scheme, respectively. This effectively overcomes the problem of shift invariance factors in real-value fields that cannot be extracted using traditional algorithms. Therefore, the proposed method can absolutely compute eigenvalue decomposition and estimate parameters in a real-value field, resulting in lower computational complexity compared with traditional methods. Simulation results verify both the correctness of our theoretical analysis and the effectiveness of the proposed algorithm.

  16. Micromachined high frequency PMN-PT/epoxy 1-3 composite ultrasonic annular array.

    Science.gov (United States)

    Liu, Changgeng; Djuth, Frank; Li, Xiang; Chen, Ruimin; Zhou, Qifa; Shung, K Kirk

    2012-04-01

    This paper reports the design, fabrication, and performance of miniature micromachined high frequency PMN-PT/epoxy 1-3 composite ultrasonic annular arrays. The PMN-PT single crystal 1-3 composites were made with micromachining techniques. The area of a single crystal pillar was 9×9 μm. The width of the kerf among pillars was ∼5 μm and the kerfs were filled with a polymer. The composite thickness was 25 μm. A six-element annular transducer of equal element area of 0.2 mm(2) with 16 μm kerf widths between annuli was produced. The aperture size the array transducer is about 1.5 mm in diameter. A novel electrical interconnection strategy for high density array elements was implemented. After the transducer was attached to the electric connection board and packaged, the array transducer was tested in a pulse/echo arrangement, whereby the center frequency, bandwidth, two-way insertion loss (IL), and cross talk between adjacent elements were measured for each annulus. The center frequency was 50 MHz and -6 dB bandwidth was 90%. The average insertion loss was 19.5 dB at 50 MHz and the crosstalk between adjacent elements was about -35 dB. The micromachining techniques described in this paper are promising for the fabrication of other types of high frequency transducers, e.g. 1D and 2D arrays.

  17. Data analysis considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues.

    Science.gov (United States)

    Jacobs, Sharoni

    2012-11-01

    The Whole Genome Sampling Analysis (WGSA) assay in combination with Affymetrix GeneChip Mapping Arrays is used for copy number analysis of high-quality DNA samples (i.e., samples that have been collected from blood, fresh or frozen tissue, or cell lines). Formalin-fixed, paraffin-embedded (FFPE) samples, however, represent the most prevalent form of archived clinical samples, but they provide additional challenges for molecular assays. FFPE processing usually results in the degradation of FFPE DNA and in the contamination and chemical modification of these DNA samples. In this article, we describe the steps needed to obtain reliable copy number predictions from degraded and contaminated FFPE samples.

  18. High-Q cavity-induced synchronization in oscillator arrays

    DEFF Research Database (Denmark)

    Filatrella, Giovanni; Pedersen, Niels Falsig; Wiesenfeld, Kurt

    2000-01-01

    A model for a large number of Josephson junctions coupled to a cavity is presented. The system displays synchronization behavior very similar to that reported in recent experiments [P. Barbara ct al., Phys. Rev. Lett. 82, 1963 (1999)]. The essential dynamical mechanism responsible for coherence...... should be generic in nonlinear oscillator systems where the interactions are mediated by a highly resonant cavity, in analogy with gas lasers....

  19. High efficiency,high power 808nm laser array and stacked arrays optimized for elevated temperature operation

    Institute of Scientific and Technical Information of China (English)

    Crump P A; Wise D; Crum T R; DeVito M; Farmer J; Grimshaw M; Huang Z; Igl S A; Macomber S; Thiagarajan P

    2004-01-01

    Operation of 808-nm laser diode pumping at elevated temperature is crucial to many applications. Reliable operation at high power is limited by high thermal load and low catastrophic optical mirror damage (COMD) threshold at elevated temperature range. We demonstrated high efficiency and high power operation at elevated temperature with high COMD power. These results were achieved through device design optimization such as growth conditions, doping profile, and materials composition of the quantum-well and other layers. Electrical-to-optical efficiency as high as 62% was obtained through lowered threshold current, lowered series resistance and increased slope efficiency. The performance of single broad-area laser diodes scales to that of high power single bars on water-cooled copper micro-channel heatsinks or conductively-cooled CS heatsinks. No reduction in bar performance or significant spectral broadening is seen when these micro-channel coolers are assembled into 6-bar and 18-bar CW stacks for the highest power levels.

  20. Detection of breast cancer by soft-copy reading of digital mammograms: comparison between a routine image-processing parameter and high-contrast parameters.

    Science.gov (United States)

    Kamitani, Takeshi; Yabuuchi, Hidetake; Soeda, Hiroyasu; Matsuo, Yoshio; Okafuji, Takashi; Sakai, Shuji; Setoguchi, Taro; Hatakenaka, Masamitsu; Ishii, Nobuhide; Honda, Hiroshi

    2010-02-01

    Recent studies have reported the clinical usefulness of the soft-copy reading of mammograms. However, image-processing parameters for soft-copy reading of digital mammograms have not been established. To compare observer performance in detecting breast cancer by soft-copy reading of digital mammograms using a routine image-processing parameter versus each of several high-contrast parameters. The mammograms of 154 breasts, including 48 abnormal breasts with breast cancer and 106 normal breasts, were examined. Cancers were classified into 34 mass-dominant cancers, 11 microcalcification-dominant cancers, two cancers showing only architectural distortion, and one cancer without abnormal findings. All mammograms were performed using a computed radiography (CR) system. Each image was processed using GA (1.2), which was the contrast parameter recommended by the manufacturer for hard-copy film, GA (1.4), GA (1.6), and GA (1.8). These images were displayed on 5-megapixel (M) liquid-crystal display monitors. Five experienced radiologists classified them into BI-RADS category 1-2 or 3-5, and were also asked to rate the images on a scale of 0 to 100 for the likelihood of the presence of masses and microcalcifications in each breast. In mass-dominant cancers of dense breast tissue, the mean sensitivities of GA (1.2), GA (1.4), GA (1.6), and GA (1.8) were 32.7, 38.2, 36.4, and 40.0, and the A(Z) values were 0.67, 0.73, 0.71, and 0.73, respectively; in microcalcification-dominant cancers, the mean sensitivities were 80.0, 74.5, 80.0, and 78.2, respectively; however, there were no significant differences among them. High-contrast parameters tended to show relatively high sensitivity and A(Z) values in the detection of masses in dense breast tissue, but relatively low sensitivity for microcalcifications.

  1. Standoff photoacoustic detections with high-sensitivity microphones and acoustic arrays

    Science.gov (United States)

    Choa, Fow-Sen; Wang, Chen-Chia; Khurgin, Jacob; Samuels, Alan; Trivedi, Sudhir; Gupta, Deepa

    2016-05-01

    Standoff detection of dangerous chemicals like explosives, nerve gases, and harmful aerosols has continuously been an important subject due to the serious concern about terrorist threats to both overseas and homeland lives and facility. Compared with other currently available standoff optical detection techniques, like Raman, photo-thermal, laser induced breakdown spectroscopy,...etc., photoacoustic (PA) sensing has the advantages of background free and very high detection sensitivity, no need of back reflection surfaces, and 1/R instead of 1/R2 signal decay distance dependence. Furthermore, there is still a great room for PA sensitivity improvement by using different PA techniques, including lockin amplifier, employing new microphones, and microphone array techniques. Recently, we have demonstrated standoff PA detection of isopropanol vapor, solid phase TNT and RDX at a standoff distance. To further calibrate the detection sensitivity, we use nerve gas simulants that were generated and calibrated by a commercial vapor generator. For field operations, array of microphones and microphone-reflector pairs can be utilized to achieve noise rejection and signal enhancement. We have experimentally demonstrated signal enhancement and noise reduction using an array of 4 microphone/4 reflector system as well as an array of 16-microphone/1 reflector. In this work we will review and compare different standoff techniques and discuss the advantages of using different photoacoustic techniques. We will also discuss new advancement of using new types of microphone and the performance comparison of using different structure of microphone arrays and combining lock-in amplifier with acoustic arrays. Demonstration of out-door real-time operations with high power mid-IR laser and microphone array will be presented.

  2. The Art of Copying

    DEFF Research Database (Denmark)

    Christensen, Hans Dam

    2017-01-01

    This article discusses copies within the field of art museums by way of mapping strategies for copy practices. This mapping leans heavily towards parts of the writings of Jacques Derrida (1930–2004). Against the backdrop of this theoretical premise, the article distinguishes five main strategies....... An informational copy is just as unique as an original object of art, and at the same time, it defines the original and is itself defined by this opposition. Lastly, the strategy for the imagined relation between original and copy follows. This strategy is dependent upon several of the previous approaches, and...

  3. Highly uniform hole spacing micro brushes based on aligned carbon nanotube arrays

    Science.gov (United States)

    Yang, Zhi; Zhu, Xingzhong; Huang, Xiaolu; Cheng, Yingwu; Liu, Yun; Geng, Huijuan; Wu, Yue; Su, Yanjie; Wei, Hao; Zhang, Yafei

    2013-11-01

    Highly uniform hole spacing micro brushes were fabricated based on aligned carbon nanotube (CNT) arrays synthesized by chemical vapor deposition method with the assistance of anodic aluminum oxide (AAO) template. Different micro brushes from CNT arrays were constructed on silicon, glass, and polyimide substrates, respectively. The micro brushes had highly uniform hole spacing originating from the regularly periodic pore structure of AAO template. The CNT arrays, serving as bristles, were firmly grafted on the substrates. The brushes can easily clean particles with scale of micrometer on the surface of silicon wafer and from the narrow spaces between the electrodes in a series of cleaning experiments. The results show the potential application of the CNT micro brushes as a cleaning tool in microelectronics manufacture field.

  4. Improvement on a 2 × 2 Elements High-Gain Circularly Polarized Antenna Array

    Directory of Open Access Journals (Sweden)

    C. Liu

    2015-01-01

    Full Text Available A novel antipodal Vivaldi antenna with tapering serrated structure at the edges is proposed. Compared with traditional Vivaldi antennas without serrated structure, the gain of the designed antenna is significantly improved in the desired frequency band (4.5–7.5 GHz. In addition, a 2 × 2 Vivaldi antenna array with an orthorhombic structure is designed and fabricated to achieve a circular polarization (CP characteristic. With this configuration, the 3 dB axial ratio bandwidth of the array reaches about 42% with respect to the center frequency of 6 GHz and a high gain is achieved as well. The novel Vivaldi antenna and CP antenna array both have ultrawide band (UWB and high-gain characteristics, which may be applied to the field of commercial communication, remote sensing, and so forth.

  5. High Gain Slot Array with Fabry-Perot Cavity Feeding Circuit

    Directory of Open Access Journals (Sweden)

    Halim Boutayeb

    2016-01-01

    Full Text Available A new approach for designing slot arrays using a Fabry-Perot cavity for the feeding circuit is presented. The proposed array has simpler and smaller feeding circuit compared to conventional feeding networks that have multiple dividers or combiners. The dividers and combiners are usually sources of losses. In addition, the profile of the proposed array is not limited by the half-wavelength resonance condition that exists for Fabry-Perot resonator antennas based on partially reflecting surfaces. The operating frequency is not sensitive to the profile of the antenna. A small profile can be achieved without the utilization of an artificial magnetic conductor or a substrate with high dielectric constant. To validate the proposed approach, full-wave numerical results are presented at 5.8 GHz showing good impedance matching, a high gain of about 22 dB, and an efficiency of 76%.

  6. Linearity Analysis on a Series-Split Capacitor Array for High-Speed SAR ADCs

    Directory of Open Access Journals (Sweden)

    Yan Zhu

    2010-01-01

    Full Text Available A novel Capacitor array structure for Successive Approximation Register (SAR ADC is proposed. This circuit efficiently utilizes charge recycling to achieve high-speed of operation and it can be applied to high-speed and low-to-medium-resolution SAR ADC. The parasitic effects and the static linearity performance, namely, the INL and DNL, of the proposed structure are theoretically analyzed and behavioral simulations are performed to demonstrate its effectiveness under those nonidealities. Simulation results show that to achieve the same conversion performance the proposed capacitor array structure can reduce the average power consumed from the reference ladder by 90% when compared to the binary-weighted splitting capacitor array structure.

  7. The characteristics of machined surface controlled by multi tip arrayed tool and high speed spindle.

    Science.gov (United States)

    Kim, Yong Woo; Choi, Soo Chang; Park, Jeong Woo; Lee, Deug Woo

    2010-07-01

    In this study, we propose one of the ultra-precision machining methods that can be adapted brittle material as well as soft material by using multi arrayed diamond tips and high speed spindle. Conventional machining method is too hard to control surface roughness and surface texture against brittle material because particles of grinding tools are irregular size and material can be fragile. Therefore we were able to design tool paths and machine controlled pattern on surface by multi arrayed diamond tips which has uniform size made in MEMS fabrication and high speed spindle of which maximum speed is about 300,000 rpm. We defined several parameters that can have effect on machining surface. Those are multi array of diamond tips (n * n), speed of the air spindle, and feeding rate. Surface roughness and surface texture can be controlled by those parameters for micro machining.

  8. Highly tunable ultra-narrow-resonances with optical nano-antenna phased arrays in the infrared

    CERN Document Server

    Li, Shi-Qiang; Guo, Peijun; Buchholz, D Bruce; Qiu, Ziwei; Ketterson, John B; Ocola, Leonidas E; Sakoda, Kazuaki; Chang, Robert P H

    2014-01-01

    We report our recent development in pursuing high Quality-Factor (high-Q factor) plasmonic resonances, with vertically aligned two dimensional (2-D) periodic nanorod arrays. The 2-D vertically aligned nano-antenna array can have high-Q resonances varying arbitrarily from near infrared to terahertz regime, as the antenna resonances of the nanorod are highly tunable through material properties, the length of the nanorod, and the orthogonal polarization direction with respect to the lattice surface,. The high-Q in combination with the small optical mode volume gives a very high Purcell factor, which could potentially be applied to various enhanced nonlinear photonics or optoelectronic devices. The 'hot spots' around the nanorods can be easily harvested as no index-matching is necessary. The resonances maintain their high-Q factor with the change of the environmental refractive index, which is of great interest for molecular sensing.

  9. Diffusion of dilute gas in arrays of randomly distributed, vertically aligned, high-aspect-ratio cylinders

    Science.gov (United States)

    Guerra, Carlos

    2017-01-01

    In this work we modelled the diffusive transport of a dilute gas along arrays of randomly distributed, vertically aligned nanocylinders (nanotubes or nanowires) as opposed to gas diffusion in long pores, which is described by the well-known Knudsen theory. Analytical expressions for (i) the gas diffusion coefficient inside such arrays, (ii) the time between collisions of molecules with the nanocylinder walls (mean time of flight), (iii) the surface impingement rate, and (iv) the Knudsen number of such a system were rigidly derived based on a random-walk model of a molecule that undergoes memoryless, diffusive reflections from nanocylinder walls assuming the molecular regime of gas transport. It can be specifically shown that the gas diffusion coefficient inside such arrays is inversely proportional to the areal density of cylinders and their mean diameter. An example calculation of a diffusion coefficient is delivered for a system of titanium isopropoxide molecules diffusing between vertically aligned carbon nanotubes. Our findings are important for the correct modelling and optimisation of gas-based deposition techniques, such as atomic layer deposition or chemical vapour deposition, frequently used for surface functionalisation of high-aspect-ratio nanocylinder arrays in solar cells and energy storage applications. Furthermore, gas sensing devices with high-aspect-ratio nanocylinder arrays and the growth of vertically aligned carbon nanotubes need the fundamental understanding and precise modelling of gas transport to optimise such processes. PMID:28144565

  10. High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip.

    Directory of Open Access Journals (Sweden)

    Yan P Yu

    Full Text Available Detection of human genome copy number variation (CNV is one of the most important analyses in diagnosing human malignancies. Genome CNV detection in formalin-fixed and paraffin-embedded (FFPE tissues remains challenging due to suboptimal DNA quality and failure to use appropriate baseline controls for such tissues. Here, we report a modified method in analyzing CNV in FFPE tissues using microarray with Affymetrix Cytoscan HD chips. Gel purification was applied to select DNA with good quality and data of fresh frozen and FFPE tissues from healthy individuals were included as baseline controls in our data analysis. Our analysis showed a 91% overlap between CNV detection by microarray with FFPE tissues and chromosomal abnormality detection by karyotyping with fresh tissues on 8 cases of lymphoma samples. The CNV overlap between matched frozen and FFPE tissues reached 93.8%. When the analyses were restricted to regions containing genes, 87.1% concordance between FFPE and fresh frozen tissues was found. The analysis was further validated by Fluorescence In Situ Hybridization on these samples using probes specific for BRAF and CITED2. The results suggested that the modified method using Affymetrix Cytoscan HD chip gave rise to a significant improvement over most of the previous methods in terms of accuracy in detecting CNV in FFPE tissues. This FFPE microarray methodology may hold promise for broad application of CNV analysis on clinical samples.

  11. Flexible, phase-matched, linear receive arrays for high-field MRI in monkeys.

    Science.gov (United States)

    Goense, Jozien; Logothetis, Nikos K; Merkle, Hellmut

    2010-10-01

    High signal-to-noise ratios (SNR) are essential for high-resolution anatomical and functional MRI. Phased arrays are advantageous for this but have the drawback that they often have inflexible and bulky configurations. Particularly in experiments where functional MRI is combined with simultaneous electrophysiology, space constraints can be prohibitive. To this end we developed a highly flexible multiple receive element phased array for use on anesthetized monkeys. The elements are interchangeable and different sizes and combinations of coil elements can be used, for instance, combinations of single and overlapped elements. The preamplifiers including control electronics are detachable and can serve a variety of prefabricated and phase matched arrays of different configurations, allowing the elements to always be placed in close proximity to the area of interest. Optimizing performance of the individual elements ensured high SNR at the cortical surface as well as in deeper laying structures. Performance of a variety of arrangements of gapped linear arrays was evaluated at 4.7 and 7T in high-resolution anatomical and functional MRI.

  12. Design Considerations for Array CGH to OligonucleotideArrays

    Energy Technology Data Exchange (ETDEWEB)

    Baldocchi, R.A.; Glynne, R.J.; Chin, K.; Kowbel, D.; Collins, C.; Mack, D.H.; Gray, J.W.

    2005-03-04

    Background: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. Methods: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. Results: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. Conclusion: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.

  13. Agrobacterium-mediated plant transformation by novel mini-T vectors in conjunction with a high-copy vir region helper plasmid.

    Science.gov (United States)

    Zyprian, E; Kado, C I

    1990-08-01

    A new binary vector system for Agrobacterium-mediated plant transformation was developed. A set of four mini-T vectors comprised of T-DNA border sequences from nopaline-type Ti-plasmid pTiC58 flanking a chimaeric hygromycin-resistance gene for selection of transformants and up to eight unique restriction sites for cloning foreign DNA was constructed on a broad-host replicon containing the oriV of plasmid pSa. In two of the constructs these multiple cloning sites are flanked by a strong promoter to activate transcription of inserted DNA in planta. High-efficiency transformation was prompted by a high-copy, stable virulence helper plasmid pUCD2614, which contains a cloned virulence region of pTiC58 and tandem copies of the par locus of plasmid pTAR. Southern blot hybridization and genetic analyses of the progeny of transformed plants showed that the hygromycin resistance gene was stably inherited.

  14. Chemiluminescent detection of sequential DNA hybridizations to high-density, filter-arrayed cDNA libraries: a subtraction method for novel gene discovery.

    Science.gov (United States)

    Guiliano, D; Ganatra, M; Ware, J; Parrot, J; Daub, J; Moran, L; Brennecke, H; Foster, J M; Supali, T; Blaxter, M; Scott, A L; Williams, S A; Slatko, B E

    1999-07-01

    A chemiluminescent approach for sequential DNA hybridizations to high-density filter arrays of cDNAs, using a biotin-based random priming method followed by a streptavidin/alkaline phosphatase/CDP-Star detection protocol, is presented. The method has been applied to the Brugia malayi genome project, wherein cDNA libraries, cosmid and bacterial artificial chromosome (BAC) libraries have been gridded at high density onto nylon filters for subsequent analysis by hybridization. Individual probes and pools of rRNA probes, ribosomal protein probes and expressed sequence tag probes show correct specificity and high signal-to-noise ratios even after ten rounds of hybridization, detection, stripping of the probes from the membranes and rehybridization with additional probe sets. This approach provides a subtraction method that leads to a reduction in redundant DNA sequencing, thus increasing the rate of novel gene discovery. The method is also applicable for detecting target sequences, which are present in one or only a few copies per cell; it has proven useful for physical mapping of BAC and cosmid high-density filter arrays, wherein multiple probes have been hybridized at one time (multiplexed) and subsequently "deplexed" into individual components for specific probe localizations.

  15. Development and validation of InnoQuant(®) HY, a system for quantitation and quality assessment of total human and male DNA using high copy targets.

    Science.gov (United States)

    Loftus, Andrew; Murphy, Gina; Brown, Hiromi; Montgomery, Anne; Tabak, Jonathan; Baus, James; Carroll, Marion; Green, André; Sikka, Suresh; Sinha, Sudhir

    2017-07-01

    The development and validation of InnoQuant(®) HY, a real-time PCR system containing four DNA targets-two RE autosomal targets of different sizes, male specific targets, and an internal positive control target-are described herein. The ratio of the two autosomal targets provides a Degradation Index, or a quantitative value of a sample's degradation state. The male specific targets are multi-copy targets located on the Y chromosome, which provides information about a sample's male DNA composition. The experimental results demonstrate InnoQuant HY as a robust qPCR method producing accurate DNA quantitation results even at low dynamic ranges, with reproducibility among population groups. The system is human specific with low level higher primate cross reactivity and is able to consistently and reproducibly detect sub-picogram concentrations of human and human male DNA. The use of high copy number Alu and SVA (>1000 copies per genome) retrotransposable elements as the two autosomal targets significantly enhances both sensitivity and reproducibility of determination of DNA quantitation as well as DNA degradation in forensic samples. The inclusion of a sensitive multi-copy Y-chromosome specific target provides accurate quantitation of DNA from a male in challenging male-female mixtures (i.e. sexual assault samples). Even in the presence of a large excess of DNA from a female, accurate quantitation was achieved with a male to female ratio of 1:128,000. Population database studies reveal an average Short/Y target ratio of the quantification values across all four populations tested was 1.124±0.282, exhibiting the system's reproducibility across multiple populations. The results from InnoQuant HY provide a tool equipping a forensic analyst with crucial data about a sample's DNA quantitation, male:female ratio, degradation state, and the presence or absence of PCR inhibitors. With the information gained from the InnoQuant HY kit, a more streamlined and efficient workflow

  16. The NumPy array: a structure for efficient numerical computation

    OpenAIRE

    Van der Walt, Stefan; Colbert, S. Chris; Varoquaux, Gaël

    2011-01-01

    International audience; In the Python world, NumPy arrays are the standard representation for numerical data. Here, we show how these arrays enable efficient implementation of numerical computations in a high-level language. Overall, three techniques are applied to improve performance: vectorizing calculations, avoiding copying data in memory, and minimizing operation counts. We first present the NumPy array structure, then show how to use it for efficient computation, and finally how to shar...

  17. Fully printed, highly sensitive multifunctional artificial electronic whisker arrays integrated with strain and temperature sensors.

    Science.gov (United States)

    Harada, Shingo; Honda, Wataru; Arie, Takayuki; Akita, Seiji; Takei, Kuniharu

    2014-04-22

    Mammalian-mimicking functional electrical devices have tremendous potential in robotics, wearable and health monitoring systems, and human interfaces. The keys to achieve these devices are (1) highly sensitive sensors, (2) economically fabricated macroscale devices on flexible substrates, and (3) multifunctions beyond mammalian functions. Although highly sensitive artificial electronic devices have been reported, none have been fabricated using cost-effective macroscale printing methods and demonstrate multifunctionalities of artificial electronics. Herein we report fully printed high-sensitivity multifunctional artificial electronic whiskers (e-whisker) integrated with strain and temperature sensors using printable nanocomposite inks. Importantly, changing the composition ratio tunes the sensitivity of strain. Additionally, the printed temperature sensor array can be incorporated with the strain sensor array beyond mammalian whisker functionalities. The sensitivity for the strain sensor is impressively high (∼59%/Pa), which is the best sensitivity reported to date (>7× improvement). As the proof-of-concept for a truly printable multifunctional artificial e-whisker array, two- and three-dimensional space and temperature distribution mapping are demonstrated. This fully printable flexible sensor array should be applicable to a wide range of low-cost macroscale electrical applications.

  18. Fabrication of High-Frequency pMUT Arrays on Silicon Substrates

    DEFF Research Database (Denmark)

    Pedersen, Thomas; Zawada, Tomasz; Hansen, Karsten

    2010-01-01

    A novel technique based on silicon micromachining for fabrication of linear arrays of high-frequency piezoelectric micromachined ultrasound transducers (pMUT) is presented. Piezoelectric elements are formed by deposition of lead zirconia titanate into etched features of a silicon substrate...

  19. Multilevel kinoform microlens arrays in fused silica for high-power laser optics

    Science.gov (United States)

    Atuchin, Victor V.; Soldatenkov, I. S.; Kirpichnikov, A. V.; Mikhailov, E. V.; Pestryakov, Efim V.; Sheglov, Dmitriy V.

    2004-03-01

    Diffraction microlens arrays has been fabricated in silica substrates by deep UV photolithography and wet chemical etching. The calculated kinoform profile has been approximated by multistep function and this microrelief has been transfered into the surface with wet etching through the photoresist mask. The diffraction efficiency of eight-level kinoform microlens is as high as 85%.

  20. The nuclear spectroscopic telescope array (NuSTAR) high-energy X-ray mission

    DEFF Research Database (Denmark)

    Madsen, Kristin K.; Harrison, Fiona A.; Hongjun An

    2014-01-01

    The Nuclear Spectroscopic Telescope Array (NuSTAR) mission was launched on 2012 June 13 and is the first focusing high-energy X-ray telescope in orbit operating above ~10 keV. NuSTAR flies two co-aligned Wolter-I conical approximation X-ray optics, coated with Pt/C and W/Si multilayers...

  1. GOSSIPO-4: an array of high resolution TDCs with a PLL control

    NARCIS (Netherlands)

    Zappon, F.; van Beuzekom, M.; Gromov, V.; Kluit, R.; Fang, X.; Kruth, A.

    2012-01-01

    GOSSIPO-4 is a prototype chip featuring an array of high resolution Time to Digital Converters with a PLL control that has been taped out the 9th of August 2011. This prototype is the successor of GOSSIPO-3 test chip and the precursor of the 65k pixel chip TimePix3. The prototype is being developed

  2. Reverse Phase Protein Arrays for High-Throughput Protein Measurements in Mammospheres

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    Protein Array (RPPA)-based readout format integrated into robotic siRNA screening. This technique would allow post-screening high-throughput quantification of protein changes. Recently, breast cancer stem cells (BCSCs) have attracted much attention, as a tumor- and metastasis-driving subpopulation...

  3. Integrated Automation of High-Throughput Screening and Reverse Phase Protein Array Sample Preparation

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    multiplexing readouts, but this has a natural limitation. High-content screening via image acquisition and analysis allows multiplexing of few parameters, but is connected to substantial time consumption and complex logistics. We report on integration of Reverse Phase Protein Arrays (RPPA)-based readouts...

  4. Dense high-aspect ratio 3D carbon pillars on interdigitated microelectrode arrays

    DEFF Research Database (Denmark)

    Amato, Letizia; Heiskanen, Arto; Hansen, Rasmus

    2015-01-01

    In this work we present high-aspect ratio carbon pillars (1.4 μm in diameter and ∼11 μm in height) on top of interdigitated electrode arrays to be used for electrochemical applications. For this purpose, different types of 2D and 3D pyrolysed carbon structures were fabricated and characterised...

  5. High field matching effects in superconducting Nb porous arrays catalyzed from anodic alumina templates

    DEFF Research Database (Denmark)

    Vinckx, W.; Vanacken, J.; Moshchalkov, V.V.;

    2007-01-01

    Vortex pinning in a superconducting Nb thin film deposited on an anodically grown alumina template is investigated. Anodic oxidation of aluminium layers permits under specific conditions the formation of highly ordered porous alumina, a membrane-like structure consisting of triangular arrays...... of parallel pores. Its pore diameter and interpore distance are set by careful tuning of the anodization parameters. A superconducting Nb thin film is deposited directly onto the alumina film. The porous alumina acts as a template and it allows Nb to form a periodic pinning array during its growth. Pinning...

  6. A novel technique for electronic phasing of high power fiber amplifier arrays

    Science.gov (United States)

    Shay, T. M.; Baker, J. T.; Sanchez, Anthony D.; Robin, C. A.; Vergien, C. L.; Zeringue, C.; Gallant, D.; Lu, Chunte A.; Pulford, Benjamin; Bronder, T. J.; Lucero, Arthur

    2009-06-01

    We report high power phase locked fiber amplifier array using the Self-Synchronous Locking of Optical Coherence by Single-detector Electronic-frequency Tagging technique. We report the first experimental results for a five element amplifier array with a total locked power of more than 725-W. We will report on experimental measurements of the phase fluctuations versus time when the control loop is closed. The rms phase error was measured to be λ/60. Recent results will be reported. To the best of the authors' knowledge this is the highest fiber laser power to be coherently combined.

  7. Preparation and hydrogen 8as sensitive characteristics of highly ordered titania nanotube arrays

    Institute of Scientific and Technical Information of China (English)

    JI HuiMing; LU HuiXiang; MA DongFang; YU JianJun; MA ShiCai

    2008-01-01

    In this paper, we report the growth and characteristics of titania nanotube arrays prepared by anodic oxidation and then annealed in an oxygen atmosphere at 500℃. The titania nanotube arrays presented high sensitivity to hydrogen gas. The crystalline phase of the samples was checked by X-ray diffraction (XRD). The differences in the nanotubes morphology attributed to the etched samples due to anodiza-tion potential, reaction time and the electrolyte concentration were analyzed by scanning electron mi-croscopy (SEM). The gas sensitive parameters of the samples were obtained from resistance, the re-sponse time and the recovery time at different temperatures.

  8. A High-Efficiency Si Nanowire Array/Perovskite Hybrid Solar Cell

    OpenAIRE

    Yan, Xin; Zhang, Chen; Wang, Jiamin; Zhang, Xia; Ren, Xiaomin

    2017-01-01

    A low-cost Si nanowire array/perovskite hybrid solar cell is proposed and simulated. The solar cell consists of a Si p-i-n nanowire array filled with CH3NH3PbI3, in which both the nanowires and perovskite absorb the incident light while the nanowires act as the channels for transporting photo-generated electrons and holes. The hybrid structure has a high absorption efficiency in a broad wavelength range of 300~800 nm. A large short-circuit current density of 28.8 mA/cm2 and remarkable convers...

  9. The High-Level Interface Definitions in the ASTRI/CTA Mini Array Software System (MASS)

    Science.gov (United States)

    Conforti, V.; Tosti, G.; Schwarz, J.; Bruno, P.; Cefal‘A, M.; Paola, A. D.; Gianotti, F.; Grillo, A.; Russo, F.; Tanci, C.; Testa, V.; Antonelli, L. A.; Canestrari, R.; Catalano, O.; Fiorini, M.; Gallozzi, S.; Giro, E.; Palombara, N. L.; Leto, G.; Maccarone, M. C.; Pareschi, G.; Stringhetti, L.; Trifoglio, M.; Vercellone, S.; Astri Collaboration; Cta Consortium

    2015-09-01

    ASTRI (Astrofisica con Specchi a Tecnologia Replicante Italiana) is a Flagship Project funded by the Italian Ministry of Education, University and Research, and led by INAF, the Italian National Institute of Astrophysics. Within this framework, INAF is currently developing an end-to-end prototype, named ASTRI SST-2M, of a Small Size Dual-Mirror Telescope for the Cherenkov Telescope Array, CTA. A second goal of the project is the realization of the ASTRI/CTA mini-array, which will be composed of seven SST-2M telescopes placed at the CTA Southern Site. The ASTRI Mini Array Software System (MASS) is designed to support the ASTRI/CTA mini-array operations. MASS is being built on top of the ALMA Common Software (ACS) framework, which provides support for the implementation of distributed data acquisition and control systems, and functionality for log and alarm management, message driven communication and hardware devices management. The first version of the MASS system, which will comply with the CTA requirements and guidelines, will be tested on the ASTRI SST-2M prototype. In this contribution we present the interface definitions of the MASS high level components in charge of the ASTRI SST-2M observation scheduling, telescope control and monitoring, and data taking. Particular emphasis is given to their potential reuse for the ASTRI/CTA mini-array.

  10. Development of 2D Bi-SQUID Arrays with High Linearity

    CERN Document Server

    Berggren, S; Longhini, P; Palacios, A; Mukhanov, O A; de Escobar, A Leese; Taylor, B J; de Andrade, M C; Nisenoff, M; Fagaly, R L; Wong, T; Cho, E; Wong, E; In, V

    2013-01-01

    We develop a two-dimensional (2D) Superconducting Quantum Interference Filter (SQIF) array based on recently introduced high-linearity tri-junction bi-SQUIDs. Our bi-SQUID SQIF array design is based on a tight integration of individual bi- SQUID cells sharing inductances with adjacent cells. We provide extensive computer simulations, analysis and experimental measurements, in which we explore the phase dynamics and linearity of the array voltage response. The non-uniformity in inductances of the bi-SQUIDs produces a pronounced zero-field single antipeak in the voltage response. The anti-peak linearity and size can be optimized by varying the critical current of the additional junction of each bi-SQUID. The layout implementation of the tight 2D array integration leads to a distinct geometrical diamond shape formed by the merged dual bi-SQUID cells. Different size 2D arrays are fabricated using standard HYPRES niobium 4.5 kA/cm2 fabrication process. The measured linearity, power gain, and noise properties will ...

  11. Chimera-free, high copy number YAC libraries and efficient methods of analysis. Final technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The first experiment involved a low chimera YAC library in recombination deficient host strains. To determine if the genetic background of the yeast host strain contributes to the formation of chimeric YACs the same YAC ligation mixture was introduced into three isogenic yeast hosts differing only in their recombination abilities. To prepare YACs, human genomic DNA was partially digested with EcoR1 and then ligated to YAC vector pCGS966 arms. DNA was size fractionated before and after ligation by preparative pulsed field gel electrophoresis (CHEF), selecting for fragments greater than 400 kb, and introduced into competent spheroplasts. CHEF gel Southern blots of resulting colony-purified YACs were probed with human DNA to determine if multiple YACs or YAC fragments were present in the same cell. The frequency of chimeric YACs was measured by fluorescence in situ hybridization (FISH) of YACs to human prometaphase spreads. YACs that hybridized to more than one location were assumed to be chimeric. In the second experiment new YAC vectors featuring tags for capture of YACs and YAC inserts were constructed. Yeast Artificial Chromosomes (YACs) have been of tremendous value in the physical mapping of the human genome. Because they can carry very large inserts, YACs are likely not only to contain entire genes but also their control elements. However, the only mode of purification of YAC DNA from current commonly used YAC libraries such as the CEPH library is by pulsed field gel electrophoresis. This is an inefficient, time consuming process and due to the single copy nature of these YACs, often result in poor yields. The vector pCGS1000 was designed to test new efficient ways of YAC DNA purification.

  12. Chimera-free, high copy number YAC libraries and efficient methods of analysis. Final technical progress report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-10-01

    The first experiment involved a low chimera YAC library in recombination deficient host strains. To determine if the genetic background of the yeast host strain contributes to the formation of chimeric YACs the same YAC ligation mixture was introduced into three isogenic yeast hosts differing only in their recombination abilities. To prepare YACs, human genomic DNA was partially digested with EcoR1 and then ligated to YAC vector pCGS966 arms. DNA was size fractionated before and after ligation by preparative pulsed field gel electrophoresis (CHEF), selecting for fragments greater than 400 kb, and introduced into competent spheroplasts. CHEF gel Southern blots of resulting colony-purified YACs were probed with human DNA to determine if multiple YACs or YAC fragments were present in the same cell. The frequency of chimeric YACs was measured by fluorescence in situ hybridization (FISH) of YACs to human prometaphase spreads. YACs that hybridized to more than one location were assumed to be chimeric. In the second experiment new YAC vectors featuring tags for capture of YACs and YAC inserts were constructed. Yeast Artificial Chromosomes (YACs) have been of tremendous value in the physical mapping of the human genome. Because they can carry very large inserts, YACs are likely not only to contain entire genes but also their control elements. However, the only mode of purification of YAC DNA from current commonly used YAC libraries such as the CEPH library is by pulsed field gel electrophoresis. This is an inefficient, time consuming process and due to the single copy nature of these YACs, often result in poor yields. The vector pCGS1000 was designed to test new efficient ways of YAC DNA purification.

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

    Science.gov (United States)

    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

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

    CERN Document Server

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

    2013-01-01

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

  15. Characterization of SPAD Array for Multifocal High-Content Screening Applications

    Directory of Open Access Journals (Sweden)

    Anthony Tsikouras

    2016-10-01

    Full Text Available Current instruments used to detect specific protein-protein interactions in live cells for applications in high-content screening (HCS are limited by the time required to measure the lifetime. Here, a 32 × 1 single-photon avalanche diode (SPAD array was explored as a detector for fluorescence lifetime imaging (FLIM in HCS. Device parameters and characterization results were interpreted in the context of the application to determine if the SPAD array could satisfy the requirements of HCS-FLIM. Fluorescence lifetime measurements were performed using a known fluorescence standard; and the recovered fluorescence lifetime matched literature reported values. The design of a theoretical 32 × 32 SPAD array was also considered as a detector for a multi-point confocal scanning microscope.

  16. Performance of compact TES arrays with integrated high-fill-fraction X-ray absorbers

    Energy Technology Data Exchange (ETDEWEB)

    Lindeman, Mark A. E-mail: lindeman@lheapop.gsfc.nasa.gov; Bandler, Simon; Brekosky, Regis P.; Chervenak, James A.; Figueroa-Feliciano, Enectali; Finkbeiner, Fred M.; Kelley, Richard L.; Saab, Tarek; Stahle, Caroline K.; Talley, D.J

    2004-03-11

    We have recently produced and tested two-dimensional arrays of Mo/Au transition-edge-sensor (TES) calorimeters with Bi/Cu absorbers. The arrays represent a significant step towards meeting the specifications of NASA's Constellation-X mission. The calorimeters are compactly spaced within 5x5 arrays of 250 {mu}m square pixels necessary for an angular resolution of 5 arcsec. Lithographically produced absorbers hang over the substrate and wiring between the TESs for high filling fraction and high quantum efficiency. We designed the calorimeters with heat capacities and thermal couplings such that X-rays produce pulses with fall times of approximately 300 {mu}s to allow relatively high count rates with low dead time. We read out up to four of the pixels simultaneously. The arrays demonstrated very good energy resolution (5 eV at 1.5 keV and 7 eV at 6 keV) and little crosstalk between neighboring pixels.

  17. Implementation of High Resolution Whole Genome Array CGH in the Prenatal Clinical Setting: Advantages, Challenges, and Review of the Literature

    Directory of Open Access Journals (Sweden)

    Paola Evangelidou

    2013-01-01

    Full Text Available Array Comparative Genomic Hybridization analysis is replacing postnatal chromosomal analysis in cases of intellectual disabilities, and it has been postulated that it might also become the first-tier test in prenatal diagnosis. In this study, array CGH was applied in 64 prenatal samples with whole genome oligonucleotide arrays (BlueGnome, Ltd. on DNA extracted from chorionic villi, amniotic fluid, foetal blood, and skin samples. Results were confirmed with Fluorescence In Situ Hybridization or Real-Time PCR. Fifty-three cases had normal karyotype and abnormal ultrasound findings, and seven samples had balanced rearrangements, five of which also had ultrasound findings. The value of array CGH in the characterization of previously known aberrations in five samples is also presented. Seventeen out of 64 samples carried copy number alterations giving a detection rate of 26.5%. Ten of these represent benign or variables of unknown significance, giving a diagnostic capacity of the method to be 10.9%. If karyotype is performed the additional diagnostic capacity of the method is 5.1% (3/59. This study indicates the ability of array CGH to identify chromosomal abnormalities which cannot be detected during routine prenatal cytogenetic analysis, therefore increasing the overall detection rate. In addition a thorough review of the literature is presented.

  18. Highly Oriented ZnO Rod Arrays on Si Substrates from Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    LIU Changsong; LI Zhiwen; ZHANG Qifeng

    2008-01-01

    Ordered zinc oxide (ZnO) rod arrays with very high orientation were fabricated on Si substrates by using a solution method. The substrate surfaces were functionalized by Self-Assembly Monolayers(SAMs). In the very early growth stage, the oriented ZnO crystals had already grown, which appeared to be themain reason why ZnO nanorods showed very high orientation. The un-dense and un-uniform SAMs provided a surface that was heterogeneous to ZnO nucleation. Consequently, highly oriented ZnO rods were selectively grown on the "coin-like" SAM-uncovered regions. The route developed here can provide some helpful information to control the nucleation and orientation of ZnO in aqueous solution. Also, the site-selective growth mechanisms can indicate a clue to grow patterned highly oriented ZnO nanorod arrays by the organic template.

  19. Ultra-Fast Processing of Gigapixel Tissue MicroArray Images Using High Performance Computing

    OpenAIRE

    Yinhai Wang; David McCleary; Ching-Wei Wang; Paul Kelly; Jackie James; Fennell, Dean A; Peter Hamilton

    2010-01-01

    Background: Tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers. The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform. Methods: A High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented in this study. Using...

  20. Highly Ordered Carbon Nanotube Arrays with Open Ends Grown in Anodic Alumina Nanoholes

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Highly ordered multiwalled carbon nanotube arrays were fabricated by pyrolysis of acetylene within anodic alumina templates.Nanotubes are very uniform in diameter and open at both ends. High resolution transmission electron microscopy and electron diffraction analysis show that the carbon nanotubes are well graphitized. These standing and open carbon nanotubes are possible to offer a potential elegant technique for electron emitting devices,chemical functionalization and nanotube composites.

  1. Modeling change from large-scale high-dimensional spatio-temporal array data

    Science.gov (United States)

    Lu, Meng; Pebesma, Edzer

    2014-05-01

    The massive data that come from Earth observation satellite and other sensors provide significant information for modeling global change. At the same time, the high dimensionality of the data has brought challenges in data acquisition, management, effective querying and processing. In addition, the output of earth system modeling tends to be data intensive and needs methodologies for storing, validation, analyzing and visualization, e.g. as maps. An important proportion of earth system observations and simulated data can be represented as multi-dimensional array data, which has received increasingly attention in big data management and spatial-temporal analysis. Study cases will be developed in natural science such as climate change, hydrological modeling, sediment dynamics, from which the addressing of big data problems is necessary. Multi-dimensional array-based database management and analytics system such as Rasdaman, SciDB, and R will be applied to these cases. From these studies will hope to learn the strengths and weaknesses of these systems, how they might work together or how semantics of array operations differ, through addressing the problems associated with big data. Research questions include: • How can we reduce dimensions spatially and temporally, or thematically? • How can we extend existing GIS functions to work on multidimensional arrays? • How can we combine data sets of different dimensionality or different resolutions? • Can map algebra be extended to an intelligible array algebra? • What are effective semantics for array programming of dynamic data driven applications? • In which sense are space and time special, as dimensions, compared to other properties? • How can we make the analysis of multi-spectral, multi-temporal and multi-sensor earth observation data easy?

  2. Self-assembled random arrays: high-performance imaging and genomics applications on a high-density microarray platform

    Science.gov (United States)

    Barker, David L.; Theriault, Greg; Che, Diping; Dickinson, Todd; Shen, Richard; Kain, Robert C.

    2003-07-01

    Illumina is developing a BeadArrayTM technology that supports SNP genotyping, mRNA expression analysis and protein expression analysis on the same platform. We use fiber-optic bundles with a density of approximately 40,000 fibers/mm2. At hte end of each fiber, a derivatized silica bead forms an array element for reading out a genotyping or expression assay data point. Each bead contains oligonucleotide probes that hybridize with high specificity to complementary sequences in a complex nucleic acid mixture. We derivatize the beads in bulk, pool them to form a quality-controlled source of microarray elements, and allow them to assemble spontaneously into pits etched into the end of each optical fiber bundle. We load our fiber bundles, containing 49,777 fibers, with up to 1520 different bead types. The presence of many beads of each type greatly improves the accuracy of each assay. As the final step in our manufacturing process, we decode the identity of each bead by a series of rapid hybridizations with fluroescent oligos. Decoding accuracy and the number of beads of each type is recorded for each array. Decoding also serves as a quality control procedure for the performance of each element in the array. To facilitate high-throughput analysis of many samples, the fiber bundles are arranged in an array matrix (SentrixTM arrays). Using a 96-bundle array matrix, up to 1520 assays can be performed on each of 96 samples simultaneously for a total of 145,920 assays. Using a 384-bundle array matrix, up to 583,680 assays can be performed simultaneously. The BeadArray platform is the highest density microarray in commercial use, requiring development of a high-performance array scanner. To meet this need, we developed the SherlockTM system, a laser-scanning confocal imaging system that automatically scans all 96 bundles of an array matrix at variable resolution down to 0.8 micron. The system scans with both 532 and 635 nm lasers simultaneously, collecting two fluorescence

  3. Investigation on transmission and reflection characteristics of plasma array to 6 GHz high-power microwave

    Science.gov (United States)

    Yang, Liu; Yang, Zhongcun; Wan, Jianing; Liu, Hao

    2016-10-01

    For the safety of electronic equipment, a double-layer barrier of cylindrical plasma array was designed, and its protective performance to high-power microwave (HPM) were analyzed and the protective performance experiment was conducted. Combining the density distribution characteristic of the discharge plasma, the shielding effectiveness of the double-layer plasma on 6GHz HPM pulse was studied. The experiment results indicate that the protective effectiveness of two layers plasma array is better than that of one layer. Two layers plasma array can make the peak electric field of transmission waveform less than interference threshold of electronic equipment to achieve better protection effectiveness. Transmission attenuation of one layer and two layers plasma array to HPM can reach -6.6066dB and -24.9357dB. The results also show that for the existence of multiple reflection, even the plasma electron density is not high enough, it can realize a strong attenuation. The experiment results in this paper are of great significance in protecting against HPM and electromagnetic pulse.

  4. MassCode liquid arrays as a tool for multiplexed high-throughput genetic profiling.

    Directory of Open Access Journals (Sweden)

    Gregory S Richmond

    Full Text Available Multiplexed detection assays that analyze a modest number of nucleic acid targets over large sample sets are emerging as the preferred testing approach in such applications as routine pathogen typing, outbreak monitoring, and diagnostics. However, very few DNA testing platforms have proven to offer a solution for mid-plexed analysis that is high-throughput, sensitive, and with a low cost per test. In this work, an enhanced genotyping method based on MassCode technology was devised and integrated as part of a high-throughput mid-plexing analytical system that facilitates robust qualitative differential detection of DNA targets. Samples are first analyzed using MassCode PCR (MC-PCR performed with an array of primer sets encoded with unique mass tags. Lambda exonuclease and an array of MassCode probes are then contacted with MC-PCR products for further interrogation and target sequences are specifically identified. Primer and probe hybridizations occur in homogeneous solution, a clear advantage over micro- or nanoparticle suspension arrays. The two cognate tags coupled to resultant MassCode hybrids are detected in an automated process using a benchtop single quadrupole mass spectrometer. The prospective value of using MassCode probe arrays for multiplexed bioanalysis was demonstrated after developing a 14plex proof of concept assay designed to subtype a select panel of Salmonella enterica serogroups and serovars. This MassCode system is very flexible and test panels can be customized to include more, less, or different markers.

  5. Application of HEMT for multiplexing large arrays of high impedance LTDs

    Energy Technology Data Exchange (ETDEWEB)

    Benoit, A.; Camus, Ph. E-mail: camus@grenoble.cnrs.fr; Cavanna, A.; Elhdiy, A.; Jin, Y.; Leclercq, S

    2004-03-11

    The development of large arrays of detectors requires using a proximate electronics at low temperatures for signal multiplexing and amplification. We report the use of commercial High Electronic Mobility Transistors (HEMT) for multiplexing signals from high impedance LTD arrays (typ. 10-100 M{omega}). The electronic architecture is based on HEMTs cooled at 0.1 K for the multiplexer and a JFET amplifier cooled at 100 K with <1 nV/Hz{sup 1/2} noise figure. For this time-multiplexing scheme, a capacitor is used to integrate the signal between measurements. Two main solutions are compared for the detectors polarization: the first uses a classical resistive method; the second uses a common capacitor allowing to polarize the detectors individually. The multiplexing ratio is mainly limited by the amplifier noise to about 20 detectors per amplifier with a pixel sampling rate of about 60 Hz. A specific development of HEMT arrays with Quantum Point Contacts (QPC-HEMT) with very small grid-to-channel capacitor ({approx}1 fF) allows minimizing the transient effects and realizing a close integration with the LTD arrays.

  6. Demonstration of nanoimprinted hyperlens array for high-throughput sub-diffraction imaging

    Science.gov (United States)

    Byun, Minsueop; Lee, Dasol; Kim, Minkyung; Kim, Yangdoo; Kim, Kwan; Ok, Jong G.; Rho, Junsuk; Lee, Heon

    2017-04-01

    Overcoming the resolution limit of conventional optics is regarded as the most important issue in optical imaging science and technology. Although hyperlenses, super-resolution imaging devices based on highly anisotropic dispersion relations that allow the access of high-wavevector components, have recently achieved far-field sub-diffraction imaging in real-time, the previously demonstrated devices have suffered from the extreme difficulties of both the fabrication process and the non-artificial objects placement. This results in restrictions on the practical applications of the hyperlens devices. While implementing large-scale hyperlens arrays in conventional microscopy is desirable to solve such issues, it has not been feasible to fabricate such large-scale hyperlens array with the previously used nanofabrication methods. Here, we suggest a scalable and reliable fabrication process of a large-scale hyperlens device based on direct pattern transfer techniques. We fabricate a 5 cm × 5 cm size hyperlenses array and experimentally demonstrate that it can resolve sub-diffraction features down to 160 nm under 410 nm wavelength visible light. The array-based hyperlens device will provide a simple solution for much more practical far-field and real-time super-resolution imaging which can be widely used in optics, biology, medical science, nanotechnology and other closely related interdisciplinary fields.

  7. High-Accuracy, Compact Scanning Method and Circuit for Resistive Sensor Arrays

    Directory of Open Access Journals (Sweden)

    Jong-Seok Kim

    2016-01-01

    Full Text Available The zero-potential scanning circuit is widely used as read-out circuit for resistive sensor arrays because it removes a well known problem: crosstalk current. The zero-potential scanning circuit can be divided into two groups based on type of row drivers. One type is a row driver using digital buffers. It can be easily implemented because of its simple structure, but we found that it can cause a large read-out error which originates from on-resistance of the digital buffers used in the row driver. The other type is a row driver composed of operational amplifiers. It, very accurately, reads the sensor resistance, but it uses a large number of operational amplifiers to drive rows of the sensor array; therefore, it severely increases the power consumption, cost, and system complexity. To resolve the inaccuracy or high complexity problems founded in those previous circuits, we propose a new row driver which uses only one operational amplifier to drive all rows of a sensor array with high accuracy. The measurement results with the proposed circuit to drive a 4 × 4 resistor array show that the maximum error is only 0.1% which is remarkably reduced from 30.7% of the previous counterpart.

  8. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates.

    Science.gov (United States)

    Holden, Matthew T; Carter, Matthew C D; Wu, Cheng-Hsien; Wolfer, Jamison; Codner, Eric; Sussman, Michael R; Lynn, David M; Smith, Lloyd M

    2015-11-17

    The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

  9. The Art of Copying

    DEFF Research Database (Denmark)

    Christensen, Hans Dam

    2017-01-01

    This article discusses copies within the field of art museums by way of mapping strategies for copy practices. This mapping leans heavily towards parts of the writings of Jacques Derrida (1930–2004). Against the backdrop of this theoretical premise, the article distinguishes five main strategies...... for the informational originalcopy will be discussed as it has a vital function in terms of talking about museum originals and copies. This is the strategy which grants the original artifacts their status as museum objects. An informational originalcopy is just as unique as an original object of art, and at the same...

  10. The use of HEMTs in multiplexing large arrays of high impedance LTDs

    Energy Technology Data Exchange (ETDEWEB)

    Yates, S.J.C. [CNRS-CRTBT, 25 Rue des Martyrs, 38042 Grenoble Cedex 9 (France)]. E-mail: stephen.yates@grenoble.cnrs.fr; Benoit, A. [CNRS-CRTBT, 25 Rue des Martyrs, 38042 Grenoble Cedex 9 (France); Jin, Y. [CNRS-LPN, Route de Nozay, 91461 Marcoussis (France); Camus, Ph. [CNRS-CRTBT, 25 Rue des Martyrs, 38042 Grenoble Cedex 9 (France); Cavanna, A. [CNRS-LPN, Route de Nozay, 91461 Marcoussis (France); Durand, T. [CNRS-CRTBT, 25 Rue des Martyrs, 38042 Grenoble Cedex 9 (France); Etienne, B. [CNRS-LPN, Route de Nozay, 91461 Marcoussis (France); Gennser, U. [CNRS-LPN, Route de Nozay, 91461 Marcoussis (France); Gremion, E. [CNRS-LPN, Route de Nozay, 91461 Marcoussis (France); Hoffmann, C. [CNRS-CRTBT, 25 Rue des Martyrs, 38042 Grenoble Cedex 9 (France); Universite Joseph Fourier, Grenoble (France); Leclercq, S. [CNRS-CRTBT, 25 Rue des Martyrs, 38042 Grenoble Cedex 9 (France); Ulysse, Ch. [CNRS-LPN, Route de Nozay, 91461 Marcoussis (France)

    2006-04-15

    The use of a multiplexing system in close proximity to the detectors simplifies the electronics associated with large arrays of Low Temperature Detectors (LTDs). Here, we report the demonstration of an array of Quantum-Point-Contact High-Electron-Mobility-Transistors (QPC-HEMTs) down to 100mK used to time multiplex the signal from 8 simulated high impedance LTDs ({approx}10M{omega}) to an individual amplifier. Capacitors in parallel with the individual LTDs integrate the signal between measurements so giving a quasi-DC measurement of the LTDs. With the high impedance of the LTD this acts as a filter which counter acts the aliasing of the Johnson noise of the LTD associated with the time-multiplexing technique.

  11. Automatic Combination of Microfluidic Nanoliter-Scale Droplet Array with High-Speed Capillary Electrophoresis

    Science.gov (United States)

    Li, Q.; Zhu, Y.; Zhang, N.-Q.; Fang, Q.

    2016-05-01

    In this paper, we developed a novel approach for interfacing a microfluidic two-dimensional droplet array to a high-speed capillary electrophoresis (HSCE) system. Picoliter-scale sample injection (ca. 200 pL) from a nanoliter-scale droplet array covered by nonvolatile oil was automatically achieved using the spontaneous injection mode, without the interference from the cover oil and the need of special droplet extraction interface as in previously reported systems. The system was applied in consecutive separations of 25 different samples of amino acids with a whole separation time less than 15 min, as well as on-line monitoring of in-droplet derivatizing reaction of amino acids by fluorescein isothiocyanate (FITC) over 3 hours. High separation speed (up to 100 samples per hour) and high separation efficiency (up to 9.22 × 105 N/m) were achieved.

  12. Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm.

    Science.gov (United States)

    Kwong, Qi Bin; Teh, Chee Keng; Ong, Ai Ling; Heng, Huey Ying; Lee, Heng Leng; Mohamed, Mohaimi; Low, Joel Zi-Bin; Apparow, Sukganah; Chew, Fook Tim; Mayes, Sean; Kulaveerasingam, Harikrishna; Tammi, Martti; Appleton, David Ross

    2016-08-01

    High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r(2) = 0.43 to 146 kb at r(2) = 0.50) when compared with the semi-wild populations (19.5 kb at r(2) = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.

  13. A TMA de-arraying method for high throughput biomarker discovery in tissue research.

    Directory of Open Access Journals (Sweden)

    Yinhai Wang

    Full Text Available BACKGROUND: Tissue MicroArrays (TMAs represent a potential high-throughput platform for the analysis and discovery of tissue biomarkers. As TMA slides are produced manually and subject to processing and sectioning artefacts, the layout of TMA cores on the final slide and subsequent digital scan (TMA digital slide is often disturbed making it difficult to associate cores with their original position in the planned TMA map. Additionally, the individual cores can be greatly altered and contain numerous irregularities such as missing cores, grid rotation and stretching. These factors demand the development of a robust method for de-arraying TMAs which identifies each TMA core, and assigns them to their appropriate coordinates on the constructed TMA slide. METHODOLOGY: This study presents a robust TMA de-arraying method consisting of three functional phases: TMA core segmentation, gridding and mapping. The segmentation of TMA cores uses a set of morphological operations to identify each TMA core. Gridding then utilises a Delaunay Triangulation based method to find the row and column indices of each TMA core. Finally, mapping correlates each TMA core from a high resolution TMA whole slide image with its name within a TMAMap. CONCLUSION: This study describes a genuine robust TMA de-arraying algorithm for the rapid identification of TMA cores from digital slides. The result of this de-arraying algorithm allows the easy partition of each TMA core for further processing. Based on a test group of 19 TMA slides (3129 cores, 99.84% of cores were segmented successfully, 99.81% of cores were gridded correctly and 99.96% of cores were mapped with their correct names via TMAMaps. The gridding of TMA cores were also extensively tested using a set of 113 pseudo slide (13,536 cores with a variety of irregular grid layouts including missing cores, rotation and stretching. 100% of the cores were gridded correctly.

  14. A TMA de-arraying method for high throughput biomarker discovery in tissue research.

    Science.gov (United States)

    Wang, Yinhai; Savage, Kienan; Grills, Claire; McCavigan, Andrena; James, Jacqueline A; Fennell, Dean A; Hamilton, Peter W

    2011-01-01

    Tissue MicroArrays (TMAs) represent a potential high-throughput platform for the analysis and discovery of tissue biomarkers. As TMA slides are produced manually and subject to processing and sectioning artefacts, the layout of TMA cores on the final slide and subsequent digital scan (TMA digital slide) is often disturbed making it difficult to associate cores with their original position in the planned TMA map. Additionally, the individual cores can be greatly altered and contain numerous irregularities such as missing cores, grid rotation and stretching. These factors demand the development of a robust method for de-arraying TMAs which identifies each TMA core, and assigns them to their appropriate coordinates on the constructed TMA slide. This study presents a robust TMA de-arraying method consisting of three functional phases: TMA core segmentation, gridding and mapping. The segmentation of TMA cores uses a set of morphological operations to identify each TMA core. Gridding then utilises a Delaunay Triangulation based method to find the row and column indices of each TMA core. Finally, mapping correlates each TMA core from a high resolution TMA whole slide image with its name within a TMAMap. This study describes a genuine robust TMA de-arraying algorithm for the rapid identification of TMA cores from digital slides. The result of this de-arraying algorithm allows the easy partition of each TMA core for further processing. Based on a test group of 19 TMA slides (3129 cores), 99.84% of cores were segmented successfully, 99.81% of cores were gridded correctly and 99.96% of cores were mapped with their correct names via TMAMaps. The gridding of TMA cores were also extensively tested using a set of 113 pseudo slide (13,536 cores) with a variety of irregular grid layouts including missing cores, rotation and stretching. 100% of the cores were gridded correctly.

  15. Arrays of single-walled carbon nanotubes with full surface coverage for high-performance electronics.

    Science.gov (United States)

    Cao, Qing; Han, Shu-jen; Tulevski, George S; Zhu, Yu; Lu, Darsen D; Haensch, Wilfried

    2013-03-01

    Single-walled carbon nanotubes have exceptional electronic properties and have been proposed as a replacement for silicon in applications such as low-cost thin-film transistors and high-performance logic devices. However, practical devices will require dense, aligned arrays of electronically pure nanotubes to optimize performance, maximize device packing density and provide sufficient drive current (or power output) for each transistor. Here, we show that aligned arrays of semiconducting carbon nanotubes can be assembled using the Langmuir-Schaefer method. The arrays have a semiconducting nanotube purity of 99% and can fully cover a surface with a nanotube density of more than 500 tubes/µm. The nanotube pitch is self-limited by the diameter of the nanotube plus the van der Waals separation, and the intrinsic mobility of the nanotubes is preserved after array assembly. Transistors fabricated using this approach exhibit significant device performance characteristics with a drive current density of more than 120 µA µm(-1), transconductance greater than 40 µS µm(-1) and on/off ratios of ∼1 × 10(3).

  16. High Field Emission Current Density from Patterned Carbon Nanotube Field Emitter Arrays with Random Growth.

    Science.gov (United States)

    Khaneja, Mamta; Ghosh, Santanu; Gautam, Seema; Kumar, Prashant; Rawat, J S; Chaudhury, P K; Vankar, V D; Kumar, Vikram

    2015-05-01

    High field emission (FE) current density from carbon nanotube (CNT) arrays grown on lithographically patterned silicon substrates is reported. A typical patterned field emitter array consists of bundles of nanotubes separated by a fixed gap and spread over the entire emission area. Emission performance from such an array having randomly oriented nanotube growth within each bundle is reported for different bundle sizes and separations. One typical sample with aligned CNTs within the bundle is also examined for comparison. It is seen that the current density from an array having random nanotube growth within the bundles is appreciably higher as compared to its aligned counterpart. The influence of structure on FE current densities as revealed by Raman spectroscopy is also seen. It is also observed that current density depends on edge length and increases with the same for all samples under study. Highest current density of -100 mA cm(-2) at an applied field of 5 V/μm is achieved from the random growth patterned sample with a bundle size of 2 μm and spacing of 4 μm between the bundles.

  17. High-resolution dynamic pressure sensor array based on piezo-phototronic effect tuned photoluminescence imaging.

    Science.gov (United States)

    Peng, Mingzeng; Li, Zhou; Liu, Caihong; Zheng, Qiang; Shi, Xieqing; Song, Ming; Zhang, Yang; Du, Shiyu; Zhai, Junyi; Wang, Zhong Lin

    2015-03-24

    A high-resolution dynamic tactile/pressure display is indispensable to the comprehensive perception of force/mechanical stimulations such as electronic skin, biomechanical imaging/analysis, or personalized signatures. Here, we present a dynamic pressure sensor array based on pressure/strain tuned photoluminescence imaging without the need for electricity. Each sensor is a nanopillar that consists of InGaN/GaN multiple quantum wells. Its photoluminescence intensity can be modulated dramatically and linearly by small strain (0-0.15%) owing to the piezo-phototronic effect. The sensor array has a high pixel density of 6350 dpi and exceptional small standard deviation of photoluminescence. High-quality tactile/pressure sensing distribution can be real-time recorded by parallel photoluminescence imaging without any cross-talk. The sensor array can be inexpensively fabricated over large areas by semiconductor product lines. The proposed dynamic all-optical pressure imaging with excellent resolution, high sensitivity, good uniformity, and ultrafast response time offers a suitable way for smart sensing, micro/nano-opto-electromechanical systems.

  18. Broadband High Efficiency Fractal-Like and Diverse Geometry Silicon Nanowire Arrays for Photovoltaic Applications

    Science.gov (United States)

    AL-Zoubi, Omar H.

    Solar energy has many advantages over conventional sources of energy. It is abundant, clean and sustainable. One way to convert solar energy directly into electrical energy is by using the photovoltaic solar cells (PVSC). Despite PVSC are becoming economically competitive, they still have high cost and low light to electricity conversion efficiency. Therefore, increasing the efficiency and reducing the cost are key elements for producing economically more competitive PVSC that would have significant impact on energy market and saving environment. A significant percentage of the PVSC cost is due to the materials cost. For that, thin films PVSC have been proposed which offer the benefits of the low amount of material and fabrication costs. Regrettably, thin film PVSC show poor light to electricity conversion efficiency because of many factors especially the high optical losses. To enhance conversion efficiency, numerous techniques have been proposed to reduce the optical losses and to enhance the absorption of light in thin film PVSC. One promising technique is the nanowire (NW) arrays in general and the silicon nanowire (SiNW) arrays in particular. The purpose of this research is to introduce vertically aligned SiNW arrays with enhanced and broadband absorption covering the entire solar spectrum while simultaneously reducing the amount of material used. To this end, we apply new concept for designing SiNW arrays based on employing diversity of physical dimensions, especially radial diversity within certain lattice configurations. In order to study the interaction of light with SiNW arrays and compute their optical properties, electromagnetic numerical modeling is used. A commercial numerical electromagnetic solver software package, high frequency structure simulation (HFSS), is utilized to model the SiNW arrays and to study their optical properties. We studied different geometries factors that affect the optical properties of SiNW arrays. Based on this study, we

  19. Transfer-free synthesis of highly ordered Ge nanowire arrays on glass substrates

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, M.; Toko, K., E-mail: toko@bk.tsukuba.ac.jp; Suemasu, T. [Institute of Applied Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573 (Japan); Jevasuwan, W.; Fukata, N. [National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044 (Japan); Saitoh, N.; Yoshizawa, N. [Electron Microscope Facility, TIA, AIST, 16-1 Onogawa, Tsukuba 305-8569 (Japan)

    2015-09-28

    Vertically aligned Ge nanowires (NWs) are directly synthesized on glass via vapor-liquid-solid (VLS) growth using chemical-vapor deposition. The use of the (111)-oriented Ge seed layer, formed by metal-induced crystallization at 325 °C, dramatically improved the density, uniformity, and crystal quality of Ge NWs. In particular, the VLS growth at 400 °C allowed us to simultaneously achieve the ordered morphology and high crystal quality of the Ge NW array. Transmission electron microscopy demonstrated that the resulting Ge NWs had no dislocations or stacking faults. Production of high-quality NW arrays on amorphous insulators will promote the widespread application of nanoscale devices.

  20. Linear array transducer for high-power airborne ultrasound using flextensional structure

    Science.gov (United States)

    Yamamoto, Jun; Mizuno, Yosuke; Tabaru, Marie; Nakamura, Kentaro

    2015-07-01

    To change the direction of ultrasonic irradiation without moving a transducer, a high-power airborne ultrasonic transducer for a one-dimensional phased array system was designed and tested. A flextensional element transducer with higher-mode bending vibration was fabricated to obtain a high vibration amplitude over a wide aperture, where a phase-compensating stepped structure was employed. The width of the main lobe at half maximum and the sidelobe level were measured to be 14.3 deg and 0.78, respectively. The maximal sound pressure of 132 dB (0 dB re. 0.02 mPa) was obtained under the applied voltage of 4.0 V. The beam steering characteristics of a phased array using eight elements were compared with the simple theory.

  1. Detection of High Energy Cosmic Rays at the Auger Engineering Radio Array

    CERN Document Server

    de Jong, Sijbrand

    2016-01-01

    Detection of (ultra-) high-energy cosmic rays with the use of radio frequency emission from extensive air showers has been proven as complimentary to existing ground array detection techniques. Great progress has been made in the understanding of the emission processes and in their Monte Carlo modelling. These have led to experimental results, notably also at the Auger Engineering Radio Array, on energy, angular and mass composition resolution of the primary cosmic rays. Recent results are reported. The measured resolutions turn out to be competitive with existing techniques and they have independent uncertainties. Implications for cross-calibration with existing techniques and for future large-scale applications of radio detection of ultra-high-energy cosmic rays are discussed.

  2. Large-scale boron nanowire nanojunctions and their highly-oriented arrays

    Institute of Scientific and Technical Information of China (English)

    CAO Limin; ZHANG Ze; WANG Wenkui

    2004-01-01

    Highly oriented multiple boron nanowire nanojunctions with unilateral feather- like morphology were first successfully prepared using a radio-frequency magnetron sputtering method. The branched boron nano-feathers always nucleate and grow on the same sidewall of the stems, and align in parallel to form multiple T- and/or Y-type nanojunctions. The diameters of the branches and the stems are in the range of 20-40 and 60-80 nm, respectively. The thinner branches and thicker stems of the boron nanowires self-assembled into large-scale, highly ordered arrays on various substrates. During the formation and self-assembly of the arrays, no template or catalyst was needed. We believe that the approach presented here can be used to fabricate heterostructures with bottom-up assembly of a wide variety of one-dimensional nanostructures via the rational design of targets and the proper control of the experimental conditions.

  3. Electrochemically Created Highly Surface Roughened Ag Nanoplate Arrays for SERS Biosensing Applications

    OpenAIRE

    Yang, Shikuan; Slotcavage, Daniel; Mai, John D.; Guo, Feng; Li, Sixing; Zhao, Yanhui; Lei, Yong; Cameron, Craig E.; Huang, Tony Jun

    2014-01-01

    Highly surface-roughened Ag nanoplate arrays are fabricated using a simple electrodeposition and in situ electrocorrosion method with inorganic borate ions as capping agent. The electrocorrosion process is induced by a change in the local pH value during the electrochemical growth, which is used to intentionally carve the electrodeposited structures. The three dimensionally arranged Ag nanoplates are integrated with substantial surface-enhanced Raman scattering (SERS) hot spots and are free o...

  4. From Nearby Low Luminosity AGN to High Redshift Radio Galaxies: Science Interests with Square Kilometre Array

    Indian Academy of Sciences (India)

    P. Kharb; D. V. Lal; V. Singh; J. Bagchi; C. H. Ishwara Chandra; A. Hota; C. Konar; Y. Wadadekar; P. Shastri; M. Das; K. Baliyan; B. B. Nath; M. Pandey-Pommier

    2016-12-01

    We present detailed science cases that a large fraction of the Indian AGN community is interested in pursuing with the upcoming Square Kilometre Array (SKA). These interests range from understanding low luminosity active galactic nuclei in the nearby Universe to powerful radio galaxies at high redshifts. Important unresolved science questions in AGN physics are discussed. Ongoing low-frequency surveys with the SKA pathfinder telescope GMRT, are highlighted.

  5. A BaF2 crystal array for high energy -ray measurements

    Indian Academy of Sciences (India)

    A Ray; S R Banerjee; P Das

    2001-07-01

    We shall discuss about the scientific motivation and construction of a 7 × 7 BaF2 crystal array at Variable Energy Cyclotron Centre, Calcutta. This detector would be used to measure high energy -ray photons from GDR decay and proton–neutron bremsstrahlung reactions at the present 88'' cyclotron and upcoming superconducting cyclotron at VECC, Calcutta. This detector can also be used to measure photons from quark–gluon plasma at the relativistic heavy ion collider (RHIC) in USA.

  6. [High resolution MR imaging of the hip using pelvic phased-array coil].

    Science.gov (United States)

    Niitsu, M; Mishima, H; Itai, Y

    1997-01-01

    A pelvic phased-array coil was applied to obtain high resolution MR images of the hip. Three-mm-thick fast spinecho images were obtained in seven hips. Images with a pelvic coil enhanced delineation of acetabular labrum and articular cartilage more clearly than those with a body coil or flexible-surface coil. The use of a pelvic coil in imaging of the hip may be of diagnostic value because of its superior delineation.

  7. High optical transmittance of aluminum ultrathin film with hexagonal nanohole arrays as transparent electrode

    KAUST Repository

    Du, Qing Guo

    2016-02-24

    We fabricate samples of aluminum ultrathin films with hexagonal nanohole arrays and characterize the transmission performance. High optical transmittance larger than 60% over a broad wavelength range from 430 nm to 750 nm is attained experimentally. The Fano-type resonance of the excited surface plasmon plaritons and the directly transmitted light attribute to both of the broadband transmission enhancement and the transmission suppression dips. © 2016 Optical Society of America.

  8. Environmental change drives accelerated adaptation through stimulated copy number variation

    Science.gov (United States)

    Hull, Ryan M.; Cruz, Cristina; Jack, Carmen V.

    2017-01-01

    Copy number variation (CNV) is rife in eukaryotic genomes and has been implicated in many human disorders, particularly cancer, in which CNV promotes both tumorigenesis and chemotherapy resistance. CNVs are considered random mutations but often arise through replication defects; transcription can interfere with replication fork progression and stability, leading to increased mutation rates at highly transcribed loci. Here we investigate whether inducible promoters can stimulate CNV to yield reproducible, environment-specific genetic changes. We propose a general mechanism for environmentally-stimulated CNV and validate this mechanism for the emergence of copper resistance in budding yeast. By analysing a large cohort of individual cells, we directly demonstrate that CNV of the copper-resistance gene CUP1 is stimulated by environmental copper. CNV stimulation accelerates the formation of novel alleles conferring enhanced copper resistance, such that copper exposure actively drives adaptation to copper-rich environments. Furthermore, quantification of CNV in individual cells reveals remarkable allele selectivity in the rate at which specific environments stimulate CNV. We define the key mechanistic elements underlying this selectivity, demonstrating that CNV is regulated by both promoter activity and acetylation of histone H3 lysine 56 (H3K56ac) and that H3K56ac is required for CUP1 CNV and efficient copper adaptation. Stimulated CNV is not limited to high-copy CUP1 repeat arrays, as we find that H3K56ac also regulates CNV in 3 copy arrays of CUP1 or SFA1 genes. The impact of transcription on DNA damage is well understood, but our research reveals that this apparently problematic association forms a pathway by which mutations can be directed to particular loci in particular environments and furthermore that this mutagenic process can be regulated through histone acetylation. Stimulated CNV therefore represents an unanticipated and remarkably controllable pathway

  9. Identification of genomic aberrations associated with disease transformation by means of high-resolution SNP array analysis in patients with myeloproliferative neoplasm.

    Science.gov (United States)

    Rumi, Elisa; Harutyunyan, Ashot; Elena, Chiara; Pietra, Daniela; Klampfl, Thorsten; Bagienski, Klaudia; Berg, Tiina; Casetti, Ilaria; Pascutto, Cristiana; Passamonti, Francesco; Kralovics, Robert; Cazzola, Mario

    2011-12-01

    Myeloproliferative neoplasms (MPN) include polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). These disorders may undergo phenotypic shifts, and may specifically evolve into secondary myelofibrosis (MF) or acute myeloid leukemia (AML). We studied genomic changes associated with these transformations in 29 patients who had serial samples collected in different phases of disease. Genomic DNA from granulocytes, i.e., the myeloproliferative genome, was processed and hybridized to genome-wide human SNP 6.0 arrays. Most patients in chronic phase had chromosomal regions with uniparental disomy (UPD) and/or copy number changes. Disease progression to secondary MF or AML was associated with the acquisition of additional chromosomal aberrations in granulocytes (P = 0.002). A close relationship was observed between aberrations of chromosome 9p (UPD and/or gain) and progression from PV to post-PV MF (P = 0.002). The acquisition of one or more aberrations involving chromosome 5, 7, or 17p was specifically associated with progression to AML (OR 5.9, 95% CI 1.2-27.7, P = 0.006), and significantly affected overall survival (HR 18, 95% CI 1.9-164, P = 0.01). These observations indicate that disease progression from chronic-phase MPN to secondary MF or AML is associated with specific chromosomal aberrations that can be detected by means of high-resolution SNP array analysis of granulocyte DNA. Copyright © 2011 Wiley-Liss, Inc.

  10. The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA.

    Science.gov (United States)

    Moritz, Rebecca L; Welch, Rodney A

    2006-11-01

    The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.

  11. High density near amorphous InSb nanowire arrays and its photo-electric performance

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Ming, E-mail: mfang@issp.ac.cn [Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanostructure, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Tan, Xiaoli [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); Liu, Mao, E-mail: mliu@issp.ac.cn [Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanostructure, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Gong, Xinxin; Zhang, Lide; Fei, Guangtao [Key Laboratory of Materials Physics, Anhui Key Laboratory of Nanomaterials and Nanostructure, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China)

    2015-03-25

    Highlights: • InSb near amorphous nanowire arrays are successfully fabricated. • The 30 nm diameter nanowire array shows a well infrared photo-electric response, and the reasons are discussed. • The reason for the black color of the InSb semiconductor is discussed. - Abstract: In this paper, we report the fabrication of high density near amorphous InSb nanowire arrays with using 30, 55 and 70 nm diameter anodic alumina oxide (AAO) template by electrodeposition method. The near amorphous structure was proved by combining the results of X-ray diffraction (XRD) and high resolution transmission electron microscopy (HRTEM). Different from the bulk material, these nanowires are black and could not be analyzed by the traditional method, and the reason was discussed. By testing of the photo-electric performance, the 30 nm diameter InSb nanowire showed the best performance, which could be used at about 260 K. The formation of the near amorphous structure was also discussed. Such high density nanoarrays may found potential application in the infrared detection field.

  12. High spatial resolution Hall sensor array for edge plasma magnetic field measurements

    Science.gov (United States)

    Liu, Yuhong; Maurer, David A.; Navratil, Gerald A.; Rivera, Nicholas

    2005-09-01

    A one-dimensional, high-spatial resolution, 20-element Hall sensor array has been developed to directly measure the edge plasma perpendicular magnetic field and its fluctuations as a function of radius with 4-mm resolution. The array employs new small-area, high-sensitivity indium antimonide (InSb) Hall probes in combination with a high-density seven-layer printed circuit board to provide for connections to supply Hall current, record the measured Hall voltage output signals, and mitigate inductive pickup. A combination of bench and in situ measurements is described that provides absolute calibration of the diagnostic array in the presence of a strong transverse magnetic field component that is approximately 1000 times greater than the perpendicular fluctuating field needed to be resolved by the diagnostic. The Hall probes calibrated using this method are capable of magnetic field measurements with a sensitivity of 7V/T over the frequency band from 0 to 20 kHz.

  13. Reprint of “Overhanging ferroelectric nanodot arrays created by high surface energy seeds”

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jiyoon [Department of Materials Science and Engineering, KAIST, Daejeon 305-701 (Korea, Republic of); Park, Kwang-Won [Department of Chemistry, Chung-Ang University, Seoul 156-756 (Korea, Republic of); Hong, Jongin, E-mail: hongj@cau.ac.kr [Department of Chemistry, Chung-Ang University, Seoul 156-756 (Korea, Republic of); No, Kwangsoo, E-mail: ksno@kaist.ac.kr [Department of Materials Science and Engineering, KAIST, Daejeon 305-701 (Korea, Republic of)

    2015-04-15

    Highlights: • We investigated that the high surface energy of TiO{sub 2}contributed to the formation of spherical PbTiO{sub 3}nanodot arrays. • The crystallinity of the TiO{sub 2}nanoseeds had an influence on ferroelectric switching properties of the PbTiO{sub 3}nanodots. • The creation of spherical nanodots can minimize the effect of substrate clamping. - Abstract: We demonstrated a facile route for the fabrication of overhanging PbTiO{sub 3} (PTO) nanodot arrays on platinized silicon substrates using PbO vapor phase reaction sputtering on micellar monolayer films of polystyrene-block-poly(ethylene oxide) (PS-b-PEO) loaded with TiO{sub 2} sol–gel precursor. We also investigated that the high surface energy of TiO{sub 2} contributes to the formation of overhanging ferroelectric PTO nanodot arrays by means of high-resolution transmission electron microscopy. Additionally, the crystallographic orientation of the nanoseeds had a significant influence on the ferroelectric switching properties of the PTO nanodots, which were determined by piezoresponse force microscopy (PFM)

  14. Development Toward a Ground-Based Interferometric Phased Array for Radio Detection of High Energy Neutrinos

    CERN Document Server

    Avva, J; Chesebro, T; Cremonisi, L; Deaconu, C; Gupta, A; Ludwig, A; Messino, W; Miki, C; Nichol, R; Oberla, E; Romero-Wolf, A; Saltzberg, D; Schlupf, C; Shipp, N; Varner, G; Vieregg, A G; Wissel, S A

    2016-01-01

    A promising method for further measurements of high energy neutrinos at the PeV scale and above is through an in-ice radio interferometric phased array, designed to look for Askaryan emission from neutrinos interacting in large volumes of glacial ice. Such a detector would be sensitive to two populations of neutrinos: the PeV-scale astrophysical neutrino flux recently detected by IceCube, and the predicted cosmogenic ultra-high energy (UHE) flux ($E>10^{17}$ eV). Characterizing these high energy neutrino populations is an important step toward understanding the most energetic cosmic accelerators, and the discovery of UHE neutrinos would allow us to probe fundamental physics at energy scales that are not achievable on Earth. We report here on studies validating the phased array technique, including measurements and a simulation of thermal noise correlations between nearby antennas, beamforming for impulsive signals, and a measurement of the expected improvement in trigger efficiency through the phased array te...

  15. High-speed imaging and wavefront sensing with an infrared avalanche photodiode array

    CERN Document Server

    Baranec, Christoph; Riddle, Reed; Hall, Donald; Jacobson, Shane; Law, Nicholas M; Chun, Mark

    2015-01-01

    Infrared avalanche photodiode arrays represent a panacea for many branches of astronomy by enabling extremely low-noise, high-speed and even photon-counting measurements at near-infrared wavelengths. We recently demonstrated the use of an early engineering-grade infrared avalanche photodiode array that achieves a correlated double sampling read noise of 0.73 e- in the lab, and a total noise of 2.52 e- on sky, and supports simultaneous high-speed imaging and tip-tilt wavefront sensing with the Robo-AO visible-light laser adaptive optics system at the Palomar Observatory 1.5-m telescope. We report here on the improved image quality achieved simultaneously at visible and infrared wavelengths by using the array as part of an image stabilization control-loop with adaptive-optics sharpened guide stars. We also discuss a newly enabled survey of nearby late M-dwarf multiplicity as well as future uses of this technology in other adaptive optics and high-contrast imaging applications.

  16. Scientific Data Services -- A High-Performance I/O System with Array Semantics

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kesheng; Byna, Surendra; Rotem, Doron; Shoshani, Arie

    2011-09-21

    As high-performance computing approaches exascale, the existing I/O system design is having trouble keeping pace in both performance and scalability. We propose to address this challenge by adopting database principles and techniques in parallel I/O systems. First, we propose to adopt an array data model because many scientific applications represent their data in arrays. This strategy follows a cardinal principle from database research, which separates the logical view from the physical layout of data. This high-level data model gives the underlying implementation more freedom to optimize the physical layout and to choose the most effective way of accessing the data. For example, knowing that a set of write operations is working on a single multi-dimensional array makes it possible to keep the subarrays in a log structure during the write operations and reassemble them later into another physical layout as resources permit. While maintaining the high-level view, the storage system could compress the user data to reduce the physical storage requirement, collocate data records that are frequently used together, or replicate data to increase availability and fault-tolerance. Additionally, the system could generate secondary data structures such as database indexes and summary statistics. We expect the proposed Scientific Data Services approach to create a “live” storage system that dynamically adjusts to user demands and evolves with the massively parallel storage hardware.

  17. High-content analysis screening for cell cycle regulators using arrayed synthetic crRNA libraries.

    Science.gov (United States)

    Strezoska, Žaklina; Perkett, Matthew R; Chou, Eldon T; Maksimova, Elena; Anderson, Emily M; McClelland, Shawn; Kelley, Melissa L; Vermeulen, Annaleen; Smith, Anja van Brabant

    2017-06-10

    The CRISPR-Cas9 system has been utilized for large-scale, loss-of-function screens mainly using lentiviral pooled formats and cell-survival phenotypic assays. Screening in an arrayed format expands the types of phenotypic readouts that can be used to now include high-content, morphology-based assays, and with the recent availability of synthetic crRNA libraries, new studies are emerging. Here, we use a cell cycle reporter cell line to perform an arrayed, synthetic crRNA:tracrRNA screen targeting 169 genes (>600 crRNAs) and used high content analysis (HCA) to identify genes that regulate the cell cycle. Seven parameters were used to classify cells into cell cycle categories and multiple parameters were combined using a new analysis technique to identify hits. Comprehensive hit follow-up experiments included target gene expression analysis, confirmation of DNA insertions/deletions, and validation with orthogonal reagents. Our results show that most hits had three or more independent crRNAs per gene that demonstrated a phenotype with consistent individual parameters, indicating that our screen produced high-confidence hits with low off-target effects and allowed us to identify hits with more subtle phenotypes. The results of our screen demonstrate the power of using arrayed, synthetic crRNAs for functional phenotypic screening using multiparameter HCA assays. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  18. 3D Nanochannel Array Platform for High-throughput Cell Manipulation and Nano-electroporation

    Science.gov (United States)

    Chang, Lingqian

    Electroporation is one of the most common non-viral methods for gene delivery. Recent progress in gene therapy has offered special opportunities to electroporation for in vitro and in vivo applications. However, conventional bulk electroporation (BEP) inevitably causes serious cell damage and stochastic transfection between cells. Microfluidic electroporation (MEP) has been claimed to provide benign single cell transfection for the last decade. Nevertheless, the intracellular transport in both MEP and BEP systems is highly diffusion-dominant, which prevents precise dose control and high uniformity. In this Ph.D. research, we developed a 3D nanochannel-electroporation (3D NEP) platform for mass cell transfection. A silicon-based nanochannel array (3D NEP) chip was designed and fabricated for cell manipulation and electroporation. The chip, designed as Z-directional microchannel - nanochannel array, was fabricated by clean room techniques including projection photolithography and deep reactive-ion etching (DRIE). The fabricated 3D NEP chip is capable of handling 40,000 cells per 1 cm2, up to 1 million per wafer (100 mm diameter). High-throughput cell manipulation technologies were investigated for precise alignment of individual cells to the nanochannel array, a key step for NEP to achieve dose control. We developed three techniques for cell trapping in this work. (1) Magnetic tweezers (MTs) were integrated on the chip to remotely control cells under a programmed magnetic field. (2) A positive dielectrophoresis (pDEP) power system was built as an alternative to trap cells onto the nanochannel array using DEP force. (3) A novel yet simple 'dipping-trap' method was used to rapidly trap cells onto a nanochannel array, aligned by a micro-cap array pattern on the 3D NEP chip, which eventually offered 70 - 90 % trapping efficiency and 90 % specificity. 3D NEP platforms were assembled for cell transfection based on the Si-based nanochannel array chip and cell manipulation

  19. Crack-free and scalable transfer of carbon nanotube arrays into flexible and highly thermal conductive composite film.

    Science.gov (United States)

    Wang, Miao; Chen, Hongyuan; Lin, Wei; Li, Zhuo; Li, Qiang; Chen, Minghai; Meng, Fancheng; Xing, Yajuan; Yao, Yagang; Wong, Ching-ping; Li, Qingwen

    2014-01-08

    Carbon nanotube (CNT) arrays show great promise in developing anisotropic thermal conductive composites for efficiently dissipating heat from high-power devices along thickness direction. However, CNT arrays are always grown on some substrates and liable to be deformed and broken into pieces during transfer and solution treatment. In the present study, we intentionally synthesized well-crystallized and large-diameter (~80 nm) multiwalled CNT (MWCNT) arrays by floating catalyst chemical vapor deposition (FCCVD) method. Such arrays provided high packing density and robust structure from collapse and crack formation during post solution treatment and therefore favored to maintain original thermal and electrical conductive paths. Under optimized condition, the CNT arrays can be transferred into flexible composite films. Furthermore, the composite film also exhibited excellent thermal conductivity at 8.2 W/(m·K) along thickness direction. Such robust, flexible, and highly thermal conductive composite film may enable some prospective applications in advanced thermal management.

  20. High-repetition-rate optical delay line using a micromirror array and galvanometer mirror for a terahertz system.

    Science.gov (United States)

    Kitahara, Hideaki; Tani, Masahiko; Hangyo, Masanori

    2009-07-01

    We developed a high-repetition-rate optical delay line based on a micromirror array and galvanometer mirror for terahertz time-domain spectroscopy. The micromirror array is fabricated by using the x-ray lithographic technology. The measurement of terahertz time-domain waveforms with the new optical delay line is demonstrated successfully up to 25 Hz.

  1. 8×8 Planar Phased Array Antenna with High Efficiency and Insensitivity Properties for 5G Mobile Base Stations

    DEFF Research Database (Denmark)

    Ojaroudiparchin, Naser; Shen, Ming; Pedersen, Gert F.

    2016-01-01

    An insensitive planar phased array antenna with high efficiency function for 5G applications is introduced in this study. 64-elements of compact slot-loop antenna elements have been used to form the 8×8 planar array. The antenna is designed on a low cost FR4 substrate and has good performance...

  2. Measuring Phased-Array Antenna Beampatterns with High Dynamic Range for the Murchison Widefield Array using 137 MHz ORBCOMM Satellites

    CERN Document Server

    Neben, A R; 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

    2015-01-01

    Detection of the fluctuations in 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 {\\it 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...

  3. Identification of rare high-risk copy number variants affecting the dopamine transporter gene in mental disorders

    DEFF Research Database (Denmark)

    Hoeffding, Louise K; Duong, Linh T T; Ingason, Andrés;

    2015-01-01

    BACKGROUND: The dopamine transporter, also known as solute carrier 6A3 (SLC6A3), plays an important role in synaptic transmission by regulating the reuptake of dopamine in the synapses. In line with this, variations in the gene encoding this transporter have been linked to both schizophrenia...... rare high-risk variants of psychiatric disorders. METHODS: We performed a systematic screening for CNVs affecting SLC6A3 in 761 healthy controls, 672 schizophrenia patients, and 194 patients with bipolar disorder in addition to 253 family members from six large pedigrees affected by mental disorders...... sizes and two affected several genes in addition to SLC6A3. CONCLUSION: Our findings suggest that rare high-risk CNVs affecting the gene encoding the dopamine transporter contribute to the pathogenesis of schizophrenia and affective disorders....

  4. High-resolution hard x-ray spectroscopy of high-temperature plasmas using an array of quantum microcalorimeters.

    Science.gov (United States)

    Thorn, Daniel B; Gu, Ming F; Brown, Greg V; Beiersdorfer, Peter; Porter, F Scott; Kilbourne, Caroline A; Kelley, Richard L

    2008-10-01

    Quantum microcalorimeters show promise in being able to fully resolve x-ray spectra from heavy highly charged ions, such as would be found in hot plasmas with temperatures in excess of 50 keV. Quantum microcalorimeter arrays are able to achieve this as they have a high-resolving power and good effective quantum efficiency for hard x-ray photons up to 60 keV. To demonstrate this, we present a measurement using an array of thin HgTe quantum microcalorimeters to measure the K-shell spectrum of hydrogenlike through carbonlike praseodymium (Z=57). With this device we are able to attain a resolving power, E/DeltaE, of 1000 at a photon energy of 37 keV.

  5. Radiative properties of high wire number tungsten arrays with implosion times up to 250 ns

    Science.gov (United States)

    Deeney, C.; Coverdale, C. A.; Douglas, M. R.; Struve, K. W.; Spielman, R. B.; Stygar, W. A.; Peterson, D. L.; Roderick, N. F.; Haines, M. G.; Beg, F. N.; Ruiz-Camacho, J.

    1999-09-01

    High wire number, 25-mm-diameter tungsten wire arrays have been imploded on the 8-MA Saturn generator [R. B. Spielman et al., AIP Conference Proceeding 195, 3 (American Institute of Physics, Woodbury, NY 1989)], operating in a long-pulse mode. By varying the mass of the arrays from 710 to 6140 μg/cm, implosion times of 130-250 ns have been obtained with implosion velocities of 50-25 cm/μs, respectively. These Z-pinch implosions produced plasmas with millimeter diameters that radiated 600-800 kJ of x-rays, with powers of 20-49 TW; the corresponding pulsewidths were 19-7.5 ns, with risetimes ranging from 6.5 to 4.0 ns. These powers and pulsewidths are similar to those achieved with 50-ns implosion times on Saturn. Two-dimensional, radiation-magnetohydrodynamic calculations indicate that the imploding shells in these long implosion time experiments are comparable in width to those in the short-pulse cases. This can be due to lower initial perturbations. A heuristic wire array model suggests that the reduced perturbations, in the long-pulse cases, may be due to the individual wire merger occurring well before the acceleration of the shell. The experiments and modeling suggest that 150-200 ns implosion time Z-pinches could be employed for high-power, x-ray source applications.

  6. Highly Transparent Dual-Sensitized Titanium Dioxide Nanotube Arrays for Spontaneous Solar Water Splitting Tandem Configuration.

    Science.gov (United States)

    Shin, Kahee; Park, Jong Hyeok

    2015-08-26

    Vertically aligned one-dimensional (1D) titanium dioxide (TiO2) arrays on transparent conducting oxide (TCO) substrates, which can act as host electron transport materials for low bandgap materials, were synthesized via a hydrothermal reaction combined with a controlled chemical etching process. By controlling the chemical etching conditions, we can maximize the light transmission properties of the 1D TiO2 arrays, which is beneficial for the front electrode in photoelectrochemical (PEC) tandem configurations. As a result, dual sensitization to form 1D TiO2@CdS@CdSe (CdS and CdSe coated 1D TiO2) results in excellent photocurrent density, as well as transparency, and the resulting material is able to pass unabsorbed photons through the front electrode into the rear bias solar cell. Owing to the improved light transmission in combination with the increased specific surface area of the obtained 1D TiO2 arrays from the controlled etching process, a high-efficiency PEC tandem device with ∼2.1% was successfully fabricated for unassisted hydrogen evolution. Efficient PEC tandem device was fabricated for unassisted solar hydrogen generation using highly transparent composite electrode composed of dual sensitization to form 1D TiO2@CdS@CdSe.

  7. High-Resolution Arrayed-Waveguide-Gratings in Astronomy: Design and Fabrication Challenges

    Directory of Open Access Journals (Sweden)

    Andreas Stoll

    2017-04-01

    Full Text Available A comprehensive design of a folded-architecture arrayed-waveguide-grating (AWG-device, targeted at applications as integrated photonic spectrographs (IPS in near-infrared astronomy, is presented. The AWG structure is designed for the astronomical H-band (1500 nm–1800 nm with a theoretical maximum resolving power R = 60,000 at 1630 nm. The geometry of the device is optimized for a compact structure with a footprint of 5.5 cm × 3.93 cm on SiO 2 platform. To evaluate the fabrication challenges of such high-resolution AWGs, effects of random perturbations of the effective refractive index (RI distribution in the free propagation region (FPR, as well as small variations of the array waveguide optical lengths are numerically investigated. The results of the investigation show a dramatic degradation of the point spread function (PSF for a random effective RI distribution with variance values above ∼ 10 - 4 for both the FPR and the waveguide array. Based on the results, requirements on the fabrication technology for high-resolution AWG-based spectrographs are given in the end.

  8. Water-photolysis properties of micron-length highly-ordered titania nanotube-arrays.

    Science.gov (United States)

    Varghese, Oomman K; Paulose, Maggie; Shankar, Karthik; Mor, Gopal K; Grimes, Craig A

    2005-07-01

    We report the water photoelectrolysis and photoelectrochemical properties of the titania nanotube arrays as a function of nanotube crystallinity, length (up to 6.4 microm), and pore size. Most noteworthy of our results, under 320-400 nm illumination (98 mW/cm2) the titania nanotube-array photoanodes (area 1 cm2), pore size 110 nm, wall thickness 20 nm, and 6 microm length, generate hydrogen by water photoelectrolysis at a rate of 7.6 mL/hr, with a photoconversion efficiency of 12.25%. The energy-time normalized hydrogen evolution rate is 80 mL/hrW, the largest reported hydrogen photoelectrolysis generation rate for any material system by a factor of four. The highly-ordered nanotubular architecture appears to allow for superior charge separation and charge transport, with a calculated quantum efficiency of over 80% for incident photons with energies larger than the titania bandgap.

  9. Fabrication of High Aspect Ratio Micro-Penning-Malmberg Gold Plated Silicon Trap Arrays

    CERN Document Server

    Narimannezhad, Alireza; Weber, Marc H; Lynn, Kelvin G

    2013-01-01

    Acquiring a portable high density charged particles trap might consist of an array of micro-Penning-Malmberg traps (microtraps) with substantially lower end barriers potential than conventional Penning-Malmberg traps [1]. We report on the progress of the fabrication of these microtraps designed for antimatter storage such as positrons. The fabrication of large length to radius aspect ratio (1000:1) microtrap arrays involved advanced techniques including photolithography, deep reactive ion etching (DRIE) of silicon wafers to achieve through-vias, gold sputtering of the wafers on the surfaces and inside the vias, and thermal compression bonding of the wafers. This paper describes the encountered issues during fabrication and addresses geometry errors and asymmetries. In order to minimize the patch effects on the lifetime of the trapped positrons, the bonded stacks were gold electroplated to achieve a uniform gold surface. We show by simulation and analytical calculation that how positrons confinement time depen...

  10. A High-Efficiency Si Nanowire Array/Perovskite Hybrid Solar Cell.

    Science.gov (United States)

    Yan, Xin; Zhang, Chen; Wang, Jiamin; Zhang, Xia; Ren, Xiaomin

    2017-12-01

    A low-cost Si nanowire array/perovskite hybrid solar cell is proposed and simulated. The solar cell consists of a Si p-i-n nanowire array filled with CH3NH3PbI3, in which both the nanowires and perovskite absorb the incident light while the nanowires act as the channels for transporting photo-generated electrons and holes. The hybrid structure has a high absorption efficiency in a broad wavelength range of 300~800 nm. A large short-circuit current density of 28.8 mA/cm(2) and remarkable conversion efficiency of 13.3% are obtained at a thin absorber thickness of 1.6 μm, which are comparable to the best results of III-V nanowire solar cells.

  11. Telescope Array Radar (TARA) observatory for Ultra-High Energy Cosmic Rays

    Energy Technology Data Exchange (ETDEWEB)

    Abbasi, R.; Othman, M. Abou Bakr [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Allen, C. [University of Kansas, Lawrence, KS 66045 (United States); Beard, L. [Purdue University, West Lafayette, IN 47907 (United States); Belz, J. [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Besson, D. [University of Kansas, Lawrence, KS 66045 (United States); Moscow Engineering and Physics Institute, 31 Kashirskaya Shosse, Moscow 115409 (Russian Federation); Byrne, M.; Farhang-Boroujeny, B.; Gardner, A. [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Gillman, W.H. [Gillman and Associates, Salt Lake City, UT 84106 (United States); Hanlon, W. [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Hanson, J. [University of Kansas, Lawrence, KS 66045 (United States); Jayanthmurthy, C. [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Kunwar, S. [University of Kansas, Lawrence, KS 66045 (United States); Larson, S.L. [Utah State University, Logan, Utah 84322 (United States); Myers, I., E-mail: isaac@cosmic.utah.edu [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Prohira, S.; Ratzlaff, K. [University of Kansas, Lawrence, KS 66045 (United States); Sokolsky, P. [University of Utah, 115 S 1400 E #201 JFB, Salt Lake City, UT 84112 (United States); Takai, H. [Brookhaven National Laboratory, Upton, NY 11973 (United States); and others

    2014-12-11

    Construction was completed during summer 2013 on the Telescope Array RAdar (TARA) bi-static radar observatory for Ultra-High Energy Cosmic Rays (UHECR). TARA is co-located with the Telescope Array, the largest “conventional” cosmic ray detector in the Northern Hemisphere, in radio-quiet Western Utah. TARA employs an 8 MW Effective Radiated Power (ERP) VHF transmitter and smart receiver system based on a 250 MS/s data acquisition system in an effort to detect the scatter of sounding radiation by UHECR-induced atmospheric ionization. TARA seeks to demonstrate bi-static radar as a useful new remote sensing technique for UHECRs. In this report, we describe the design and performance of the TARA transmitter and receiver systems.

  12. High reproducibility and sensitivity of bifacial copper nanowire array for detection of glucose

    Directory of Open Access Journals (Sweden)

    Hanqing Zhang

    2017-06-01

    Full Text Available The ordered bifacial copper nanowire array (Cu BNWA was synthesized by a template assisted electrochemical deposition method. The morphology and structure of the as-prepared samples were investigated by field emission scanning electron microscope (FESEM and X-ray diffraction (XRD. The results show that the ordered Cu nanowire array with uniform geometrical dimensions covered both side of the Cu substrate. When used as the electrode for glucose detection, the minimum detectable concentration of glucose can be reached as low as 0.2 mM. Impressively, the sample still showed high sensitivity and stability for glucose detection after two months placement in ambient environment. These excellent performances of the Cu BNWA make it a promising non-enzyme glucose detection sensor for various applications.

  13. Wafer-scale high-throughput ordered growth of vertically aligned ZnO nanowire arrays.

    Science.gov (United States)

    Wei, Yaguang; Wu, Wenzhuo; Guo, Rui; Yuan, Dajun; Das, Suman; Wang, Zhong Lin

    2010-09-01

    This article presents an effective approach for patterned growth of vertically aligned ZnO nanowire (NW) arrays with high throughput and low cost at wafer scale without using cleanroom technology. Periodic hole patterns are generated using laser interference lithography on substrates coated with the photoresist SU-8. ZnO NWs are selectively grown through the holes via a low-temperature hydrothermal method without using a catalyst and with a superior control over orientation, location/density, and as-synthesized morphology. The development of textured ZnO seed layers for replacing single crystalline GaN and ZnO substrates extends the large-scale fabrication of vertically aligned ZnO NW arrays on substrates of other materials, such as polymers, Si, and glass. This combined approach demonstrates a novel method of manufacturing large-scale patterned one-dimensional nanostructures on various substrates for applications in energy harvesting, sensing, optoelectronics, and electronic devices.

  14. Telescope Array Radar (TARA) observatory for Ultra-High Energy Cosmic Rays

    Science.gov (United States)

    Abbasi, R.; Othman, M. Abou Bakr; Allen, C.; Beard, L.; Belz, J.; Besson, D.; Byrne, M.; Farhang-Boroujeny, B.; Gardner, A.; Gillman, W. H.; Hanlon, W.; Hanson, J.; Jayanthmurthy, C.; Kunwar, S.; Larson, S. L.; Myers, I.; Prohira, S.; Ratzlaff, K.; Sokolsky, P.; Takai, H.; Thomson, G. B.; Von Maluski, D.

    2014-12-01

    Construction was completed during summer 2013 on the Telescope Array RAdar (TARA) bi-static radar observatory for Ultra-High Energy Cosmic Rays (UHECR). TARA is co-located with the Telescope Array, the largest "conventional" cosmic ray detector in the Northern Hemisphere, in radio-quiet Western Utah. TARA employs an 8 MW Effective Radiated Power (ERP) VHF transmitter and smart receiver system based on a 250 MS/s data acquisition system in an effort to detect the scatter of sounding radiation by UHECR-induced atmospheric ionization. TARA seeks to demonstrate bi-static radar as a useful new remote sensing technique for UHECRs. In this report, we describe the design and performance of the TARA transmitter and receiver systems.

  15. A High-Efficiency Si Nanowire Array/Perovskite Hybrid Solar Cell

    Science.gov (United States)

    Yan, Xin; Zhang, Chen; Wang, Jiamin; Zhang, Xia; Ren, Xiaomin

    2017-01-01

    A low-cost Si nanowire array/perovskite hybrid solar cell is proposed and simulated. The solar cell consists of a Si p-i-n nanowire array filled with CH3NH3PbI3, in which both the nanowires and perovskite absorb the incident light while the nanowires act as the channels for transporting photo-generated electrons and holes. The hybrid structure has a high absorption efficiency in a broad wavelength range of 300 800 nm. A large short-circuit current density of 28.8 mA/cm2 and remarkable conversion efficiency of 13.3% are obtained at a thin absorber thickness of 1.6 μm, which are comparable to the best results of III-V nanowire solar cells.

  16. Characteristics of a four element gyromagnetic nonlinear transmission line array high power microwave source

    Science.gov (United States)

    Johnson, J. M.; Reale, D. V.; Krile, J. T.; Garcia, R. S.; Cravey, W. H.; Neuber, A. A.; Dickens, J. C.; Mankowski, J. J.

    2016-05-01

    In this paper, a solid-state four element array gyromagnetic nonlinear transmission line high power microwave system is presented as well as a detailed description of its subsystems and general output capabilities. This frequency agile S-band source is easily adjusted from 2-4 GHz by way of a DC driven biasing magnetic field and is capable of generating electric fields of 7.8 kV/m at 10 m correlating to 4.2 MW of RF power with pulse repetition frequencies up to 1 kHz. Beam steering of the array at angles of ±16.7° is also demonstrated, and the associated general radiation pattern is detailed.

  17. Telescope Array Radar (TARA) Observatory for Ultra-High Energy Cosmic Rays

    CERN Document Server

    Abbasi, R; Allen, C; Beard, L; Belz, J; Besson, D; Byrne, M; Farhang-Boroujeny, B; Gardner, A; Gillman, W H; Hanlon, W; Hanson, J; Jayanthmurthy, C; Kunwar, S; Larson, S L; Myers, I; Prohyra, S; Ratzlaff, K; Sokolsky, P; Takai, H; Thomson, G B; Von Maluski, D

    2014-01-01

    Construction was completed during summer 2013 on the Telescope Array RAdar (TARA) bi-static radar observatory for Ultra-High Energy Cosmic Rays (UHECR). TARA is co-located with the Telescope Array, the largest "conventional" cosmic ray detector in the Northern Hemisphere, in radio-quiet Western Utah. TARA employs an 8 MW Effective Radiated Power (ERP) VHF transmitter and smart receiver system based on a 250 MS/s data acquisition system in an effort to detect the scatter of sounding radiation by UHECR-induced atmospheric ionization. TARA seeks to demonstrate bi-static radar as a useful new remote sensing technique for UHECRs, extending their detection aperture far beyond what is accessible by conventional means. In this report, we describe the design and performance of the TARA transmitter and receiver systems.

  18. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel; Scheel, M.; Hansen, Niclas Tue

    2011-01-01

    To search for disease‐related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk...

  19. Physical state & copy number of high risk human papillomavirus type 16 DNA in progression of cervical cancer

    Directory of Open Access Journals (Sweden)

    Shirish Shukla

    2014-01-01

    Full Text Available Background & objectives: High-risk human papilloma virus (HR-HPV infection and its integration in host genome is a key event in malignant transformation of cervical cells. HPV16 being a dominant HR-HPV type, we undertook this study to analyze if viral load and physical state of the virus correlated with each other in the absence of other confounding variables and examined their potential as predictors of progressive cervical lesions. Methods: Both, viral load and integration status of HPV16 were determined by real time URR PCR and estimation of E2:E6 ratio in a total of 130 PGMY-RLB -confirmed, monotypic HPV16-infected cervical DNA samples from biopsies of cytology-confirmed low grade (LSIL, 30 and high grade (HSIL, 30, and invasive carcinoma, (squamous cell carcinoma SCC, 70 cases. Results: Investigation of DNA samples revealed a gradual increase in HPV16 viral load over several magnitudes and increased frequency of integration from LSIL to HSIL and HSIL to invasive cancer in relation to the severity of lesions in monotypic HPV16-infected cervical tissues. In a substantial number of precancer (11/60 and cancer cases (29/70, HPV16 was detected in concomitant mixed form. The concomitant form of HPV16 genome carried significantly higher viral load. Interpretation & conclusions: Overall, viral load and integration increased with disease severity and could be useful biomarkers in disease progression, at least, in HPV16-infected cervical pre-cancer and cancer lesions.

  20. Compact printed two dipole array antenna with a high front-back ratio for ultra-high-frequency radio-frequency identification handheld reader applications

    DEFF Research Database (Denmark)

    Liu, Qi; Zhang, Shuai; He, Sailing

    2015-01-01

    A printed two-dipole array antenna with a high front-back ratio is proposed for ultra-high-frequency (UHF) radio-frequency identification handheld readers. The proposed antenna is a parasitic dual-element array with the ends of both elements folded back towards each other for additional coupling...

  1. Optimization of Fixed Microphone Array in High Speed Train Noises Identification Based on Far-Field Acoustic Holography

    Directory of Open Access Journals (Sweden)

    Rujia Wang

    2017-01-01

    Full Text Available Acoustical holography has been widely applied for noise sources location and sound field measurement. Performance of the microphones array directly determines the sound source recognition method. Therefore, research is very important to the performance of the microphone array, its array of applications, selection, and how to design instructive. In this paper, based on acoustic holography moving sound source identification theory, the optimization method is applied in design of the microphone array, we select the main side lobe ratio and the main lobe area as the optimization objective function and then put the optimization method use in the sound source identification based on holography, and finally we designed this paper to optimize microphone array and compare the original array of equally spaced array with optimization results; by analyzing the optimization results and objectives, we get that the array can be achieved which is optimized not only to reduce the microphone but also to change objective function results, while improving the far-field acoustic holography resolving effect. Validation experiments have showed that the optimization method is suitable for high speed trains sound source identification microphone array optimization.

  2. Real-time volumetric visualization of high-resolution array and toroidal volume search sonar data

    Science.gov (United States)

    Cross, Robert A.

    1998-09-01

    The Advanced Volume Visualization Display (AVVD) research program is a joint research program between the Fraunhofer Center for Research in Computer Graphics, Inc. and Innovative Research and Development Corp. It is dedicated the application of the human visual system to real-time visualization of high- resolution volumetric sensor data sets. The AVVD program has successfully demonstrated its application to undersea imaging using data from the Naval Undersea Warfare Center -- Division Newport's High Resolution Array (HRA), and from the Naval Surface Warfare Center -- Coastal System Stations's Toroidal Volume Search Sonar (TVSS).

  3. Resonant transmission of light in arrays of high-index dielectric nanoparticles

    CERN Document Server

    Savelev, Roman S; Petrov, Mihail I; Krasnok, Alexander E; Belov, Pavel A; Kivshar, Yuri S

    2015-01-01

    We study numerically, analytically and experimentally the resonant transmission of light in a waveguide formed by a periodic array of high-index dielectric nanoparticles with a side-coupled resonator. We demonstrate that a resonator with high enough Q-factor provides the conditions for the Fano-type interference allowing to control the resonant transmission of light. We suggest a practical realization of this resonant effect based on the quadrupole resonance of a dielectric particle and demonstrate it experimentally for ceramic spheres at microwaves.

  4. A frogspawn-inspired hierarchical porous NaTi2(PO4)3-C array for high-rate and long-life aqueous rechargeable sodium batteries

    Science.gov (United States)

    Zhao, Baidan; Lin, Bo; Zhang, Sen; Deng, Chao

    2015-11-01

    Hollow micro/nano-arrays have attracted tremendous attention in the field of energy conversion and storage, but such structures usually compromise the volumetric energy density of the electrode materials. Frogspawn consists of a spawn core and a transparent jelly shell organized in a hierarchical porous array, which exhibits superior mechanical strength and high-efficiency oxygen permeability. It can be used as a model for designing a new high-performance electrode material, which has advantages such as a high surface area, fast mass transport and superior durability. Herein, we report a frogspawn-like NaTi2(PO4)3/C array prepared by a facile preform impregnation strategy. The framework is formed by a hollow carbon sphere connected by the NaTi2(PO4)3/C skeleton, and its hollow is filled with the NaTi2(PO4)3 nanospheres. The whole hierarchical porous three-dimensional array copies the structure of a frogspawn. This unique structure not only enables easy electrolyte percolation and fast electron/ion transport, but also enhances the reversible capacity and cycling durability. When it is applied as an anode of the aqueous sodium ion battery, it exhibits favorable high rate capability and superior cycling stability, and retains 89% of the initial capacity after two thousand cycles at 20 C. Moreover, the full cell using the frogspawn-inspired NaTi2(PO4)3-C as the anode and Na0.44MnO2 as the cathode is capable of ultralong cycling up to one thousand cycles at alternate 10 and 60 C, which is among the best of state-of-the-art aqueous sodium ion systems. Therefore, the frogspawn-inspired architecture provides a new strategy to the tailored design of polyanion materials for high-power applications.Hollow micro/nano-arrays have attracted tremendous attention in the field of energy conversion and storage, but such structures usually compromise the volumetric energy density of the electrode materials. Frogspawn consists of a spawn core and a transparent jelly shell organized in

  5. The Klinefelter syndrome is associated with high recurrence of copy number variations on the X chromosome with a potential role in the clinical phenotype.

    Science.gov (United States)

    Rocca, M S; Pecile, V; Cleva, L; Speltra, E; Selice, R; Di Mambro, A; Foresta, C; Ferlin, A

    2016-03-01

    The Klinefelter syndrome (KS) is the most frequent sex chromosomal disorder in males, characterized by at least one supernumerary X chromosome (most frequent karyotype 47,XXY). This syndrome presents with a broad range of phenotypes. The common characteristics include small testes and infertility, but KS subjects are at increased risk of hypogonadism, cognitive dysfunction, obesity, diabetes, metabolic syndrome, osteoporosis, and autoimmune disorders, which are present in variable proportion. Although part of the clinical variability might be linked to a different degree of testicular function observed in KS patients, genetic mechanisms of the supernumerary X chromosome might contribute. Gene-dosage effects and parental origin of the supernumerary X chromosome have been suggested to this regard. No study has been performed analyzing the genetic constitution of the X chromosome in terms of copy number variations (CNVs) and their possible involvement in phenotype of KS. To this aim, we performed a SNP arrays analysis on 94 KS and 85 controls. We found that KS subjects have more frequently than controls X-linked CNVs (39/94, [41.5%] with respect to 12/42, [28.6%] of females, and 8/43, [18.6%] of males, p < 0.01). The number of X-linked CNVs in KS patients was 4.58 ± 1.92 CNVs/subject, significantly higher with respect to that found in control females (1.50 ± 1.29 CNVs/subject) and males (1.14 ± 0.37 CNVs/subject). Importantly, 94.4% X-linked CNVs in KS subjects were duplications, higher with respect to control males (50.0%, p < 0.001) and females (83.3%, p = 0.1). Half of the X-linked CNVs fell within regions encompassing genes and most of them (90%) included genes escaping X-inactivation in the regions of X-Y homology, particularly in the pseudoautosomal region 1 (PAR1) and Xq21.31. This study described for the first time the genetic properties of the X chromosome in KS and suggests that X-linked CNVs (especially duplications) might contribute to the clinical

  6. A High-Frequency High Frame Rate Duplex Ultrasound Linear Array Imaging System for Small Animal Imaging

    Science.gov (United States)

    Zhang, Lequan; Xu, Xiaochen; Hu, Changhong; Sun, Lei; Yen, Jesse T.; Cannata, Jonathan M.; Shung, K. Kirk

    2010-01-01

    High-frequency (HF) ultrasound imaging has been shown to be useful for non-invasively imaging anatomical structures of the eye and small animals in biological and pharmaceutical research, achieving superior spatial resolution. Cardiovascular research utilizing mice requires not only real-time B-scan imaging, but also ultrasound Doppler to evaluate both anatomy and blood flow of the mouse heart. This paper reports the development of a high frequency ultrasound duplex imaging system capable of both B-mode imaging and Doppler flow measurements, using a 64-element linear array. The system included a HF pulsed-wave Doppler module, a 32-channel HF B-mode imaging module, a PC with a 200 MS/s 14-bit A/D card, and real-time LabView software. A 50dB signal-to-noise ratio (SNR) and a depth of penetration of larger than 12 mm were achieved using a 35 MHz linear array with 50 μm pitch. The two-way beam widths were determined to be 165 μm to 260 μm and the clutter energy to total energy ratio (CTR) were 9.1 dB to 12 dB, when the array was electronically focused at different focal points at depths from 4.8 mm to 9.6 mm. The system is capable of acquiring real-time B-mode images at a rate greater than 400 frames per second (fps) for a 4.8 × 13 mm field of view, using a 30 MHz 64-element linear array with 100 μm pitch. Sample in vivo cardiac high frame rate images and duplex images of mouse hearts are shown to assess its current imaging capability and performance for small animals. PMID:20639149

  7. Front-end receiver electronics for high-frequency monolithic CMUT-on-CMOS imaging arrays.

    Science.gov (United States)

    Gurun, Gokce; Hasler, Paul; Degertekin, F

    2011-08-01

    This paper describes the design of CMOS receiver electronics for monolithic integration with capacitive micromachined ultrasonic transducer (CMUT) arrays for highfrequency intravascular ultrasound imaging. A custom 8-inch (20-cm) wafer is fabricated in a 0.35-μm two-poly, four-metal CMOS process and then CMUT arrays are built on top of the application specific integrated circuits (ASICs) on the wafer. We discuss advantages of the single-chip CMUT-on-CMOS approach in terms of receive sensitivity and SNR. Low-noise and high-gain design of a transimpedance amplifier (TIA) optimized for a forward-looking volumetric-imaging CMUT array element is discussed as a challenging design example. Amplifier gain, bandwidth, dynamic range, and power consumption trade-offs are discussed in detail. With minimized parasitics provided by the CMUT-on-CMOS approach, the optimized TIA design achieves a 90 fA/√Hz input-referred current noise, which is less than the thermal-mechanical noise of the CMUT element. We show successful system operation with a pulseecho measurement. Transducer-noise-dominated detection in immersion is also demonstrated through output noise spectrum measurement of the integrated system at different CMUT bias voltages. A noise figure of 1.8 dB is obtained in the designed CMUT bandwidth of 10 to 20 MHz.

  8. Design and development of high frequency matrix phased-array ultrasonic probes

    Science.gov (United States)

    Na, Jeong K.; Spencer, Roger L.

    2012-05-01

    High frequency matrix phased-array (MPA) probes have been designed and developed for more accurate and repeatable assessment of weld conditions of thin sheet metals commonly used in the auto industry. Unlike the line focused ultrasonic beam generated by a linear phased-array (LPA) probe, a MPA probe can form a circular shaped focused beam in addition to the typical beam steering capabilities of phased-array probes. A CIVA based modeling and simulation method has been used to design the probes in terms of various probe parameters such as number of elements, element size, overall dimensions, frequency etc. Challenges associated with the thicknesses of thin sheet metals have been resolved by optimizing these probe design parameters. A further improvement made on the design of the MPA probe proved that a three-dimensionally shaped matrix element can provide a better performing probe at a much lower probe manufacturing cost by reducing the total number of elements and lowering the operational frequency. This three dimensional probe naturally matches to the indentation shape of the weld on the thin sheet metals and hence a wider inspection area with the same level of spatial resolution obtained by a twodimensional flat MPA probe operating at a higher frequency. The two aspects, a wider inspection area and a lower probe manufacturing cost, make this three-dimensional MPA sensor more attractive to auto manufacturers demanding a quantitative nondestructive inspection method.

  9. High-performance SPAD array detectors for parallel photon timing applications

    Science.gov (United States)

    Rech, I.; Cuccato, A.; Antonioli, S.; Cammi, C.; Gulinatti, A.; Ghioni, M.

    2012-02-01

    Over the past few years there has been a growing interest in monolithic arrays of single photon avalanche diodes (SPAD) for spatially resolved detection of faint ultrafast optical signals. SPADs implemented in planar technologies offer the typical advantages of microelectronic devices (small size, ruggedness, low voltage, low power, etc.). Furthermore, they have inherently higher photon detection efficiency than PMTs and are able to provide, beside sensitivities down to single-photons, very high acquisition speeds. In order to make SPAD array more and more competitive in time-resolved application it is necessary to face problems like electrical crosstalk between adjacent pixel, moreover all the singlephoton timing electronics with picosecond resolution has to be developed. In this paper we present a new instrument suitable for single-photon imaging applications and made up of 32 timeresolved parallel channels. The 32x1 pixel array that includes SPAD detectors represents the system core, and an embedded data elaboration unit performs on-board data processing for single-photon counting applications. Photontiming information is exported through a custom parallel cable that can be connected to an external multichannel TCSPC system.

  10. High frequency glow discharges at atmospheric pressure with micro-structured electrode arrays

    Science.gov (United States)

    Baars-Hibbe, L.; Sichler, P.; Schrader, C.; Lucas, N.; Gericke, K.-H.; Büttgenbach, S.

    2005-02-01

    Micro-structured electrode (MSE) arrays allow the generation of large-area uniform glow discharges over a wide pressure range up to atmospheric pressure. The electrode widths, thicknesses and distances in the micrometre range are realized by means of modern micro-machining and galvanic techniques. The electrode distance, the gap width d, is small enough to generate sufficiently high electric field strengths to ignite gas discharges by applying only moderate radio frequency (RF, 13.56 MHz) voltages (80-390 V in Ne, He, Ar, N2 and air). The non-thermal plasma system is characterized by a special probe measuring the electric parameters. We tested MSE arrays with d = 70, 25 and 15 µm. The MSE driven plasmas show a different behaviour from conventional RF discharge plasmas. Due to the very small electrode gap width we can describe the behaviour of the charged particles in the RF field of our system with the dc Townsend breakdown theory, depending on the pressure range and gas. With decreasing pressure, the gas discharges, especially in Ne and He, are increasingly dominated by field electron emission. With the MSE arrays as plasma sources several applications were developed and successfully tested, e.g. decomposition of waste gases and sterilization of food packaging materials at atmospheric pressure.

  11. Highly sensitive label-free dual sensor array for rapid detection of wound bacteria.

    Science.gov (United States)

    Sheybani, Roya; Shukla, Anita

    2017-06-15

    Wound infections are a critical healthcare concern worldwide. Rapid and effective antibiotic treatments that can mitigate infection severity and prevent the spread of antibiotic resistance are contingent upon timely infection detection. In this work, dual electrochemical pH and cell-attachment sensor arrays were developed for the real-time spatial and temporal monitoring of potential wound infections. Biocompatible polymeric device coatings were integrated to stabilize the sensors and promote bacteria attachment while preventing non-specific cell and protein fouling. High sensitivity (bacteria concentration of 10(2) colony forming units (CFU)/mL and -88.1±6.3mV/pH over a pH range of 1-13) and stability over 14 days were achieved without the addition of biological recognition elements. The dual sensor array was demonstrated to successfully monitor the growth of both gram-positive (Staphylococcus aureus and Streptococcus pyogenes) and gram-negative bacteria (Pseudomonas aeruginosa and Escherichia coli) over time through lag and log growth phases and following antibiotic administration and in simulated shallow wounds conditions. The versatile fabrication methods utilized in sensor development, superior sensitivity, prolonged stability, and lack of non-specific sensor fouling may enable long-term in situ sensor array operation in low resource settings. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Optimizing Concentric Circular Antenna Arrays for High-Altitude Platforms Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yasser Albagory

    2014-04-01

    Full Text Available Wireless Sensor Networks (WSN has gained interest in many applications and it becomes important to improve its performance. Antennas and communication performance are most important issues of WSN. In this paper, an adaptive concentric circular array (CCA is proposed to improve the link between the sink and sensor nodes. This technique is applied to the new High – Altitude Platform (HAP Wireless Sensor Network (WSN. The proposed array technique is applied for two coverage scenarios; a wider coverage cell of 30 km radius and a smaller cell of 8 km radius. The feasibility of the link is discussed where it shows the possibility of communications between the HAP sink station and sensor nodes located on the ground. The proposed CCA array is optimized using a modified Dolph-Chebyshev feeding function. A comparison with conventional antenna models in literature shows that the link performance in terms of bit energy to noise power spectral density ratio can be improved by up to 11.37 dB for cells of 8 km radius and 16.8 dB in the case of 30 km radius cells that make the link at 2.4 GHz feasible and realizable compared to using conventional antenna techniques.

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

    Science.gov (United States)

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

    2014-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Casini G.

    2014-03-01

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

  15. Parallel and series FED microstrip array with high efficiency and low cross polarization

    Science.gov (United States)

    Huang, John (Inventor)

    1995-01-01

    A microstrip array antenna for vertically polarized fan beam (approximately 2 deg x 50 deg) for C-band SAR applications with a physical area of 1.7 m by 0.17 m comprises two rows of patch elements and employs a parallel feed to left- and right-half sections of the rows. Each section is divided into two segments that are fed in parallel with the elements in each segment fed in series through matched transmission lines for high efficiency. The inboard section has half the number of patch elements of the outboard section, and the outboard sections, which have tapered distribution with identical transmission line sections, terminated with half wavelength long open-circuit stubs so that the remaining energy is reflected and radiated in phase. The elements of the two inboard segments of the two left- and right-half sections are provided with tapered transmission lines from element to element for uniform power distribution over the central third of the entire array antenna. The two rows of array elements are excited at opposite patch feed locations with opposite (180 deg difference) phases for reduced cross-polarization.

  16. Choosing processor array configuration by performance modeling for a highly parallel linear algebra algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Littlefield, R.J.; Maschhoff, K.J.

    1991-04-01

    Many linear algebra algorithms utilize an array of processors across which matrices are distributed. Given a particular matrix size and a maximum number of processors, what configuration of processors, i.e., what size and shape array, will execute the fastest The answer to this question depends on tradeoffs between load balancing, communication startup and transfer costs, and computational overhead. In this paper we analyze in detail one algorithm: the blocked factored Jacobi method for solving dense eigensystems. A performance model is developed to predict execution time as a function of the processor array and matrix sizes, plus the basic computation and communication speeds of the underlying computer system. In experiments on a large hypercube (up to 512 processors), this model has been found to be highly accurate (mean error {approximately} 2%) over a wide range of matrix sizes (10 {times} 10 through 200 {times} 200) and processor counts (1 to 512). The model reveals, and direct experiment confirms, that the tradeoffs mentioned above can be surprisingly complex and counterintuitive. We propose decision procedures based directly on the performance model to choose configurations for fastest execution. The model-based decision procedures are compared to a heuristic strategy and shown to be significantly better. 7 refs., 8 figs., 1 tab.

  17. Plasma nitriding induced growth of Pt-nanowire arrays as high performance electrocatalysts for fuel cells.

    Science.gov (United States)

    Du, Shangfeng; Lin, Kaijie; Malladi, Sairam K; Lu, Yaxiang; Sun, Shuhui; Xu, Qiang; Steinberger-Wilckens, Robert; Dong, Hanshan

    2014-09-22

    In this work, we demonstrate an innovative approach, combing a novel active screen plasma (ASP) technique with green chemical synthesis, for a direct fabrication of uniform Pt nanowire arrays on large-area supports. The ASP treatment enables in-situ N-doping and surface modification to the support surface, significantly promoting the uniform growth of tiny Pt nuclei which directs the growth of ultrathin single-crystal Pt nanowire (2.5-3 nm in diameter) arrays, forming a three-dimensional (3D) nano-architecture. Pt nanowire arrays in-situ grown on the large-area gas diffusion layer (GDL) (5 cm(2)) can be directly used as the catalyst electrode in fuel cells. The unique design brings in an extremely thin electrocatalyst layer, facilitating the charge transfer and mass transfer properties, leading to over two times higher power density than the conventional Pt nanoparticle catalyst electrode in real fuel cell environment. Due to the similar challenges faced with other nanostructures and the high availability of ASP for other material surfaces, this work will provide valuable insights and guidance towards the development of other new nano-architectures for various practical applications.

  18. SNP discovery and development of a high-density genotyping array for sunflower.

    Directory of Open Access Journals (Sweden)

    Eleni Bachlava

    Full Text Available Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs. Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.. This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.

  19. SNP discovery and development of a high-density genotyping array for sunflower.

    Science.gov (United States)

    Bachlava, Eleni; Taylor, Christopher A; Tang, Shunxue; Bowers, John E; Mandel, Jennifer R; Burke, John M; Knapp, Steven J

    2012-01-01

    Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.

  20. High-frequency Ultrasound Doppler System for Biomedical Applications with a 30 MHz Linear Array

    Science.gov (United States)

    Xu, Xiaochen; Sun, Lei; Cannata, Jonathan M.; Yen, Jesse T.; Shung, K. Kirk

    2008-01-01

    In this paper, we report the development of the first high-frequency (HF) pulsed-wave Doppler system using a 30 MHz linear array transducer to assess the cardiovascular functions in small animal. This array based pulsed-wave Doppler system included a 16-channel HF analog beamformer, a HF pulsed-wave Doppler module, timing circuits, HF bipolar pulsers, and analog front-ends. The beamformed echoes acquired by the 16 channel analog beamformer, were directly fed to the HF pulsed-wave Doppler module. Then the in-phase and quadrature-phase (IQ) audio Doppler signals were digitized by either a sound card or a Gage digitizer and stored in a PC. The Doppler spectrogram was displayed on a PC in real time. The two-way beam-widths were determined to be 160 μm to 320 μm when the array was electronically focused at different focal points at depths from 5–10 mm. A micro flow phantom, consisting of a polyimide tube with inner diameter of 127 μm, and the wire phantom were used to evaluate and calibrate the system. The results show that the system is capable of detecting motion velocity of the wire phantom as low as 0.1 mm/s, and detecting blood-mimicking flow velocity in the 127 μm tube lower than 7 mm/s. The system was subsequently used to measure the blood flow in vivo in two mouse abdominal superficial vessels with diameters of approximately 200 μm, and a mouse aorta close to the heart. These results demonstrated that this system may become an indispensable part of the current HF array based imaging systems for small animal studies. PMID:17993243

  1. Identification of RCN1 and RSA3 as ethanol-tolerant genes in Saccharomyces cerevisiae using a high copy barcoded library.

    Science.gov (United States)

    Anderson, Michael J; Barker, Sarah L; Boone, Charlie; Measday, Vivien

    2012-02-01

    Saccharomyces cerevisiae (S. cerevisiae) encounters a multitude of stresses during industrial processes such as wine fermentation including ethanol toxicity. High levels of ethanol reduce the viability of yeast and may prevent completion of fermentation. The identification of ethanol-tolerant genes is important for creating stress-resistant industrial yeast, and S. cerevisiae genomic resources have been utilized for this purpose. We have employed a molecular barcoded yeast open reading frame (MoBY-ORF) high copy plasmid library to identify ethanol-tolerant genes in both the S. cerevisiae S288C laboratory and M2 wine strains. We find that increased dosage of either RCN1 or RSA3 improves tolerance of S288C and M2 to toxic levels of ethanol. RCN1 is a regulator of calcineurin, whereas RSA3 has a role in ribosome maturation. Additional fitness advantages conferred upon overproduction of RCN1 and RSA3 include increased resistance to cell wall degradation, heat, osmotic and oxidative stress. We find that the M2 wine yeast strain is generally more tolerant of stress than S288C with the exception of translation inhibition, which affects M2 growth more severely than S288C. We conclude that regulation of ribosome biogenesis and ultimately translation is a critical factor for S. cerevisiae survival during industrial-related environmental stress. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  2. Stable high-copy-number integration of Aspergillus oryzae alpha-AMYLASE cDNA in an industrial baker's yeast strain.

    Science.gov (United States)

    Nieto, A; Prieto, J A; Sanz, P

    1999-01-01

    The Aspergillus oryzae alpha-amylase cDNA was placed under the control of the Saccharomyces cerevisiae actin promoter (pACT1) and introduced into the ribosomal DNA locus of an industrial baker's yeast strain. To obtain a strain eligible for commercial use, we constructed an integrative cassette lacking bacterial DNA sequences but containing the alpha-amylase cDNA and ribosomal DNA sequences to target the integration to this locus. High-copy-number integrants were obtained including a defective TRP1d promoter in the integrative cassette. We selected one transformant, Rib-AMY (CECT10872), in which the multi-integrated sequences were stable even after 200 generations of growth in nonselective medium. This transformant also expressed and secreted high levels of alpha-amylase. Bread made with this strain had a higher volume, lower density, and softer crumbs than bread made with a control strain. The Rib-AMY transformant also was useful in retarding bread firming. This new strain fulfills all the requirements for commercial utilization and should reduce or eliminate the requirement for addition of exogenous alpha-amylase to the flour, reducing allergenic work-related symptoms due to this enzyme.

  3. Synthetic microfluidic paper: high surface area and high porosity polymer micropillar arrays.

    Science.gov (United States)

    Hansson, Jonas; Yasuga, Hiroki; Haraldsson, Tommy; van der Wijngaart, Wouter

    2016-01-21

    We introduce Synthetic Microfluidic Paper, a novel porous material for microfluidic applications that consists of an OSTE polymer that is photostructured in a well-controlled geometry of slanted and interlocked micropillars. We demonstrate the distinct benefits of Synthetic Microfluidic Paper over other porous microfluidic materials, such as nitrocellulose, traditional paper and straight micropillar arrays: in contrast to straight micropillar arrays, the geometry of Synthetic Microfluidic Paper was miniaturized without suffering capillary collapse during manufacturing and fluidic operation, resulting in a six-fold increased internal surface area and a three-fold increased porous fraction. Compared to commercial nitrocellulose materials for capillary assays, Synthetic Microfluidic Paper shows a wider range of capillary pumping speed and four times lower device-to-device variation. Compared to the surfaces of the other porous microfluidic materials that are modified by adsorption, Synthetic Microfluidic Paper contains free thiol groups and has been shown to be suitable for covalent surface chemistry, demonstrated here for increasing the material hydrophilicity. These results illustrate the potential of Synthetic Microfluidic Paper as a porous microfluidic material with improved performance characteristics, especially for bioassay applications such as diagnostic tests.

  4. BioMEA: a versatile high-density 3D microelectrode array system using integrated electronics.

    Science.gov (United States)

    Charvet, Guillaume; Rousseau, Lionel; Billoint, Olivier; Gharbi, Sadok; Rostaing, Jean-Pierre; Joucla, Sébastien; Trevisiol, Michel; Bourgerette, Alain; Chauvet, Philippe; Moulin, Céline; Goy, François; Mercier, Bruno; Colin, Mikael; Spirkovitch, Serge; Fanet, Hervé; Meyrand, Pierre; Guillemaud, Régis; Yvert, Blaise

    2010-04-15

    Microelectrode arrays (MEAs) offer a powerful tool to both record activity and deliver electrical microstimulations to neural networks either in vitro or in vivo. Microelectronics microfabrication technologies now allow building high-density MEAs containing several hundreds of microelectrodes. However, dense arrays of 3D micro-needle electrodes, providing closer contact with the neural tissue than planar electrodes, are not achievable using conventional isotropic etching processes. Moreover, increasing the number of electrodes using conventional electronics is difficult to achieve into compact devices addressing all channels independently for simultaneous recording and stimulation. Here, we present a full modular and versatile 256-channel MEA system based on integrated electronics. First, transparent high-density arrays of 3D-shaped microelectrodes were realized by deep reactive ion etching techniques of a silicon substrate reported on glass. This approach allowed achieving high electrode aspect ratios, and different shapes of tip electrodes. Next, we developed a dedicated analog 64-channel Application Specific Integrated Circuit (ASIC) including one amplification stage and one current generator per channel, and analog output multiplexing. A full modular system, called BIOMEA, has been designed, allowing connecting different types of MEAs (64, 128, or 256 electrodes) to different numbers of ASICs for simultaneous recording and/or stimulation on all channels. Finally, this system has been validated experimentally by recording and electrically eliciting low-amplitude spontaneous rhythmic activity (both LFPs and spikes) in the developing mouse CNS. The availability of high-density MEA systems with integrated electronics will offer new possibilities for both in vitro and in vivo studies of large neural networks.

  5. Fabrication of highly ordered TiO2 nanorod/nanotube adjacent arrays for photoelectrochemical applications.

    Science.gov (United States)

    Zhang, Haimin; Liu, Porun; Liu, Xiaolu; Zhang, Shanqing; Yao, Xiangdong; An, Taicheng; Amal, Rose; Zhao, Huijun

    2010-07-06

    This work reports a facile approach to fabricate a perpendicularly aligned and highly ordered TiO(2) nanorod/nanotube (NR/NT) adjacent film by directly anodizing a modified titanium foil. The titanium foil substrate was modified with a layer of crystalline TiO(2) film via a hydrothermal process in 0.05 M (NH(4))(2)S(2)O(8). The resultant NR/NT architecture consists of a highly ordered nanorod top layer that directly adjoins to a highly ordered nanotube array bottom layer. The thickness of the top nanorod layer was approximately 90 nm with average nanorod diameter of 22 nm after 20 min of anodization. The thickness of the bottom nanotube array layer was found to be ca. 250 nm after 20 min of anodization, having an average outer and inner tubular diameters of 120 and 80 nm, respectively. A broad implication of the method is that a simple modification to the substrate surface can lead to new forms of nanostructures. For as-anodized NR/NT samples, XRD analysis reveals that the nanorods are of anatase TiO(2) crystalline form while the nanotubes are amorphous. Anatase TiO(2) crystalline form of NR/NT film with high crystallinity can be obtained by thermally treating the as-anodized sample at 450 degrees C for 2 h in air. The resultant NR/NT film was used as a photoanode for photoactivity evaluation. Comparing with a nanotube array photoanode prepared by direct anodization of unmodified titanium foil, the NR/NT photoanode exhibits a unique feature of selective photocatalytic oxidation toward organics, which makes it very attractive to photocatalytic degradation of organic pollutants, sensing, and other applications.

  6. High fill-factor multilevel Fresnel zone plate arrays by femtosecond laser direct writing

    Science.gov (United States)

    Niu, Li-Gang; Wang, Dian; Jiang, Tong; Wu, Si-Zhu; Li, Ai-Wu; Song, Jun-Feng

    2011-02-01

    Fresnel zone plate arrays (FZPAs), as a kind of an important integrated micro-optical device, have attracted great attention. However, the fill factor of present FZPAs by femtosecond technology is a little low, which leads to serious light loss and low signal-to-noise. Here we reported high fill-factor square and hexagonal FZPAs by femtosecond laser two-photon polymerization of the resin SU-8. Their optical focusing and imaging properties showed the high uniformity and high fidelity of these FZPAs. Moreover, 100% fill-factor FZPAs were demonstrated by optimal theoretical design and experimental parameters. With this high quality FZPAs, clear imaging "F" was obtained. At last, high-level phase type FZPAs were prepared to further enhance the diffractive efficiency to as much as 75%.

  7. An open label phase II study evaluating first-line EGFR tyrosine kinase inhibitor erlotinib in non-small cell lung cancer patients with tumors showing high EGFR gene copy number

    Science.gov (United States)

    Kowalczyk, Anna; Suszko-Kazarnowicz, Malgorzata; Duchnowska, Renata; Szczesna, Aleksandra; Ratajska, Magdalena; Sowa, Aleksander; Limon, Janusz; Biernat, Wojciech; Burzykowski, Tomasz; Jassem, Jacek; Dziadziuszko, Rafal

    2017-01-01

    Background First-line treatment with epidermal growth factor receptor (EGFR) inhibitors in NSCLC is effective in patients with activating EGFR mutations. The activity of erlotinib in patients harboring high EGFR gene copy number has been considered debatable. Patients and Methods A multicenter, open-label, single-arm phase II clinical trial was performed to test the efficacy of erlotinib in the first-line treatment of NSCLC patients harboring high EGFR gene copy number defined as =4 copies in =40% of cells. Findings Between December 2007 and April 2011, tumor samples from 149 subjects were screened for EGFR gene copy number by fluorescence in-situ hybridization (FISH), Out of 49 patients with positive EGFR FISH test, 45 were treated with erlotinib. Median PFS in the intent-to-treat population was 3.3 months (95%CI: 1.83.9 months), and median overall survival was 7.9 months (95% CI: 5.112.6 months). Toxicity profile of erlotinib was consistent with its known safety profile. The trial was stopped prematurely at 63% of originally planned sample size due to accumulating evidence that EGFR gene copy number should not be used to select NSCLC patients to first-line therapy with EGFR TKI. Data on erlotinib efficacy according to EGFR, KRAS and BRAF mutations are additionally presented. Interpretation This trial argues against using high gene copy number for selection of NSCLC patients to first-line therapy with EGFR TKIs. The study adds to the discussion on efficacy of other targeted agents in patients with target gene amplified tumors. PMID:27924059

  8. One-Step Electrodeposited Nickel Cobalt Sulfide Nanosheet Arrays for High-Performance Asymmetric Supercapacitors

    KAUST Repository

    Chen, Wei

    2014-09-23

    A facile one-step electrodeposition method is developed to prepare ternary nickel cobalt sulfide interconnected nanosheet arrays on conductive carbon substrates as electrodes for supercapacitors, resulting in exceptional energy storage performance. Taking advantages of the highly conductive, mesoporous nature of the nanosheets and open framework of the three-dimensional nanoarchitectures, the ternary sulfide electrodes exhibit high specific capacitance (1418 F g(-1) at 5 A g(-1) and 1285 F g(-1) at 100 A g(-1)) with excellent rate capability. An asymmetric supercapacitor fabricated by the ternary sulfide nanosheet arrays as positive electrode and porous graphene film as negative electrode demonstrates outstanding electrochemical performance for practical energy storage applications. Our asymmetric supercapacitors show a high energy density of 60 Wh kg(-1) at a power density of 1.8 kW kg(-1). Even when charging the cell within 4.5 s, the energy density is still as high as 33 Wh kg(-1) at an outstanding power density of 28.8 kW kg(-1) with robust long-term cycling stability up to 50 000 cycles.

  9. Design of DSP-based high-power digital solar array simulator

    Science.gov (United States)

    Zhang, Yang; Liu, Zhilong; Tong, Weichao; Feng, Jian; Ji, Yibo

    2013-12-01

    To satisfy rigid performance specifications, a feedback control was presented for zoom optical lens plants. With the increasing of global energy consumption, research of the photovoltaic(PV) systems get more and more attention. Research of the digital high-power solar array simulator provides technical support for high-power grid-connected PV systems research.This paper introduces a design scheme of the high-power digital solar array simulator based on TMS320F28335. A DC-DC full-bridge topology was used in the system's main circuit. The switching frequency of IGBT is 25kHz.Maximum output voltage is 900V. Maximum output current is 20A. Simulator can be pre-stored solar panel IV curves.The curve is composed of 128 discrete points .When the system was running, the main circuit voltage and current values was feedback to the DSP by the voltage and current sensors in real-time. Through incremental PI,DSP control the simulator in the closed-loop control system. Experimental data show that Simulator output voltage and current follow a preset solar panels IV curve. In connection with the formation of high-power inverter, the system becomes gridconnected PV system. The inverter can find the simulator's maximum power point and the output power can be stabilized at the maximum power point (MPP).

  10. Monolithic, High-Speed Fiber-Optic Switching Array for Lidar

    Science.gov (United States)

    Suckow, Will; Roberts, Tony; Switzer, Gregg; Terwilliger, Chelle

    2011-01-01

    Current fiber switch technologies use mechanical means to redirect light beams, resulting in slow switch time, as well as poor reliability due to moving parts wearing out quickly at high speeds. A non-mechanical ability to switch laser output into one of multiple fibers within a fiber array can provide significant power, weight, and costs savings to an all-fiber system. This invention uses an array of crystals that act as miniature prisms to redirect light as an electric voltage changes the prism s properties. At the heart of the electro-optic fiber-optic switch is an electro- optic crystal patterned with tiny prisms that can deflect the beam from the input fiber into any one of the receiving fibers arranged in a linear array when a voltage is applied across the crystal. Prism boundaries are defined by a net dipole moment in the crystal lattice that has been poled opposite to the surrounding lattice fabricated using patterned, removable microelectrodes. When a voltage is applied across the crystal, the resulting electric field changes the index of refraction within the prism boundaries relative to the surrounding substrate, causing light to deflect slightly according to Snell s Law. There are several materials that can host the necessary monolithic poled pattern (including, but not limited to, SLT, KTP, LiNbO3, and Mg:LiNbO3). Be cause this is a solid-state system without moving parts, it is very fast, and does not wear down easily. This invention is applicable to all fiber networks, as well as industries that use such networks. The unit comes in a compact package, can handle both low and high voltages, and has a high reliability (100,000 hours without maintenance).

  11. High Current ESD Test of Advanced Triple Junction Solar Array Coupon

    Science.gov (United States)

    Wright, Kenneth H., Jr.; Schneider, Todd A.; Vaughn, Jason A.; Hoang, Bao; Wong, Frankie

    2015-01-01

    A test was conducted on an Advanced Triple Junction (ATJ) coupon that was part of a risk reduction effort in the development of a high-powered solar array design by SSL. The ATJ coupon was a small, 4-cell, two-string configuration that has served as the basic test coupon design used in previous SSL environmental aging campaigns. The coupon has many attributes of the flight design; e.g., substrate structure with graphite face sheets, integrated by-pass diodes, cell interconnects, RTV grout, wire routing, etc. The objective of the present test was to evaluate the performance of the coupon after being subjected to induced electrostatic discharge testing at two string voltages (100 V, 150 V) and four array current (1.65 A, 2.0 A, 2.475 A, and 3.3 A). An ESD test circuit, unique to SSL solar array design, was built that simulates the effect of missing cells and strings in a full solar panel with special primary arc flashover circuitry. A total of 73 primary arcs were obtained that included 7 temporary sustained arcs (TSA) events. The durations of the TSAs ranged from 50 micros to 2.9 ms. All TSAs occurred at a string voltage of 150 V. Post-test Large Area Pulsed Solar Simulator (LAPSS), Dark I-V, and By-Pass Diode tests showed that no degradation occurred due to the TSA events. In addition, the post-test insulation resistance measured was > 50 G-ohms between cells and substrate. These test results indicate a robust design for application to a high-current, high-power mission application.

  12. High-accuracy infra-red thermography method using reflective marker arrays

    Science.gov (United States)

    Kirollos, Benjamin; Povey, Thomas

    2017-09-01

    In this paper, we describe a new method for high-accuracy infra-red (IR) thermography measurements in situations with significant spatial variation in reflected radiation from the surroundings, or significant spatial variation in surface emissivity due to viewing angle non-uniformity across the field of view. The method employs a reflective marker array (RMA) on the target surface—typically, high emissivity circular dots—and an integrated image analysis algorithm designed to require minimal human input. The new technique has two particular advantages which make it suited to high-accuracy measurements in demanding environments: (i) it allows the reflected radiation component to be calculated directly, in situ, and as a function of position, overcoming a key problem in measurement environments with non-uniform and unsteady stray radiation from the surroundings; (ii) using image analysis of the marker array (via apparent aspect ratio of the circular reflective markers), the local viewing angle of the target surface can be estimated, allowing corrections for angular variation of local emissivity to be performed without prior knowledge of the geometry. A third advantage of the technique is that allows for simple focus-stacking algorithms due to increased image entropy. The reflective marker array method is demonstrated for an isothermal, hemispherical object exposed to an external IR source arranged to give a significant non-uniform reflected radiation term. This is an example of a challenging environment, both because of the significant non-uniform reflected radiation term, and also the significant variation in target emissivity due to surface angle variation. We demonstrate that the new RMA IR technique leads to significantly lower error in evaluated surface temperature than conventional IR techniques. The method is applicable to any complex radiative environment.

  13. DNA replication stress restricts ribosomal DNA copy number.

    Science.gov (United States)

    Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

    2017-09-15

    Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen the yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

  14. Super-Resolution Imaging by Arrays of High-Index Spheres Embedded in Transparent Matrices

    CERN Document Server

    Allen, Kenneth W; Li, Yangcheng; Limberopoulos, Nicholaos I; Walker, Dennis E; Urbas, Augustine M; Astratov, Vasily N

    2014-01-01

    We fabricated thin-films made from polydimethylsiloxane (PDMS) with embedded high-index (n~1.9-2.2) microspheres for super-resolution imaging applications. To control the position of microspheres, such films can be translated along the surface of the nanoplasmonic structure to be imaged. Microsphere-assisted imaging, through these matrices, provided lateral resolution of ~{\\lambda}/7 in nanoplasmonic dimer arrays with an illuminating wavelength {\\lambda}=405 nm. Such thin films can be used as contact optical components to boost the resolution capability of conventional microscopes.

  15. High-efficiency fabrication of aspheric microlens arrays by holographic femtosecond laser-induced photopolymerization

    Science.gov (United States)

    Hu, Yanlei; Chen, Yuhang; Ma, Jianqiang; Li, Jiawen; Huang, Wenhao; Chu, Jiaru

    2013-09-01

    Manufacture of aspheric microlens has always been technically challenging for conventional approaches due to their complex curved profile and tiny sizes. Two-photon polymerization is capable of producing arbitrary shape with high spatial resolution, apart from the disadvantage of ultra-low rate of yield resulting from point-by-point writing strategy. Here, we report parallel fabrication of aspheric microlens arrays (AMLAs) by taking advantage of holographic femtosecond laser direct-writing. The inherent constraints of the spatial light modulator are taken into consideration for achieving improved intensity uniformity and enhanced diffraction efficiency. Closely-packed AMLAs with designable optical parameters are readily fabricated with excellent optical performance.

  16. Simulation study of a high power density rectenna array for biomedical implantable devices

    Science.gov (United States)

    Day, John; Yoon, Hargsoon; Kim, Jaehwan; Choi, Sang H.; Song, Kyo D.

    2016-04-01

    The integration of wireless power transmission devices using microwaves into the biomedical field is close to a practical reality. Implanted biomedical devices need a long lasting power source or continuous power supply. Recent development of high efficiency rectenna technology enables continuous power supply to these implanted devices. Due to the size limit of most of medical devices, it is imperative to minimize the rectenna as well. The research reported in this paper reviews the effects of close packing the rectenna elements which show the potential of directly empowering the implanted devices, especially within a confined area. The rectenna array is tested in the X band frequency range.

  17. Characterization of a highly-segmented silicon prototype for the TRACE array

    Directory of Open Access Journals (Sweden)

    Gelain M.

    2014-03-01

    Full Text Available In view of the construction of novel and high-sensitive instrumentation for the emerging ISOL facilities new prototypes have being implemented and tested. The contribution focuses at the investigation of the detection efficiency of an innovative silicon-pad prototype, which is the key element for the construction of the TRACE array, pursued for the SPES facility based at the Legnaro National Laboratories (Italy. The inter-pad size has been estimated by using a commercial 100-MHz-14-bit CAEN digitizer for sampling the signals obtained by an alpha-source scan over the inter-pad region.

  18. High power telecommunication-compatible photoconductive terahertz emitters based on plasmonic nano-antenna arrays

    Science.gov (United States)

    Yardimci, Nezih Tolga; Lu, Hong; Jarrahi, Mona

    2016-11-01

    We present a high-power and broadband photoconductive terahertz emitter operating at telecommunication optical wavelengths, at which compact and high-performance fiber lasers are commercially available. The presented terahertz emitter utilizes an ErAs:InGaAs substrate to achieve high resistivity and short carrier lifetime characteristics required for robust operation at telecommunication optical wavelengths. It also uses a two-dimensional array of plasmonic nano-antennas to offer significantly higher optical-to-terahertz conversion efficiencies compared to the conventional photoconductive emitters, while maintaining broad operation bandwidths. We experimentally demonstrate pulsed terahertz radiation over 0.1-5 THz frequency range with the power levels as high as 300 μW. This is the highest-reported terahertz radiation power from a photoconductive emitter operating at telecommunication optical wavelengths.

  19. High power telecommunication-compatible photoconductive terahertz emitters based on plasmonic nano-antenna arrays.

    Science.gov (United States)

    Yardimci, Nezih Tolga; Lu, Hong; Jarrahi, Mona

    2016-11-07

    We present a high-power and broadband photoconductive terahertz emitter operating at telecommunication optical wavelengths, at which compact and high-performance fiber lasers are commercially available. The presented terahertz emitter utilizes an ErAs:InGaAs substrate to achieve high resistivity and short carrier lifetime characteristics required for robust operation at telecommunication optical wavelengths. It also uses a two-dimensional array of plasmonic nano-antennas to offer significantly higher optical-to-terahertz conversion efficiencies compared to the conventional photoconductive emitters, while maintaining broad operation bandwidths. We experimentally demonstrate pulsed terahertz radiation over 0.1-5 THz frequency range with the power levels as high as 300 μW. This is the highest-reported terahertz radiation power from a photoconductive emitter operating at telecommunication optical wavelengths.

  20. Centrifugal micro-channel array droplet generation for highly parallel digital PCR.

    Science.gov (United States)

    Chen, Zitian; Liao, Peiyu; Zhang, Fangli; Jiang, Mengcheng; Zhu, Yusen; Huang, Yanyi

    2017-01-17

    Stable water-in-oil emulsion is essential to digital PCR and many other bioanalytical reactions that employ droplets as microreactors. We developed a novel technology to produce monodisperse emulsion droplets with high efficiency and high throughput using a bench-top centrifuge. Upon centrifugal spinning, the continuous aqueous phase is dispersed into monodisperse droplet jets in air through a micro-channel array (MiCA) and then submerged into oil as a stable emulsion. We performed dPCR reactions with a high dynamic range through the MiCA approach, and demonstrated that this cost-effective method not only eliminates the usage of complex microfluidic devices and control systems, but also greatly suppresses the loss of materials and cross-contamination. MiCA-enabled highly parallel emulsion generation combines both easiness and robustness of picoliter droplet production, and breaks the technical challenges by using conventional lab equipment and supplies.

  1. High-throughput fiber-array transvaginal ultrasound/photoacoustic probe for ovarian cancer imaging

    Science.gov (United States)

    Salehi, Hassan S.; Kumavor, Patrick D.; Alqasemi, Umar; Li, Hai; Wang, Tianheng; Zhu, Quing

    2014-03-01

    A high-throughput ultrasound/photoacoustic probe for delivering high contrast and signal-to-noise ratio images was designed, constructed, and tested. The probe consists of a transvaginal ultrasound array integrated with four 1mm-core optical fibers and a sheath. The sheath encases transducer and is lined with highly reflecting aluminum for high intensity light output and uniformity while at the same time remaining below the maximum permissible exposure (MPE) recommended by the American National Standards Institute (ANSI). The probe design was optimized by simulating the light fluence distribution in Zemax. The performance of the probe was evaluated by experimental measurements of the fluence and real-time imaging of polyethylene-tubing filled with blood. These results suggest that our probe has great potential for in vivo imaging and characterization of ovarian cancer.

  2. A High Performance Backend for Array-Oriented Programming on Next-Generation Processing Units

    DEFF Research Database (Denmark)

    Lund, Simon Andreas Frimann

    and the efficient execution of them on high performance systems. This work investigates the requirements for, and the implementation of, a high performance backend supporting these goals. This involves an outline of the hardware available today, in the near future and how to program it for high performance......The financial crisis, which started in 2008, spawned the HIPERFIT research center as a preventive measure against future financial crises. The goal of prevention is to be met by improving mathematical models for finance, the verifiable description of them in domain-specific languages....... The main challenge is to bridge the gaps between performance, productivity and portability. A declarative high-level array-oriented programming model is explored to achieve this goal and a backend implemented to support it. Different strategies to the backend design and application of optimizations...

  3. A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors.

    Science.gov (United States)

    Kang, Seok Hee; Hwang, Wan Sik; Lin, Zhiqun; Kwon, Se Hun; Hong, Suck Won

    2015-12-01

    Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.

  4. High resolution velocity structure beneath Mount Vesuvius from seismic array data

    Science.gov (United States)

    Scarpa, Roberto; Tronca, Fabrizio; Bianco, Francesca; Del Pezzo, Edoardo

    2002-11-01

    A high resolution P-wave image of Mt. Vesuvius edifice has been derived from simultaneous inversion of travel times and hypocentral parameters of local earthquakes, land based shots and small aperture array data. The results give details down to 300-500 m. The relocated local seismicity appears to extend down to 5 km below the central crater, distributed in a major cluster, centered at 3 km below the central crater and in a minor group, with diffuse hypocenters inside the volcanic edifice. The two clusters are separated by an anomalously high Vp region at around 1 km depth. A zone with high Vp/Vs in the upper layers is interpreted as produced by the presence of intense fluid circulation. The highest energy quakes (up to M = 3.6) are located in the deeper cluster, in a high P-wave velocity zone. Our results favor an interpretation in terms of absence of shallow magma reservoirs.

  5. High power external cavity laser diode arrays for the generation of hyperpolarized noble gases

    Science.gov (United States)

    Blasche, Gregory Paul

    Hyperpolarized noble gas magnetic resonance imaging promises to be a useful medical diagnostic tool due to its ability to image airways and brain function. A current limitation to widespread use is the time needed to generate gas quantities large enough for clinical patient imaging. Here I investigate line-narrowing of laser diode arrays in order to optimize the generation of hyperpolarized noble gases. Hyperpolarized noble gases are nuclear spin-½ isotopes that are polarized externally to have a large excess population of metastable spin up nuclei. When inhaled and imaged, they provide a novel tool for scientific studies and medical diagnosis in the human body. The gases are generated through a spin-exchange process via the spin-conserving hyperfine interaction of noble gas nuclei and optically pumped alkali metals. The net amount of polarized gas is limited by the optical power which is absorbed by the alkali metals as this is the first stage in the spin-exchange process. Laser diode arrays are typically used because they have a high available power for relatively low cost. Unfortunately, they are optically inefficient due to the factor of twenty larger inherent linewidth relative to the pressure broadened absorption linewidth of the alkali metal. In order to increase the efficiency of the system, I have designed and built an external cavity around the laser diode array consisting of a diffraction grating which acts as a wavelength dependent mirror tuned to the alkali metal rubidium absorption frequency. This causes the laser to operate solely at the desired wavelength, reducing the linewidth. External cavities have long been used for single element laser diodes. I extend this technique to laser diode arrays by imaging the diodes onto the grating using a set of imaging lenses forming individual cavities. I discuss the limitations on the power and linewidth achievable due to the optics of the cavity, as well as limitations caused by non-uniform heating effects

  6. Use of ubiquitous, highly heterozygous copy number variants and digital droplet polymerase chain reaction to monitor chimerism after allogeneic haematopoietic stem cell transplantation.

    Science.gov (United States)

    Whitlam, John B; Ling, Ling; Swain, Michael; Harrington, Tom; Mirochnik, Oksana; Brooks, Ian; Cronin, Sara; Challis, Jackie; Petrovic, Vida; Bruno, Damien L; Mechinaud, Francoise; Conyers, Rachel; Slater, Howard

    2017-01-29

    Chimerism analysis has an important role in the management of allogeneic hematopoietic stem cell transplantation. It informs response to disease relapse, graft rejection, and graft-versus-host disease. We have developed a method for chimerism analysis using ubiquitous copy number variation (CNV), which has the benefit of a "negative background" against which multiple independent informative markers are quantified using digital droplet polymerase chain reaction. A panel of up to 38 CNV markers with homozygous deletion frequencies of approximately 0.4-0.6 were used. Sensitivity, precision, reproducibility, and informativity were assessed. CNV chimerism results were compared against established fluorescence in situ hybridization, single nucleotide polymorphism, and short tandem repeat-based methods with excellent correlation. Using 30 ng of input DNA per well, the limit of detection was 0.05% chimerism and the limit of quantification was 0.5% chimerism. High informativity was seen with a median of four informative markers detectable per individual in 39 recipients and 43 donor genomes studied. The strength of this approach was exemplified in a multiple donor case involving four genomes (three related). The precision, sensitivity, and informativity of this approach recommend it for use in clinical practice.

  7. Improved performance of high average power semiconductor arrays for applications in diode pumped solid state lasers

    Energy Technology Data Exchange (ETDEWEB)

    Beach, R.; Emanuel, M.; Benett, W.; Freitas, B.; Ciarlo, D.; Carlson, N.; Sutton, S.; Skidmore, J.; Solarz, R.

    1994-01-01

    The average power performance capability of semiconductor diode laser arrays has improved dramatically over the past several years. These performance improvements, combined with cost reductions pursued by LLNL and others in the fabrication and packaging of diode lasers, have continued to reduce the price per average watt of laser diode radiation. Presently, we are at the point where the manufacturers of commercial high average power solid state laser systems used in material processing applications can now seriously consider the replacement of their flashlamp pumps with laser diode pump sources. Additionally, a low cost technique developed and demonstrated at LLNL for optically conditioning the output radiation of diode laser arrays has enabled a new and scalable average power diode-end-pumping architecture that can be simply implemented in diode pumped solid state laser systems (DPSSL`s). This development allows the high average power DPSSL designer to look beyond the Nd ion for the first time. Along with high average power DPSSL`s which are appropriate for material processing applications, low and intermediate average power DPSSL`s are now realizable at low enough costs to be attractive for use in many medical, electronic, and lithographic applications.

  8. Observations with the High Altitude GAmma Ray (HAGAR) telescope array in the Indian Himalayas

    Science.gov (United States)

    Britto, R. J.; Acharya, B. S.; Anupama, G. C.; Bhatt, N.; Bhattacharjee, P.; Bhattacharya, S. S.; Chitnis, V. R.; Cowsik, R.; Dorji, N.; Duhan, S. K.; Gothe, K. S.; Kamath, P. U.; Koul, R.; Mahesh, P. K.; Mitra, A.; Nagesh, B. K.; Parmar, N. K.; Prabhu, T. P.; Rannot, R. C.; Rao, S. K.; Saha, L.; Saleem, F.; Saxena, A. K.; Sharma, S. K.; Shukla, A.; Singh, B. B.; Srinivasan, R.; Srinivasulu, G.; Sudersanan, P. V.; Tickoo, A. K.; Tsewang, D.; Upadhya, S.; Vishwanath, P. R.; Yadav, K. K.

    2010-12-01

    For several decades, it was thought that astrophysical sources emit high energy photons within the energy range of the gamma-ray region of the electromagnetic spectrum also. These photons originate from interactions of high energy particles from sources involving violent phenomena in the Universe (supernovae, pulsars, Active Galactic Nuclei, etc.) with gas and radiation fields. Since the first reliable detections of cosmic gamma rays in the 1970's, improvements in instrumentation have led gamma-ray astronomy to an established branch of modern Astrophysics, with a constant increase in the number of detected sources. But the 30-300 GeV energy range remained sparsely explored until the launch of the Fermi space telescope in June 2008. The ground-based gamma-ray telescope array HAGAR is the first array of atmospheric Cherenkov telescopes established at a so high altitude (4270 m a.s.l.), and was designed to reach a relatively low energy threshold with quite a low mirror area (31 m^2). It is located at Hanle in India, in the Ladakh region of the Himalayas. Regular source observations have begun with the complete setup of 7 telescopes on Sept. 2008. We report and discuss our estimation of the systematics through dark region studies, and present preliminary results from gamma-ray sources in this paper.

  9. High Current ESD Test of Advanced Triple Junction Solar Array Coupon

    Science.gov (United States)

    Wright, Kenneth H., Jr.; Schneider, Todd A.; Vaughn, Jason A.; Hoang, Bao; Wong, Frankie

    2014-01-01

    Testing was conducted on an Advanced Triple Junction (ATJ) coupon that was part of a risk reduction effort in the development of a high-powered solar array design by Space Systems Loral, LLC (SSL). The ATJ coupon was a small, 4-cell, two-string configuration of flight-type design that has served as the basic test coupon design used in previous SSL environmental aging campaigns. The objective of the present test was to evaluate the performance of the coupon after being subjected to induced electrostatic discharge (ESD) testing at two string voltages (100 V, 150 V) and four string currents (1.65 A, 2.0 A, 2.475 A, and 3.3 A). An ESD test circuit, unique to SSL solar array design, was built that simulates the effect of missing cells and strings in a full solar panel with special primary arc flashover circuitry. A total of 73 primary arcs were obtained that included 7 temporary sustained arcs (TSA) events. The durations of the TSAs ranged from 50 micro-seconds to 2.75 milli-seconds. All TSAs occurred at a string voltage of 150 V. Post-ESD functional testing showed that no degradation occurred due to the TSA events. These test results point to a robust design for application to a high-current, high-power mission.

  10. A large array of high-performance artificial stars using airship-supported small mirrors

    Science.gov (United States)

    Content, Robert; Foxwell, Mark; Murray, Graham J.

    2004-10-01

    We propose a practical system that can provide a large number of high performance artificial stars, of the order of a few hundred, using an array of small mirrors on an airship supported platform illuminated from the ground by a laser. Our concept offers several advantages over other guide star schemes: Airborne mirror arrays can furnish tip-tilt information; they also permit a considerable reduction in the total ground-laser power required; high intensity guide stars with very small angular image size are possible; and finally they offer very low scattered parasite laser light. More basic & simpler launch-laser & AO technologies can therefore be employed, with potentially huge cost savings, with potentially significant improvement in the quality of the AO correction. The general platform scheme and suitable lift technologies are also discussed. A novel concept for achieving precise positioning is presented whereby the platform & the lifting vehicle are linked by a tether, the platform having a degree of independent control. Our proposal would employ as the lift vehicle an autonomous high altitude airship of the type currently under widespread development in the commercial sector, for use as hubs for telecommunication networks, mobile telephone relay stations, etc.

  11. High-resolution genome-wide array-based comparative genome hybridization reveals cryptic chromosome changes in AML and MDS cases with trisomy 8 as the sole cytogenetic aberration.

    Science.gov (United States)

    Paulsson, K; Heidenblad, M; Strömbeck, B; Staaf, J; Jönsson, G; Borg, A; Fioretos, T; Johansson, B

    2006-05-01

    Although trisomy 8 as the sole chromosome aberration is the most common numerical abnormality in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), little is known about its pathogenetic effects. Considering that +8 is a frequent secondary change in AML/MDS, cryptic--possibly primary--genetic aberrations may occur in cases with trisomy 8 as the apparently single anomaly. However, no such hidden anomalies have been reported. We performed a high-resolution genome-wide array-based comparative genome hybridization (array CGH) analysis of 10 AML/MDS cases with isolated +8, utilizing a 32K bacterial artificial chromosome array set, providing >98% coverage of the genome with a resolution of 100 kb. Array CGH revealed intrachromosomal imbalances, not corresponding to known genomic copy number polymorphisms, in 4/10 cases, comprising nine duplications and hemizygous deletions ranging in size from 0.5 to 2.2 Mb. A 1.8 Mb deletion at 7p14.1, which had occurred prior to the +8, was identified in MDS transforming to AML. Furthermore, a deletion including ETV6 was present in one case. The remaining seven imbalances involved more than 40 genes. The present results show that cryptic genetic abnormalities are frequent in trisomy 8-positive AML/MDS cases and that +8 as the sole cytogenetic aberration is not always the primary genetic event.

  12. Water-cooled hard-soldered kilowatt laser diode arrays operating at high duty cycle

    Science.gov (United States)

    Klumel, Genady; Karni, Yoram; Oppenhaim, Jacob; Berk, Yuri; Shamay, Moshe; Tessler, Renana; Cohen, Shalom; Risemberg, Shlomo

    2010-04-01

    High brightness laser diode arrays are increasingly found in defense applications either as efficient optical pumps or as direct energy sources. In many instances, duty cycles of 10- 20 % are required, together with precise optical collimation. System requirements are not always compatible with the use of microchannel based cooling, notwithstanding their remarkable efficiency. Simpler but effective solutions, which will not involve high fluid pressure drops as well as deionized water, are needed. The designer is faced with a number of challenges: effective heat removal, minimization of the built- in and operational stresses as well as precise and accurate fast axis collimation. In this article, we report on a novel laser diode array which includes an integral tap water cooling system. Robustness is achieved by all around hard solder bonding of passivated 940nm laser bars. Far field mapping of the beam, after accurate fast axis collimation will be presented. It will be shown that the design of water cooling channels , proper selection of package materials, careful design of fatigue sensitive parts and active collimation technique allow for long life time and reliability, while not compromising the laser diode array efficiency, optical power density ,brightness and compactness. Main performance characteristics are 150W/bar peak optical power, 10% duty cycle and more than 50% wall plug efficiency with less than 1° fast axis divergence. Lifetime of 0.5 Gshots with less than 10% power degradation has been proved. Additionally, the devices have successfully survived harsh environmental conditions such as thermal cycling of the coolant temperature and mechanical shocks.

  13. Fast Growth of Highly Ordered TiO2 Nanotube Arrays on Si Substrate under High-Field Anodization

    Science.gov (United States)

    Song, Jingnan; Zheng, Maojun; Zhang, Bin; Li, Qiang; Wang, Faze; Ma, Liguo; Li, Yanbo; Zhu, Changqing; Ma, Li; Shen, Wenzhong

    2017-04-01

    Highly ordered TiO2 nanotube arrays (NTAs) on Si substrate possess broad applications due to its high surface-to-volume ratio and novel functionalities, however, there are still some challenges on facile synthesis. Here, we report a simple and cost-effective high-field (90-180 V) anodization method to grow highly ordered TiO2 NTAs on Si substrate, and investigate the effect of anodization time, voltage, and fluoride content on the formation of TiO2 NTAs. The current density-time curves, recorded during anodization processes, can be used to determine the optimum anodization time. It is found that the growth rate of TiO2 NTAs is improved significantly under high field, which is nearly 8 times faster than that under low fields (40-60 V). The length and growth rate of the nanotubes are further increased with the increase of fluoride content in the electrolyte.

  14. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer

    Directory of Open Access Journals (Sweden)

    Kenter Gemma G

    2007-02-01

    Full Text Available Abstract Background Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH and microsatellite marker analysis for the detection of loss of heterozygosity (LOH. Currently, high throughput methods such as array comparative genomic hybridization (array CGH, single nucleotide polymorphism array (SNP array and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression. Results Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH. Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR. Conclusion This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene

  15. Large-area, high-intensity PV arrays for systems using dish concentrating optics

    Energy Technology Data Exchange (ETDEWEB)

    Ward, J.S.; Duda, A.; Zweibel, K.; Coutts, T.J. [National Renewable Energy Lab., Golden, CO (United States)

    1998-09-01

    In this paper, the authors report on efforts to fabricate monolithic interconnected modules (MIMs) using III-V semiconductors with bandgaps appropriate for the terrestrial solar spectrum. The small size of the component cells comprising the MIM allows for operation at extremely high flux densities and relaxes the requirement for a small spot size to be generated by the optics. This makes possible a PV option for the large dish concentrator systems that have been developed by the solar thermal community for use with Stirling engines. Additionally, the highly effective back-surface reflector integrated into the MIM design is an effective tool for thermal management of the array. Development of this technology would radically alter the projections for PV manufacturing capacity because of the potential for extremely high power generation per unit area of semiconductor material.

  16. A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control

    NARCIS (Netherlands)

    Van Dyk, E.; Reinders, M.J.T.; Wessels, L.F.A.

    2013-01-01

    Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC,

  17. Association between genetic subgroups of pancreatic ductal adenocarcinoma defined by high density 500 K SNP-arrays and tumor histopathology.

    Directory of Open Access Journals (Sweden)

    María Laura Gutiérrez

    Full Text Available The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP-arrays to define those chromosomal regions which most commonly harbour copy number (CN alterations and loss of heterozygozity (LOH in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70% extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9 versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11. From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterozygozity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.

  18. Copy number variation across European populations.

    Directory of Open Access Journals (Sweden)

    Wanting Chen

    Full Text Available Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations.

  19. High-energy sources at low radio frequency: the Murchison Widefield Array view of Fermi blazars

    CERN Document Server

    Giroletti, M; D'Abrusco, R; Lico, R; Burlon, D; Hurley-Walker, N; Johnston-Hollitt, M; Morgan, J; Pavlidou, V; Bell, M; Bernardi, G; Bhat, R; Bowman, J D; Briggs, F; Cappallo, R J; Corey, B E; Deshpande, A A; Ewall-Rice, A; Emrich, D; Gaensler, B M; Goeke, R; Greenhill, L J; Hazelton, B J; Hindson, L; Kaplan, D L; Kasper, J C; Kratzenberg, E; Feng, L; Jacobs, D; Kurdryavtseva, N; Lenc, E; Lonsdale, C J; Lynch, M J; McKinley, B; McWhirter, S R; Mitchell, D A; Morales, M F; Morgan, E; Oberoi, D; Offringa, A R; Ord, S M; Pindor, B; Prabu, T; Procopio, P; Riding, J; Rogers, A E E; Roshi, A; Shankar, N Udaya; Srivani, K S; Subrahmanyan, R; Tingay, S J; Waterson, M; Wayth, R B; Webster, R L; Whitney, A R; Williams, A; Williams, C L

    2016-01-01

    Low-frequency radio arrays are opening a new window for the study of the sky, both to study new phenomena and to better characterize known source classes. Being flat-spectrum sources, blazars are so far poorly studied at low radio frequencies. We characterize the spectral properties of the blazar population at low radio frequency compare the radio and high-energy properties of the gamma-ray blazar population, and search for radio counterparts of unidentified gamma-ray sources. We cross-correlated the 6,100 deg^2 Murchison Widefield Array Commissioning Survey catalogue with the Roma blazar catalogue, the third catalogue of active galactic nuclei detected by Fermi-LAT, and the unidentified members of the entire third catalogue of gamma-ray sources detected by \\fermilat. When available, we also added high-frequency radio data from the Australia Telescope 20 GHz catalogue. We find low-frequency counterparts for 186 out of 517 (36%) blazars, 79 out of 174 (45%) gamma-ray blazars, and 8 out of 73 (11%) gamma-ray bl...

  20. Development of a 64 channel ultrasonic high frequency linear array imaging system

    Science.gov (United States)

    Hu, ChangHong; Zhang, Lequan; Cannata, Jonathan M.; Yen, Jesse; Shung, K. Kirk

    2011-01-01

    In order to improve the lateral resolution and extend the field of view of a previously reported 48 element 30 MHz ultrasound linear array and 16-channel digital imaging system, the development of a 256 element 30 MHz linear array and an ultrasound imaging system with increased channel count has been undertaken. This paper reports the design and testing of a 64 channel digital imaging system which consists of an analog front-end pulser/receiver, 64 channels of Time-Gain Compensation (TGC), 64 channels of high-speed digitizer as well as a beamformer. A Personal Computer (PC) is used as the user interface to display real-time images. This system is designed as a platform for the purpose of testing the performance of high frequency linear arrays that have been developed in house. Therefore conventional approaches were taken it its implementation. Flexibility and ease of use are of primary concern whereas consideration of cost-effectiveness and novelty in design are only secondary. Even so, there are many issues at higher frequencies but do not exist at lower frequencies need to be solved. The system provides 64 channels of excitation pulsers while receiving simultaneously at a 20 MHz–120 MHz sampling rate to 12-bits. The digitized data from all channels are first fed through Field Programmable Gate Arrays (FPGAs), and then stored in memories. These raw data are accessed by the beamforming processor to re-build the image or to be downloaded to the PC for further processing. The beamformer that applies delays to the echoes of each channel is implemented with the strategy that combines coarse (8.3ns) and fine delays (2 ns). The coarse delays are integer multiples of the sampling clock rate and are achieved by controlling the write enable pin of the First-In-First-Out (FIFO) memory to obtain valid beamforming data. The fine delays are accomplished with interpolation filters. This system is capable of achieving a maximum frame rate of 50 frames per second. Wire phantom

  1. Development of a 64 channel ultrasonic high frequency linear array imaging system.

    Science.gov (United States)

    Hu, ChangHong; Zhang, Lequan; Cannata, Jonathan M; Yen, Jesse; Shung, K Kirk

    2011-12-01

    In order to improve the lateral resolution and extend the field of view of a previously reported 48 element 30 MHz ultrasound linear array and 16-channel digital imaging system, the development of a 256 element 30 MHz linear array and an ultrasound imaging system with increased channel count has been undertaken. This paper reports the design and testing of a 64 channel digital imaging system which consists of an analog front-end pulser/receiver, 64 channels of Time-Gain Compensation (TGC), 64 channels of high-speed digitizer as well as a beamformer. A Personal Computer (PC) is used as the user interface to display real-time images. This system is designed as a platform for the purpose of testing the performance of high frequency linear arrays that have been developed in house. Therefore conventional approaches were taken it its implementation. Flexibility and ease of use are of primary concern whereas consideration of cost-effectiveness and novelty in design are only secondary. Even so, there are many issues at higher frequencies but do not exist at lower frequencies need to be solved. The system provides 64 channels of excitation pulsers while receiving simultaneously at a 20-120 MHz sampling rate to 12-bits. The digitized data from all channels are first fed through Field Programmable Gate Arrays (FPGAs), and then stored in memories. These raw data are accessed by the beamforming processor to re-build the image or to be downloaded to the PC for further processing. The beamformer that applies delays to the echoes of each channel is implemented with the strategy that combines coarse (8.3 ns) and fine delays (2 ns). The coarse delays are integer multiples of the sampling clock rate and are achieved by controlling the write enable pin of the First-In-First-Out (FIFO) memory to obtain valid beamforming data. The fine delays are accomplished with interpolation filters. This system is capable of achieving a maximum frame rate of 50 frames per second. Wire phantom images

  2. LDRD final report on Bloch Oscillations in two-dimensional nanostructure arrays for high frequency applications.

    Energy Technology Data Exchange (ETDEWEB)

    Lyo, Sungkwun Kenneth; Pan, Wei; Reno, John Louis; Wendt, Joel Robert; Barton, Daniel Lee

    2008-09-01

    We have investigated the physics of Bloch oscillations (BO) of electrons, engineered in high mobility quantum wells patterned into lateral periodic arrays of nanostructures, i.e. two-dimensional (2D) quantum dot superlattices (QDSLs). A BO occurs when an electron moves out of the Brillouin zone (BZ) in response to a DC electric field, passing back into the BZ on the opposite side. This results in quantum oscillations of the electron--i.e., a high frequency AC current in response to a DC voltage. Thus, engineering a BO will yield continuously electrically tunable high-frequency sources (and detectors) for sensor applications, and be a physics tour-de-force. More than a decade ago, Bloch oscillation (BO) was observed in a quantum well superlattice (QWSL) in short-pulse optical experiments. However, its potential as electrically biased high frequency source and detector so far has not been realized. This is partially due to fast damping of BO in QWSLs. In this project, we have investigated the possibility of improving the stability of BO by fabricating lateral superlattices of periodic coupled nanostructures, such as metal grid, quantum (anti)dots arrays, in high quality GaAs/Al{sub x}Ga{sub 1-x}As heterostructures. In these nanostructures, the lateral quantum confinement has been shown theoretically to suppress the optical-phonon scattering, believed to be the main mechanism for fast damping of BO in QWSLs. Over the last three years, we have made great progress toward demonstrating Bloch oscillations in QDSLs. In the first two years of this project, we studied the negative differential conductance and the Bloch radiation induced edge-magnetoplasmon resonance. Recently, in collaboration with Prof. Kono's group at Rice University, we investigated the time-domain THz magneto-spectroscopy measurements in QDSLs and two-dimensional electron systems. A surprising DC electrical field induced THz phase flip was observed. More measurements are planned to investigate this

  3. High Resolution Imagery and Three-line Array Imagery Automatic Registration for China’s TH-1 Satellite Imagery

    OpenAIRE

    2014-01-01

    An automatic image registration method of high resolution (HR) imagery and three-line array imagery for China’s TH-1 mapping satellite is invented. The 2m resolution HR imagery is normalized to 5m resolution three-line array imagery firstly. Then using precise point prediction model (P3M) matching method, thousands of correspondent points can be matched. Based on these matched points, feature points collected on HR imagery can be converted onto three-line array imagery automatically. Conseque...

  4. Optimized high-power diode laser, laser arrays, and bars for pump applications

    Science.gov (United States)

    Hülsewede, R.; Schulze, H.; Sebastian, J.; Schröder, D.; Meusel, J.; Wolf, J.; Hennig, P.

    2009-02-01

    Broad area diode laser and diode laser bars are the most efficient light sources. In comparison to solid state laser or gas laser systems the over all beam quality of the diode laser is poor. Thus most application of diode laser bars is high efficient pumping of solid state lasers converting the beam quality and scaling the power of laser systems within the kW range. The pump efficiency and the beam coupling efficiency of the diode laser pumped systems has to be increased to meet the increasing laser market demands for reduced costs. JENOPTIK Diode Lab GmbH (JDL) has optimized their high power brilliance bars to enable reliable high power operation especially, for the 9xx nm wavelength range and low far field divergences. Superior reliability with long operation time of 13,000 hours and high power operation of 200 W are demonstrated for high power bars high filling factor mounted on passively cooled heat sinks. Smaller far field divergence at high power levels requires longer cavity length and higher efficiencies in the beam coupling needs requires lower filling factors. The new high brilliance bars and arrays with 20% filling factor are showing high power operation up to 95 W and a slow axis beam divergence of less than 8° (95% power content).

  5. Watermark copy attack

    OpenAIRE

    Kutter, Martin; Voloshynovskyy, Svyatoslav; Herrigel, Alexander

    2000-01-01

    Research in digital watermarking has progressed along two paths. While new watermarking technologies are being developed, some researchers are also investigating di erent ways of attacking digital watermarks. Common attacks to watermarks usually aim to destroy theembedded watermark or to impair its detection. In this paper we propose a conceptually new attack for digitally watermarked images. The proposed attack doesnot destroy anembedded watermark, but copies it from one image to a di erent ...

  6. Understanding the dynamics of superparamagnetic particles under the influence of high field gradient arrays.

    Science.gov (United States)

    Barnsley, Lester C; Carugo, Dario; Aron, Miles; Stride, Eleanor

    2017-03-21

    The aim of this study was to characterize the behaviour of superparamagnetic particles in magnetic drug targeting (MDT) schemes. A 3-dimensional mathematical model was developed, based on the analytical derivation of the trajectory of a magnetized particle suspended inside a fluid channel carrying laminar flow and in the vicinity of an external source of magnetic force. Semi-analytical expressions to quantify the proportion of captured particles, and their relative accumulation (concentration) as a function of distance along the wall of the channel were also derived. These were expressed in terms of a non-dimensional ratio of the relevant physical and physiological parameters corresponding to a given MDT protocol. The ability of the analytical model to assess magnetic targeting schemes was tested against numerical simulations of particle trajectories. The semi-analytical expressions were found to provide good first-order approximations for the performance of MDT systems in which the magnetic force is relatively constant over a large spatial range. The numerical model was then used to test the suitability of a range of different designs of permanent magnet assemblies for MDT. The results indicated that magnetic arrays that emit a strong magnetic force that varies rapidly over a confined spatial range are the most suitable for concentrating magnetic particles in a localized region. By comparison, commonly used magnet geometries such as button magnets and linear Halbach arrays result in distributions of accumulated particles that are less efficient for delivery. The trajectories predicted by the numerical model were verified experimentally by acoustically focusing magnetic microbeads flowing in a glass capillary channel, and optically tracking their path past a high field gradient Halbach array.

  7. Understanding the dynamics of superparamagnetic particles under the influence of high field gradient arrays

    Science.gov (United States)

    Barnsley, Lester C.; Carugo, Dario; Aron, Miles; Stride, Eleanor

    2017-03-01

    The aim of this study was to characterize the behaviour of superparamagnetic particles in magnetic drug targeting (MDT) schemes. A 3-dimensional mathematical model was developed, based on the analytical derivation of the trajectory of a magnetized particle suspended inside a fluid channel carrying laminar flow and in the vicinity of an external source of magnetic force. Semi-analytical expressions to quantify the proportion of captured particles, and their relative accumulation (concentration) as a function of distance along the wall of the channel were also derived. These were expressed in terms of a non-dimensional ratio of the relevant physical and physiological parameters corresponding to a given MDT protocol. The ability of the analytical model to assess magnetic targeting schemes was tested against numerical simulations of particle trajectories. The semi-analytical expressions were found to provide good first-order approximations for the performance of MDT systems in which the magnetic force is relatively constant over a large spatial range. The numerical model was then used to test the suitability of a range of different designs of permanent magnet assemblies for MDT. The results indicated that magnetic arrays that emit a strong magnetic force that varies rapidly over a confined spatial range are the most suitable for concentrating magnetic particles in a localized region. By comparison, commonly used magnet geometries such as button magnets and linear Halbach arrays result in distributions of accumulated particles that are less efficient for delivery. The trajectories predicted by the numerical model were verified experimentally by acoustically focusing magnetic microbeads flowing in a glass capillary channel, and optically tracking their path past a high field gradient Halbach array.

  8. Chirp-coded excitation imaging with a high-frequency ultrasound annular array.

    Science.gov (United States)

    Mamou, Jonathan; Ketterling, Jeffrey A; Silverman, Ronald H

    2008-02-01

    High-frequency ultrasound (HFU, > 15 MHz) is an effective means of obtaining fine-resolution images of biological tissues for applications such as opthalmologic, dermatologic, and small animal imaging. HFU has two inherent drawbacks. First, HFU images have a limited depth of field (DOF) because of the short wavelength and the low fixed F-number of conventional HFU transducers. Second, HFU can be used to image only a few millimeters deep into a tissue because attenuation increases with frequency. In this study, a five-element annular array was used in conjunction with a synthetic-focusing algorithm to extend the DOF. The annular array had an aperture of 10 mm, a focal length of 31 mm, and a center frequency of 17 MHz. To increase penetration depth, 8-micros, chirp-coded signals were designed, input into an arbitrary waveform generator, and used to excite each array element. After data acquisition, the received signals were linearly filtered to restore axial resolution and increase the SNR. To compare the chirpcoded imaging method with conventional impulse imaging in terms of resolution, a 25-microm diameter wire was scanned and the -6-dB axial and lateral resolutions were computed at depths ranging from 20.5 to 40.5 mm. The results demonstrated that chirp-coded excitation did not degrade axial or lateral resolution. A tissue-mimicking phantom containing 10-microm glass beads was scanned, and backscattered signals were analyzed to evaluate SNR and penetration depth. Finally, ex vivo ophthalmic images were formed and chirpcoded images showed features that were not visible in conventional impulse images.

  9. High density array fabrication and readout method for a fiber optic biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Pinkel, Daniel (Walnut Creek, CA); Gray, Joe (San Francisco, CA)

    1997-01-01

    The invention relates to the fabrication and use of biosensors comprising a plurality of optical fibers each fiber having attached to its "sensor end" biological "binding partners" (molecules that specifically bind other molecules to form a binding complex such as antibody-antigen, lectin-carbohydrate, nucleic acid-nucleic acid, biotin-avidin, etc.). The biosensor preferably bears two or more different species of biological binding partner. The sensor is fabricated by providing a plurality of groups of optical fibers. Each group is treated as a batch to attach a different species of biological binding partner to the sensor ends of the fibers comprising that bundle. Each fiber, or group of fibers within a bundle, may be uniquely identified so that the fibers, or group of fibers, when later combined in an array of different fibers, can be discretely addressed. Fibers or groups of fibers are then selected and discretely separated from different bundles. The discretely separated fibers are then combined at their sensor ends to produce a high density sensor array of fibers capable of assaying simultaneously the binding of components of a test sample to the various binding partners on the different fibers of the sensor array. The transmission ends of the optical fibers are then discretely addressed to detectors--such as a multiplicity of optical sensors. An optical signal, produced by binding of the binding partner to its substrate to form a binding complex, is conducted through the optical fiber or group of fibers to a detector for each discrete test. By examining the addressed transmission ends of fibers, or groups of fibers, the addressed transmission ends can transmit unique patterns assisting in rapid sample identification by the sensor.

  10. High density array fabrication and readout method for a fiber optic biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Pinkel, D.; Gray, J.

    1997-11-25

    The invention relates to the fabrication and use of biosensors comprising a plurality of optical fibers each fiber having attached to its ``sensor end`` biological ``binding partners`` (molecules that specifically bind other molecules to form a binding complex such as antibody-antigen, lectin-carbohydrate, nucleic acid-nucleic acid, biotin-avidin, etc.). The biosensor preferably bears two or more different species of biological binding partner. The sensor is fabricated by providing a plurality of groups of optical fibers. Each group is treated as a batch to attach a different species of biological binding partner to the sensor ends of the fibers comprising that bundle. Each fiber, or group of fibers within a bundle, may be uniquely identified so that the fibers, or group of fibers, when later combined in an array of different fibers, can be discretely addressed. Fibers or groups of fibers are then selected and discretely separated from different bundles. The discretely separated fibers are then combined at their sensor ends to produce a high density sensor array of fibers capable of assaying simultaneously the binding of components of a test sample to the various binding partners on the different fibers of the sensor array. The transmission ends of the optical fibers are then discretely addressed to detectors--such as a multiplicity of optical sensors. An optical signal, produced by binding of the binding partner to its substrate to form a binding complex, is conducted through the optical fiber or group of fibers to a detector for each discrete test. By examining the addressed transmission ends of fibers, or groups of fibers, the addressed transmission ends can transmit unique patterns assisting in rapid sample identification by the sensor. 9 figs.

  11. High density array fabrication and readout method for a fiber optic biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Pinkel, Daniel (Walnut Creek, CA); Gray, Joe (San Francisco, CA); Albertson, Donna G. (Lafayette, CA)

    2002-01-01

    The invention relates to the fabrication and use of biosensors comprising a plurality of optical fibers each fiber having attached to its "sensor end" biological "binding partners" (molecules that specifically bind other molecules to form a binding complex such as antibody-antigen, lectin-carbohydrate, nucleic acid-nucleic acid, biotin-avidin, etc.). The biosensor preferably bears two or more different species of biological binding partner. The sensor is fabricated by providing a plurality of groups of optical fibers. Each group is treated as a batch to attach a different species of biological binding partner to the sensor ends of the fibers comprising that bundle. Each fiber, or group of fibers within a bundle, may be uniquely identified so that the fibers, or group of fibers, when later combined in an array of different fibers, can be discretely addressed. Fibers or groups of fibers are then selected and discretely separated from different bundles. The discretely separated fibers are then combined at their sensor ends to produce a high density sensor array of fibers capable of assaying simultaneously the binding of components of a test sample to the various binding partners on the different fibers of the sensor array. The transmission ends of the optical fibers are then discretely addressed to detectors--such as a multiplicity of optical sensors. An optical signal, produced by binding of the binding partner to its substrate to form a binding complex, is conducted through the optical fiber or group of fibers to a detector for each discrete test. By examining the addressed transmission ends of fibers, or groups of fibers, the addressed transmission ends can transmit unique patterns assisting in rapid sample identification by the sensor.

  12. High density array fabrication and readout method for a fiber optic biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Pinkel, Daniel (Walnut Creek, CA); Gray, Joe (San Francisco, CA); Albertson, Donna G. (Lafayette, CA)

    2000-01-01

    The invention relates to the fabrication and use of biosensors comprising a plurality of optical fibers each fiber having attached to its "sensor end" biological "binding partners" (molecules that specifically bind other molecules to form a binding complex such as antibody-antigen, lectin-carbohydrate, nucleic acid-nucleic acid, biotin-avidin, etc.). The biosensor preferably bears two or more different species of biological binding partner. The sensor is fabricated by providing a plurality of groups of optical fibers. Each group is treated as a batch to attach a different species of biological binding partner to the sensor ends of the fibers comprising that bundle. Each fiber, or group of fibers within a bundle, may be uniquely identified so that the fibers, or group of fibers, when later combined in an array of different fibers, can be discretely addressed. Fibers or groups of fibers are then selected and discretely separated from different bundles. The discretely separated fibers are then combined at their sensor ends to produce a high density sensor array of fibers capable of assaying simultaneously the binding of components of a test sample to the various binding partners on the different fibers of the sensor array. The transmission ends of the optical fibers are then discretely addressed to detectors--such as a multiplicity of optical sensors. An optical signal, produced by binding of the binding partner to its substrate to form a binding complex, is conducted through the optical fiber or group of fibers to a detector for each discrete test. By examining the addressed transmission ends of fibers, or groups of fibers, the addressed transmission ends can transmit unique patterns assisting in rapid sample identification by the sensor.

  13. High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction--universal array approach.

    Science.gov (United States)

    Candela, Marco; Consolandi, Clarissa; Severgnini, Marco; Biagi, Elena; Castiglioni, Bianca; Vitali, Beatrice; De Bellis, Gianluca; Brigidi, Patrizia

    2010-04-19

    Affecting the core functional microbiome, peculiar high level taxonomic unbalances of the human intestinal microbiota have been recently associated with specific diseases, such as obesity, inflammatory bowel diseases, and intestinal inflammation. In order to specifically monitor microbiota unbalances that impact human physiology, here we develop and validate an original DNA-microarray (HTF-Microbi.Array) for the high taxonomic level fingerprint of the human intestinal microbiota. Based on the Ligase Detection Reaction-Universal Array (LDR-UA) approach, the HTF-Microbi.Array enables specific detection and approximate relative quantification of 16S rRNAs from 30 phylogenetically related groups of the human intestinal microbiota. The HTF-Microbi.Array was used in a pilot study of the faecal microbiota of eight young adults. Cluster analysis revealed the good reproducibility of the high level taxonomic microbiota fingerprint obtained for each of the subject. The HTF-Microbi.Array is a fast and sensitive tool for the high taxonomic level fingerprint of the human intestinal microbiota in terms of presence/absence of the principal groups. Moreover, analysis of the relative fluorescence intensity for each probe pair of our LDR-UA platform can provide estimation of the relative abundance of the microbial target groups within each samples. Focusing the phylogenetic resolution at division, order and cluster levels, the HTF-Microbi.Array is blind with respect to the inter-individual variability at the species level.

  14. Facile fabrication, characterization, and enhanced photoelectrocatalytic degradation performance of highly oriented TiO2 nanotube arrays

    Science.gov (United States)

    Zhao, Qidong; Li, Xinyong; Wang, Ning; Hou, Yang; Quan, Xie; Chen, Guohua

    2009-11-01

    Highly ordered TiO2 nanotube arrays were successfully fabricated using ethanol and water mixture electrolytes (40 vol% ethanol and 0.2 wt% hydrofluoric acid) by a facile electrochemical anodization method. The as-prepared nanotube arrays were grown perpendicular to the titanium substrate with about 90 nm in diameter, 20 nm in wall thickness, and around 500 nm in length. The formation mechanism of the samples is briefly discussed. A blue shift in the spectrum of UV-Vis absorption was observed with respect to a piece of the sol-gel derived TiO2 film. Moreover, photocurrent response and photoelectrocatalytic degradation of methyl orange under ultraviolet light irradiation were adopted to evaluate the photoelectrocatalytic properties of the TiO2 nanotube arrays. We demonstrate that the highly ordered TiO2 nanotube arrays possess much better photoelectrocatalytic activity than the sol-gel derived TiO2 film and good stability.

  15. Fabrication and characterization of gold nanocrown arrays on a gold film for a high-sensitivity surface plasmon resonance biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Munsik; Kim, Nak-hyeon; Eom, Seyoung [Department of Biomedical Engineering, Kyung Hee University, Yongin 446-701 (Korea, Republic of); Kim, Tae Woo [School of East–West Medical Science, Kyung Hee University, Yongin 446-701 (Korea, Republic of); Byun, Kyung Min, E-mail: kmbyun@khu.ac.kr [Department of Biomedical Engineering, Kyung Hee University, Yongin 446-701 (Korea, Republic of); Park, Hyeong-Ho, E-mail: hyeongho.park@kanc.re.kr [Nano Process Division, Korea Advanced Nano Fab Center, Suwon 443-270 (Korea, Republic of)

    2015-07-31

    We report on a versatile method to fabricate gold nanocrown arrays on a thin gold film based on ultraviolet nanoimprint lithography and tilted evaporation technique. We realize highly ordered 2-dimensional nanocrown arrays and characterize their sizes and morphologies using scanning electron microscopy. To demonstrate an enhanced surface plasmon resonance (SPR) detection by the fabricated gold nanocrown samples, biosensing experiments are performed by measuring SPR angle shift for biotin–streptavidin interaction and bulk refractive index change of dielectric medium. We hope that the suggested plasmonic platform with a high sensitivity could be extended to a variety of biomolecular binding reactions. - Highlights: • Gold nanocrown arrays are produced by nanoimprint lithography and tilted evaporation. • Use of gold nanocrown arrays can improve the sensor sensitivity significantly. • Improved sensitivity is due to enhanced field–matter interaction at gold nanocrowns.

  16. High-resolution analysis of DNA copy number alterations in rectal cancer. Correlation with metastasis, survival, and mRNA expression

    Energy Technology Data Exchange (ETDEWEB)

    Doyen, Jerome; Gerard, Jean-Pierre [Centre Antoine-Lacassagne, Department of Radiation Oncology, Nice (France); University of Nice Sophia-Antipolis, Nice (France); Letouze, Eric; Marisa, Laetitia; Reynies, Aurelien de [Ligue Nationale Contre Le Cancer, Programme Cartes d' Identite des Tumeurs, Paris (France); Milano, Gerard; Etienne-Grimaldi, Marie-Christine [University of Nice Sophia-Antipolis, Nice (France); Centre Antoine-Lacassagne, Oncopharmacology Unit, Nice (France); Olschwang, Sylviane [INSERM U1068, Marseille (France); Gaedcke, Jochen; Ghadimi, Michael [University Medical Center Goettingen, Department of General and Visceral Surgery, Goettingen (Germany)

    2014-11-15

    This study aimed to determine the candidate genes and chromosomal imbalances capable of predicting occurrences of metastasis in patients with rectal cancer. Fresh frozen tumor tissues from 80 patients with rectal cancer were prospectively collected and analyzed using Affymetrix HG-U133 Plus 2.0 gene expression arrays and high-resolution Illumina single-nucleotide polymorphism (SNP) arrays. Endpoints of the study were metastasis-free survival (MFS) and cancer-specific survival (CSS). The median follow-up was 102 months (1-146). Deletions of 8p and 1p36-35 correlated with worse MFS (p = 0.005 and p = 0.01, respectively) and CSS (p = 0.001 and p = 0.01, respectively). Multivariate analysis identified 8p deletion as an independent prognostic factor for MFS (p = 0.04) and CSS (p = 0.003); 97 genes located on the 8p chromosome were significantly underexpressed in tumors with 8p deletion. This study shows for the first time in rectal cancer an independent correlation of 8p deletion with MFS and CSS and highlights potential new tumor suppressor genes. (orig.) [German] Diese Studie zielt darauf ab, Kandidatengene und chromosomale Ungleichgewichte vorherzusagen und das Auftreten von Metastasen bei Rektumkarzinompatienten zu bestimmen. Frisch gefrorenes Tumorgewebe von 80 Patienten mit Rektumkarzinom wurde prospektiv erfasst und mit Affymetrix-(HG-U133-Plus-2.0)-Genexpressionsarrays und hochaufloesenden Illumina-Single-Nukleotid-Polymorphismus-(SNP-)Arrays analysiert. Endpunkte der Studie waren fernmetastasenfreies Ueberleben (MFU) und krebsspezifisches Ueberleben (KSU). Die mediane Nachbeobachtungszeit betrug 102 Monate (1-146 Monate). Die Deletionen von 8p und 1p36-35 waren mit schlechterem MFU (jeweils p = 0,005 und p = 0,01) und KSU (jeweils p = 0,001 und p = 0,01) korreliert. Die multivariate Analyse identifizierte - 8p als unabhaengigen prognostischen Faktor fuer MFU (p = 0,04) und KSU (p = 0,003). In Tumoren mit einer 8p-Deletion waren 97 Gene auf Chromosom 8p

  17. Utilization of graphene electrode in transparent microwell arrays for high throughput cell trapping and lysis.

    Science.gov (United States)

    Ameri, S Kabiri; Singh, P K; Sonkusale, S

    2014-11-15

    Here we present a high-throughput, transparent microfluidic device with embedded microwell arrays sandwiched between transparent electrodes made from graphene (at the bottom) and indium tin oxide (at the top) for dielectrophoretic cell trapping and electrical lysis. Graphene suppresses unwanted faradaic reaction effects on the cells and the medium that is typically observed in ITO based electrodes from application of DC field for electrical lysis. This is because graphene is more electrochemically inert than indium tin oxide (ITO) where ITO undergoes reduction-oxidation (redox) reaction in the presence of electrolyte in most standard cell media. This redox process also compromises ITO's electrical properties and optical transparency over multiple use. The presented microfluidic device shows high efficiency for cell trapping and lysis and an electrochemically stable behavior for long operational life.

  18. Evaluation of high frequency ghost cavitation emissions for two different seismic air-gun arrays using numerical modelling

    Science.gov (United States)

    Khodabandeloo, Babak; Landrø, Martin

    2017-04-01

    Sound is deployed by marine mammals for variety of vital purposes such as finding food, communication, echolocation, etc. On the other hand human activities generate underwater noise. One major type of acoustic source is marine seismic acquisition which is carried out to image layers beneath the seabed exploiting reflected acoustic and elastic waves. Air-gun arrays are the most common and efficient marine seismic sources. Field measurements using broad band hydrophones have revealed that acoustic energies emitted by air-gun arrays contains frequencies from a few Hz up to tens of kHz. Frequencies below 200 Hz benefit seismic imaging and the rest is normally considered as wasted energy. On the other hand, the high frequency range (above 200 Hz) overlaps with hearing curves of many marine mammals and especially toothed whales and may have an impact on their behavior. A phenomenon called ghost cavitation is recently recognized to be responsible for a major part of these high frequencies (> 5 kHz). Acoustic pressure waves of individual air guns reflected from sea surface can cause the hydrostatic pressure to drop towards zero close to the source array. In these regions there is a high probability for water vapor cavity growth and subsequent collapse. We have simulated ghost cavitation cloud using numerical modelling and the results are validated by comparing with field measurements. The model is used to compare the amount of high frequency noise due to ghost cavitation for two different air gun arrays. Both of the arrays have three subarrays but the array distance for the one with 2730 in3 air volume is 6 meters and for the slightly bigger array (3250 in3 in air volume) the subarrays are separated by 8 meters. Simulation results indicate that the second array, despite larger subarray distance, generates stronger ghost cavitation signal.

  19. A robust penalized method for the analysis of noisy DNA copy number data

    Directory of Open Access Journals (Sweden)

    Huang Jian

    2010-09-01

    Full Text Available Abstract Background Deletions and amplifications of the human genomic DNA copy number are the causes of numerous diseases, such as, various forms of cancer. Therefore, the detection of DNA copy number variations (CNV is important in understanding the genetic basis of many diseases. Various techniques and platforms have been developed for genome-wide analysis of DNA copy number, such as, array-based comparative genomic hybridization (aCGH and high-resolution mapping with high-density tiling oligonucleotide arrays. Since complicated biological and experimental processes are often associated with these platforms, data can be potentially contaminated by outliers. Results We propose a penalized LAD regression model with the adaptive fused lasso penalty for detecting CNV. This method contains robust properties and incorporates both the spatial dependence and sparsity of CNV into the analysis. Our simulation studies and real data analysis indicate that the proposed method can correctly detect the numbers and locations of the true breakpoints while appropriately controlling the false positives. Conclusions The proposed method has three advantages for detecting CNV change points: it contains robustness properties; incorporates both spatial dependence and sparsity; and estimates the true values at each marker accurately.

  20. Bimetallic gold-silver nanoplate array as a highly active SERS substrate for detection of streptavidin/biotin assemblies.

    Science.gov (United States)

    Bi, Liyan; Dong, Jian; Xie, Wei; Lu, Wenbo; Tong, Wei; Tao, Lin; Qian, Weiping

    2013-12-17

    The silver-modified gold nanoplate arrays as bimetallic surface-enhanced Raman scattering (SERS) substrates were optimized for the surface-enhanced Raman detection of streptavidin/biotin monolayer assemblies. The bimetallic gold-silver nanoplate arrays were fabricated by coating silver nanoparticles uniformly on the gold nanoplate arrays. Depending on silver nanoparticle coating, the localized surface plasmon resonance (LSPR) peak of the bimetallic gold-silver nanoplate arrays blue-shifted and broadened significantly. The common probe molecule, Niel Blue A sulfate (NBA) was used for testing the SERS activity of the bimetallic gold-silver nanoplate arrays. The SERS intensity increased with the silver nanoparticle coating, due to a large number of hot spots and nanoparticle interfaces. The platforms were tested against a monolayer of streptavidin functionalized over the bimetallic gold-silver nanoplate arrays showing that good quality spectra could be acquired with a short acquisition time. The supramolecular interaction between streptavidin (strep) and biotin showed subsequent modification of Raman spectra that implied a change of the secondary structure of the host biomolecule. And the detection concentration for biotin by this method was as low as 1.0 nM. The enhanced SERS performance of such bimetallic gold-silver nanoplate arrays could spur further interest in the integration of highly sensitive biosensors for rapid, nondestructive, and quantitative bioanalysis, particularly in microfluidics.

  1. Wafer-Scale High-Throughput Ordered Growth of Vertically Aligned ZnO Nanowire Arrays

    KAUST Repository

    Wei, Yaguang

    2010-09-08

    This article presents an effective approach for patterned growth of vertically aligned ZnO nanowire (NW) arrays with high throughput and low cost at wafer scale without using cleanroom technology. Periodic hole patterns are generated using laser interference lithography on substrates coated with the photoresist SU-8. ZnO NWs are selectively grown through the holes via a low-temperature hydrothermal method without using a catalyst and with a superior control over orientation, location/density, and as-synthesized morphology. The development of textured ZnO seed layers for replacing single crystalline GaN and ZnO substrates extends the large-scale fabrication of vertically aligned ZnO NW arrays on substrates of other materials, such as polymers, Si, and glass. This combined approach demonstrates a novel method of manufacturing large-scale patterned one-dimensional nanostructures on various substrates for applications in energy harvesting, sensing, optoelectronics, and electronic devices. © 2010 American Chemical Society.

  2. MEASURING HIGH-PRECISION ASTROMETRY WITH THE INFRARED ARRAY CAMERA ON THE SPITZER SPACE TELESCOPE

    Energy Technology Data Exchange (ETDEWEB)

    Esplin, T. L.; Luhman, K. L., E-mail: taran.esplin@psu.edu [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States)

    2016-01-15

    The Infrared Array Camera (IRAC) on the Spitzer Space Telescope currently offers the greatest potential for high-precision astrometry of faint mid-IR sources across arcminute-scale fields, which would be especially valuable for measuring parallaxes of cold brown dwarfs in the solar neighborhood and proper motions of obscured members of nearby star-forming regions. To more fully realize IRAC's astrometric capabilities, we have sought to minimize the largest sources of uncertainty in astrometry with its 3.6 and 4.5 μm bands. By comparing different routines that estimate stellar positions, we have found that Point Response Function (PRF) fitting with the Spitzer Science Center's Astronomical Point Source Extractor produces both the smallest systematic errors from varying intra-pixel sensitivity and the greatest precision in measurements of positions. In addition, self-calibration has been used to derive new 7th and 8th order distortion corrections for the 3.6 and 4.5 μm arrays of IRAC, respectively. These corrections are suitable for data throughout the mission of Spitzer when a time-dependent scale factor is applied to the corrections. To illustrate the astrometric accuracy that can be achieved by combining PRF fitting with our new distortion corrections, we have applied them to archival data for a nearby star-forming region, arriving at total astrometric errors of ∼20 and 70 mas at signal to noise ratios of 100 and 10, respectively.

  3. High sensitive photonic crystal multiplexed biosensor array using H0 sandwiched cavities

    Science.gov (United States)

    Arafa, Safia; Bouchemat, Mohamed; Bouchemat, Touraya; Benmerkhi, Ahlem

    2017-03-01

    We theoretically investigate a high sensitive photonic crystal integrated biosensor array structure which is potentially used for label-free multiplexed sensing. The proposed device consists of an array of three sandwiched H0 cavities patterned above silicon on insulator (SOI) substrate; each cavity has been designed for different cavity spacing and different resonant wavelength. Results obtained by performing finite-difference time-domain (FDTD) simulations, indicate that the response of each detection unit shifts independently in terms of refractive index variations. The optimized design makes possible the combination of sensing as a function of location, as well as a function of time in the same platform. A refractive index sensitivity of 520nm/RIU and a quality factor over 104 are both achieved with an accompanied crosstalk of less than -26 dB. In addition, the device presents an improved detection limit (DL) of 1.24.10-6 RIU and a wide measurement range. These features make the designed device a promising element for performing label-free multiplexed detection in monolithic substrate for medical diagnostics and environmental monitoring.

  4. Formation and dissolution of microbubbles on highly-ordered plasmonic nanopillar arrays

    Science.gov (United States)

    Liu, Xiumei; Bao, Lei; Dipalo, Michele; De Angelis, Francesco; Zhang, Xuehua

    2015-01-01

    Bubble formation from plasmonic heating of nanostructures is of great interest in many applications. In this work, we study experimentally the intrinsic effects of the number of three-dimensional plasmonic nanostructures on the dynamics of microbubbles, largely decoupled from the effects of dissolved air. The formation and dissolution of microbubbles is observed on exciting groups of 1, 4, and 9 nanopillars. Our results show that the power threshold for the bubble formation depends on the number density of the nanopillars in highly-ordered arrays. In the degassed water, both the growth rate and the maximal radius of the plasmonic microbubbles increase with an increase of the illuminated pillar number, due to the heat balance between the heat loss across the bubble and the collective heating generated from the nanopillars. Interestingly, our results show that the bubble dissolution is affected by the spatial arrangement of the underlying nanopillars, due to the pinning effect on the bubble boundary. The bubbles on nanopillar arrays dissolve in a jumping mode with step-wise features on the dissolution curves, prior to a smooth dissolution phase for the bubble pinned by a single pillar. The insight from this work may facilitate the design of nanostructures for efficient energy conversion. PMID:26687143

  5. High sensitive photonic crystal multiplexed biosensor array using H0 sandwiched cavities

    Directory of Open Access Journals (Sweden)

    Arafa Safia

    2017-01-01

    Full Text Available We theoretically investigate a high sensitive photonic crystal integrated biosensor array structure which is potentially used for label-free multiplexed sensing. The proposed device consists of an array of three sandwiched H0 cavities patterned above silicon on insulator (SOI substrate; each cavity has been designed for different cavity spacing and different resonant wavelength. Results obtained by performing finite-difference time-domain (FDTD simulations, indicate that the response of each detection unit shifts independently in terms of refractive index variations. The optimized design makes possible the combination of sensing as a function of location, as well as a function of time in the same platform. A refractive index sensitivity of 520nm/RIU and a quality factor over 104 are both achieved with an accompanied crosstalk of less than -26 dB. In addition, the device presents an improved detection limit (DL of 1.24.10-6 RIU and a wide measurement range. These features make the designed device a promising element for performing label-free multiplexed detection in monolithic substrate for medical diagnostics and environmental monitoring.

  6. A new active array MST radar system with enhanced capabilities for high resolution atmospheric observations

    Science.gov (United States)

    Durga rao, Meka; Jayaraman, Achuthan; Patra, Amit; Venkat Ratnam, Madineni; Narayana Rao, T.; Kamaraj, Pandian; Jayaraj, Katta; Kmv, Prasad; Kamal Kumar, J.; Raghavendra, J.; Prasad, T. Rajendra; Thriveni, A.; Yasodha, Polisetti

    2016-07-01

    A new version of the 53-MHz MST Radar, using the 1024 solid state Transmit-Receive Modules (TRM), necessary feeder network, multi-channel receiver and a modified radar controller has been established using the existing antenna array of 1024 crossed Yagis. The new system has been configured for steering the beam on a pulse-to-pulse basis in all 360o azimuth and 20o zenith angle, providing enhanced capability to study the Mesosphere-Stratosphere-Troposphere and Ionosphere. The multi channel receiver system has been designed for Spaced Antenna (SA) and Interferometry/ Iamging applications. The new system has also been configured for radiating in circular polarization for its application in the Ionosphere Incoherent Scatter mode. The new active array MST radar at Very-High-Frequency (53-MHz) located at Gadanki (13.45°N, 79.18°E), a tropical station in India, will be used to enhance the observations of winds, turbulence during the passage of convective events over the radar site as deep convection occurs very often at tropical latitudes. The new configuration with enhanced average power, beam agility with multi-channel experiments will be a potential source for studying middle atmosphere and ionosphere. In this paper, we present the system configuration, new capabilities and the first results obtained using the new version of the MST Radar.

  7. Organic/IR-Semiconductor heterojunctions for low-cost, high temperature IR arrays

    Science.gov (United States)

    Jones, Colin E.

    1992-08-01

    This program evaluated a new technology for producing infrared photo-diodes in HgCdTe and InSb using evaporated organic heterojunctions. High quantum-efficiency IR detectors were demonstrated with the organic process comparable to commercial IR detectors. The organic photodiodes at room temperature were better than commercial detectors. They had lower leakage currents and higher resistance-area products (RoAs). Detector arrays made with the organics can operate at higher temperatures than the current detectors. Initial data at low temperatures were poorer than commercial detectors with lower RoAs and slightly higher 1/f noise. This comparison at low temperature may change with further optimization of the organic process. The organic diode process is very simple, low cost and non-damaging to the HgCdTe or InSb. It involves thermal evaporation of the organic onto the HgCdTe or InSb followed by evaporation of metal contacts through a shadow mask. Phase 1 demonstrated organic/HaCdTe IR detectors with quantum efficiencies similar to commercial devices operating at higher temperatures. The technology is ready for a Phase 2 to further optimize the processing for IR arrays and to increase yields.

  8. The Cherenkov Telescope Array: Exploring the Very-high-energy Sky from ESO's Paranal Site

    Science.gov (United States)

    Hofmann, W.

    2017-06-01

    The Cherenkov Telescope Array (CTA) is a next-generation observatory for ground-based very-high-energy gamma-ray astronomy, using the imaging atmospheric Cherenkov technique to detect and reconstruct gamma-ray induced air showers. The CTA project is planning to deploy 19 telescopes on its northern La Palma site, and 99 telescopes on its southern site at Paranal, covering the 20 GeV to 300 TeV energy domain and offering vastly improved performance compared to currently operating Cherenkov telescopes. The combination of three different telescope sizes (23-, 12- and 4-metre) allows cost-effective coverage of the wide energy range. CTA will be operated as a user facility, dividing observation time between a guest observer programme and large Key Science Projects (KSPs), and the data will be made public after a one-year proprietary period. The history of the project, the implementation of the arrays, and some of the major science goals and KSPs, are briefly summarised.

  9. Measuring High-Precision Astrometry with the Infrared Array Camera on the Spitzer Space Telescope

    CERN Document Server

    Esplin, T L

    2015-01-01

    The Infrared Array Camera (IRAC) on the Spitzer Space Telescope currently offers the greatest potential for high-precision astrometry of faint mid-IR sources across arcminute-scale fields, which would be especially valuable for measuring parallaxes of cold brown dwarfs in the solar neighborhood and proper motions of obscured members of nearby star-forming regions. To more fully realize IRAC's astrometric capabilities, we have sought to minimize the largest sources of uncertainty in astrometry with its 3.6 and 4.5 $\\mu$m bands. By comparing different routines that estimate stellar positions, we have found that Point Response Function (PRF) fitting with the Spitzer Science Center's Astronomical Point Source Extractor produces both the smallest systematic errors from varying intra-pixel sensitivity and the greatest precision in measurements of positions. In addition, self-calibration has been used to derive new 7$^{\\rm th}$ and 8$^{\\rm th}$ order distortion corrections for the 3.6 and 4.5 $\\mu$m arrays of IRAC, ...

  10. Optical investigations of high pressure glow discharges based on MSE arrays

    Energy Technology Data Exchange (ETDEWEB)

    Penache, C.; Hohn, O.; Schmidt-Boecking, H. [Frankfurt Univ. (Germany); Spielberger, L. [Deutsche Gesellschaft fuer Technische Zusammenarbeit GmbH (GTZ), Eschborn (Germany); Braeuning-Demian, A.; Penache, D. [Gesellschaft fuer Schwerionenforschung mbH, Darmstadt (Germany)

    2001-07-01

    The micro-structure-electrode (MSE) arrays are providing a non-thermal high pressure plasma. These arrays consist of a matrix of holes perforated in a thin multilayer made out of two metallic foils separated by a dielectric. The holes diameter and the thickness of the insulator spacer need to be around 100 {mu}m to allow for the MSE operation at pressure ranging from 0.1 to 1 bar and above. In this work single direct current microdischarges and systems of parallel operated holes in argon at 0.2 bar have been optically investigated. The spatial distribution of the emitted light has been monitored by a digital camera connected to an optical microscope. The UV photon emission has been recorded by a position sensitive photon detector allowing for space and time resolved measurements. Its time resolution of about 1 nsec makes possible the investigation of fast processes, e.g. the constriction of the discharge. Due to its typical position resolution of 100 {mu}m, this detector needs to be used in combination with an optical system allowing for the magnification of the discharge area. The optical appearance show a stable, volume filling glow discharge, fact proved also by the typical current-voltage characteristic.

  11. High-density flexible interconnect for two-dimensional ultrasound arrays.

    Science.gov (United States)

    Fiering, J O; Hultman, P; Lee, W; Light, E D; Smith, S W

    2000-01-01

    We present a method for fabricating flexible multilayer circuits for interconnection to 2-D array ultrasound transducers. In addition, we describe four 2-D arrays in which such flexible interconnect is implemented, including transthoracic arrays with 438 channels operating at up to 7 MHz and intracardiac catheter arrays with 70 channels operating at up to 7 MHz. We employ thin and thick film microfabrication techniques to batch produce the interconnect circuits with minimum dimensions of 12-mum lines, 40-mum vias, and 150-mum array pitch. The arrays show 50-Omega insertion loss of -60 to -84 dB and a fractional bandwidth of 27 to 67%. The arrays are used to obtain real time, in vivo volumetric scans.

  12. SNP Array in Hematopoietic Neoplasms: A Review

    Directory of Open Access Journals (Sweden)

    Jinming Song

    2015-12-01

    Full Text Available Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH studies. Single nucleotide polymorphism (SNP arrays offer high-resolution identification of copy number variants (CNVs and acquired copy-neutral loss of heterozygosity (LOH/uniparental disomy (UPD that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.

  13. High-throughput genotyping of copy number variation in glutathione S-transferases M1 and T1 using real-time PCR in 20,687 individuals

    DEFF Research Database (Denmark)

    Norskov, M.S.; Frikke-Schmidt, R.; Loft, S.;

    2009-01-01

    OBJECTIVES: Characteristic for the genes encoding glutathione S-transferase (GST) M1 and GSTT1 is a null allele, suggested to increase susceptibility to chronic diseases. We report an optimized method for the determination of copy number variation (CNV) in GST genes. DESIGN AND METHODS: Real-time...

  14. High copy number variation of cancer-related microRNA genes and frequent amplification of DICER1 and DROSHA in lung cancer

    Science.gov (United States)

    Czubak, Karol; Lewandowska, Marzena Anna; Klonowska, Katarzyna; Roszkowski, Krzysztof; Kowalewski, Janusz; Figlerowicz, Marek; Kozlowski, Piotr

    2015-01-01

    A growing body of evidence indicates that miRNAs may be a class of genetic elements that can either drive or suppress oncogenesis. In this study we analyzed the somatic copy number variation of 14 miRNA genes frequently found to be either over- or underexpressed in lung cancer, as well as two miRNA biogenesis genes, DICER1 and DROSHA, in non-small-cell lung cancer (NSCLC). Our analysis showed that most analyzed miRNA genes undergo substantial copy number alteration in lung cancer. The most frequently amplified miRNA genes include the following: miR-30d, miR-21, miR-17 and miR-155. We also showed that both DICER1 and DROSHA are frequently amplified in NSCLC. The copy number variation of DICER1 and DROSHA correlates well with their expression and survival of NSCLC and other cancer patients. The increased expression of DROSHA and DICER1 decreases and increases the survival, respectively. In conclusion, our results show that copy number variation may be an important mechanism of upregulation/downregulation of miRNAs in cancer and suggest an oncogenic role for DROSHA. PMID:26156018

  15. Navigating Earthquake Physics with High-Resolution Array Back-Projection

    Science.gov (United States)

    Meng, Lingsen

    Understanding earthquake source dynamics is a fundamental goal of geophysics. Progress toward this goal has been slow due to the gap between state-of-art earthquake simulations and the limited source imaging techniques based on conventional low-frequency finite fault inversions. Seismic array processing is an alternative source imaging technique that employs the higher frequency content of the earthquakes and provides finer detail of the source process with few prior assumptions. While the back-projection provides key observations of previous large earthquakes, the standard beamforming back-projection suffers from low resolution and severe artifacts. This thesis introduces the MUSIC technique, a high-resolution array processing method that aims to narrow the gap between the seismic observations and earthquake simulations. The MUSIC is a high-resolution method taking advantage of the higher order signal statistics. The method has not been widely used in seismology yet because of the nonstationary and incoherent nature of the seismic signal. We adapt MUSIC to transient seismic signal by incorporating the Multitaper cross-spectrum estimates. We also adopt a "reference window" strategy that mitigates the "swimming artifact," a systematic drift effect in back projection. The improved MUSIC back projections allow the imaging of recent large earthquakes in finer details which give rise to new perspectives on dynamic simulations. In the 2011 Tohoku-Oki earthquake, we observe frequency-dependent rupture behaviors which relate to the material variation along the dip of the subduction interface. In the 2012 off-Sumatra earthquake, we image the complicated ruptures involving orthogonal fault system and an usual branching direction. This result along with our complementary dynamic simulations probes the pressure-insensitive strength of the deep oceanic lithosphere. In another example, back projection is applied to the 2010 M7 Haiti earthquake recorded at regional distance. The

  16. THE MINIMUM WIDTH OF THE ARRIVAL DIRECTION DISTRIBUTION OF ULTRA-HIGH-ENERGY COSMIC RAYS DETECTED WITH THE YAKUTSK ARRAY

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, A. A., E-mail: ivanov@ikfia.ysn.ru [Shafer Institute for Cosmophysical Research and Aeronomy, 31 Lenin Avenue, Yakutsk 677980 (Russian Federation)

    2015-05-10

    This paper presents the results of searches for anisotropy in the arrival directions of ultra-high-energy cosmic rays (CRs) detected with the Yakutsk Array during the 1974–2008 observational period as well as searches in available data from other giant extensive air shower arrays working at present. A method of analysis based on a comparison of the minimum width of distributions in equatorial coordinates is used. As a result, a hypothesis of isotropy in arrival directions is rejected at the 99.5% significance level. The observed decrease in the minimum width of the distribution can be explained by the presence of CR sources in energy intervals and sky regions according to recent indications inferred from data of the Yakutsk Array and Telescope Array experiments.

  17. A minimal width of the arrival direction distribution of ultra-high energy cosmic rays detected with the Yakutsk array

    CERN Document Server

    Ivanov, A A

    2015-01-01

    This paper presents the results of searches for anisotropy in arrival directions of ultra-high energy cosmic rays detected with the Yakutsk Array during the 1974--2008 observational period together with available data from other giant extensive air shower arrays working at present. A method of analysis based on a comparison of the minimal width of distributions in equatorial coordinates is applied. As a result, a hypothesis of isotropy in arrival directions is rejected at the $99.5\\%$ significance level. The observed decrease in the minimal width of distribution can be explained by the presence of cosmic ray sources in energy intervals and sky regions according to the recent indications inferred from data of the Yakutsk Array and Telescope Array experiments.

  18. Microbowl-arrayed surface generated by EBL of negative-tone SU-8 for highly adhesive hydrophobicity

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiangmeng, E-mail: xiangmengli2010@stu.xjtu.edu.cn; Shao, Jinyou, E-mail: jyshao@mail.xjtu.edu.cn; Ding, Yucheng, E-mail: ycding@mail.xjtu.edu.cn; Tian, Hongmiao, E-mail: tian.hongmiao@stu.xjtu.edu.cn

    2014-07-01

    A unique microbowl-arrayed surface demonstrates highly adhesive hydrophobicity similar to a rose-petal. Such a textured surface is generated by electron beam lithography on negative-tone SU-8 resist with X–Y cross-lines scanning. The microbowl array patterned surface possesses an advancing contact angle of 160° and a contact angle hysteresis of 90°, and it is capable of holding a 50 μl aqueous droplet as positioned perpendicularly. The wetting properties of adhesive hydrophobicity can be tuned by varying the exposure dosage in EBL as well as the thickness of the fluorocarbon deposition, both of which can change the curvature of microbowl array with submicron-ridges. Therefore, the contact state on such microbowl-arrayed surfaces can be varied from Cassie–Baxter's to Wenzel's model.

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

    Directory of Open Access Journals (Sweden)

    Qiu-jiong Zhao

    2016-01-01

    Full Text Available 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.

  20. Robust Adaptable Video Copy Detection

    DEFF Research Database (Denmark)

    Assent, Ira; Kremer, Hardy

    2009-01-01

    Video copy detection should be capable of identifying video copies subject to alterations e.g. in video contrast or frame rates. We propose a video copy detection scheme that allows for adaptable detection of videos that are altered temporally (e.g. frame rate change) and/or visually (e.g. change...... in contrast). Our query processing combines filtering and indexing structures for efficient multistep computation of video copies under this model. We show that our model successfully identifies altered video copies and does so more reliably than existing models....

  1. Robust Adaptable Video Copy Detection

    DEFF Research Database (Denmark)

    Assent, Ira; Kremer, Hardy

    2009-01-01

    Video copy detection should be capable of identifying video copies subject to alterations e.g. in video contrast or frame rates. We propose a video copy detection scheme that allows for adaptable detection of videos that are altered temporally (e.g. frame rate change) and/or visually (e.g. change...... in contrast). Our query processing combines filtering and indexing structures for efficient multistep computation of video copies under this model. We show that our model successfully identifies altered video copies and does so more reliably than existing models....

  2. Three-dimensional nanotube electrode arrays for hierarchical tubular structured high-performance pseudocapacitors

    Science.gov (United States)

    Gao, Yuan; Lin, Yuanjing; Chen, Jiaqi; Lin, Qingfeng; Wu, Yue; Su, Wenjun; Wang, Wenli; Fan, Zhiyong

    2016-07-01

    Ordered three-dimensional (3-D) tubular arrays are highly attractive candidates for high performance pseudocapacitor electrodes. Here, we report 3-D fluorine doped tin oxide (FTO) tubular arrays fabricated by a cost-effective ultrasonic spray pyrolysis (USP) method in anodic aluminum oxide (AAO) channels with high uniformity. The large surface area of such a structure leads to remarkable surface area enhancement up to 51.8 times compared to a planar structure. Combining with electrochemically deposited manganese dioxide (MnO2) nanoflakes on the inner side wall of the FTO nanotubes, the unique hierarchical tubular structured pseudocapacitor electrode demonstrated the highest areal capacitance of 193.8 mF cm-2 at the scan rate of 5 mV s-1 and 184 mF cm-2 at the discharge current density of 0.6 mA cm-2, which is 18.5 times that of a planar electrode. And it also showed a volumetric capacitance of 112.6 F cm-3 at the scan rate of 5 mV s-1 and 108.8 F cm-3 at the discharge current density of 0.6 mA cm-2. In addition, the cyclic stability test also indicated that a nanostructured pseudocapacitive electrode has a much larger capacitance retention after 3000 cycles of the charge-discharge process compared with a planar electrode, primarily due to the mechanical stability of the nanostructure. Moreover, pseudocapacitor device fabrication based on such electrodes shows the volumetric capacitance of 17.5 F cm-3, and the highest specific energy of 1.56 × 10-3 Wh cm-3. With the merit of facile fabrication procedures and largely enhanced electrochemical performance, such a 3-D structure has high potency for energy storage systems for a wide range of practical applications.Ordered three-dimensional (3-D) tubular arrays are highly attractive candidates for high performance pseudocapacitor electrodes. Here, we report 3-D fluorine doped tin oxide (FTO) tubular arrays fabricated by a cost-effective ultrasonic spray pyrolysis (USP) method in anodic aluminum oxide (AAO) channels with

  3. Fabrication of ordered NiO coated Si nanowire array films as electrodes for a high performance lithium ion battery.

    Science.gov (United States)

    Qiu, M C; Yang, L W; Qi, X; Li, Jun; Zhong, J X

    2010-12-01

    Highly ordered NiO coated Si nanowire array films are fabricated as electrodes for a high performance lithium ion battery via depositing Ni on electroless-etched Si nanowires and subsequently annealing. The structures and morphologies of as-prepared films are characterized by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. When the potential window versus lithium was controlled, the coated NiO can be selected to be electrochemically active to store and release Li+ ions, while highly conductive crystalline Si cores function as nothing more than a stable mechanical support and an efficient electrical conducting pathway. The hybrid nanowire array films exhibit superior cyclic stability and reversible capacity compared to that of NiO nanostructured films. Owing to the ease of large-scale fabrication and superior electrochemical performance, these hybrid nanowire array films will be promising anode materials for high performance lithium-ion batteries.

  4. High Sensitivity Terahertz Detection through Large-Area Plasmonic Nano-Antenna Arrays

    Science.gov (United States)

    Yardimci, Nezih Tolga; Jarrahi, Mona

    2017-01-01

    Plasmonic photoconductive antennas have great promise for increasing responsivity and detection sensitivity of conventional photoconductive detectors in time-domain terahertz imaging and spectroscopy systems. However, operation bandwidth of previously demonstrated plasmonic photoconductive antennas has been limited by bandwidth constraints of their antennas and photoconductor parasitics. Here, we present a powerful technique for realizing broadband terahertz detectors through large-area plasmonic photoconductive nano-antenna arrays. A key novelty that makes the presented terahertz detector superior to the state-of-the art is a specific large-area device geometry that offers a strong interaction between the incident terahertz beam and optical pump at the nanoscale, while maintaining a broad operation bandwidth. The large device active area allows robust operation against optical and terahertz beam misalignments. We demonstrate broadband terahertz detection with signal-to-noise ratio levels as high as 107 dB. PMID:28205615

  5. Improved high-fidelity transport of trapped-ion qubits through a multi-dimensional array

    CERN Document Server

    Blakestad, R B; VanDevender, A P; Wesenberg, J H; Biercuk, M J; Leibfried, D; Wineland, D J

    2011-01-01

    We have demonstrated transport of Be+ ions through a 2D Paul-trap array that incorporates an X-junction, while maintaining the ions near the motional ground-state of the confining potential well. We expand on the first report of the experiment [1], including a detailed discussion of how the transport potentials were calculated. Two main mechanisms that caused motional excitation during transport are explained, along with the methods used to mitigate such excitation. We reduced the motional excitation below the results in Ref. [1] by a factor of approximately 50. The effect of a mu-metal shield on qubit coherence is also reported. Finally, we examined a method for exchanging energy between multiple motional modes on the few-quanta level, which could be useful for cooling motional modes without directly accessing the modes with lasers. These results establish how trapped ions can be transported in a large-scale quantum processor with high fidelity.

  6. High Sensitivity Terahertz Detection through Large-Area Plasmonic Nano-Antenna Arrays

    Science.gov (United States)

    Yardimci, Nezih Tolga; Jarrahi, Mona

    2017-02-01

    Plasmonic photoconductive antennas have great promise for increasing responsivity and detection sensitivity of conventional photoconductive detectors in time-domain terahertz imaging and spectroscopy systems. However, operation bandwidth of previously demonstrated plasmonic photoconductive antennas has been limited by bandwidth constraints of their antennas and photoconductor parasitics. Here, we present a powerful technique for realizing broadband terahertz detectors through large-area plasmonic photoconductive nano-antenna arrays. A key novelty that makes the presented terahertz detector superior to the state-of-the art is a specific large-area device geometry that offers a strong interaction between the incident terahertz beam and optical pump at the nanoscale, while maintaining a broad operation bandwidth. The large device active area allows robust operation against optical and terahertz beam misalignments. We demonstrate broadband terahertz detection with signal-to-noise ratio levels as high as 107 dB.

  7. Determination of acaricides in honey by high-performance liquid chromatography with photodiode array detection.

    Science.gov (United States)

    Martel, Anne-Claire; Zeggane, Sarah

    2002-04-19

    Rapid analytical methods are described to control quality of honeys, concerning residues of acaricides applied in hives to prevent Varroa jacobsoni infestation. A liquid-liquid extraction with hexane-propanol-2-ammonia (60 ml:30 ml:0.28%) was used for the simultaneous analysis of coumaphos, bromopropylate, amitraz and fluvalinate. For thymol, one clean up on a solid-phase extraction C18 (500 mg, 6 ml) column was performed; for rotenone, a liquid extraction with dichloromethane was realised. Quantitative recoveries obtained with honey were satisfactory and were superior to 80%. All acaricides are identified by reversed-phase high-performance liquid chromatography with photodiode array detection. Quantification limits obtained were below maximal residue limits when these exist.

  8. The Effect of Mutual Coupling on a High Altitude Platform Diversity System Using Compact Antenna Arrays

    Directory of Open Access Journals (Sweden)

    Tommy Hult

    2010-01-01

    Full Text Available We analyze the destructive effects of mutual coupling and spatial correlation between the separate antenna elements on a combined diversity system consisting of multiple HAPs (High-Altitude Platforms employing various compact MIMO (Multiple-Input Multiple-Output antenna array configurations, in order to enhance the mutual information in HAP communication links. In addition, we assess the influence of the separation angle between HAPs on system performance, and determine the optimal separation angles that maximize the total mutual information of the system for various compact MIMO antennas. Simulation results show that although the mutual information is degraded by mutual coupling and spatial correlation, the proposed HAP diversity system still provides better performance compared to a nondiversity system for all tested scenarios.

  9. Identifying firing mammalian neurons in networks with high-resolution multi-transistor array (MTA)

    Science.gov (United States)

    Lambacher, A.; Vitzthum, V.; Zeitler, R.; Eickenscheidt, M.; Eversmann, B.; Thewes, R.; Fromherz, P.

    2011-01-01

    The electrical activity of a network of mammalian neurons is mapped with a Multi-Transistor Array (MTA) fabricated with extended CMOS technology. The spatial resolution is 7.4 μm on an area of 1 mm2 at a sampling frequency of 6 kHz for a complete readout of 16,384 sensor transistors. Action potentials give rise to extracellular voltages with amplitudes in a range of 500 μV. On the basis of the high resolution in space and time, correlation algorithms are used to identify single action potentials with amplitudes as low as about 200μV, and to assign the signals to the activity of individual neurons even in a dense network.

  10. Micro mirror arrays as high-resolution spatial light modulators for photoactivation and optogenetics

    Science.gov (United States)

    Rückerl, F.; Kielhorn, Martin; Tinevez, J.-Y.; Heber, J.; Heintzmann, R.; Shorte, S.

    2013-03-01

    The ability to control the illumination and imaging paths of optical microscopes is an essential part of advanced fluorescence microscopy, and a powerful tool for optogenetics. In order to maximize the visualization and the image quality of the objects under observation we use programmable, fast Micro Mirror Arrays (MMAs) as high-resolution Spatial Light Modulators (SLMs). Using two 256x256 MMAs in a mirror-based illumination setup allows for fast angular-spatial control at a wide range of wavelengths (300-1000nm). Additionally, the illumination intensity can be controlled at 10-bit resolution. The setup allows selective illumination of subcellular regions of interest enabling the precise, localized activation of fluorescent probes and the activation and deactivation of subcellular and cellular signaling cascades using photo-activated ion-channels. Furthermore, inasmuch as phototoxicity is dependent on the rate of photo illumination [1] we show that our system, which provides fast, compartmentalized illumination is minimally phototoxic.

  11. High-performance timing electronics for single photon avalanche diode arrays

    Science.gov (United States)

    Acconcia, G.; Crotti, M.; Rech, I.; Ghioni, M.

    2015-05-01

    Time correlated photon counting techniques have been proved to be very effective, especially when very fast and faint optical signals have to be recorded with extremely high precision. Nowadays, a steadily increasing number of applications require not only high performance in terms of photon detection efficiency, time resolution and linearity but also a high number of pixels operating in parallel. In order to combine the features of the most performing detectors and state of art timing electronics, an innovative architecture has been conceived and the main circuits have been designed. The system will employ dense arrays of custom technology Single Photon Avalanche Diode (SPAD) detectors, in order to perform a truly concurrent analysis of the sample, while it will have only a small number of acquisition chains with the ultimate purpose of obtaining very high performance while limiting area occupation and power dissipation. To this aim, three main circuits have been designed: first of all, a pick-up circuit capable of directly reading the signal coming from the sensor; secondly, a timing circuit to measure the arrival time of the each photon with picoseconds resolution and very high linearity and finally, a circuit to perform a dynamic binding between the many sensors and the few conversion chains.

  12. Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468

    Directory of Open Access Journals (Sweden)

    Andreas Antje

    2010-03-01

    Full Text Available Abstract Background Increased transcription of oncogenes like the epidermal growth factor receptor (EGFR is frequently caused by amplification of the whole gene or at least of regulatory sequences. Aim of this study was to pinpoint mechanistic parameters occurring during egfr copy number gains leading to a stable EGFR overexpression and high sensitivity to extracellular signalling. A deeper understanding of those marker events might improve early diagnosis of cancer in suspect lesions, early detection of cancer progression and the prediction of egfr targeted therapies. Methods The basal-like/stemness type breast cancer cell line subpopulation MDA-MB-468 CD44high/CD24-/low, carrying high egfr amplifications, was chosen as a model system in this study. Subclones of the heterogeneous cell line expressing low and high EGF receptor densities were isolated by cell sorting. Genomic profiling was carried out for these by means of SNP array profiling, qPCR and FISH. Cell cycle analysis was performed using the BrdU quenching technique. Results Low and high EGFR expressing MDA-MB-468 CD44+/CD24-/low subpopulations separated by cell sorting showed intermediate and high copy numbers of egfr, respectively. However, during cell culture an increase solely for egfr gene copy numbers in the intermediate subpopulation occurred. This shift was based on the formation of new cells which regained egfr gene copies. By two parametric cell cycle analysis clonal effects mediated through growth advantage of cells bearing higher egfr gene copy numbers could most likely be excluded for being the driving force. Subsequently, the detection of a fragile site distal to the egfr gene, sustaining uncapped telomere-less chromosomal ends, the ladder-like structure of the intrachromosomal egfr amplification and a broader range of egfr copy numbers support the assumption that dynamic chromosomal rearrangements, like breakage-fusion-bridge-cycles other than proliferation drive the gain

  13. High-Power Amplifier Compatible Internally Sensed Optical Phased Array for Space Debris Tracking and Maneuvering

    Science.gov (United States)

    Roberts, L.; Francis, S.; Sibley, P.; Ward, R.; Smith, C.; McClelland, D.; Shaddock, D.

    2016-09-01

    Optical phased arrays (OPAs) provide a way to scale optical power beyond the capabilities of conventional CW lasers via coherent beam combination. By stabilising the relative output phase of multiple spatially separate lasers, OPAs form a coherent optical wavefront in the far field. Since the phase of each laser can be controlled independently, OPAs also have the ability to manipulate the distribution of optical power in the far field, and therefore may provide the capability to compensate for atmospheric turbulence. Combined with their inherent scalability and high power handling capabilities, OPAs are a promising technology for CW space debris ranging and manoeuvring. The OPA presented here is unique in its ability to sense the phase of each laser internally, without requiring any external sampling optics between it and the telescope. This allows the internally sensed OPA to be constructed entirely within fibre, utilising high-power fiber amplifiers to scale optical power beyond the limits of any conventional single lasers. The total power that can be delivered by each emitter in the OPA is limited only by the onset of stimulated Brillouin scattering, a non-linear effect that clamps the amount of power that can be delivered through a fiber waveguide. A three element internally sensed OPA developed at the Australian National University has been demonstrated to coherently combine three commercial 15 Watt fiber amplifiers with an output phase stability of one 200th of a wavelength. We have also demonstrated the ability to dynamically manipulate the distribution of optical power in the far-field at a bandwidth of up to 10 kHz. Since the OPA's control system is implemented using field-programmable gate-array technology, the system may be scaled beyond 100 emitters, potentially reaching the kilowatt level optical powers required to perturb the orbit of space debris.

  14. High-speed X-ray imaging pixel array detector for synchrotron bunch isolation

    Energy Technology Data Exchange (ETDEWEB)

    Philipp, Hugh T., E-mail: htp2@cornell.edu; Tate, Mark W.; Purohit, Prafull; Shanks, Katherine S.; Weiss, Joel T. [Cornell University, Ithaca, NY 14853 (United States); Gruner, Sol M. [Cornell University, Ithaca, NY 14853 (United States); Cornell University, Ithaca, NY 14853 (United States)

    2016-01-28

    A high-speed pixel array detector for time-resolved X-ray imaging at synchrotrons has been developed. The ability to isolate single synchrotron bunches makes it ideal for time-resolved dynamical studies. A wide-dynamic-range imaging X-ray detector designed for recording successive frames at rates up to 10 MHz is described. X-ray imaging with frame rates of up to 6.5 MHz have been experimentally verified. The pixel design allows for up to 8–12 frames to be stored internally at high speed before readout, which occurs at a 1 kHz frame rate. An additional mode of operation allows the integration capacitors to be re-addressed repeatedly before readout which can enhance the signal-to-noise ratio of cyclical processes. This detector, along with modern storage ring sources which provide short (10–100 ps) and intense X-ray pulses at megahertz rates, opens new avenues for the study of rapid structural changes in materials. The detector consists of hybridized modules, each of which is comprised of a 500 µm-thick silicon X-ray sensor solder bump-bonded, pixel by pixel, to an application-specific integrated circuit. The format of each module is 128 × 128 pixels with a pixel pitch of 150 µm. In the prototype detector described here, the three-side buttable modules are tiled in a 3 × 2 array with a full format of 256 × 384 pixels. The characteristics, operation, testing and application of the detector are detailed.

  15. Fabrication of micro-pin array with high aspect ratio on stainless steel using nanosecond laser beam machining

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Se Won [School of Mechanical and Aerospace Engineering, Seoul National University, Gwanak 599 Gwanak-ro, Gwanak-Gu, Seoul, 151-744 (Korea, Republic of); Shin, Hong Shik, E-mail: shinhs05@ut.ac.kr [Department of Energy System Engineering, Korea National University of Transportation, Chungju, Chungbuk, 380-702 (Korea, Republic of); Chu, Chong Nam [School of Mechanical and Aerospace Engineering, Seoul National University, Gwanak 599 Gwanak-ro, Gwanak-Gu, Seoul, 151-744 (Korea, Republic of)

    2013-01-01

    Highlights: Black-Right-Pointing-Pointer A high aspect ratio micro-pin array was fabricated by laser beam machining using the piling of a recast layer. Black-Right-Pointing-Pointer The recast layer could be piled due to the chromium oxide with high surface tension and viscosity of chromium oxide. Black-Right-Pointing-Pointer The machining characteristics for a high aspect ratio micro-pin array were investigated according to laser beam parameters. Black-Right-Pointing-Pointer Experiments for attaching force relative to the surface roughness of the subject plane were carried out. Black-Right-Pointing-Pointer The developed micro-pin array was successfully attached to vertical wall. - Abstract: In this paper, a micro-pin array with a high aspect ratio was fabricated on AISI 304 using laser beam ablation for attachment to a vertical wall. In recent times, there has been research in various fields, including robotics and bio-MEMS, regarding attachment to vertical walls, and micro-pin arrays may offer the best solution. For vertical wall attachment, the micro-pin should have a high aspect ratio, long length, and sharp tip. The recast layer could be piled due to the chromium oxide with high surface tension and viscosity of chromium oxide, and it composed the micro-pins with high aspect ratio. X-ray photoelectron spectroscopy (XPS) was used to identify the characteristics of the piled recast layer. The machining characteristics for a high aspect ratio micro-pin array were investigated according to laser beam machining parameters. In addition, experiments for attaching force relative to the surface roughness of the subject plane were carried out.

  16. Highly informative single-copy nuclear microsatellite DNA markers developed using an AFLP-SSR approach in black spruce (Picea mariana and red spruce (P. rubens.

    Directory of Open Access Journals (Sweden)

    Yong-Zhong Shi

    Full Text Available Microsatellites or simple sequence repeats (SSRs are highly informative molecular markers for various biological studies in plants. In spruce (Picea and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana and red spruce (Picea rubens using a simple but efficient method based on a combination of AFLP and microsatellite technologies.A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67 in black spruce and from 0.161 to 0.851 (mean = 0.62 in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies.The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for

  17. Core-shell diode array for high performance particle detectors and imaging sensors: status of the development

    Science.gov (United States)

    Jia, G.; Hübner, U.; Dellith, J.; Dellith, A.; Stolz, R.; Plentz, J.; Andrä, G.

    2017-02-01

    We propose a novel high performance radiation detector and imaging sensor by a ground-breaking core-shell diode array design. This novel core-shell diode array are expected to have superior performance respect to ultrahigh radiation hardness, high sensitivity, low power consumption, fast signal response and high spatial resolution simultaneously. These properties are highly desired in fundamental research such as high energy physics (HEP) at CERN, astronomy and future x-ray based protein crystallography at x-ray free electron laser (XFEL) etc.. This kind of detectors will provide solutions for these fundamental research fields currently limited by instrumentations. In this work, we report our progress on the development of core-shell diode array for the applications as high performance imaging sensors and particle detectors. We mainly present our results in the preparation of high aspect ratio regular silicon rods by metal assisted wet chemical etching technique. Nearly 200 μm deep and 2 μm width channels with high aspect ratio have been etched into silicon. This result will open many applications not only for the core-shell diode array, but also for a high density integration of 3D microelectronics devices.

  18. Spectrally narrowed external-cavity high-power stack of laser diode arrays.

    Science.gov (United States)

    Zhu, H; Ruset, I C; Hersman, F W

    2005-06-01

    We describe an effective external cavity for narrowing the spectral linewidth of a multiarray stack of laser diode arrays. For a commercially available 279-W free-running five-array laser diode array operating at 60 A, we narrow the spectral linewidth to 0.40 nm at FWHM with 115 W of cw power output. This technique leads to the possibility of higher-efficiency, lower-cost production of hyperpolarized noble gases for magnetic resonance imaging.

  19. Nuclear structure at high spin using multidetector gamma array and ancillary detectors

    Indian Academy of Sciences (India)

    S Muralithar

    2014-04-01

    A multidetector gamma array (GDA), for studying nuclear structure was built with ancillary devices namely gamma multiplicity filter and charged particle detector array. This facility was designed for in-beam gamma spectroscopy measurements in fusion evaporation reactions at Inter-University Accelerator Centre, New Delhi. Description of the facility and in-beam performance with two experimental studies done are presented. This array was used in a number of nuclear spectroscopic and reaction investigations.

  20. Identifying single copy orthologs in Metazoa.

    Directory of Open Access Journals (Sweden)

    Christopher J Creevey

    2011-12-01

    Full Text Available The identification of single copy (1-to-1 orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene.Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence.To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis to 99.8% (human with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.

  1. High Dynamic Range adaptive ΔΣ-based Focal Plane Array architecture

    KAUST Repository

    Yao, Shun

    2012-10-16

    In this paper, an Adaptive Delta-Sigma based architecture for High Dynamic Range (HDR) Focal Plane Arrays is presented. The noise shaping effect of the Delta-Sigma modulation in the low end, and the distortion noise induced in the high end of Photo-diode current were analyzed in detail. The proposed architecture can extend the DR for about 20N log2 dB at the high end of Photo-diode current with an N bit Up-Down counter. At the low end, it can compensate for the larger readout noise by employing Extended Counting. The Adaptive Delta-Sigma architecture employing a 4-bit Up-Down counter achieved about 160dB in the DR, with a Peak SNR (PSNR) of 80dB at the high end. Compared to the other HDR architectures, the Adaptive Delta-Sigma based architecture provides the widest DR with the best SNR performance in the extended range.

  2. High-Performance MWIR HgCdTe on Si Substrate Focal Plane Array Development

    Science.gov (United States)

    Bommena, R.; Ketharanathan, S.; Wijewarnasuriya, P. S.; Dhar, N. K.; Kodama, R.; Zhao, J.; Buurma, C.; Bergeson, J. D.; Aqariden, F.; Velicu, S.

    2015-09-01

    The development of low noise-equivalent differential temperature (NEDT), high-operability midwave infrared (MWIR) focal plane arrays (FPAs) fabricated from molecular beam epitaxial (MBE)-grown HgCdTe on Si-based substrates is reported. High-quality n-type MWIR HgCdTe layers with a cutoff wavelength of 4.90 μm at 77 K and a carrier concentration of 1-2 × 1015 cm-3 were grown on CdTe/Si substrates by MBE. Highly uniform composition and thickness over 3-inch areas were demonstrated, and low surface defect densities (voids ~5 × 102 cm-2, micro-defects ~5 × 103 cm-2) and etch pit density (~3.5 × 106 cm-2) were measured. This material was used to fabricate 320 × 256, 30 μm pitch FPAs with planar device architecture; arsenic implantation was used to achieve p-type doping. Radiometric and noise characterization was also performed. A low NEDT of 13.8 m K at 85 K for a 1 ms integration time with f/#2 optics was measured. The NEDT operability was 99% at 120 K with a mean dark current noise of 8.14 × 10-13 A/pixel. High-quality thermal images were obtained from the FPA up to a temperature of 150 K.

  3. Investigation of the Optical and Sensing Characteristics of Nanoparticle Arrays for High Temperature Applications

    Science.gov (United States)

    Dharmalingam, Gnanaprakash

    The monitoring of polluting gases such as CO and NOx emitted from gas turbines in power plants and aircraft is important in order to both reduce the effects of such gases on the environment as well as to optimize the performance of the respective power system. The need for emissions monitoring systems is further realized from increased regulatory requirements that are being instituted as a result of the environmental impact from increased air travel. Specifically, it is estimated that the contributions from aircraft emissions to total NOx emissions will increase from 4% to 17% between 2008 and 2020. Extensive fuel cost savings as well as a reduced environmental impact would therefore be realized if this increased air traffic utilized next generation jet turbines which used a emission/performance control sensing system. These future emissions monitoring systems must be sensitive and selective to the emission gases, reliable and stable under harsh environmental conditions where the operation temperatures are in excess of 500 °C within a highly reactive environment. Plasmonics based chemical sensors which use nanocomposites comprised of a combination of gold nano particles and Yttria Stabilized Zirconia (YSZ) has enabled the sensitive (PPM) and stable detection (100s of hrs) of H2, NO2 and CO at temperatures of 500 °C. The detection method involves measuring the change in the localized Surface Plasmon Resonance (LSPR) characteristics of the Au- YSZ nano composite and in particular, the plasmon peak position. Selectivity remains a challenging parameter to optimize and a layer by layer sputter deposition approach has been recently demonstrated to modify the resulting sensing properties through a change in the morphology of the deposited films. The material properties of the films have produced a unique sensing behavior in terms of a preferential response to H2 compared to CO. Although this is a very good benefit, it is expected that further enhancements would be

  4. Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data

    Directory of Open Access Journals (Sweden)

    Smith Richard JH

    2005-02-01

    Full Text Available Abstract Background The identification of disease-associated genes using single nucleotide polymorphisms (SNPs has been increasingly reported. In particular, the Affymetrix Mapping 10 K SNP microarray platform uses one PCR primer to amplify the DNA samples and determine the genotype of more than 10,000 SNPs in the human genome. This provides the opportunity for large scale, rapid and cost-effective genotyping assays for linkage analysis. However, the analysis of such datasets is nontrivial because of the large number of markers, and visualizing the linkage scores in the context of genome maps remains less automated using the current linkage analysis software packages. For example, the haplotyping results are commonly represented in the text format. Results Here we report the development of a novel software tool called CompareLinkage for automated formatting of the Affymetrix Mapping 10 K genotype data into the "Linkage" format and the subsequent analysis with multi-point linkage software programs such as Merlin and Allegro. The new software has the ability to visualize the results for all these programs in dChip in the context of genome annotations and cytoband information. In addition we implemented a variant of the Lander-Green algorithm in the dChipLinkage module of dChip software (V1.3 to perform parametric linkage analysis and haplotyping of SNP array data. These functions are integrated with the existing modules of dChip to visualize SNP genotype data together with LOD score curves. We have analyzed three families with recessive and dominant diseases using the new software programs and the comparison results are presented and discussed. Conclusions The CompareLinkage and dChipLinkage software packages are freely available. They provide the visualization tools for high-density oligonucleotide SNP array data, as well as the automated functions for formatting SNP array data for the linkage analysis programs Merlin and Allegro and calling

  5. Delta-Doping at Wafer Level for High Throughput, High Yield Fabrication of Silicon Imaging Arrays

    Science.gov (United States)

    Hoenk, Michael E. (Inventor); Nikzad, Shoulch (Inventor); Jones, Todd J. (Inventor); Greer, Frank (Inventor); Carver, Alexander G. (Inventor)

    2014-01-01

    Systems and methods for producing high quantum efficiency silicon devices. A silicon MBE has a preparation chamber that provides for cleaning silicon surfaces using an oxygen plasma to remove impurities and a gaseous (dry) NH3 + NF3 room temperature oxide removal process that leaves the silicon surface hydrogen terminated. Silicon wafers up to 8 inches in diameter have devices that can be fabricated using the cleaning procedures and MBE processing, including delta doping.

  6. Aluminum-based one- and two-dimensional micro fin array structures: high-throughput fabrication and heat transfer testing

    Science.gov (United States)

    Primeaux, Philip A.; Zhang, Bin; Zhang, Xiaoman; Miller, Jacob; Meng, W. J.; KC, Pratik; Moore, Arden L.

    2017-02-01

    Microscale fin array structures were replicated onto surfaces of aluminum 1100 and aluminum 6061 alloy (Al1100/Al6061) sheet metals through room-temperature instrumented roll molding. Aluminum-based micro fin arrays were replicated at room temperature, and the fabrication process is one with high throughput and low cost. One-dimensional (1D) micro fin arrays were made through one-pass rolling, while two-dimensional (2D) micro fin arrays were made by sequential 90° cross rolling with the same roller sleeve. For roll molding of 1D micro fins, fin heights greater than 600 µm were achieved and were shown to be proportional to the normal load force per feature width. At a given normal load force, the fin height was further shown to scale inversely with the hardness of the sheet metal. For sequential 90° cross rolling, morphologies of roll molded 2D micro fin arrays were examined, which provided clues to understand how plastic deformation occurred under cross rolling conditions. A series of pool boiling experiments on low profile Al micro fin array structures were performed within Novec 7100, a widely used commercial dielectric coolant. Results for both horizontal and vertical surface orientations show that roll molded Al micro fin arrays can increase heat flux at fixed surface temperature as compared to un-patterned Al sheet. The present results further suggest that many factors beyond just increased surface area can influence heat transfer performance, including surface finish and the important multiphase transport mechanisms in and around the fin geometry. These factors must also be considered when designing and optimizing micro fin array structures for heat transfer applications.

  7. Single-copy insertion of transgenes in Caenorhabditis elegans

    DEFF Research Database (Denmark)

    Frøkjaer-Jensen, Christian; Davis, M Wayne; Hopkins, Christopher E;

    2008-01-01

    At present, transgenes in Caenorhabditis elegans are generated by injecting DNA into the germline. The DNA assembles into a semistable extrachromosomal array composed of many copies of injected DNA. These transgenes are typically overexpressed in somatic cells and silenced in the germline. We have...

  8. High sensitive immunoassay for multiplex mycotoxin detection with photonic crystal microsphere suspension array.

    Science.gov (United States)

    Deng, Guozhe; Xu, Kun; Sun, Yue; Chen, Yu; Zheng, Tiesong; Li, Jianlin

    2013-03-05

    A novel, sensitive, and high throughput competitive immunoassay for multiplex mycotoxins was established by immobilizing the artificial antigens (Ags) of mycotoxins on the surfaces of three kinds of silica photonic crystal microsphere (SPCM) suspension arrays. The SPCMs were encoded by their reflectance peak positions. Aflatoxin B1 (AFB1), fumonisin B1 (FB1), and citrinin (CIT) spiked in the cereals were extracted, and the fluorescein isothiocyanate (FITC) labeled antibodies (Abs) of these mycotoxins were added into the centrifuge tube which contained the SPCMs of the modified artificial antigens (Ags). The fluorescence signal was collected by an array fluorescent scanner. The limit of detection (LOD) was as low as 0.5, 1, and 0.8 pg/mL for AFB1, FB1, and CIT, respectively. The new method provided a wide linear detection range from 0.001 to 10, 0.001 to 10, and 0.001 to 1 ng/mL for AFB1, FB1, and CIT, respectively. The mean recovery rates are in range of 74.7 ± 4.0% to 127.9 ± 4.4% for the three mycotoxins in corn, peanuts, and wheat. The developed method for mycotoxins was used to assay the AFB1, FB1, and CIT level in 10 naturally contaminated cereal samples, and the results of detection were in agreement with that of a classic enzyme-linked immunosorbent assay (ELISA) method. This method saves a large amount of reagents (10 μL volume) and detection time (<3 h) for multiplex mycotoxin assay.

  9. Highly integrated optical phased arrays: photonic integrated circuits for optical beam shaping and beam steering

    Directory of Open Access Journals (Sweden)

    Heck Martijn J.R.

    2017-01-01

    Full Text Available Technologies for efficient generation and fast scanning of narrow free-space laser beams find major applications in three-dimensional (3D imaging and mapping, like Lidar for remote sensing and navigation, and secure free-space optical communications. The ultimate goal for such a system is to reduce its size, weight, and power consumption, so that it can be mounted on, e.g. drones and autonomous cars. Moreover, beam scanning should ideally be done at video frame rates, something that is beyond the capabilities of current opto-mechanical systems. Photonic integrated circuit (PIC technology holds the promise of achieving low-cost, compact, robust and energy-efficient complex optical systems. PICs integrate, for example, lasers, modulators, detectors, and filters on a single piece of semiconductor, typically silicon or indium phosphide, much like electronic integrated circuits. This technology is maturing fast, driven by high-bandwidth communications applications, and mature fabrication facilities. State-of-the-art commercial PICs integrate hundreds of elements, and the integration of thousands of elements has been shown in the laboratory. Over the last few years, there has been a considerable research effort to integrate beam steering systems on a PIC, and various beam steering demonstrators based on optical phased arrays have been realized. Arrays of up to thousands of coherent emitters, including their phase and amplitude control, have been integrated, and various applications have been explored. In this review paper, I will present an overview of the state of the art of this technology and its opportunities, illustrated by recent breakthroughs.

  10. Very large array observations of ammonia in high-mass star formation regions

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Xing; Gu, Qiusheng [School of Astronomy and Space Science, Nanjing University, Nanjing, Jiangsu 210093 (China); Zhang, Qizhou [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Liu, Hauyu Baobab [Academia Sinica Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 106, Taiwan (China); Wang, Junzhi [Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030 (China)

    2014-08-01

    We report systematic mapping observations of the NH{sub 3} (1, 1) and (2, 2) inversion lines toward 62 high-mass star-forming regions using the Very Large Array (VLA) in its D and DnC array configurations. The VLA images cover a spatial dynamic range from 40'' to 3'', allowing us to trace gas kinematics from ∼1 pc scales to ≲0.1 pc scales. Based on the NH{sub 3} morphology and the infrared nebulosity on 1 pc scales, we categorize three subclasses in the sample: filaments, hot cores, and NH{sub 3}-dispersed sources. The ubiquitous gas filaments found on 1 pc scales have a typical width of ∼0.1 pc and often contain regularly spaced fragments along the major axis. The spacing of the fragments and the column densities is consistent with the turbulent supported fragmentation of cylinders. Several sources show multiple filaments that converge toward a center where the velocity field in the filaments is consistent with gas flows. We derive rotational temperature maps for the entire sample. For the three hot core sources, we find a projected radial temperature distribution that is best fit by power-law indices from –0.18 to –0.35. We identify 174 velocity-coherent ∼0.1 pc scale dense cores from the entire sample. The mean physical properties for these cores are 1.1 km s{sup –1} in intrinsic linewidth, 18 K in NH{sub 3} rotational temperature, 2.3 × 10{sup 15} cm{sup –2} in NH{sub 3} gas column density, and 67 M{sub ☉} in molecular mass. The dense cores identified from the filamentary sources are closer to being virialized. Dense cores in the other two categories of sources appear to be dynamically unstable.

  11. Decoding continuous limb movements from high-density epidural electrode arrays using custom spatial filters

    Science.gov (United States)

    Marathe, A. R.; Taylor, D. M.

    2013-06-01

    Objective. Our goal was to identify spatial filtering methods that would improve decoding of continuous arm movements from epidural field potentials as well as demonstrate the use of the epidural signals in a closed-loop brain-machine interface (BMI) system in monkeys. Approach. Eleven spatial filtering options were compared offline using field potentials collected from 64-channel high-density epidural arrays in monkeys. Arrays were placed over arm/hand motor cortex in which intracortical microelectrodes had previously been implanted and removed leaving focal cortical damage but no lasting motor deficits. Spatial filters tested included: no filtering, common average referencing (CAR), principle component analysis, and eight novel modifications of the common spatial pattern (CSP) algorithm. The spatial filtering method and decoder combination that performed the best offline was then used online where monkeys controlled cursor velocity using continuous wrist position decoded from epidural field potentials in real time. Main results. Optimized CSP methods improved continuous wrist position decoding accuracy by 69% over CAR and by 80% compared to no filtering. Kalman decoders performed better than linear regression decoders and benefitted from including more spatially-filtered signals but not from pre-smoothing the calculated power spectra. Conversely, linear regression decoders required fewer spatially-filtered signals and were improved by pre-smoothing the power values. The ‘position-to-velocity’ transformation used during online control enabled the animals to generate smooth closed-loop movement trajectories using the somewhat limited position information available in the epidural signals. The monkeys’ online performance significantly improved across days of closed-loop training. Significance. Most published BMI studies that use electrocorticographic signals to decode continuous limb movements either use no spatial filtering or CAR. This study suggests a

  12. Measuring High-Precision Astrometry with the Infrared Array Camera on the Spitzer Space Telescope

    Science.gov (United States)

    Esplin, T. L.; Luhman, K. L.

    2016-01-01

    The Infrared Array Camera (IRAC) on the Spitzer Space Telescope currently offers the greatest potential for high-precision astrometry of faint mid-IR sources across arcminute-scale fields, which would be especially valuable for measuring parallaxes of cold brown dwarfs in the solar neighborhood and proper motions of obscured members of nearby star-forming regions. To more fully realize IRAC's astrometric capabilities, we have sought to minimize the largest sources of uncertainty in astrometry with its 3.6 and 4.5 μm bands. By comparing different routines that estimate stellar positions, we have found that Point Response Function (PRF) fitting with the Spitzer Science Center's Astronomical Point Source Extractor produces both the smallest systematic errors from varying intra-pixel sensitivity and the greatest precision in measurements of positions. In addition, self-calibration has been used to derive new 7th and 8th order distortion corrections for the 3.6 and 4.5 μm arrays of IRAC, respectively. These corrections are suitable for data throughout the mission of Spitzer when a time-dependent scale factor is applied to the corrections. To illustrate the astrometric accuracy that can be achieved by combining PRF fitting with our new distortion corrections, we have applied them to archival data for a nearby star-forming region, arriving at total astrometric errors of ∼20 and 70 mas at signal to noise ratios of 100 and 10, respectively. Based on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA.

  13. Highly integrated optical phased arrays: photonic integrated circuits for optical beam shaping and beam steering

    Science.gov (United States)

    Heck, Martijn J. R.

    2017-01-01

    Technologies for efficient generation and fast scanning of narrow free-space laser beams find major applications in three-dimensional (3D) imaging and mapping, like Lidar for remote sensing and navigation, and secure free-space optical communications. The ultimate goal for such a system is to reduce its size, weight, and power consumption, so that it can be mounted on, e.g. drones and autonomous cars. Moreover, beam scanning should ideally be done at video frame rates, something that is beyond the capabilities of current opto-mechanical systems. Photonic integrated circuit (PIC) technology holds the promise of achieving low-cost, compact, robust and energy-efficient complex optical systems. PICs integrate, for example, lasers, modulators, detectors, and filters on a single piece of semiconductor, typically silicon or indium phosphide, much like electronic integrated circuits. This technology is maturing fast, driven by high-bandwidth communications applications, and mature fabrication facilities. State-of-the-art commercial PICs integrate hundreds of elements, and the integration of thousands of elements has been shown in the laboratory. Over the last few years, there has been a considerable research effort to integrate beam steering systems on a PIC, and various beam steering demonstrators based on optical phased arrays have been realized. Arrays of up to thousands of coherent emitters, including their phase and amplitude control, have been integrated, and various applications have been explored. In this review paper, I will present an overview of the state of the art of this technology and its opportunities, illustrated by recent breakthroughs.

  14. Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

    Directory of Open Access Journals (Sweden)

    Rosenstiel Philip

    2010-04-01

    Full Text Available Abstract Background The beta-defensin gene cluster (DEFB at chromosome 8p23.1 is one of the most copy number (CN variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease, the role of multisite sequence variations (MSV is less well understood and to date has only been reported for prostate cancer. Simultaneous assessment of MSVs and CNs can be achieved by PCR, cloning and Sanger sequencing, however, these methods are labour and cost intensive as well as prone to methodological bias introduced by bacterial cloning. Here, we demonstrate that amplicon sequencing of pooled individual PCR products by the 454 technology allows in-depth determination of MSV haplotypes and estimation of DEFB CNs in parallel. Results Six PCR products spread over ~87 kb of DEFB and harbouring 24 known MSVs were amplified from 11 DNA samples, pooled and sequenced on a Roche 454 GS FLX sequencer. From ~142,000 reads, ~120,000 haplotype calls (HC were inferred that identified 22 haplotypes ranging from 2 to 7 per amplicon. In addition to the 24 known MSVs, two additional sequence variations were detected. Minimal CNs were estimated from the ratio of HCs and compared to absolute CNs determined by alternative methods. Concordance in CNs was found for 7 samples, the CNs differed by one in 2 samples and the estimated minimal CN was half of the absolute in one sample. For 7 samples and 2 amplicons, the 454 haplotyping results were compared to those by cloning/Sanger sequencing. Intrinsic problems related to chimera formation during PCR and differences between haplotyping by 454 and cloning/Sanger sequencing are discussed. Conclusion Deep amplicon sequencing using the 454 technology yield thousands of HCs per amplicon for an affordable price and may represent an effective method for parallel haplotyping and CN estimation in small to medium-sized cohorts. The

  15. Tailor-made rylene arrays for high performance n-channel semiconductors.

    Science.gov (United States)

    Jiang, Wei; Li, Yan; Wang, Zhaohui

    2014-10-21

    Rylene dyes, made up of naphthalene units linked in peri-positions, are emerging as promising key building blocks to create π-functional materials. Chemists have found uses for these ribbonlike structures in a wide range of applications of optoelectronic devices. Because their structure combines two sets of six-membered electron-withdrawing dicarboxylic imide rings, rylene diimides exhibit enhanced solubility, excellent chemical and thermal stabilities, high electron affinities, and remarkable electron-transporting properties. Among them, perylene diimide (PDI) and naphthalene diimide (NDI) derivatives are important representatives improving the performance of electron-transporting technologies, relative to their p-channel counterparts. Pioneering works by Müllen and Langhals have inspired chemists to extend the π-conjugation along the peri-positions of rylene diimides, which generally results in impressive bathochromic shifts and a nearly linear increase in the extinction coefficient. In addition, in the past years, researchers have focused on π-expansion of NDI or PDI systems through bay-functionalization with carbocyclic and heterocyclic rings annulated onto the skeleton. However, chemists have rarely investigated lateral expansion via both bay- and nonbay-functionalization to construct homologous series of rylene arrays with different electronic delocalization and fine-tuned flexible linkage. This is probably due to the lack of effective procedures for the (multi) carbon-carbon formation and annulation of electron-deficient rylene imide units. In this Account, we discuss our recent progress in the design and synthesis of laterally expanded rylene dyes based on homocoupling and cross-coupling reactions of core-functionalized PDIs and NDIs to achieve novel high performance n-channel organic semiconducting materials. These new achievements offer us opportunities to learn fundamental issues about how chemical and physical properties alter with incremental

  16. Homogeneous vertical ZnO nanorod arrays with high conductivity on an in situ Gd nanolayer

    KAUST Repository

    Flemban, Tahani H.

    2015-10-30

    We demonstrate a novel, one-step, catalyst-free method fo