High-resolution array CGH clarifies events occurring on 8p in carcinogenesis

International Nuclear Information System (INIS)

Cooke, Susanna L; Pole, Jessica CM; Chin, Suet-Feung; Ellis, Ian O; Caldas, Carlos; Edwards, Paul AW

2008-01-01

Rearrangement of the short arm of chromosome 8 (8p) is very common in epithelial cancers such as breast cancer. Usually there is an unbalanced translocation breakpoint in 8p12 (29.7 Mb – 38.5 Mb) with loss of distal 8p, sometimes with proximal amplification of 8p11-12. Rearrangements in 8p11-12 have been investigated using high-resolution array CGH, but the first 30 Mb of 8p are less well characterised, although this region contains several proposed tumour suppressor genes. We analysed the whole of 8p by array CGH at tiling-path BAC resolution in 32 breast and six pancreatic cancer cell lines. Regions of recurrent rearrangement distal to 8p12 were further characterised, using regional fosmid arrays. FISH, and quantitative RT-PCR on over 60 breast tumours validated the existence of similar events in primary material. We confirmed that 8p is usually lost up to at least 30 Mb, but a few lines showed focal loss or copy number steps within this region. Three regions showed rearrangements common to at least two cases: two regions of recurrent loss and one region of amplification. Loss within 8p23.3 (0 Mb – 2.2 Mb) was found in six cell lines. Of the genes always affected, ARHGEF10 showed a point mutation of the remaining normal copies in the DU4475 cell line. Deletions within 12.7 Mb – 19.1 Mb in 8p22, in two cases, affected TUSC3. A novel amplicon was found within 8p21.3 (19.1 Mb – 23.4 Mb) in two lines and one of 98 tumours. The pattern of rearrangements seen on 8p may be a consequence of the high density of potential targets on this chromosome arm, and ARHGEF10 may be a new candidate tumour suppressor gene

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing

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Jackson Stuart

2010-04-01

Full Text Available Abstract Background DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. Results We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. Conclusion The described assay outputs absolute copy number, outputs an error estimate (p-value, and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.

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

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Liao, Can; Fu, Fang; Yang, Xin; Sun, Yi-Min; Li, Dong-Zhi

2011-06-01

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. 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. 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. 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.

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.

Peer-to-peer computing for secure high performance data copying

International Nuclear Information System (INIS)

Hanushevsky, A.; Trunov, A.; Cottrell, L.

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 (sfcp), bbcp incorporates significant improvements performance and usability. As with sfcp, bbcp uses 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 specify, 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 recoverability, 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, the authors present the bbcp architecture, it's various features, and the reasons for their inclusion

Peer-to-Peer Computing for Secure High Performance Data Copying

International Nuclear Information System (INIS)

2002-01-01

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 (sfcp), bbcp incorporates significant improvements performance and usability. As with sfcp, bbcp uses 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 specify, 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 recoverability, 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

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

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Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A; Guimarães, Bruna V A; Duarte, Luiz Cláudio Pires; Rogatto, Sílvia R; Gomez, Ricardo Santiago; Gomes, Carolina Cavaliéri

2017-05-01

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 different clinical behaviors. We assessed copy number alterations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) in UA (n = 2), MA (n = 3), and AC (n = 1) using the CytoScan HD Array (Affymetrix) and the BRAFV600E status. RT-qPCR was applied in four selected genes (B4GALT1, BAG1, PKD1L2, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. 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, 1q32.3, and 9p21.1 and loss of 16q23.2). We found positive correlation between rare CNA gene dosage and the expression of B4GALT1, BAG1, PKD1L2, and PPP2R5A. The AC and 1 UA were BRAF wild-type; however, this UA showed rare genomic alterations encompassing genes associated with RAF/MAPK activation. 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. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Integrative Genomics Reveals Mechanisms of Copy Number Alterations Responsible for Transcriptional Deregulation in Colorectal Cancer

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Camps, Jordi; Nguyen, Quang Tri; Padilla-Nash, Hesed M.; Knutsen, Turid; McNeil, Nicole E.; Wangsa, Danny; Hummon, Amanda B.; Grade, Marian; Ried, Thomas; Difilippantonio, Michael J.

2016-01-01

To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. We revealed a preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines, a novel mechanism of DNA breakage in cancer. The integration of gene expression and aCGH led to the identification of 157 genes localized within high-level copy number changes whose transcriptional deregulation was significantly affected across all of the samples, thereby suggesting that these genes play a functional role in CRC. Genomic amplification at 8q24 was the most recurrent event and led to the overexpression of MYC and FAM84B. Copy number dependent gene expression resulted in deregulation of known cancer genes such as APC, FGFR2, and ERBB2. The identification of only 36 genes whose localization near a breakpoint could account for their observed deregulated expression demonstrates that the major mechanism for transcriptional deregulation in CRC is genomic copy number changes resulting from chromosomal aberrations. PMID:19691111

Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis.

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Joel A Malek

Full Text Available Ovarian cancer is the most deadly gynecological cancer. The high rate of mortality is due to the large tumor burden with extensive metastatic lesion of the abdominal cavity. Despite initial chemosensitivity and improved surgical procedures, abdominal recurrence remains an issue and results in patients' poor prognosis. Transcriptomic and genetic studies have revealed significant genome pathologies in the primary tumors and yielded important information regarding carcinogenesis. There are, however, few studies on genetic alterations and their consequences in peritoneal metastatic tumors when compared to their matched ovarian primary tumors. We used high-density SNP arrays to investigate copy number variations in matched primary and metastatic ovarian cancer from 9 patients. Here we show that copy number variations acquired by ovarian tumors are significantly different between matched primary and metastatic tumors and these are likely due to different functional requirements. We show that these copy number variations clearly differentially affect specific pathways including the JAK/STAT and cytokine signaling pathways. While many have shown complex involvement of cytokines in the ovarian cancer environment we provide evidence that ovarian tumors have specific copy number variation differences in many of these genes.

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

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Neuvial Pierre

2010-05-01

Full Text Available Abstract Background High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses. Results We propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances. Conclusions TumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH in the tumor from allelic signals of Affymetrix or Illumina origin. We also conclude that high-precision allelic estimates can be obtained from a single pair of tumor-normal hybridizations, if TumorBoost is combined with single-array preprocessing methods such as (allele-specific CRMA v2 for Affymetrix or BeadStudio's (proprietary XY-normalization method for Illumina. A bounded-memory implementation is available in the open-source and cross-platform R package aroma.cn, which is part of the Aroma Project (http://www.aroma-project.org/.

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

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Tyson, Jess; Majerus, Tamsin Mo; Walker, Susan; Armour, John Al

2009-09-28

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. 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. 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.

Copy number variations in Saudi family with intellectual disability and epilepsy.

Science.gov (United States)

Naseer, Muhammad I; Chaudhary, Adeel G; Rasool, Mahmood; Kalamegam, Gauthaman; Ashgan, Fai T; Assidi, Mourad; Ahmed, Farid; Ansari, Shakeel A; Zaidi, Syed Kashif; Jan, Mohammed M; Al-Qahtani, Mohammad H

2016-10-17

Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs) are considered as important reason for the numerous neurodevelopmental disorders along with intellectual disability and epilepsy. DNA array based studies contribute to explain a more severe clinical presentation of the disease but interoperation of many detected CNVs are still challenging. In order to study novel CNVs with epilepsy related genes in Saudi family with six affected and two normal individuals with several forms of epileptic seizures, intellectual disability (ID), and minor dysmorphism, we performed the high density whole genome Agilent sure print G3 Hmn CGH 2x 400 K array-CGH chips analysis. Our results showed de novo deletions, duplications and deletion plus duplication on differential chromosomal regions in the affected individuals that were not shown in the normal fathe and normal kids by using Agilent CytoGenomics 3.0.6.6 softwear. Copy number gain were observed in the chromosome 1, 16 and 22 with LCE3C, HPR, GSTT2, GSTTP2, DDT and DDTL genes respectively whereas the deletions observed in the chromosomal regions 8p23-p21 (4303127-4337759) and the potential gene in this region is CSMD1 (OMIM: 612279). Moreover, the array CGH results deletions and duplication were also validated by using primer design of deleted regions utilizing the flanked SNPs using simple PCR and also by using quantitative real time PCR. We found some of the de novo deletions and duplication in our study in Saudi family with intellectual disability and epilepsy. Our results suggest that array-CGH should be used as a first line of genetic test for epilepsy except there is a strong indication for a monogenic syndrome. The advanced high through put array-CGH technique used in this study aim to collect the data base and to identify new mechanisms describing epileptic disorder, may help to improve the clinical

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

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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.

CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

Science.gov (United States)

Marzouka, Nour-Al-Dain; Nordlund, Jessica; Bäcklin, Christofer L; Lönnerholm, Gudmar; Syvänen, Ann-Christine; Carlsson Almlöf, Jonas

2016-04-01

The Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may result in erroneous CNV calling. Therefore, a baseline correction process is needed. We suggest the maximum peak of probe segment density to correct the shift in the intensities in cancer samples. CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http://cran.r-project.org nour.marzouka@medsci.uu.se Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Partitioning of copy-number genotypes in pedigrees

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Andelfinger Gregor U

2010-05-01

Full Text Available Abstract Background Copy number variations (CNVs and polymorphisms (CNPs have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results We have developed CNGen, a new software for the partitioning of copy number polymorphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible the use CNPs and CNVs for linkage analysis. It was implemented with the Python interpreter version 2.5.2. It was successfully tested on current Linux, Windows and Mac OS workstations.

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

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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.

Copy number variations in Saudi family with intellectual disability and epilepsy

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Muhammad I. Naseer

2016-10-01

Full Text Available Abstract Background Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs are considered as important reason for the numerous neurodevelopmental disorders along with intellectual disability and epilepsy. DNA array based studies contribute to explain a more severe clinical presentation of the disease but interoperation of many detected CNVs are still challenging. Results In order to study novel CNVs with epilepsy related genes in Saudi family with six affected and two normal individuals with several forms of epileptic seizures, intellectual disability (ID, and minor dysmorphism, we performed the high density whole genome Agilent sure print G3 Hmn CGH 2x 400 K array-CGH chips analysis. Our results showed de novo deletions, duplications and deletion plus duplication on differential chromosomal regions in the affected individuals that were not shown in the normal fathe and normal kids by using Agilent CytoGenomics 3.0.6.6 softwear. Copy number gain were observed in the chromosome 1, 16 and 22 with LCE3C, HPR, GSTT2, GSTTP2, DDT and DDTL genes respectively whereas the deletions observed in the chromosomal regions 8p23-p21 (4303127–4337759 and the potential gene in this region is CSMD1 (OMIM: 612279. Moreover, the array CGH results deletions and duplication were also validated by using primer design of deleted regions utilizing the flanked SNPs using simple PCR and also by using quantitative real time PCR. Conclusions We found some of the de novo deletions and duplication in our study in Saudi family with intellectual disability and epilepsy. Our results suggest that array-CGH should be used as a first line of genetic test for epilepsy except there is a strong indication for a monogenic syndrome. The advanced high through put array-CGH technique used in this study aim to collect the data base and to identify new mechanisms describing

The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

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Oga Atsunori

2008-12-01

Full Text Available Abstract Background The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Methods Initially, the DNA copy number aberrations (DCNAs were analyzed by array-based comparative genomic hybridization (aCGH in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. Results By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set. In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. Conclusion These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma.

The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

International Nuclear Information System (INIS)

Furuya, Tomoko; Uchiyama, Tetsuji; Adachi, Atsushi; Okada, Takae; Nakao, Motonao; Oga, Atsunori; Yang, Song-Ju; Kawauchi, Shigeto; Sasaki, Kohsuke

2008-01-01

The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome) mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Initially, the DNA copy number aberrations (DCNAs) were analyzed by array-based comparative genomic hybridization (aCGH) in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set). In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma

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

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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.

Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays

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Zhu, Caiye; Fan, Hongying; Yuan, Zehu; Hu, Shijin; Ma, Xiaomeng; Xuan, Junli; Wang, Hongwei; Zhang, Li; Wei, Caihong; Zhang, Qin; Zhao, Fuping; Du, Lixin

2016-01-01

Chinese indigenous sheep can be classified into three types based on tail morphology: fat-tailed, fat-rumped, and thin-tailed sheep, of which the typical breeds are large-tailed Han sheep, Altay sheep, and Tibetan sheep, respectively. To unravel the genetic mechanisms underlying the phenotypic differences among Chinese indigenous sheep with tails of three different types, we used ovine high-density 600K SNP arrays to detect genome-wide copy number variation (CNV). In large-tailed Han sheep, A...

A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH.

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Birte Möhlendick

Full Text Available Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH of single cells. The protocol is based on an established adapter-linker PCR (WGAM and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost- effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.

Large-area high-power VCSEL pump arrays optimized for high-energy lasers

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Wang, Chad; Geske, Jonathan; Garrett, Henry; Cardellino, Terri; Talantov, Fedor; Berdin, Glen; Millenheft, David; Renner, Daniel; Klemer, Daniel

2012-06-01

Practical, large-area, high-power diode pumps for one micron (Nd, Yb) as well as eye-safer wavelengths (Er, Tm, Ho) are critical to the success of any high energy diode pumped solid state laser. Diode efficiency, brightness, availability and cost will determine how realizable a fielded high energy diode pumped solid state laser will be. 2-D Vertical-Cavity Surface-Emitting Laser (VCSEL) arrays are uniquely positioned to meet these requirements because of their unique properties, such as low divergence circular output beams, reduced wavelength drift with temperature, scalability to large 2-D arrays through low-cost and high-volume semiconductor photolithographic processes, high reliability, no catastrophic optical damage failure, and radiation and vacuum operation tolerance. Data will be presented on the status of FLIR-EOC's VCSEL pump arrays. Analysis of the key aspects of electrical, thermal and mechanical design that are critical to the design of a VCSEL pump array to achieve high power efficient array performance will be presented.

High-spin research with HERA [High Energy-Resolution Array

International Nuclear Information System (INIS)

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

Genome-Wide Association of Copy Number Polymorphisms and Kidney Function.

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Man Li

Full Text Available Genome-wide association studies (GWAS using single nucleotide polymorphisms (SNPs have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR, a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea. We used hidden Markov models (HMMs to identify copy number polymorphic regions (CNPs from high-throughput SNP arrays for 2,514 African (AA and 8,645 European ancestry (EA participants in the Atherosclerosis Risk in Communities (ARIC study. Separately for the EA and AA cohorts, we used Bayesian Gaussian mixture models to estimate copy number at regions identified by the HMM or previously reported in the HapMap Project. We identified 312 and 464 autosomal CNPs among individuals of EA and AA, respectively. Multivariate models adjusted for SNP-derived covariates of population structure identified one CNP in the EA cohort near genome-wide statistical significance (Bonferroni-adjusted p = 0.067 located on chromosome 5 (876-880kb. Overall, our findings suggest a limited role of CNPs in explaining eGFR variability.

Identification of copy number variants in horses

KAUST Repository

Doan, R.

2012-03-01

Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.

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

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Wei Wang

Full Text Available 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.

Beneficial effect of a high number of copies of salivary amylase AMY1 gene on obesity risk in Mexican children.

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Mejía-Benítez, María A; Bonnefond, Amélie; Yengo, Loïc; Huyvaert, Marlène; Dechaume, Aurélie; Peralta-Romero, Jesús; Klünder-Klünder, Miguel; García Mena, Jaime; El-Sayed Moustafa, Julia S; Falchi, Mario; Cruz, Miguel; Froguel, Philippe

2015-02-01

Childhood obesity is a major public health problem in Mexico, affecting one in every three children. Genome-wide association studies identified genetic variants associated with childhood obesity, but a large missing heritability remains to be elucidated. We have recently shown a strong association between a highly polymorphic copy number variant encompassing the salivary amylase gene (AMY1 also known as AMY1A) and obesity in European and Asian adults. In the present study, we aimed to evaluate the association between AMY1 copy number and obesity in Mexican children. We evaluated the number of AMY1 copies in 597 Mexican children (293 obese children and 304 normal weight controls) through highly sensitive digital PCR. The effect of AMY1 copy number on obesity status was assessed using a logistic regression model adjusted for age and sex. We identified a marked effect of AMY1 copy number on reduced risk of obesity (OR per estimated copy 0.84, with the number of copies ranging from one to 16 in this population; p = 4.25 × 10(-6)). The global association between AMY1 copy number and reduced risk of obesity seemed to be mostly driven by the contribution of the highest AMY1 copy number. Strikingly, all children with >10 AMY1 copies were normal weight controls. Salivary amylase initiates the digestion of dietary starch, which is highly consumed in Mexico. Our current study suggests putative benefits of high number of AMY1 copies (and related production of salivary amylase) on energy metabolism in Mexican children.

Advantage of using allele-specific copy numbers when testing for association in regions with common copy number variants.

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Gaëlle Marenne

Full Text Available Copy number variants (CNV can be called from SNP-arrays; however, few studies have attempted to combine both CNV and SNP calls to test for association with complex diseases. Even when SNPs are located within CNVs, two separate association analyses are necessary, to compare the distribution of bi-allelic genotypes in cases and controls (referred to as SNP-only strategy and the number of copies of a region (referred to as CNV-only strategy. However, when disease susceptibility is actually associated with allele specific copy-number states, the two strategies may not yield comparable results, raising a series of questions about the optimal analytical approach. We performed simulations of the performance of association testing under different scenarios that varied genotype frequencies and inheritance models. We show that the SNP-only strategy lacks power under most scenarios when the SNP is located within a CNV; frequently it is excluded from analysis as it does not pass quality control metrics either because of an increased rate of missing calls or a departure from fitness for Hardy-Weinberg proportion. The CNV-only strategy also lacks power because the association testing depends on the allele which copy number varies. The combined strategy performs well in most of the scenarios. Hence, we advocate the use of this combined strategy when testing for association with SNPs located within CNVs.

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

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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.

Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

International Nuclear Information System (INIS)

Savola, Suvi; Knuutila, Sakari; Klami, Arto; Tripathi, Abhishek; Niini, Tarja; Serra, Massimo; Picci, Piero; Kaski, Samuel; Zambelli, Diana; Scotlandi, Katia

2009-01-01

Ewing sarcoma family of tumors (ESFT), characterized by t(11;22)(q24;q12), is one of the most common tumors of bone in children and young adults. In addition to EWS/FLI1 gene fusion, copy number changes are known to be significant for the underlying neoplastic development of ESFT and for patient outcome. Our genome-wide high-resolution analysis aspired to pinpoint genomic regions of highest interest and possible target genes in these areas. Array comparative genomic hybridization (CGH) and expression arrays were used to screen for copy number alterations and expression changes in ESFT patient samples. A total of 31 ESFT samples were analyzed by aCGH and in 16 patients DNA and RNA level data, created by expression arrays, was integrated. Time of the follow-up of these patients was 5–192 months. Clinical outcome was statistically evaluated by Kaplan-Meier/Logrank methods and RT-PCR was applied on 42 patient samples to study the gene of the highest interest. Copy number changes were detected in 87% of the cases. The most recurrent copy number changes were gains at 1q, 2, 8, and 12, and losses at 9p and 16q. Cumulative event free survival (ESFT) and overall survival (OS) were significantly better (P < 0.05) for primary tumors with three or less copy number changes than for tumors with higher number of copy number aberrations. In three samples copy number imbalances were detected in chromosomes 11 and 22 affecting the FLI1 and EWSR1 loci, suggesting that an unbalanced t(11;22) and subsequent duplication of the derivative chromosome harboring fusion gene is a common event in ESFT. Further, amplifications on chromosomes 20 and 22 seen in one patient sample suggest a novel translocation type between EWSR1 and an unidentified fusion partner at 20q. In total 20 novel ESFT associated putative oncogenes and tumor suppressor genes were found in the integration analysis of array CGH and expression data. Quantitative RT-PCR to study the expression levels of the most interesting

High Frequency High Spectral Resolution Focal Plane Arrays for AtLAST

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Baryshev, Andrey

2018-01-01

Large collecting area single dish telescope such as ATLAST will be especially effective for medium (R 1000) and high (R 50000) spectral resolution observations. Large focal plane array is a natural solution to increase mapping speed. For medium resolution direct detectors with filter banks (KIDs) and or heterodyne technology can be employed. We will analyze performance limits of comparable KID and SIS focal plane array taking into account quantum limit and high background condition of terrestrial observing site. For large heterodyne focal plane arrays, a high current density AlN junctions open possibility of large instantaneous bandwidth >40%. This and possible multi frequency band FPSs presents a practical challenge for spatial sampling and scanning strategies. We will discuss phase array feeds as a possible solution, including a modular back-end system, which can be shared between KID and SIS based FPA. Finally we will discuss achievable sensitivities and pixel co unts for a high frequency (>500 GHz) FPAs and address main technical challenges: LO distribution, wire counts, bias line multiplexing, and monolithic vs. discrete mixer component integration.

High-power, ultralow-mass solar arrays: FY-77 solar arrays technology readiness assessment report, volume 2

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Costogue, E. N.; Young, L. E.; Brandhorst, H. W., Jr.

1978-01-01

Development efforts are reported in detail for: (1) a lightweight solar array system for solar electric propulsion; (2) a high efficiency thin silicon solar cell; (3) conceptual design of 200 W/kg solar arrays; (4) fluorocarbon encapsulation for silicon solar cell array; and (5) technology assessment of concentrator solar arrays.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

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Moreau Yves

2005-05-01

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

Tubular fluoropolymer arrays with high piezoelectric response

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Zhukov, Sergey; Eder-Goy, Dagmar; Biethan, Corinna; Fedosov, Sergey; Xu, Bai-Xiang; von Seggern, Heinz

2018-01-01

Polymers with electrically charged internal air cavities called ferroelectrets exhibit a pronounced piezoelectric effect and are regarded as soft functional materials suitable for sensor and actuator applications. In this work, a simple method for fabricating piezoelectret arrays with open-tubular channels is introduced. A set of individual fluoroethylenepropylene (FEP) tubes is compressed between two heated metal plates. The squeezed FEP tubes are melted together at +270 °C. The resulting structure is a uniform, multi-tubular, flat array that reveals a strong piezoelectric response after a poling step. The fabricated arrays have a high ratio between piezoelectrically active and non-active areas. The optimal charging voltage and stability of the piezoelectric coefficients with pressures and frequency were experimentally investigated for two specific array structures with wall thickness of 50 and 120 μm. The array fabricated from 50 μm thick FEP tubes reveals a stable and high piezoelectric coefficient of {d}33 = 120-160 pC N-1 with a flat frequency response between 0.1 Hz and 10 kHz for pressures between 1 and 100 kPa. An increase of wall thickness to 120 μm is accompanied by a more than twofold decrease in the piezoelectric coefficient as a result of a simultaneously higher effective array stiffness and lower remanent polarization. The obtained experimental results can be used to optimize the array design with regard to the electromechanical performance.

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

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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.

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.

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

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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/.

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

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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.

Telescoping Solar Array Concept for Achieving High Packaging Efficiency

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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.

Characterization of High-power Quasi-cw Laser Diode Arrays

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Stephen, Mark A.; Vasilyev, Aleksey; Troupaki, Elisavet; Allan, Graham R.; Kashem, Nasir B.

2005-01-01

NASA s requirements for high reliability, high performance satellite laser instruments have driven the investigation of many critical components; specifically, 808 nm laser diode array (LDA) pump devices. Performance and comprehensive characterization data of Quasi-CW, High-power, laser diode arrays is presented.

Incidental copy-number variants identified by routine genome testing in a clinical population

Science.gov (United States)

Boone, Philip M.; Soens, Zachry T.; Campbell, Ian M.; Stankiewicz, Pawel; Cheung, Sau Wai; Patel, Ankita; Beaudet, Arthur L.; Plon, Sharon E.; Shaw, Chad A.; McGuire, Amy L.; Lupski, James R.

2013-01-01

Purpose Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained. Methods Array comparative genomic hybridization, a method for genome-wide detection of DNA copy-number variants, was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. Multigene copy-number variants affecting dominant, adult-onset cancer syndrome genes were also assessed. Results In our cohort, 83 single-gene copy-number variants affected 40 unique genes associated with dominant, adult-onset disorders and unrelated to the patients’ referring diagnoses (i.e., incidental) were found. Fourteen of these copy-number variants are likely disease-predisposing, 25 are likely benign, and 44 are of unknown clinical consequence. When incidental copy-number variants spanning up to 20 genes were considered, 27 copy-number variants affected 17 unique genes associated with dominant, adult-onset cancer predisposition. Conclusion Copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing. Some of these mutations may be medically actionable, enabling disease surveillance or prevention; however, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient. PMID:22878507

Phenotypic manifestations of copy number variation in chromosome 16p13.11

NARCIS (Netherlands)

Nagamani, Sandesh C. Sreenath; Erez, Ayelet; Bader, Patricia; Lalani, Seema R.; Scott, Daryl A.; Scaglia, Fernando; Plon, Sharon E.; Tsai, Chun-Hui; Reimschisel, Tyler; Roeder, Elizabeth; Malphrus, Amy D.; Eng, Patricia A.; Hixson, Patricia M.; Kang, Sung-Hae L.; Stankiewicz, Pawel; Patel, Ankita; Cheung, Sau Wai

The widespread clinical utilization of array comparative genome hybridization, has led to the unraveling of many new copy number variations (CNVs). Although some of these CNVs are clearly pathogenic, the phenotypic consequences of others, such as those in 16p13.11 remain unclear. Whereas deletions

Nonparametric testing for DNA copy number induced differential mRNA gene expression

NARCIS (Netherlands)

van Wieringen, W.N.; van de Wiel, M.A.

2009-01-01

The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two platforms may uncover meaningful biological relationships that further our understanding of cancer.

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

Science.gov (United States)

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

2009-01-01

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

Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast

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Hawthorn Lesleyann

2010-08-01

Full Text Available Abstract Background A major challenge in the interpretation of genomic profiling data generated from breast cancer samples is the identification of driver genes as distinct from bystander genes which do not impact tumorigenesis. One way to assess the relative importance of alterations in the transcriptome profile is to combine parallel analyses that assess changes in the copy number alterations (CNAs. This integrated analysis permits the identification of genes with altered expression that map within specific chromosomal regions which demonstrate copy number alterations, providing a mechanistic approach to identify the 'driver genes'. Methods We have performed whole genome analysis of CNAs using the Affymetrix 250K Mapping array on 22 infiltrating ductal carcinoma samples (IDCs. Analysis of transcript expression alterations was performed using the Affymetrix U133 Plus2.0 array on 16 IDC samples. Fourteen IDC samples were analyzed using both platforms and the data integrated. We also incorporated data from loss of heterozygosity (LOH analysis to identify genes showing altered expression in LOH regions. Results Common chromosome gains and amplifications were identified at 1q21.3, 6p21.3, 7p11.2-p12.1, 8q21.11 and 8q24.3. A novel amplicon was identified at 5p15.33. Frequent losses were found at 1p36.22, 8q23.3, 11p13, 11q23, and 22q13. Over 130 genes were identified with concurrent increases or decreases in expression that mapped to these regions of copy number alterations. LOH analysis revealed three tumors with whole chromosome or p arm allelic loss of chromosome 17. Genes were identified that mapped to copy neutral LOH regions. LOH with accompanying copy loss was detected on Xp24 and Xp25 and genes mapping to these regions with decreased expression were identified. Gene expression data highlighted the PPARα/RXRα Activation Pathway as down-regulated in the tumor samples. Conclusion We have demonstrated the utility of the application of

Genome-wide copy number variation (CNV) in patients with autoimmune Addison's disease

Science.gov (United States)

2011-01-01

Background Addison's disease (AD) is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV) could add to the repertoire of genetic susceptibility to autoimmune AD. Methods A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352) and healthy controls (n = 353) by duplex Taqman real-time polymerase chain reaction assays. Results We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. Conclusions We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28) and T cell maturation (ADAM3A). Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity. PMID:21851588

Genome-wide copy number variation (CNV in patients with autoimmune Addison's disease

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Brønstad Ingeborg

2011-08-01

Full Text Available Abstract Background Addison's disease (AD is caused by an autoimmune destruction of the adrenal cortex. The pathogenesis is multi-factorial, involving genetic components and hitherto unknown environmental factors. The aim of the present study was to investigate if gene dosage in the form of copy number variation (CNV could add to the repertoire of genetic susceptibility to autoimmune AD. Methods A genome-wide study using the Affymetrix GeneChip® Genome-Wide Human SNP Array 6.0 was conducted in 26 patients with AD. CNVs in selected genes were further investigated in a larger material of patients with autoimmune AD (n = 352 and healthy controls (n = 353 by duplex Taqman real-time polymerase chain reaction assays. Results We found that low copy number of UGT2B28 was significantly more frequent in AD patients compared to controls; conversely high copy number of ADAM3A was associated with AD. Conclusions We have identified two novel CNV associations to ADAM3A and UGT2B28 in AD. The mechanism by which this susceptibility is conferred is at present unclear, but may involve steroid inactivation (UGT2B28 and T cell maturation (ADAM3A. Characterization of these proteins may unravel novel information on the pathogenesis of autoimmunity.

A frogspawn-inspired hierarchical porous NaTi2(PO4)3-C array for high-rate and long-life aqueous rechargeable sodium batteries

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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

Copy Counts

Science.gov (United States)

Beaumont, Lee R.

1970-01-01

The level of difficulty of straight copy, which is used to measure typewriting speed, is influenced by syllable intensity (the average number of syllables per word), stroke intensity (average number of strokes per word), and high-frequency words. (CH)

CGHnormaliter: a bioconductor package for normalization of array CGH data with many CNAs.

NARCIS (Netherlands)

van Houte, B.P.P.; Binsl, T.W.; Hettling, H.; Heringa, J.

2010-01-01

Summary: CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). CGHnormaliter

ArrayBridge: Interweaving declarative array processing with high-performance computing

Energy Technology Data Exchange (ETDEWEB)

Xing, Haoyuan [The Ohio State Univ., Columbus, OH (United States); Floratos, Sofoklis [The Ohio State Univ., Columbus, OH (United States); Blanas, Spyros [The Ohio State Univ., Columbus, OH (United States); Byna, Suren [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prabhat, Prabhat [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wu, Kesheng [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brown, Paul [Paradigm4, Inc., Waltham, MA (United States)

2017-05-04

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.

Genomic Diversity Using Copy Number Variations in Worldwide Chicken Populations

Directory of Open Access Journals (Sweden)

Erica Gorla

2018-06-01

Full Text Available Recently, many studies in livestock have focused on the identification of Copy Number Variants (CNVs using high-density Single Nucleotide Polymorphism (SNP arrays, but few have focused on studying chicken ecotypes coming from many locations. CNVs are polymorphisms, which may influence phenotype and are an important source of genetic variation in populations. The aim of this study was to explore the genetic difference and structure, using a high density SNP chip in 936 individuals from seven different countries (Brazil, Italy, Egypt, Mexico, Rwanda, Sri Lanka and Uganda. The DNA was genotyped with the Affymetrix Axiom®600k Chicken Genotyping Array and processed with stringent quality controls to obtain 559,201 SNPs in 915 individuals. The Log R Ratio (LRR and the B Allele Frequency of SNPs were used to perform the CNV calling with PennCNV software based on a Hidden Markov Model analysis and the LRR was used to perform CNV detection with SVS Golden Helix software.After filtering, a total of 19,027 CNVs were detected with the SVS software, while 9,065 CNVs were identified with the Penn CNV software. The CNVs were summarized in 7,001 Copy Number Variant Regions (CNVRs and 4,414 CNVRs, using the software BedTool.The consensus analysis across the CNVRs allowed the identification of 2,820 consensus CNVR, of which 1,721 were gain, 637 loss and 462 complex, for a total length of 53 Mb corresponding to the 5 % of the GalGal5 chicken autosomes. Only the consensus CNV regions obtained from both detections were considered for further analysis.The intersection analysis performed between the chicken gene database (Gallus_gallus-5.0 and the 1,927 consensus CNVRs allowed the identification (within or partial overlap of a total of 2,354 unique genes with an official gene ID.  The CNVRs identified here represent the first comprehensive mapping in several worldwide populations, using a high-density SNP chip.

Advanced statistical tools for SNP arrays : signal calibration, copy number estimation and single array genotyping

NARCIS (Netherlands)

Rippe, Ralph Christian Alexander

2012-01-01

Fluorescence bias in in signals from individual SNP arrays can be calibrated using linear models. Given the data, the system of equations is very large, so a specialized symbolic algorithm was developed. These models are also used to illustrate that genomic waves do not exist, but are merely an

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

Directory of Open Access Journals (Sweden)

Victor Renault

Full Text Available Copy number variations (CNV include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information.To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer, a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs Affymetrix SNP Array data (Fig 1A. Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test, validated by another cohort of HCCs (p-value of 5.6e-7 (Fig 2B.aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/.aCNViewer@cephb.fr.

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.

Science.gov (United States)

Renault, Victor; Tost, Jörg; Pichon, Fabien; Wang-Renault, Shu-Fang; Letouzé, Eric; Imbeaud, Sandrine; Zucman-Rossi, Jessica; Deleuze, Jean-François; How-Kit, Alexandre

2017-01-01

Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

Science.gov (United States)

Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

2010-02-04

Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics

Directory of Open Access Journals (Sweden)

Rappaport Eric F

2010-02-01

Full Text Available Abstract Background Recent studies have shown that copy number variations (CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. Results We developed a suite of software tools and resources (CNV Workshop for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. Conclusions To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and

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.

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

Science.gov (United States)

Weitemier, Kevin; 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).

High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia.

Science.gov (United States)

Nik-Zainal, Serena; Strick, Reiner; Storer, Mekayla; Huang, Ni; Rad, Roland; Willatt, Lionel; Fitzgerald, Tomas; Martin, Vicki; Sandford, Richard; Carter, Nigel P; Janecke, Andreas R; Renner, Stefan P; Oppelt, Patricia G; Oppelt, Peter; Schulze, Christine; Brucker, Sara; Hurles, Matthew; Beckmann, Matthias W; Strissel, Pamela L; Shaw-Smith, Charles

2011-03-01

Congenital malformations involving the Müllerian ducts are observed in around 5% of infertile women. Complete aplasia of the uterus, cervix, and upper vagina, also termed Müllerian aplasia or Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome, occurs with an incidence of around 1 in 4500 female births, and occurs in both isolated and syndromic forms. Previous reports have suggested that a proportion of cases, especially syndromic cases, are caused by variation in copy number at different genomic loci. In order to obtain an overview of the contribution of copy number variation to both isolated and syndromic forms of Müllerian aplasia, copy number assays were performed in a series of 63 cases, of which 25 were syndromic and 38 isolated. A high incidence (9/63, 14%) of recurrent copy number variants in this cohort is reported here. These comprised four cases of microdeletion at 16p11.2, an autism susceptibility locus not previously associated with Müllerian aplasia, four cases of microdeletion at 17q12, and one case of a distal 22q11.2 microdeletion. Microdeletions at 16p11.2 and 17q12 were found in 4/38 (10.5%) cases with isolated Müllerian aplasia, and at 16p11.2, 17q12 and 22q11.2 (distal) in 5/25 cases (20%) with syndromic Müllerian aplasia. The finding of microdeletion at 16p11.2 in 2/38 (5%) of isolated and 2/25 (8%) of syndromic cases suggests a significant contribution of this copy number variant alone to the pathogenesis of Müllerian aplasia. Overall, the high incidence of recurrent copy number variants in all forms of Müllerian aplasia has implications for the understanding of the aetiopathogenesis of the condition, and for genetic counselling in families affected by it.

Decreases in average bacterial community rRNA operon copy number during succession.

Science.gov (United States)

Nemergut, Diana R; Knelman, Joseph E; Ferrenberg, Scott; Bilinski, Teresa; Melbourne, Brett; Jiang, Lin; Violle, Cyrille; Darcy, John L; Prest, Tiffany; Schmidt, Steven K; Townsend, Alan R

2016-05-01

Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

Array CGH analysis of a cohort of Russian patients with intellectual disability.

Science.gov (United States)

Kashevarova, Anna A; Nazarenko, Lyudmila P; Skryabin, Nikolay A; Salyukova, Olga A; Chechetkina, Nataliya N; Tolmacheva, Ekaterina N; Sazhenova, Elena A; Magini, Pamela; Graziano, Claudio; Romeo, Giovanni; Kučinskas, Vaidutis; Lebedev, Igor N

2014-02-15

The use of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated the identification of many new microdeletion/microduplication syndromes (MMSs). Furthermore, this method has allowed for the identification of copy number variations (CNVs) whose pathogenic role has yet to be uncovered. Here, we report on our application of array CGH for the identification of pathogenic CNVs in 79 Russian children with intellectual disability (ID). Twenty-six pathogenic or likely pathogenic changes in copy number were detected in 22 patients (28%): 8 CNVs corresponded to known MMSs, and 17 were not associated with previously described syndromes. In this report, we describe our findings and comment on genes potentially associated with ID that are located within the CNV regions. Copyright © 2013 Elsevier B.V. All rights reserved.

Estimating the Probability of Traditional Copying, Conditional on Answer-Copying Statistics.

Science.gov (United States)

Allen, Jeff; Ghattas, Andrew

2016-06-01

Statistics for detecting copying on multiple-choice tests produce p values measuring the probability of a value at least as large as that observed, under the null hypothesis of no copying. The posterior probability of copying is arguably more relevant than the p value, but cannot be derived from Bayes' theorem unless the population probability of copying and probability distribution of the answer-copying statistic under copying are known. In this article, the authors develop an estimator for the posterior probability of copying that is based on estimable quantities and can be used with any answer-copying statistic. The performance of the estimator is evaluated via simulation, and the authors demonstrate how to apply the formula using actual data. Potential uses, generalizability to other types of cheating, and limitations of the approach are discussed.

Conducting polymer nanowire arrays for high performance supercapacitors.

Science.gov (United States)

Wang, Kai; Wu, Haiping; Meng, Yuena; Wei, Zhixiang

2014-01-15

This Review provides a brief summary of the most recent research developments in the fabrication and application of one-dimensional ordered conducting polymers nanostructure (especially nanowire arrays) and their composites as electrodes for supercapacitors. By controlling the nucleation and growth process of polymerization, aligned conducting polymer nanowire arrays and their composites with nano-carbon materials can be prepared by employing in situ chemical polymerization or electrochemical polymerization without a template. This kind of nanostructure (such as polypyrrole and polyaniline nanowire arrays) possesses high capacitance, superior rate capability ascribed to large electrochemical surface, and an optimal ion diffusion path in the ordered nanowire structure, which is proved to be an ideal electrode material for high performance supercapacitors. Furthermore, flexible, micro-scale, threadlike, and multifunctional supercapacitors are introduced based on conducting polyaniline nanowire arrays and their composites. These prototypes of supercapacitors utilize the high flexibility, good processability, and large capacitance of conducting polymers, which efficiently extend the usage of supercapacitors in various situations, and even for a complicated integration system of different electronic devices. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High voltage load resistor array

Science.gov (United States)

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.

Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468

International Nuclear Information System (INIS)

Agelopoulos, Konstantin; Buerger, Horst; Brandt, Burkhard; Greve, Burkhard; Schmidt, Hartmut; Pospisil, Heike; Kurtz, Stefan; Bartkowiak, Kai; Andreas, Antje; Wieczorek, Marek; Korsching, Eberhard

2010-01-01

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. The basal-like/stemness type breast cancer cell line subpopulation MDA-MB-468 CD44 high /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. 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 of egfr copies. Progressive genome modulation

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.

FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.

Science.gov (United States)

Mader, Malte; Simon, Ronald; Steinbiss, Sascha; Kurtz, Stefan

2011-07-28

The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists. FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at http://www.zbh.uni-hamburg.de/fishoracle.

Inferring Variation in Copy Number Using High Throughput Sequencing Data in R.

Science.gov (United States)

Knaus, Brian J; Grünwald, Niklaus J

2018-01-01

Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori . Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR . This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions. This provides a non-parametric summary of the frequency that alleles were sequenced at. The method is applicable to organisms that have reference genomes that consist of full chromosomes or sub-chromosomal contigs. In contrast to other software designed to detect copy number variation, our method does not rely on an assumption of base ploidy, but instead infers it. We validated these approaches with the model system of Saccharomyces cerevisiae and applied it to the oomycete Phytophthora infestans , both known to vary in copy number. This functionality has been incorporated into the current release of the R package vcfR to provide modular and flexible methods to investigate copy number variation in genomic projects.

Impact of constitutional copy number variants on biological pathway evolution.

Science.gov (United States)

Poptsova, Maria; Banerjee, Samprit; Gokcumen, Omer; Rubin, Mark A; Demichelis, Francesca

2013-01-23

Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations.

Excitation of high density surface plasmon polariton vortex array

Science.gov (United States)

Kuo, Chun-Fu; Chu, Shu-Chun

2018-06-01

This study proposes a method to excite surface plasmon polariton (SPP) vortex array of high spatial density on metal/air interface. A doughnut vector beam was incident at four rectangularly arranged slits to excite SPP vortex array. The doughnut vector beam used in this study has the same field intensity distribution as the regular doughnut laser mode, TEM01* mode, but a different polarization distribution. The SPP vortex array is achieved through the matching of both polarization state and phase state of the incident doughnut vector beam with the four slits. The SPP field distribution excited in this study contains stable array-distributed time-varying optical vortices. Theoretical derivation, analytical calculation and numerical simulation were used to discuss the characteristics of the induced SPP vortex array. The period of the SPP vortex array induced by the proposed method had only half SPPs wavelength. In addition, the vortex number in an excited SPP vortex array can be increased by enlarging the structure.

Coded aperture subreflector array for high resolution radar imaging

Science.gov (United States)

Lynch, Jonathan J.; Herrault, Florian; Kona, Keerti; Virbila, Gabriel; McGuire, Chuck; Wetzel, Mike; Fung, Helen; Prophet, Eric

2017-05-01

HRL Laboratories has been developing a new approach for high resolution radar imaging on stationary platforms. High angular resolution is achieved by operating at 235 GHz and using a scalable tile phased array architecture that has the potential to realize thousands of elements at an affordable cost. HRL utilizes aperture coding techniques to minimize the size and complexity of the RF electronics needed for beamforming, and wafer level fabrication and integration allow tiles containing 1024 elements to be manufactured with reasonable costs. This paper describes the results of an initial feasibility study for HRL's Coded Aperture Subreflector Array (CASA) approach for a 1024 element micromachined antenna array with integrated single-bit phase shifters. Two candidate electronic device technologies were evaluated over the 170 - 260 GHz range, GaN HEMT transistors and GaAs Schottky diodes. Array structures utilizing silicon micromachining and die bonding were evaluated for etch and alignment accuracy. Finally, the overall array efficiency was estimated to be about 37% (not including spillover losses) using full wave array simulations and measured device performance, which is a reasonable value at 235 GHz. Based on the measured data we selected GaN HEMT devices operated passively with 0V drain bias due to their extremely low DC power dissipation.

Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors

NARCIS (Netherlands)

Jong, C.; Marchiori, E.; van der Vaart, A.W.; Chin, S.F.; Carvalho, B; Tijssen, M.; Eijk, P.P.; van den IJssel, P.; Grabsch, H.; Quirke, P.; Oudejans, J.J.; Meijer, G.J.; Caldas, C.; Ylstra, B.

2007-01-01

A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array comparative genomic hybridization (array CGH); however, the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized.

High copy number of highly similar mariner-like transposons in planarian (Platyhelminthe): evidence for a trans-phyla horizontal transfer.

Science.gov (United States)

Garcia-Fernàndez, J; Bayascas-Ramírez, J R; Marfany, G; Muñoz-Mármol, A M; Casali, A; Baguñà, J; Saló, E

1995-05-01

Several DNA sequences similar to the mariner element were isolated and characterized in the platyhelminthe Dugesia (Girardia) tigrina. They were 1,288 bp long, flanked by two 32 bp-inverted repeats, and contained a single 339 amino acid open-reading frame (ORF) encoding the transposase. The number of copies of this element is approximately 8,000 per haploid genome, constituting a member of the middle-repetitive DNA of Dugesia tigrina. Sequence analysis of several elements showed a high percentage of conservation between the different copies. Most of them presented an intact ORF and the standard signals of actively expressed genes, which suggests that some of them are or have recently been functional transposons. The high degree of similarity shared with other mariner elements from some arthropods, together with the fact that this element is undetectable in other planarian species, strongly suggests a case of horizontal transfer between these two distant phyla.

Experimental Study of Arcing on High-voltage Solar Arrays

Science.gov (United States)

Vayner, Boris; Galofaro, Joel; Ferguson, Dale

2005-01-01

The main obstacle to the implementation of a high-voltage solar array in space is arcing on the conductor-dielectric junctions exposed to the surrounding plasma. One obvious solution to this problem would be the installation of fully encapsulated solar arrays which were not having exposed conductors at all. However, there are many technological difficulties that must be overcome before the employment of fully encapsulated arrays will turn into reality. An alternative solution to raise arc threshold by modifications of conventionally designed solar arrays looks more appealing, at least in the nearest future. A comprehensive study of arc inception mechanism [1-4] suggests that such modifications can be done in the following directions: i) to insulate conductor-dielectric junction from a plasma environment (wrapthrough interconnects); ii) to change a coverglass geometry (overhang); iii) to increase a coverglass thickness; iiii) to outgas areas of conductor-dielectric junctions. The operation of high-voltage array in LEO produces also the parasitic current power drain on the electrical system. Moreover, the current collected from space plasma by solar arrays determines the spacecraft floating potential that is very important for the design of spacecraft and its scientific apparatus. In order to verify the validity of suggested modifications and to measure current collection five different solar array samples have been tested in large vacuum chamber. Each sample (36 silicon based cells) consists of three strings containing 12 cells connected in series. Thus, arc rate and current collection can be measured on every string independently, or on a whole sample when strings are connected in parallel. The heater installed in the chamber provides the possibility to test samples under temperature as high as 80 C that simulates the LEO operational temperature. The experimental setup is described below.

Gauge field copies

International Nuclear Information System (INIS)

Bollini, C.G.; Giambiagi, J.J.; Tiomno, J.

1979-01-01

The construction of field strength copies without any gauge constraint is discussed. Several examples are given, one of which is not only a field strength copy but also (at the same time) a 'current copy'. (author) [pt

Wire array z-pinch insights for high X-ray power generation

International Nuclear Information System (INIS)

Sanford, T.W.L.; Marder, B.M.; Desjarlais, M.P.

1998-01-01

The discovery that the use of very large numbers of wires enables high x-ray power to be generated from wire-array z-pinches represents a breakthrough in load design for large pulsed power generators, and has permitted high temperatures to be generated in radiation cavities on Saturn and Z. In this paper, changes in x-ray emission characteristics as a function of wire number, array mass, and load radius, for 20-mm-long aluminum arrays on Saturn that led to these breakthrough hohlraum results, are discussed and compared with a few related emission characteristics of high-wire-number aluminum and tungsten arrays on Z. X-ray measurement comparisons with analytic models and 2-D radiation-magnetohydrodynamic (RMHC) code simulations in the x-y and r-z planes provide confidence in the ability of the models and codes to predict future x-ray performance with very-large-number wire arrays

Wire array z-pinch insights for high X-ray power generation

Energy Technology Data Exchange (ETDEWEB)

Sanford, T.W.L.; Marder, B.M.; Desjarlais, M.P. [and others

1998-12-31

The discovery that the use of very large numbers of wires enables high x-ray power to be generated from wire-array z-pinches represents a breakthrough in load design for large pulsed power generators, and has permitted high temperatures to be generated in radiation cavities on Saturn and Z. In this paper, changes in x-ray emission characteristics as a function of wire number, array mass, and load radius, for 20-mm-long aluminum arrays on Saturn that led to these breakthrough hohlraum results, are discussed and compared with a few related emission characteristics of high-wire-number aluminum and tungsten arrays on Z. X-ray measurement comparisons with analytic models and 2-D radiation-magnetohydrodynamic (RMHC) code simulations in the x-y and r-z planes provide confidence in the ability of the models and codes to predict future x-ray performance with very-large-number wire arrays.

Wire array z-pinch insights for high x-ray power generation

Energy Technology Data Exchange (ETDEWEB)

Sanford, T.W.L.; Mock, R.C.; Marder, B.M. [and others

1997-12-31

The discovery that the use of very large numbers of wires enables high x-ray power to be generated from wire-array z-pinches represents a breakthrough in load design for large pulsed power generators, and has permitted high temperatures to be generated in radiation cavities on Saturn and Z. In this paper, changes in x-ray emission characteristics as a function of wire number, array mass, and load radius, for 20-mm-long aluminum arrays on Saturn that led to these breakthrough hohlraum results, are discussed and compared with a few related emission characteristics of high-wire-number aluminum and tungsten arrays on Z. X-ray measurement comparisons with analytic models and 2-D radiation-magnetohydrodynamic (RMHC) code simulations in the x-y and r-z planes provide confidence in the ability of the models and codes to predict future x-ray performance with very-large-number wire arrays.

Wire array z-pinch insights for high x-ray power generation

Energy Technology Data Exchange (ETDEWEB)

Sanford, T.W.L.; Mock, R.C.; Nash, T.J. [and others

1998-08-01

The discovery that the use of very large numbers of wires enables high x-ray power to be generated from wire-array z-pinches represents a breakthrough in load design for large pulsed power generators, and has permitted high temperatures to be generated in radiation cavities on Saturn. In this paper, changes in x-ray emission characteristics as a function of wire number, array mass, and load radius, for 20-mm-long aluminum arrays on Saturn that led to these breakthrough hohlraum results, are discussed and compared with a few related emission characteristics of high-wire-number aluminum and tungsten arrays on Z. X=ray measurement comparisons with analytic models and 2-D radiation-magnetohydrodynamic (RMHC) code simulations in the x-y and r-z planes provide confidence in the ability of the models and codes to predict future x-ray performance with very-large-number wire arrays.

Wire array z-pinch insights for high x-ray power generation

International Nuclear Information System (INIS)

Sanford, T.W.L.; Mock, R.C.; Marder, B.M.

1998-08-01

The discovery that the use of very large numbers of wires enables high x-ray power to be generated from wire-array z-pinches represents a breakthrough in load design for large pulsed power generators, and has permitted high temperatures to be generated in radiation cavities on Saturn and Z. In this paper, changes in x-ray emission characteristics as a function of wire number, array mass, and load radius, for 20-mm-long aluminum arrays on Saturn that led to these breakthrough hohlraum results, are discussed and compared with a few related emission characteristics of high-wire-number aluminum and tungsten arrays on Z. X=ray measurement comparisons with analytic models and 2-D radiation-magnetohydrodynamic (RMHC) code simulations in the x-y and r-z planes provide confidence in the ability of the models and codes to predict future x-ray performance with very-large-number wire arrays

Symmetric aluminum-wire arrays generate high-quality Z pinches at large array radii

International Nuclear Information System (INIS)

Sanford, T.W.; Mock, R.C.; Spielman, R.B.; Peterson, D.L.; Mosher, D.; Roderick, N.F.

1998-01-01

A Saturn-accelerator study of annular, aluminum-wire array, Z-pinch implosions, in the calculated high-wire-number plasma-shell regime [Phys. Rev. Lett. 77, 5063 (1996)], shows that the radiated x-ray pulse width increases from about 4 nsec to about 7 nsec, when the radius of the array is increased from 8.75 to 20 mm at a fixed array mass of 0.6 mg. Eulerian radiation- magnetohydrodynamic code (E-RMHC) simulations in the r-z plane suggest that this pulse-width increase with radius is due to the faster growth of the shell thickness (that arises from a two-stage development in the magnetic Rayleigh - Taylor instability) relative to the increase in the shell implosion velocity. Over the array radii explored, the measured peak total x-ray power of ∼40 TW and energy of ∼325 kJ show little change outside of a ±15% shot-to-shot fluctuation and are consistent with the E-RMHC simulations. Similarly, the measured peak K-shell (lines plus continuum) power of ∼8 TW and energy of ∼70 kJ show little change with radius. The minimal change in K-shell yield is in agreement with simple K-shell radiation scaling models that assume a fixed radial compression for all initial array radii. These results suggest that the improved uniformity provided by the large number of wires in the initial array reduces the disruptive effects of the Rayleigh - Taylor instability observed in small-wire-number imploding loads. copyright 1998 American Institute of Physics

Symmetric aluminum-wire arrays generate high-quality Z pinches at large array radii

Science.gov (United States)

Sanford, T. W. L.; Mock, R. C.; Spielman, R. B.; Peterson, D. L.; Mosher, D.; Roderick, N. F.

1998-10-01

A Saturn-accelerator study of annular, aluminum-wire array, Z-pinch implosions, in the calculated high-wire-number plasma-shell regime [Phys. Rev. Lett. 77, 5063 (1996)], shows that the radiated x-ray pulse width increases from about 4 nsec to about 7 nsec, when the radius of the array is increased from 8.75 to 20 mm at a fixed array mass of 0.6 mg. Eulerian radiation- magnetohydrodynamic code (E-RMHC) simulations in the r-z plane suggest that this pulse-width increase with radius is due to the faster growth of the shell thickness (that arises from a two-stage development in the magnetic Rayleigh-Taylor instability) relative to the increase in the shell implosion velocity. Over the array radii explored, the measured peak total x-ray power of ˜40 TW and energy of ˜325 kJ show little change outside of a ±15% shot-to-shot fluctuation and are consistent with the E-RMHC simulations. Similarly, the measured peak K-shell (lines plus continuum) power of ˜8 TW and energy of ˜70 kJ show little change with radius. The minimal change in K-shell yield is in agreement with simple K-shell radiation scaling models that assume a fixed radial compression for all initial array radii. These results suggest that the improved uniformity provided by the large number of wires in the initial array reduces the disruptive effects of the Rayleigh-Taylor instability observed in small-wire-number imploding loads.

Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

NARCIS (Netherlands)

Armour, J.A.; Palla, R.; Zeeuwen, P.L.J.M.; Heijer, M. den; Schalkwijk, J.; Hollox, E.J.

2007-01-01

Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and

Very high frequency (beyond 100 MHz) PZT kerfless linear arrays.

Science.gov (United States)

Wu, Da-Wei; Zhou, Qifa; Geng, Xuecang; Liu, Chang-Geng; Djuth, Frank; Shung, K Kirk

2009-10-01

This paper presents the design, fabrication, and measurements of very high frequency kerfless linear arrays prepared from PZT film and PZT bulk material. A 12-microm PZT thick film fabricated from PZT-5H powder/solution composite and a piece of 15-microm PZT-5H sheet were used to fabricate 32-element kerfless high-frequency linear arrays with photolithography. The PZT thick film was prepared by spin-coating of PZT sol-gel composite solution. The thin PZT-5H sheet sample was prepared by lapping a PZT-5H ceramic with a precision lapping machine. The measured results of the 2 arrays were compared. The PZT film array had a center frequency of 120 MHz, a bandwidth of 60% with a parylene matching layer, and an insertion loss of 41 dB. The PZT ceramic sheet array was found to have a center frequency of 128 MHz with a poorer bandwidth (40% with a parylene matching layer) but a better sensitivity (28 dB insertion loss).

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.

A Low VSWR and High Efficiency Waveguide Feed Antenna Array

Directory of Open Access Journals (Sweden)

Zhao Xiao-Fang

2018-01-01

Full Text Available A low VSWR and high efficiency antenna array operating in the Ku band for satellite communications is presented in this paper. To achieve high radiation efficiency and broad enough bandwidth, all-metal radiation elements and full-corporate waveguide feeding network are employed. As the general milling method is used in the multilayer antenna array fabrication, the E-plane waveguide feeding network is adopted here to suppress the wave leakage caused by the imperfect connectivity between adjacent layers. A 4 × 8 elements array prototype was fabricated and tested for verification. The measured results of proposed antenna array show bandwidth of 6.9% (13.9–14.8 GHz for VSWR < 1.5. Furthermore, antenna gain and efficiency of higher than 22.2 dBi and 80% are also exhibited, respectively.

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.

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...

Symmetric aluminum-wire arrays generate high-quality Z pinches at large array radii

Energy Technology Data Exchange (ETDEWEB)

Sanford, T.W.; Mock, R.C.; Spielman, R.B. [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185 (United States); Peterson, D.L. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545-0010 (United States); Mosher, D. [Naval Research Laboratory, Pulsed Power Physics Branch, Washington, DC 20375 (United States); Roderick, N.F. [University of New Mexico, Albuquerque, New Mexico 87131 (United States)

1998-10-01

A Saturn-accelerator study of annular, aluminum-wire array, Z-pinch implosions, in the calculated high-wire-number plasma-shell regime [Phys. Rev. Lett. {bold 77}, 5063 (1996)], shows that the radiated x-ray pulse width increases from about 4 nsec to about 7 nsec, when the radius of the array is increased from 8.75 to 20 mm at a fixed array mass of 0.6 mg. Eulerian radiation- magnetohydrodynamic code (E-RMHC) simulations in the r-z plane suggest that this pulse-width increase with radius is due to the faster growth of the shell thickness (that arises from a two-stage development in the magnetic Rayleigh{endash}Taylor instability) relative to the increase in the shell implosion velocity. Over the array radii explored, the measured peak total x-ray power of {approximately}40 TW and energy of {approximately}325 kJ show little change outside of a {plus_minus}15{percent} shot-to-shot fluctuation and are consistent with the E-RMHC simulations. Similarly, the measured peak {ital K}-shell (lines plus continuum) power of {approximately}8 TW and energy of {approximately}70 kJ show little change with radius. The minimal change in {ital K}-shell yield is in agreement with simple {ital K}-shell radiation scaling models that assume a fixed radial compression for all initial array radii. These results suggest that the improved uniformity provided by the large number of wires in the initial array reduces the disruptive effects of the Rayleigh{endash}Taylor instability observed in small-wire-number imploding loads. {copyright} {ital 1998 American Institute of Physics.}

Identification of copy number variants defining genomic differences among major human groups.

Directory of Open Access Journals (Sweden)

Lluís Armengol

Full Text Available BACKGROUND: Understanding the genetic contribution to phenotype variation of human groups is necessary to elucidate differences in disease predisposition and response to pharmaceutical treatments in different human populations. METHODOLOGY/PRINCIPAL FINDINGS: We have investigated the genome-wide profile of structural variation on pooled samples from the three populations studied in the HapMap project by comparative genome hybridization (CGH in different array platforms. We have identified and experimentally validated 33 genomic loci that show significant copy number differences from one population to the other. Interestingly, we found an enrichment of genes related to environment adaptation (immune response, lipid metabolism and extracellular space within these regions and the study of expression data revealed that more than half of the copy number variants (CNVs translate into gene-expression differences among populations, suggesting that they could have functional consequences. In addition, the identification of single nucleotide polymorphisms (SNPs that are in linkage disequilibrium with the copy number alleles allowed us to detect evidences of population differentiation and recent selection at the nucleotide variation level. CONCLUSIONS: Overall, our results provide a comprehensive view of relevant copy number changes that might play a role in phenotypic differences among major human populations, and generate a list of interesting candidates for future studies.

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...

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

Directory of Open Access Journals (Sweden)

Xiaohong R Yang

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

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

Science.gov (United States)

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

2008-02-01

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

The Role of Constitutional Copy Number Variants in Breast Cancer

Science.gov (United States)

Walker, Logan C.; Wiggins, George A.R.; Pearson, John F.

2015-01-01

Constitutional copy number variants (CNVs) include inherited and de novo deviations from a diploid state at a defined genomic region. These variants contribute significantly to genetic variation and disease in humans, including breast cancer susceptibility. Identification of genetic risk factors for breast cancer in recent years has been dominated by the use of genome-wide technologies, such as single nucleotide polymorphism (SNP)-arrays, with a significant focus on single nucleotide variants. To date, these large datasets have been underutilised for generating genome-wide CNV profiles despite offering a massive resource for assessing the contribution of these structural variants to breast cancer risk. Technical challenges remain in determining the location and distribution of CNVs across the human genome due to the accuracy of computational prediction algorithms and resolution of the array data. Moreover, better methods are required for interpreting the functional effect of newly discovered CNVs. In this review, we explore current and future application of SNP array technology to assess rare and common CNVs in association with breast cancer risk in humans. PMID:27600231

Piezoelectric Nanotube Array for Broadband High-Frequency Ultrasonic Transducer.

Science.gov (United States)

Liew, Weng Heng; Yao, Kui; Chen, Shuting; Tay, Francis Eng Hock

2018-03-01

Piezoelectric materials are vital in determining ultrasonic transducer and imaging performance as they offer the function for conversion between mechanical and electrical energy. Ultrasonic transducers with high-frequency operation suffer from performance degradation and fabrication difficulty of the demanded piezoelectric materials. Hence, we propose 1-D polymeric piezoelectric nanostructure with controlled nanoscale features to overcome the technical limitations of high-frequency ultrasonic transducers. For the first time, we demonstrate the integration of a well-aligned piezoelectric nanotube array to produce a high-frequency ultrasonic transducer with outstanding performance. We find that nanoconfinement-induced polarization orientation and unique nanotube structure lead to significantly improved piezoelectric and ultrasonic transducing performance over the conventional piezoelectric thin film. A large bandwidth, 126% (-6 dB), is achieved at high center frequency, 108 MHz. Transmission sensitivity of nanotube array is found to be 46% higher than that of the monolithic thin film transducer attributed to the improved electromechanical coupling effectiveness and impedance match. We further demonstrate high-resolution scanning, ultrasonic imaging, and photoacoustic imaging using the obtained nanotube array transducers, which is valuable for biomedical imaging applications in the future.

Using Copy Number Alterations to Identify New Therapeutic Targets for Bladder Carcinoma

Directory of Open Access Journals (Sweden)

Donatella Conconi

2016-02-01

Full Text Available Bladder cancer represents the ninth most widespread malignancy throughout the world. It is characterized by the presence of two different clinical and prognostic subtypes: non-muscle-invasive bladder cancers (NMIBCs and muscle-invasive bladder cancers (MIBCs. MIBCs have a poor outcome with a common progression to metastasis. Despite improvements in knowledge, treatment has not advanced significantly in recent years, with the absence of new therapeutic targets. Because of the limitations of current therapeutic options, the greater challenge will be to identify biomarkers for clinical application. For this reason, we compared our array comparative genomic hybridization (array-CGH results with those reported in literature for invasive bladder tumors and, in particular, we focused on the evaluation of copy number alterations (CNAs present in biopsies and retained in the corresponding cancer stem cell (CSC subpopulations that should be the main target of therapy. According to our data, CCNE1, MYC, MDM2 and PPARG genes could be interesting therapeutic targets for bladder CSC subpopulations. Surprisingly, HER2 copy number gains are not retained in bladder CSCs, making the gene-targeted therapy less interesting than the others. These results provide precious advice for further study on bladder therapy; however, the clinical importance of these results should be explored.

Detection of copy number variations and their effects in Chinese bulls

KAUST Repository

Zhang, Liangzhi

2014-06-17

Background: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.Results: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more " loss" events than both " gain" and " both" ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits.Conclusions: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle\\'s evolution and breeding researches. 2014 Zhang et al.; licensee BioMed Central Ltd.

Developing high coercivity in large diameter cobalt nanowire arrays

Science.gov (United States)

Montazer, A. H.; Ramazani, A.; Almasi Kashi, M.; Zavašnik, J.

2016-11-01

Regardless of the synthetic method, developing high magnetic coercivity in ferromagnetic nanowires (NWs) with large diameters has been a challenge over the past two decades. Here, we report on the synthesis of highly coercive cobalt NW arrays with diameters of 65 and 80 nm, which are embedded in porous anodic alumina templates with high-aspect-ratio pores. Using a modified electrochemical deposition method enabled us to reach room temperature coercivity and remanent ratio up to 3000 Oe and 0.70, respectively, for highly crystalline as-synthesized hcp cobalt NW arrays with a length of 8 μm. The first-order reversal curve (FORC) analysis showed the presence of both soft and hard magnetic phases along the length of the resulting NWs. To develop higher coercive fields, the length of the NWs was then gradually reduced in order from bottom to top, thereby reaching NW sections governed by the hard phase. Consequently, this resulted in record high coercivities of 4200 and 3850 Oe at NW diameters of 65 and 80 nm, respectively. In this case, the FORC diagrams confirmed a significant reduction in interactions between the magnetic phases of the remaining sections of NWs. At this stage, x-ray diffraction (XRD) and dark-field transmission electron microscopy analyses indicated the formation of highly crystalline bamboo-like sections along the [0 0 2] direction during a progressive pulse-controlled electrochemical growth of NW arrays under optimized parameters. Our results both provide new insights into the growth process, crystalline characteristics and magnetic phases along the length of large diameter NW arrays and, furthermore, develop the performance of pure 3d transition magnetic NWs.

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.

Getting DNA copy numbers without control samples.

Science.gov (United States)

Ortiz-Estevez, Maria; Aramburu, Ander; Rubio, Angel

2012-08-16

The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias.We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package

EUROGAM: A high efficiency escape suppressed spectrometer array

Energy Technology Data Exchange (ETDEWEB)

Nolan, P J [Liverpool Univ. (United Kingdom). Oliver Lodge Lab.

1992-08-01

EUROGAM is a UK-France collaboration to develop and build a high efficiency escape suppressed spectrometer array. The project has involved the development of both germanium (Ge) and bismuth germanate (BGO) detectors to produce crystals which are both bigger and have a more complex geometry. As a major investment for the future, the collaboration has developed a new electronics and data acquisition system based on the VXI and VME standards. The array will start its experimental programme in mid 1992 at the Nuclear Structure Facility at Daresbury, U.K. At this stage it will have a total photopeak efficiency (for 1.33 MeV gamma-rays) of {approx} 4.5%. This will give an improvement in sensitivity (relative to presently operating arrays) of a factor of about 10. When EUROGAM moves to France in mid 1993 its photopeak efficiency will have increased to about 8.5% which will result in an increase in sensitivity of a further factor of about 10. In this article I will concentrate on the array which will operate at Daresbury in 1992 and only briefly cover the developments which will take place for the full array before it is used in France in 1993. (author). 13 refs., 2 tabs., 10 figs.

EUROGAM: A high efficiency escape suppressed spectrometer array

International Nuclear Information System (INIS)

Nolan, P.J.

1992-01-01

EUROGAM is a UK-France collaboration to develop and build a high efficiency escape suppressed spectrometer array. The project has involved the development of both germanium (Ge) and bismuth germanate (BGO) detectors to produce crystals which are both bigger and have a more complex geometry. As a major investment for the future, the collaboration has developed a new electronics and data acquisition system based on the VXI and VME standards. The array will start its experimental programme in mid 1992 at the Nuclear Structure Facility at Daresbury, U.K. At this stage it will have a total photopeak efficiency (for 1.33 MeV gamma-rays) of ∼ 4.5%. This will give an improvement in sensitivity (relative to presently operating arrays) of a factor of about 10. When EUROGAM moves to France in mid 1993 its photopeak efficiency will have increased to about 8.5% which will result in an increase in sensitivity of a further factor of about 10. In this article I will concentrate on the array which will operate at Daresbury in 1992 and only briefly cover the developments which will take place for the full array before it is used in France in 1993. (author). 13 refs., 2 tabs., 10 figs

Phase-locked, high power, mid-infrared quantum cascade laser arrays

Science.gov (United States)

Zhou, W.; Slivken, S.; Razeghi, M.

2018-04-01

We demonstrate phase-locked, high power quantum cascade laser arrays, which are combined using a monolithic, tree array multimode interferometer, with emission wavelengths around 4.8 μm. A maximum output power of 15 W was achieved from an eight-element laser array, which has only a slightly higher threshold current density and a similar slope efficiency compared to a Fabry-Perot laser of the same length. Calculated multimode interferometer splitting loss is on the order of 0.27 dB for the in-phase supermode. In-phase supermode operation with nearly ideal behavior is demonstrated over the working current range of the array.

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...

Three gangliogliomas: results of GTG-banding, SKY, genome-wide high resolution SNP-array, gene expression and review of the literature.

Science.gov (United States)

Xu, Li-Xin; Holland, Heidrun; Kirsten, Holger; Ahnert, Peter; Krupp, Wolfgang; Bauer, Manfred; Schober, Ralf; Mueller, Wolf; Fritzsch, Dominik; Meixensberger, Jürgen; Koschny, Ronald

2015-04-01

According to the World Health Organization gangliogliomas are classified as well-differentiated and slowly growing neuroepithelial tumors, composed of neoplastic mature ganglion and glial cells. It is the most frequent tumor entity observed in patients with long-term epilepsy. Comprehensive cytogenetic and molecular cytogenetic data including high-resolution genomic profiling (single nucleotide polymorphism (SNP)-array) of gangliogliomas are scarce but necessary for a better oncological understanding of this tumor entity. For a detailed characterization at the single cell and cell population levels, we analyzed genomic alterations of three gangliogliomas using trypsin-Giemsa banding (GTG-banding) and by spectral karyotyping (SKY) in combination with SNP-array and gene expression array experiments. By GTG and SKY, we could confirm frequently detected chromosomal aberrations (losses within chromosomes 10, 13 and 22; gains within chromosomes 5, 7, 8 and 12), and identify so far unknown genetic aberrations like the unbalanced non-reciprocal translocation t(1;18)(q21;q21). Interestingly, we report on the second so far detected ganglioglioma with ring chromosome 1. Analyses of SNP-array data from two of the tumors and respective germline DNA (peripheral blood) identified few small gains and losses and a number of copy-neutral regions with loss of heterozygosity (LOH) in germline and in tumor tissue. In comparison to germline DNA, tumor tissues did not show substantial regions with significant loss or gain or with newly developed LOH. Gene expression analyses of tumor-specific genes revealed similarities in the profile of the analyzed samples regarding different relevant pathways. Taken together, we describe overlapping but also distinct and novel genetic aberrations of three gangliogliomas. © 2014 Japanese Society of Neuropathology.

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.

A swimming pool array for ultra high energy showers

Science.gov (United States)

Yodh, Gaurang B.; Shoup, Anthony; Barwick, Steve; Goodman, Jordan A.

1992-11-01

A very preliminary design concept for an array using water Cherenkov counters, built out of commercially available backyard swimming pools, to sample the electromagnetic and muonic components of ultra high energy showers at large lateral distances is presented. The expected performance of the pools is estimated using the observed lateral distributions by scintillator and water Cherenkov arrays at energies above 1019 eV and simulations.

Array-CGH Analysis in a Cohort of Phenotypically Well-Characterized Individuals with "Essential" Autism Spectrum Disorders

Science.gov (United States)

Napoli, Eleonora; Russo, Serena; Casula, Laura; Alesi, Viola; Amendola, Filomena Alessandra; Angioni, Adriano; Novelli, Antonio; Valeri, Giovanni; Menghini, Deny; Vicari, Stefano

2018-01-01

Copy-number variants (CNVs) are associated with susceptibility to autism spectrum disorder (ASD). To detect the presence of CNVs, we conducted an array-comparative genomic hybridization (array-CGH) analysis in 133 children with "essential" ASD phenotype. Genetic analyses documented that 12 children had causative CNVs (C-CNVs), 29…

Diagnostic Interpretation of Array Data Using Public Databases and Internet Sources

NARCIS (Netherlands)

de Leeuw, Nicole; Dijkhuizen, Trijnie; Hehir-Kwa, Jayne Y.; Carter, Nigel P.; Feuk, Lars; Firth, Helen V.; Kuhn, Robert M.; Ledbetter, David H.; Martin, Christa Lese; van Ravenswaaij-Arts, Conny M. A.; Scherer, Steven W.; Shams, Soheil; Van Vooren, Steven; Sijmons, Rolf; Swertz, Morris; Hastings, Ros

The range of commercially available array platforms and analysis software packages is expanding and their utility is improving, making reliable detection of copy-number variants (CNVs) relatively straightforward. Reliable interpretation of CNV data, however, is often difficult and requires

Hardened Solar Array High Temperature Adhesive.

Science.gov (United States)

1981-04-01

SHERWOOO. D SASIU.IS F3361S-0-C-201S UNCLASSI ED 1AC-SCG-IOOIIR AFVAL-TR-OL-201? NLm,,hinii EhhhEE11I1 AFWAL-TR-81- 2017 i : HARDENED SOLAR ARRAY D HIGH...Tg and as a consequence forms a film on the container and also precipitates as tacky waxlike particles, rather than the desired flocullated

Assessment of copy number variations in 120 patients with Poland syndrome.

Science.gov (United States)

Vaccari, Carlotta Maria; Tassano, Elisa; Torre, Michele; Gimelli, Stefania; Divizia, Maria Teresa; Romanini, Maria Victoria; Bossi, Simone; Musante, Ilaria; Valle, Maura; Senes, Filippo; Catena, Nunzio; Bedeschi, Maria Francesca; Baban, Anwar; Calevo, Maria Grazia; Acquaviva, Massimo; Lerone, Margherita; Ravazzolo, Roberto; Puliti, Aldamaria

2016-11-25

Poland Syndrome (PS) is a rare congenital disorder presenting with agenesis/hypoplasia of the pectoralis major muscle variably associated with thoracic and/or upper limb anomalies. Most cases are sporadic, but familial recurrence, with different inheritance patterns, has been observed. The genetic etiology of PS remains unknown. Karyotyping and array-comparative genomic hybridization (CGH) analyses can identify genomic imbalances that can clarify the genetic etiology of congenital and neurodevelopmental disorders. We previously reported a chromosome 11 deletion in twin girls with pectoralis muscle hypoplasia and skeletal anomalies, and a chromosome six deletion in a patient presenting a complex phenotype that included pectoralis muscle hypoplasia. However, the contribution of genomic imbalances to PS remains largely unknown. To investigate the prevalence of chromosomal imbalances in PS, standard cytogenetic and array-CGH analyses were performed in 120 PS patients. Following the application of stringent filter criteria, 14 rare copy number variations (CNVs) were identified in 14 PS patients in different regions outside known common copy number variations: seven genomic duplications and seven genomic deletions, enclosing the two previously reported PS associated chromosomal deletions. These CNVs ranged from 0.04 to 4.71 Mb in size. Bioinformatic analysis of array-CGH data indicated gene enrichment in pathways involved in cell-cell adhesion, DNA binding and apoptosis processes. The analysis also provided a number of candidate genes possibly causing the developmental defects observed in PS patients, among others REV3L, a gene coding for an error-prone DNA polymerase previously associated with Möbius Syndrome with variable phenotypes including pectoralis muscle agenesis. A number of rare CNVs were identified in PS patients, and these involve genes that represent candidates for further evaluation. Rare inherited CNVs may contribute to, or represent risk factors of PS

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

Directory of Open Access Journals (Sweden)

Angela Stokes

Full Text Available 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

High-Performance Flexible Force and Temperature Sensing Array with a Robust Structure

Science.gov (United States)

Kim, Min-Seok; Song, Han-Wook; Park, Yon-Kyu

We have developed a flexible tactile sensor array capable of sensing physical quantities, e.g. force and temperature with high-performances and high spatial resolution. The fabricated tactile sensor consists of 8 × 8 force measuring array with 1 mm spacing and a thin metal (copper) temperature sensor. The flexible force sensing array consists of sub-millimetre-size bar-shaped semi-conductor strain gage array attached to a thin and flexible printed circuit board covered by stretchable elastomeric material on both sides. This design incorporates benefits of both materials; the semi-conductor's high performance and the polymer's mechanical flexibility and robustness, while overcoming their drawbacks of those two materials. Special fabrication processes, so called “dry-transfer technique” have been used to fabricate the tactile sensor along with standard micro-fabrication processes.

Colloidal silica films for high-capacity DNA arrays

Science.gov (United States)

Glazer, Marc Irving

The human genome project has greatly expanded the amount of genetic information available to researchers, but before this vast new source of data can be fully utilized, techniques for rapid, large-scale analysis of DNA and RNA must continue to develop. DNA arrays have emerged as a powerful new technology for analyzing genomic samples in a highly parallel format. The detection sensitivity of these arrays is dependent on the quantity and density of immobilized probe molecules. We have investigated substrates with a porous, "three-dimensional" surface layer as a means of increasing the surface area available for the synthesis of oligonucleotide probes, thereby increasing the number of available probes and the amount of detectable bound target. Porous colloidal silica films were created by two techniques. In the first approach, films were deposited by spin-coating silica colloid suspensions onto flat glass substrates, with the pores being formed by the natural voids between the solid particles (typically 23nm pores, 35% porosity). In the second approach, latex particles were co-deposited with the silica and then pyrolyzed, creating films with larger pores (36 nm), higher porosity (65%), and higher surface area. For 0.3 mum films, enhancements of eight to ten-fold and 12- to 14-fold were achieved with the pure silica films and the films "templated" with polymer latex, respectively. In gene expression assays for up to 7,000 genes using complex biological samples, the high-capacity films provided enhanced signals and performed equivalently or better than planar glass on all other functional measures, confirming that colloidal silica films are a promising platform for high-capacity DNA arrays. We have also investigated the kinetics of hybridization on planar glass and high-capacity substrates. Adsorption on planar arrays is similar to ideal Langmuir-type adsorption, although with an "overshoot" at high solution concentration. Hybridization on high-capacity films is

Fast commutation of high current in double wire array Z-pinch loads

International Nuclear Information System (INIS)

Davis, J.; Gondarenko, N.A.; Velikovich, A.L.

1997-01-01

A dynamic model of multi-MA current commutation in a double wire array Z-pinch load is proposed and studied theoretically. Initially, the load is configured as nested concentric wire arrays, with the current driven through the outer array and imploding it. Once the outer array or the annular plasma shell formed from it approaches the inner array, the imploded plasma might penetrate through the gaps between the wires, but the azimuthal magnetic field is trapped due to both the high conductivity of the inner wires and the inductive coupling between the two parts of the array, causing a rapid switching of the total current to the inner part of the array. copyright 1997 American Institute of Physics

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.

Single-Step Fabrication of High-Density Microdroplet Arrays of Low-Surface-Tension Liquids.

Science.gov (United States)

Feng, Wenqian; Li, Linxian; Du, Xin; Welle, Alexander; Levkin, Pavel A

2016-04-01

A facile approach for surface patterning that enables single-step fabrication of high-density arrays of low-surface-tension organic-liquid microdroplets is described. This approach enables miniaturized and parallel high-throughput screenings in organic solvents, formation of homogeneous arrays of hydrophobic nanoparticles, polymer micropads of specific shapes, and polymer microlens arrays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Worst-case-efficient dynamic arrays in practice

DEFF Research Database (Denmark)

Katajainen, Jyrki

2016-01-01

The basic operations of a dynamic array are operator[], push back, and pop back. This study is an examination of variations of dynamic arrays that support these operations at O(1) worst-case cost. In the literature, many solutions have been proposed, but little information is available on their m......The basic operations of a dynamic array are operator[], push back, and pop back. This study is an examination of variations of dynamic arrays that support these operations at O(1) worst-case cost. In the literature, many solutions have been proposed, but little information is available...... on their mutual superiority. Most library implementations only guarantee O(1) amortized cost per operation. Four variations with good worst-case performance were benchmarked: (1) resizable array relying on doubling, halving, and incremental copying; (2) level-wiseallocated pile; (3) sliced array with fixed......-capacity slices; and (4) blockwise-allocated pile. Let |V| denote the size of the values of type V and |V*| the size of the pointers to values of type V, both measured in bytes. For an array of n values and a slice of S values, the space requirements of the considered variations were at most 12|V|n+O(|V*|), 2|V...

Accurate measurement of transgene copy number in crop plants using droplet digital PCR.

Science.gov (United States)

Collier, Ray; Dasgupta, Kasturi; Xing, Yan-Ping; Hernandez, Bryan Tarape; Shao, Min; Rohozinski, Dominica; Kovak, Emma; Lin, Jeanie; de Oliveira, Maria Luiza P; Stover, Ed; McCue, Kent F; Harmon, Frank G; Blechl, Ann; Thomson, James G; Thilmony, Roger

2017-06-01

Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

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.)

High Rate User Ka-Band Phased Array Antenna Test Results

Science.gov (United States)

Caroglanian, Armen; Perko, Kenneth; Seufert, Steve; Dod, Tom; Warshowsky, Jay; Day, John H. (Technical Monitor)

2001-01-01

The High Rate User Phased Array Antenna (HRUPAA) is a Ka-Band planar phased array designed by the Harris Corporation for the NASA Goddard Space Flight Center. The HRUPAA permits a satellite to downlink data either to a ground station or through the Tracking and Data Relay Satellite System (TDRSS). The HRUPAA is scanned electronically by ground station / user satellite command over a 120 degree cone angle. The phased array has the advantage of not imparting attitude disturbances to the user spacecraft. The 288-element transmit-only array has distributed RF amplifiers integrated behind each of the printed patch antenna elements. The array has 33 dBW EIRP and is left-hand circularly polarized. An engineering model of a partially populated array has been developed and delivered to NASA Goddard Space Flight Center. This report deals with the testing of the engineering model at the Goddard Antenna Range near-field and compact range facilities. The antenna specifications are described first, followed by the test plan and test results.

High throughput screening of human subtelomeric DNA for copy number changes using multiplex amplifiable probe hybridisation (MAPH).

Science.gov (United States)

Hollox, E J; Atia, T; Cross, G; Parkin, T; Armour, J A L

2002-11-01

Subtelomeric regions of the human genome are gene rich, with a high level of sequence polymorphism. A number of clinical conditions, including learning disability, have been attributed to subtelomeric deletions or duplications, but screening for deletion in these regions using conventional cytogenetic methods and fluorescence in situ hybridisation (FISH) is laborious. Here we report that a new method, multiplex amplifiable probe hybridisation (MAPH), can be used to screen for copy number at subtelomeric regions. We have constructed a set of MAPH probes with each subtelomeric region represented at least once, so that one gel lane can assay copy number at all chromosome ends in one person. Each probe has been sequenced and, where possible, its position relative to the telomere determined by comparison with mapped clones. The sensitivity of the probes has been characterised on a series of cytogenetically verified positive controls and 83 normal controls were used to assess the frequency of polymorphic copy number with no apparent phenotypic effect. We have also used MAPH to test a cohort of 37 people selected from males referred for fragile X syndrome testing and found six changes that were confirmed by dosage PCR. MAPH can be used to screen subtelomeric regions of chromosomes for deletions and duplications before confirmation by FISH or dosage PCR. The high throughput nature of this technique allows it to be used for large scale screening of subtelomeric copy number, before confirmation by FISH. In practice, the availability of a rapid and efficient screen may allow subtelomeric analysis to be applied to a wider selection of patients than is currently possible using FISH alone.

Thermoelastic expansion vs. piezoelectricity for high-frequency, 2-D arrays.

Science.gov (United States)

Buma, Takashi; Spisar, Monica; O'Donnell, Matthew

2003-08-01

Optical generation using the thermoelastic effect has traditionally suffered from low conversion efficiency. We previously demonstrated increased efficiency of nearly 20 dB with an optical absorbing layer consisting of a mixture of polydimethylsiloxane (PDMS) and carbon black spin coated onto a glass microscope slide. In this paper we show that the radiated power from a black PDMS film is comparable to a 20 MHz piezoelectric two-dimensional (2-D) array element. Furthermore, we predict that a thermoelastic array element can produce similar acoustic power levels compared to ideal piezoelectric 2-D array elements at frequencies in the 100 MHz regime. We believe these results show that thermoelastic generation of ultrasound is a promising alternative to piezoelectricity for high-frequency, 2-D arrays.

Novel candidate genes and regions for childhood apraxia of speech identified by array comparative genomic hybridization.

Science.gov (United States)

Laffin, Jennifer J S; Raca, Gordana; Jackson, Craig A; Strand, Edythe A; Jakielski, Kathy J; Shriberg, Lawrence D

2012-11-01

The goal of this study was to identify new candidate genes and genomic copy-number variations associated with a rare, severe, and persistent speech disorder termed childhood apraxia of speech. Childhood apraxia of speech is the speech disorder segregating with a mutation in FOXP2 in a multigenerational London pedigree widely studied for its role in the development of speech-language in humans. A total of 24 participants who were suspected to have childhood apraxia of speech were assessed using a comprehensive protocol that samples speech in challenging contexts. All participants met clinical-research criteria for childhood apraxia of speech. Array comparative genomic hybridization analyses were completed using a customized 385K Nimblegen array (Roche Nimblegen, Madison, WI) with increased coverage of genes and regions previously associated with childhood apraxia of speech. A total of 16 copy-number variations with potential consequences for speech-language development were detected in 12 or half of the 24 participants. The copy-number variations occurred on 10 chromosomes, 3 of which had two to four candidate regions. Several participants were identified with copy-number variations in two to three regions. In addition, one participant had a heterozygous FOXP2 mutation and a copy-number variation on chromosome 2, and one participant had a 16p11.2 microdeletion and copy-number variations on chromosomes 13 and 14. Findings support the likelihood of heterogeneous genomic pathways associated with childhood apraxia of speech.

[Analysis of genomic copy number variations in two sisters with primary amenorrhea and hyperandrogenism].

Science.gov (United States)

Zhang, Yanliang; Xu, Qiuyue; Cai, Xuemei; Li, Yixun; Song, Guibo; Wang, Juan; Zhang, Rongchen; Dai, Yong; Duan, Yong

2015-12-01

To analyze genomic copy number variations (CNVs) in two sisters with primary amenorrhea and hyperandrogenism. G-banding was performed for karyotype analysis. The whole genome of the two sisters were scanned and analyzed by array-based comparative genomic hybridization (array-CGH). The results were confirmed with real-time quantitative PCR (RT-qPCR). No abnormality was found by conventional G-banded chromosome analysis. Array-CGH has identified 11 identical CNVs from the sisters which, however, overlapped with CNVs reported by the Database of Genomic Variants (http://projects.tcag.ca/variation/). Therefore, they are likely to be benign. In addition, a -8.44 Mb 9p11.1-p13.1 duplication (38,561,587-47,002,387 bp, hg18) and a -80.9 kb 4q13.2 deletion (70,183,990-70,264,889 bp, hg18) were also detected in the elder and younger sister, respectively. The relationship between such CNVs and primary amenorrhea and hyperandrogenism was however uncertain. RT-qPCR results were in accordance with array-CGH. Two CNVs were detected in two sisters by array-CGH, for which further studies are needed to clarify their correlation with primary amenorrhea and hyperandrogenism.

Lectin-Array Blotting.

Science.gov (United States)

Pazos, Raquel; Echevarria, Juan; Hernandez, Alvaro; Reichardt, Niels-Christian

2017-09-01

Aberrant protein glycosylation is a hallmark of cancer, infectious diseases, and autoimmune or neurodegenerative disorders. Unlocking the potential of glycans as disease markers will require rapid and unbiased glycoproteomics methods for glycan biomarker discovery. The present method is a facile and rapid protocol for qualitative analysis of protein glycosylation in complex biological mixtures. While traditional lectin arrays only provide an average signal for the glycans in the mixture, which is usually dominated by the most abundant proteins, our method provides individual lectin binding profiles for all proteins separated in the gel electrophoresis step. Proteins do not have to be excised from the gel for subsequent analysis via the lectin array but are transferred by contact diffusion from the gel to a glass slide presenting multiple copies of printed lectin arrays. Fluorescently marked glycoproteins are trapped by the printed lectins via specific carbohydrate-lectin interactions and after a washing step their binding profile with up to 20 lectin probes is analyzed with a fluorescent scanner. The method produces the equivalent of 20 lectin blots in a single experiment, giving detailed insight into the binding epitopes present in the fractionated proteins. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

How bio-questionable are the different recombinant human erythropoietin copy products in Thailand?

Science.gov (United States)

Halim, Liem Andhyk; Brinks, Vera; Jiskoot, Wim; Romeijn, Stefan; Praditpornsilpa, Kearkiat; Assawamakin, Anunchai; Schellekens, Huub

2014-05-01

The high prevalence of pure red cell aplasia in Thailand has been associated with the sharp increase in number of recombinant human erythropoietin (rhEPO) copy products, based on a classical generic regulatory pathway, which have entered the market. This study aims to assess the quality of rhEPO copy products being used in Thailand. Twelve rhEPO copy products were purchased from pharmacies in Thailand, shipped under controlled cold chain conditions to the Netherlands and characterized using (1) high performance size-exclusion chromatography, (2) asymmetrical flow field-flow fractionation, (3) sodium dodecyl sulfate polyacrylamide gel electrophoresis in combination with (4) Western blotting and additionally tested for (5) host cell protein impurities as well as (6) endotoxin contamination. Some of the tested rhEPO copy products showed high aggregate levels and contained a substantial amount of protein fragments. Also, one of rhEPO copy products had a high endotoxin level, exceeding the FDA limit. Our observations show that some of the tested copy products on the Thai market differ significantly from the originator rhEPO product, Epogen®. This comparison study supports a link between the quality attributes of copy rhEPO products and their immunogenicity.

Demonstration of Millimeter Wave 5G Setup Employing High-Gain Vivaldi Array

Directory of Open Access Journals (Sweden)

Waleed Tariq Sethi

2018-01-01

Full Text Available We present a 4 × 4 slot-coupled Vivaldi antenna (SCVA array unit cell, which offers wide bandwidth and high gain (~23 dBi at the millimeter wave (mmW frequencies of 28 GHz and 38 GHz. A single SCVA element is first presented, which has a bandwidth of 25–40 GHz with an average gain of ~13 dBi at the frequencies of interest. This antenna element is then used to design a 1 × 4 linear SCVA array matched to a 50 Ω impedance via a modified Wilkinson power divider (WPD. Next, the 1 × 4 linear array is used to construct a 4 × 4 antenna array unit cell. The proposed 4 × 4 antenna array unit cell is fabricated, and the characteristics of its elements (i.e., the single SCVA, 1 × 4 linear array, and WPD are thoroughly investigated. Further, the 4 × 4 array is tested for signal reception of various digital modulation formats at lab environment using high-speed digital signal oscilloscope. In particular, a 2.5 Gbps data rate is successfully transmitted achieving receiver sensitivity of −50 dBm at 2 × 10−3 bit error rate (BER for 32 quadrature amplitude modulation (QAM with a system baud rate of 500 MHz. The wide bandwidth and high gain along with the excellent performance of the proposed 4 × 4 antenna array unit cell makes it an excellent candidate for future 5G wireless communication applications.

Custom ceramic microchannel-cooled array for high-power fiber-coupled application

Science.gov (United States)

Junghans, Jeremy; Feeler, Ryan; Stephens, Ed

2018-03-01

A low-SWaP (Size, Weight and Power) diode array has been developed for a high-power fiber-coupled application. High efficiency ( 65%) diodes enable high optical powers while minimizing thermal losses. A large amount of waste heat is still generated and must be extracted. Custom ceramic microchannel-coolers (MCCs) are used to dissipate the waste heat. The custom ceramic MCC was designed to accommodate long cavity length diodes and micro-lenses. The coolers provide similar thermal performance as copper MCCs however they are not susceptible to erosion and can be cooled with standard filtered water. The custom ceramic micro-channel cooled array was designed to be a form/fit replacement for an existing copperbased solution. Each array consisted of three-vertically stacked MCCs with 4 mm CL, 976 nm diodes and beamshaping micro-optics. The erosion and corrosion resistance of ceramic array is intended to mitigate the risk of copperbased MCC corrosion failures. Elimination of the water delivery requirements (pH, resistivity and dissolved oxygen control) further reduces the system SWaP while maintaining reliability. The arrays were fabricated and fully characterized. This work discusses the advantages of the ceramic MCC technology and describes the design parameters that were tailored for the fiber-coupled application. Additional configuration options (form/fit, micro-lensing, alternate coolants, etc.) and on-going design improvements are also discussed.

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...

Spatial normalization of array-CGH data

Directory of Open Access Journals (Sweden)

Brennetot Caroline

2006-05-01

Full Text Available Abstract Background Array-based comparative genomic hybridization (array-CGH is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the true biological signal. We investigated various sources of systematic variation in array-CGH data and identified two distinct types of spatial effect of no biological relevance as the predominant experimental artifacts: continuous spatial gradients and local spatial bias. Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments. Results We show that existing normalization techniques do not correct these spatial effects properly. We therefore developed an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It is based on the combination of a spatial segmentation algorithm called NEM (Neighborhood Expectation Maximization and spatial trend estimation. We defined quality criteria for array-CGH data, demonstrating significant improvements in data quality with our method for three data sets coming from two different platforms (198, 175 and 26 BAC-arrays. Conclusion We have designed an automatic algorithm for the spatial normalization of BAC CGH-array data, preventing the misinterpretation of experimental artifacts as biologically relevant outliers in the genomic profile. This algorithm is implemented in the R package MANOR (Micro-Array NORmalization, which is described at http://bioinfo.curie.fr/projects/manor and available from the Bioconductor site http://www.bioconductor.org. It can also be tested on the CAPweb bioinformatics platform at http://bioinfo.curie.fr/CAPweb.

Material versatility using replica molding for large-scale fabrication of high aspect-ratio, high density arrays of nano-pillars

International Nuclear Information System (INIS)

Li, Y; Menon, C; Ng, H W; Gates, B D

2014-01-01

Arrays of high aspect-ratio (AR) nano-pillars have attracted a lot of interest for various applications, such as for use in solar cells, surface acoustic sensors, tissue engineering, bio-inspired adhesives and anti-reflective surfaces. Each application may require a different structural material, which can vary in the required chemical composition and mechanical properties. In this paper, a low cost fabrication procedure is proposed for large scale, high AR and high density arrays of nano-pillars. The proposed method enables the replication of a master with high fidelity, using the subsequent replica molds multiple times, and preparing arrays of nano-pillars in a variety of different materials. As an example applied to bio-inspired dry adhesion, polymeric arrays of nano-pillars are prepared in this work. Thermoset and thermoplastic nano-pillar arrays are examined using an atomic force microscope to assess their adhesion strength and its uniformity. Results indicate the proposed method is robust and can be used to reliably prepare nano-structures with a high AR. (paper)

Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease

Science.gov (United States)

Aldhous, Marian C.; Abu Bakar, Suhaili; Prescott, Natalie J.; Palla, Raquel; Soo, Kimberley; Mansfield, John C.; Mathew, Christopher G.; Satsangi, Jack; Armour, John A.L.

2010-01-01

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case–control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case–control studies. PMID:20858604

Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease.

Science.gov (United States)

Aldhous, Marian C; Abu Bakar, Suhaili; Prescott, Natalie J; Palla, Raquel; Soo, Kimberley; Mansfield, John C; Mathew, Christopher G; Satsangi, Jack; Armour, John A L

2010-12-15

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case-control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case-control studies.

Robust Adaptable Video Copy Detection

DEFF Research Database (Denmark)

Assent, Ira; Kremer, Hardy

2009-01-01

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.......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...

Micro-machined high-frequency (80 MHz) PZT thick film linear arrays.

Science.gov (United States)

Zhou, Qifa; Wu, Dawei; Liu, Changgeng; Zhu, Benpeng; Djuth, Frank; Shung, K

2010-10-01

This paper presents the development of a micromachined high-frequency linear array using PZT piezoelectric thick films. The linear array has 32 elements with an element width of 24 μm and an element length of 4 mm. Array elements were fabricated by deep reactive ion etching of PZT thick films, which were prepared from spin-coating of PZT sol-gel composite. Detailed fabrication processes, especially PZT thick film etching conditions and a novel transferring-and-etching method, are presented and discussed. Array designs were evaluated by simulation. Experimental measurements show that the array had a center frequency of 80 MHz and a fractional bandwidth (-6 dB) of 60%. An insertion loss of -41 dB and adjacent element crosstalk of -21 dB were found at the center frequency.

Spatiotemporal norepinephrine mapping using a high-density CMOS microelectrode array.

Science.gov (United States)

Wydallis, John B; Feeny, Rachel M; Wilson, William; Kern, Tucker; Chen, Tom; Tobet, Stuart; Reynolds, Melissa M; Henry, Charles S

2015-10-21

A high-density amperometric electrode array containing 8192 individually addressable platinum working electrodes with an integrated potentiostat fabricated using Complementary Metal Oxide Semiconductor (CMOS) processes is reported. The array was designed to enable electrochemical imaging of chemical gradients with high spatiotemporal resolution. Electrodes are arranged over a 2 mm × 2 mm surface area into 64 subarrays consisting of 128 individual Pt working electrodes as well as Pt pseudo-reference and auxiliary electrodes. Amperometric measurements of norepinephrine in tissue culture media were used to demonstrate the ability of the array to measure concentration gradients in complex media. Poly(dimethylsiloxane) microfluidics were incorporated to control the chemical concentrations in time and space, and the electrochemical response at each electrode was monitored to generate electrochemical heat maps, demonstrating the array's imaging capabilities. A temporal resolution of 10 ms can be achieved by simultaneously monitoring a single subarray of 128 electrodes. The entire 2 mm × 2 mm area can be electrochemically imaged in 64 seconds by cycling through all subarrays at a rate of 1 Hz per subarray. Monitoring diffusional transport of norepinephrine is used to demonstrate the spatiotemporal resolution capabilities of the system.

Getting DNA copy numbers without control samples

Directory of Open Access Journals (Sweden)

Ortiz-Estevez Maria

2012-08-01

Full Text Available Abstract Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm, a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM, Ovarian, Prostate and Lung Cancer experiments have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs. These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the

The Cherenkov Telescope Array For Very High-Energy Astrophysics

Science.gov (United States)

Kaaret, Philip

2015-08-01

The field of very high energy (VHE) astrophysics had been revolutionized by the results from ground-based gamma-ray telescopes, including the current imaging atmospheric Cherenkov telescope (IACT) arrays: HESS, MAGIC and VERITAS. A worldwide consortium of scientists from 29 countries has formed to propose the Cherenkov Telescope Array (CTA) that will capitalize on the power of this technique to greatly expand the scientific reach of ground-based gamma-ray telescopes. CTA science will include key topics such as the origin of cosmic rays and cosmic particle acceleration, understanding extreme environments in regions close to neutron stars and black holes, and exploring physics frontiers through, e.g., the search for WIMP dark matter, axion-like particles and Lorentz invariance violation. CTA is envisioned to consist of two large arrays of Cherenkov telescopes, one in the southern hemisphere and one in the north. Each array will contain telescopes of different sizes to provide a balance between cost and array performance over an energy range from below 100 GeV to above 100 TeV. Compared to the existing IACT arrays, CTA will have substantially better angular resolution and energy resolution, will cover a much wider energy range, and will have up to an order of magnitude better sensitivity. CTA will also be operated as an open observatory and high-level CTA data will be placed into the public domain; these aspects will enable broad participation in CTA science from the worldwide scientific community to fully capitalize on CTA's potential. This talk will: 1) review the scientific motivation and capabilities of CTA, 2) provide an overview of the technical design and the status of prototype development, and 3) summarize the current status of the project in terms of its proposed organization and timeline. The plans for access to CTA data and opportunities to propose for CTA observing time will be highlighed.Presented on behalf of the CTA Consortium.

Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma.

Science.gov (United States)

Gu, De-Leung; Chen, Yen-Hsieh; Shih, Jou-Ho; Lin, Chi-Hung; Jou, Yuh-Shan; Chen, Chian-Feng

2013-12-21

High-throughput short-read sequencing of exomes and whole cancer genomes in multiple human hepatocellular carcinoma (HCC) cohorts confirmed previously identified frequently mutated somatic genes, such as TP53, CTNNB1 and AXIN1, and identified several novel genes with moderate mutation frequencies, including ARID1A, ARID2, MLL, MLL2, MLL3, MLL4, IRF2, ATM, CDKN2A, FGF19, PIK3CA, RPS6KA3, JAK1, KEAP1, NFE2L2, C16orf62, LEPR, RAC2, and IL6ST. Functional classification of these mutated genes suggested that alterations in pathways participating in chromatin remodeling, Wnt/β-catenin signaling, JAK/STAT signaling, and oxidative stress play critical roles in HCC tumorigenesis. Nevertheless, because there are few druggable genes used in HCC therapy, the identification of new therapeutic targets through integrated genomic approaches remains an important task. Because a large amount of HCC genomic data genotyped by high density single nucleotide polymorphism arrays is deposited in the public domain, copy number alteration (CNA) analyses of these arrays is a cost-effective way to reveal target genes through profiling of recurrent and overlapping amplicons, homozygous deletions and potentially unbalanced chromosomal translocations accumulated during HCC progression. Moreover, integration of CNAs with other high-throughput genomic data, such as aberrantly coding transcriptomes and non-coding gene expression in human HCC tissues and rodent HCC models, provides lines of evidence that can be used to facilitate the identification of novel HCC target genes with the potential of improving the survival of HCC patients.

Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing.

Science.gov (United States)

Yi, Guoqiang; Qu, Lujiang; Liu, Jianfeng; Yan, Yiyuan; Xu, Guiyun; Yang, Ning

2014-11-07

Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed a genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 8,840 CNV regions (CNVRs) covering 98.2 Mb and representing 9.4% of the chicken genome were identified, ranging in size from 1.1 to 268.8 kb with an average of 11.1 kb. Sequencing-based predictions were confirmed at a high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson's correlation coefficients between sequencing and aCGH results ranged from 0.435 to 0.755, and qPCR experiments revealed a positive validation rate of 91.71% and a false negative rate of 22.43%. In total, 2,214 (25.0%) predicted CNVRs span 2,216 (36.4%) RefSeq genes associated with specific biological functions. Besides two previously reported copy number variable genes EDN3 and PRLR, we also found some promising genes with potential in phenotypic variation. Two genes, FZD6 and LIMS1, related to disease susceptibility/resistance are covered by CNVRs. The highly duplicated SOCS2 may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3 may have great economic importance in poultry breeding. Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.

Growth of high-aspect ratio horizontally-aligned ZnO nanowire arrays.

Science.gov (United States)

Soman, Pranav; Darnell, Max; Feldman, Marc D; Chen, Shaochen

2011-08-01

A method of fabricating horizontally-aligned zinc-oxide (ZnO) nanowire (NW) arrays with full control over the width and length is demonstrated. SEM images reveal the hexagonal structure typical of zinc oxide NWs. Arrays of high-aspect ratio horizontal ZnO NWs are fabricated by making use of the lateral overgrowth from dot patterns created by electron beam lithography (EBL). An array of patterned wires are lifted off and transferred to a flexible PDMS substrate with possible applications in several key nanotechnology areas.

Hard-copy versus soft-copy with and without simple image manipulation for detection of pulmonary nodules and masses

International Nuclear Information System (INIS)

Kosuda, S.; Kaji, T.; Iwasaki, Y.; Kusano, S.; Kobayashi, H.; Watanabe, M.

2000-01-01

To compare interpretation performance on soft-copy presentations, with and without simple image manipulation, and on unmodified hard-copy presentations with regard to detection of pulmonary nodules and masses. Material and Methods: Fifty chest digital radiograph combinations of patients with a total of 60 nodules, 32 of which were 2.0 cm in diameter, were selected for the study. Three readers evaluated three separate image formats: unmodified hard- and soft-copies, and soft-copies with simple image manipulation of lung and mediastinum window settings, and zooming. The screen display was 1600x1200 pixels with 8 bits/pixel. Results: The sensitivity, accuracy, detectability, and Az value of the soft-copy systems were clearly inferior to hard-copy evaluation. The mean Az values were 0.921 for unmodified hard-copy, 0.820 for image-manipulated soft-copy, and 0.781 for unmodified soft-copy. Conclusion: Soft-copy interpretations were not as sensitive in detecting pulmonary nodules and masses as hard-copy evaluation

Characterization of Copy Number Variation’s Potential Role in Marek’s Disease

Directory of Open Access Journals (Sweden)

Lingyang Xu

2017-05-01

Full Text Available Marek’s Disease (MD is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. Chicken Lines 63 and 72, as well as their recombinant congenic strains (RCS with varied susceptibility to MD, are ideal models to study the complex mechanisms of genetic resistance to MD. In this study, we investigated copy number variation (CNV in these inbred chicken lines using the Affymetrix Axiom HD 600 K SNP genotyping array. We detected 393 CNV segments across all ten chicken lines, of which 12 CNVs were specifically identified in Line 72. We then assessed genetic structure based on CNV and observed markedly different patterns. Finally, we validated two deletion events in Line 72 and correlated them with genes expression using qPCR and RNA-seq, respectively. Our combined results indicated that these two CNV deletions were likely to contribute to MD susceptibility.

A superconducting quadrupole array for transport of multiple high current beams

International Nuclear Information System (INIS)

Faltens, A.; Shuman, D.

1999-01-01

We present a conceptual design of a superconducting quadrupole magnet array for the side-by-side transport of multiple high current particle beams in induction linear accelerators. The magnetic design uses a modified cosine 20 current distribution inside a square cell boundary. Each interior magnet's neighbors serve as the return flux paths and the poles are placed as close as possible to each other to facilitate this. No iron is present in the basic 2-D magnetic design; it will work at any current level without correction windings. Special 1/8th quadrupoles are used along the transverse periphery of the array to contain and channel flux back into the array, making every channel look as part of an infinite array. This design provides a fixed dimension array boundary equal to the quadrupole radius that can be used for arrays of any number of quadrupole channels, at any field level. More importantly, the design provides magnetic field separation between the array and the induction cores which may be surrounding it. Flux linkage between these two components can seriously affect the operation of both of them

Modular Ultra-High Power Solar Array Architecture, Phase I

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...

Molecular Dynamics Simulation of High Density DNA Arrays

Directory of Open Access Journals (Sweden)

Rudolf Podgornik

2018-01-01

Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

Copy number alterations in small intestinal neuroendocrine tumors determined by array comparative genomic hybridization

International Nuclear Information System (INIS)

Hashemi, Jamileh; Fotouhi, Omid; Sulaiman, Luqman; Kjellman, Magnus; Höög, Anders; Zedenius, Jan; Larsson, Catharina

2013-01-01

Small intestinal neuroendocrine tumors (SI-NETs) are typically slow-growing tumors that have metastasized already at the time of diagnosis. The purpose of the present study was to further refine and define regions of recurrent copy number (CN) alterations (CNA) in SI-NETs. Genome-wide CNAs was determined by applying array CGH (a-CGH) on SI-NETs including 18 primary tumors and 12 metastases. Quantitative PCR analysis (qPCR) was used to confirm CNAs detected by a-CGH as well as to detect CNAs in an extended panel of SI-NETs. Unsupervised hierarchical clustering was used to detect tumor groups with similar patterns of chromosomal alterations based on recurrent regions of CN loss or gain. The log rank test was used to calculate overall survival. Mann–Whitney U test or Fisher’s exact test were used to evaluate associations between tumor groups and recurrent CNAs or clinical parameters. The most frequent abnormality was loss of chromosome 18 observed in 70% of the cases. CN losses were also frequently found of chromosomes 11 (23%), 16 (20%), and 9 (20%), with regions of recurrent CN loss identified in 11q23.1-qter, 16q12.2-qter, 9pter-p13.2 and 9p13.1-11.2. Gains were most frequently detected in chromosomes 14 (43%), 20 (37%), 4 (27%), and 5 (23%) with recurrent regions of CN gain located to 14q11.2, 14q32.2-32.31, 20pter-p11.21, 20q11.1-11.21, 20q12-qter, 4 and 5. qPCR analysis confirmed most CNAs detected by a-CGH as well as revealed CNAs in an extended panel of SI-NETs. Unsupervised hierarchical clustering of recurrent regions of CNAs revealed two separate tumor groups and 5 chromosomal clusters. Loss of chromosomes 18, 16 and 11 and again of chromosome 20 were found in both tumor groups. Tumor group II was enriched for alterations in chromosome cluster-d, including gain of chromosomes 4, 5, 7, 14 and gain of 20 in chromosome cluster-b. Gain in 20pter-p11.21 was associated with short survival. Statistically significant differences were observed between primary

Affordable High Performance Electromagnetically Clean Solar Arrays, Phase I

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...

Active phase correction of high resolution silicon photonic arrayed waveguide gratings.

Science.gov (United States)

Gehl, M; Trotter, D; Starbuck, A; Pomerene, A; Lentine, A L; DeRose, C

2017-03-20

Arrayed waveguide gratings provide flexible spectral filtering functionality for integrated photonic applications. Achieving narrow channel spacing requires long optical path lengths which can greatly increase the footprint of devices. High index contrast waveguides, such as those fabricated in silicon-on-insulator wafers, allow tight waveguide bends which can be used to create much more compact designs. Both the long optical path lengths and the high index contrast contribute to significant optical phase error as light propagates through the device. Therefore, silicon photonic arrayed waveguide gratings require active or passive phase correction following fabrication. Here we present the design and fabrication of compact silicon photonic arrayed waveguide gratings with channel spacings of 50, 10 and 1 GHz. The largest device, with 11 channels of 1 GHz spacing, has a footprint of only 1.1 cm2. Using integrated thermo-optic phase shifters, the phase error is actively corrected. We present two methods of phase error correction and demonstrate state-of-the-art cross-talk performance for high index contrast arrayed waveguide gratings. As a demonstration of possible applications, we perform RF channelization with 1 GHz resolution. Additionally, we generate unique spectral filters by applying non-zero phase offsets calculated by the Gerchberg Saxton algorithm.

Prognostic Impact of Array-based Genomic Profiles in Esophageal Squamous Cell Cancer

International Nuclear Information System (INIS)

Carneiro, Ana; Isinger, Anna; Karlsson, Anna; Johansson, Jan; Jönsson, Göran; Bendahl, Pär-Ola; Falkenback, Dan; Halvarsson, Britta; Nilbert, Mef

2008-01-01

Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and a major cause of cancer related mortality. Although distinct genetic alterations have been linked to ESCC development and prognosis, the genetic alterations have not gained clinical applicability. We applied array-based comparative genomic hybridization (aCGH) to obtain a whole genome copy number profile relevant for identifying deranged pathways and clinically applicable markers. A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC. Potential interdependent alterations and deranged pathways were identified and copy number changes were correlated to stage, differentiation and survival. Copy number alterations affected median 19% of the genome and included recurrent gains of chromosome regions 5p, 7p, 7q, 8q, 10q, 11q, 12p, 14q, 16p, 17p, 19p, 19q, and 20q and losses of 3p, 5q, 8p, 9p and 11q. High-level amplifications were observed in 30 regions and recurrently involved 7p11 (EGFR), 11q13 (MYEOV, CCND1, FGF4, FGF3, PPFIA, FAD, TMEM16A, CTTS and SHANK2) and 11q22 (PDFG). Gain of 7p22.3 predicted nodal metastases and gains of 1p36.32 and 19p13.3 independently predicted poor survival in multivariate analysis. aCGH profiling verified genetic complexity in ESCC and herein identified imbalances of multiple central tumorigenic pathways. Distinct gains correlate with clinicopathological variables and independently predict survival, suggesting clinical applicability of genomic profiling in ESCC

Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component.

Science.gov (United States)

Alonso, M Henar; Aussó, Susanna; Lopez-Doriga, Adriana; Cordero, David; Guinó, Elisabet; Solé, Xavier; Barenys, Mercè; de Oca, Javier; Capella, Gabriel; Salazar, Ramón; Sanz-Pamplona, Rebeca; Moreno, Victor

2017-07-25

Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression. Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes. All analyses were adjusted for the quantity of stroma in each sample, which was inferred from gene expression data. High heterogeneity among samples was observed; the proportion of altered genome ranged between 0.04 and 26.6%. Recurrent CNA regions with gains were frequent in chromosomes 7p, 8q, 13q, and 20, whereas 8p, 17p, and 18 cumulated losses. A significant positive correlation was observed between the number of somatic mutations and total CNA (Spearman's r=0.42, P=0.006). Approximately 37% of genes located in CNA regions changed their level of expression and the average partial correlation (adjusted for stromal content) with copy number was 0.54 (interquartile range 0.20 to 0.81). Altered genes showed enrichment in pathways relevant for CRC. Tumours classified as CMS2 and CMS4 by the consensus molecular subtyping showed higher frequency of CNA. Losses of one small region in 1p36.33, with gene CDK11B, were associated with poor prognosis. More than 66% of the recurrent CNA were validated in the The Cancer Genome Atlas (TCGA) data when analysed with the same procedure. Furthermore, 79% of the genes with altered expression in our data were validated in the TCGA. Although CNA are frequent events in microsatellite stable CRC, few focal recurrent regions were found. These aberrations have strong effects on gene expression and contribute to deregulate relevant cancer pathways. Owing to the diploid nature of stromal cells, it is important to

cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate.

Science.gov (United States)

Clevert, Djork-Arné; Mitterecker, Andreas; Mayr, Andreas; Klambauer, Günter; Tuefferd, Marianne; De Bondt, An; Talloen, Willem; Göhlmann, Hinrich; Hochreiter, Sepp

2011-07-01

Cost-effective oligonucleotide genotyping arrays like the Affymetrix SNP 6.0 are still the predominant technique to measure DNA copy number variations (CNVs). However, CNV detection methods for microarrays overestimate both the number and the size of CNV regions and, consequently, suffer from a high false discovery rate (FDR). A high FDR means that many CNVs are wrongly detected and therefore not associated with a disease in a clinical study, though correction for multiple testing takes them into account and thereby decreases the study's discovery power. For controlling the FDR, we propose a probabilistic latent variable model, 'cn.FARMS', which is optimized by a Bayesian maximum a posteriori approach. cn.FARMS controls the FDR through the information gain of the posterior over the prior. The prior represents the null hypothesis of copy number 2 for all samples from which the posterior can only deviate by strong and consistent signals in the data. On HapMap data, cn.FARMS clearly outperformed the two most prevalent methods with respect to sensitivity and FDR. The software cn.FARMS is publicly available as a R package at http://www.bioinf.jku.at/software/cnfarms/cnfarms.html.

Oxide-confined 2D VCSEL arrays for high-density inter/intra-chip interconnects

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King, Roger; Michalzik, Rainer; Jung, Christian; Grabherr, Martin; Eberhard, Franz; Jaeger, Roland; Schnitzer, Peter; Ebeling, Karl J.

1998-04-01

We have designed and fabricated 4 X 8 vertical-cavity surface-emitting laser (VCSEL) arrays intended to be used as transmitters in short-distance parallel optical interconnects. In order to meet the requirements of 2D, high-speed optical links, each of the 32 laser diodes is supplied with two individual top contacts. The metallization scheme allows flip-chip mounting of the array modules junction-side down on silicon complementary metal oxide semiconductor (CMOS) chips. The optical and electrical characteristics across the arrays with device pitch of 250 micrometers are quite homogeneous. Arrays with 3 micrometers , 6 micrometers and 10 micrometers active diameter lasers have been investigated. The small devices show threshold currents of 600 (mu) A, single-mode output powers as high as 3 mW and maximum wavelength deviations of only 3 nm. The driving characteristics of all arrays are fully compatible to advanced 3.3 V CMOS technology. Using these arrays, we have measured small-signal modulation bandwidths exceeding 10 GHz and transmitted pseudo random data at 8 Gbit/s channel over 500 m graded index multimode fiber. This corresponds to a data transmission rate of 256 Gbit/s per array of 1 X 2 mm2 footprint area.

Screening for common copy-number variants in cancer genes.

Science.gov (United States)

Tyson, Jess; Majerus, Tamsin M O; Walker, Susan; Armour, John A L

2010-12-01

For most cases of colorectal cancer that arise without a family history of the disease, it is proposed that an appreciable heritable component of predisposition is the result of contributions from many loci. Although progress has been made in identifying single nucleotide variants associated with colorectal cancer risk, the involvement of low-penetrance copy number variants is relatively unexplored. We have used multiplex amplifiable probe hybridization (MAPH) in a fourfold multiplex (QuadMAPH), positioned at an average resolution of one probe per 2 kb, to screen a total of 1.56 Mb of genomic DNA for copy number variants around the genes APC, AXIN1, BRCA1, BRCA2, CTNNB1, HRAS, MLH1, MSH2, and TP53. Two deletion events were detected, one upstream of MLH1 in a control individual and the other in APC in a colorectal cancer patient, but these do not seem to correspond to copy number polymorphisms with measurably high population frequencies. In summary, by means of our QuadMAPH assay, copy number measurement data were of sufficient resolution and accuracy to detect any copy number variants with high probability. However, this study has demonstrated a very low incidence of deletion and duplication variants within intronic and flanking regions of these nine genes, in both control individuals and colorectal cancer patients. Copyright © 2010 Elsevier Inc. All rights reserved.

Hierarchically structured Co₃O₄@Pt@MnO₂ nanowire arrays for high-performance supercapacitors.

Science.gov (United States)

Xia, Hui; Zhu, Dongdong; Luo, Zhentao; Yu, Yue; Shi, Xiaoqin; Yuan, Guoliang; Xie, Jianping

2013-10-17

Here we proposed a novel architectural design of a ternary MnO2-based electrode - a hierarchical Co3O4@Pt@MnO2 core-shell-shell structure, where the complemental features of the three key components (a well-defined Co3O4 nanowire array on the conductive Ti substrate, an ultrathin layer of small Pt nanoparticles, and a thin layer of MnO2 nanoflakes) are strategically combined into a single entity to synergize and construct a high-performance electrode for supercapacitors. Owing to the high conductivity of the well-defined Co3O4 nanowire arrays, in which the conductivity was further enhanced by a thin metal (Pt) coating layer, in combination with the large surface area provided by the small MnO2 nanoflakes, the as-fabricated Co3O4@Pt@MnO2 nanowire arrays have exhibited high specific capacitances, good rate capability, and excellent cycling stability. The architectural design demonstrated in this study provides a new approach to fabricate high-performance MnO2-based nanowire arrays for constructing next-generation supercapacitors.

Copying of holograms by spot scanning approach.

Science.gov (United States)

Okui, Makoto; Wakunami, Koki; Oi, Ryutaro; Ichihashi, Yasuyuki; Jackin, Boaz Jessie; Yamamoto, Kenji

2018-05-20

To replicate holograms, contact copying has conventionally been used. In this approach, a photosensitive material is fixed together with a master hologram and illuminated with a coherent beam. This method is simple and enables high-quality copies; however, it requires a large optical setup for large-area holograms. In this paper, we present a new method of replicating holograms that uses a relatively compact optical system even for the replication of large holograms. A small laser spot that irradiates only part of the hologram is used to reproduce the hologram by scanning the spot over the whole area of the hologram. We report on the results of experiments carried out to confirm the copy quality, along with a guide to design scanning conditions. The results show the potential effectiveness of the large-area hologram replication technology using a relatively compact apparatus.

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.

A Meta-Analysis of Multiple Matched Copy Number and Transcriptomics Data Sets for Inferring Gene Regulatory Relationships

Science.gov (United States)

Newton, Richard; Wernisch, Lorenz

2014-01-01

Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments. PMID:25148247

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

International Nuclear Information System (INIS)

Lindeman, Mark A.; 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.

2004-01-01

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 μm 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 μs 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

Highly Integrated, Reconfigurable, Large-Area, Flexible Radar Antenna Arrays, Phase I

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...

Highly scalable parallel processing of extracellular recordings of Multielectrode Arrays.

Science.gov (United States)

Gehring, Tiago V; Vasilaki, Eleni; Giugliano, Michele

2015-01-01

Technological advances of Multielectrode Arrays (MEAs) used for multisite, parallel electrophysiological recordings, lead to an ever increasing amount of raw data being generated. Arrays with hundreds up to a few thousands of electrodes are slowly seeing widespread use and the expectation is that more sophisticated arrays will become available in the near future. In order to process the large data volumes resulting from MEA recordings there is a pressing need for new software tools able to process many data channels in parallel. Here we present a new tool for processing MEA data recordings that makes use of new programming paradigms and recent technology developments to unleash the power of modern highly parallel hardware, such as multi-core CPUs with vector instruction sets or GPGPUs. Our tool builds on and complements existing MEA data analysis packages. It shows high scalability and can be used to speed up some performance critical pre-processing steps such as data filtering and spike detection, helping to make the analysis of larger data sets tractable.

Chimpanzees copy dominant and knowledgeable individuals: implications for cultural diversity.

Science.gov (United States)

Kendal, Rachel; Hopper, Lydia M; Whiten, Andrew; Brosnan, Sarah F; Lambeth, Susan P; Schapiro, Steven J; Hoppitt, Will

2015-01-01

Evolutionary theory predicts that natural selection will fashion cognitive biases to guide when, and from whom, individuals acquire social information, but the precise nature of these biases, especially in ecologically valid group contexts, remains unknown. We exposed four captive groups of chimpanzees ( Pan troglodytes ) to a novel extractive foraging device and, by fitting statistical models, isolated four simultaneously operating transmission biases. These include biases to copy (i) higher-ranking and (ii) expert individuals, and to copy others when (iii) uncertain or (iv) of low rank. High-ranking individuals were relatively un-strategic in their use of acquired knowledge, which, combined with the bias for others to observe them, may explain reports that high innovation rates (in juveniles and subordinates) do not generate a correspondingly high frequency of traditions in chimpanzees. Given the typically low rank of immigrants in chimpanzees, a 'copying dominants' bias may contribute to the observed maintenance of distinct cultural repertoires in neighboring communities despite sharing similar ecology and knowledgeable migrants. Thus, a copying dominants strategy may, as often proposed for conformist transmission, and perhaps in concert with it, restrict the accumulation of traditions within chimpanzee communities whilst maintaining cultural diversity.

Association tests and software for copy number variant data

Directory of Open Access Journals (Sweden)

Plagnol Vincent

2009-01-01

Full Text Available Abstract Recent studies have suggested that copy number variation (CNV significantly contributes to genetic predisposition to several common disorders. These findings, combined with the imperfect tagging of CNVs by single nucleotide polymorphisms (SNPs, have motivated the development of association studies directly targeting CNVs. Several assays, including comparative genomic hybridisation arrays, SNP genotyping arrays, or DNA quantification through real-time polymerase chain reaction analysis, allow direct assessment of CNV status in cohorts sufficiently large to provide adequate statistical power for association studies. When analysing data provided by these assays, association tests for CNV data are not fundamentally different from SNP-based association tests. The main difference arises when the quality of the CNV assay is not sufficient to convert unequivocally the raw measurement into discrete calls -- a common issue, given the technological limitations of current CNV assays. When this is the case, association tests are more appropriately based on the raw continuous measurement provided by the CNV assay, instead of potentially inaccurate discrete calls, thus motivating the development of new statistical methods. Here, the programs available for CNV association testing for case control or family data are reviewed, using either discrete calls or raw continuous data.

High luminosity operation of large solid angle scintillator arrays in Jefferson Lab Hall A

International Nuclear Information System (INIS)

Ran Shneor

2003-01-01

This thesis describes selected aspects of high luminosity operation of large solid angle scintillator arrays in Hall A of the CEBAF (Central Electron Beam Accelerator Facility) at TJNAF (Thomas Jefferson National Accelerator Facility ). CEBAF is a high current, high duty factor electron accelerator with a maximum beam energy of about 6 GeV and a maximum current of 200 (micro)A. Operating large solid angle scintillator arrays in high luminosity environment presents several problems such as high singles rates, low signal to noise ratios and shielding requirements. To demonstrate the need for large solid angle and momentum acceptance detectors as a third arm in Hall A, we will give a brief overview of the physics motivating five approved experiments, which utilize scintillator arrays. We will then focus on the design and assembly of these scintillator arrays, with special focus on the two new detector packages built for the Short Range Correlation experiment E01-015. This thesis also contains the description and results of different tests and calibrations which where conducted for these arrays. We also present the description of a number of tests which were done in order to estimate the singles rates, data reconstruction, filtering techniques and shielding required for these counters

Integrative analysis of copy number alteration and gene expression profiling in ovarian clear cell adenocarcinoma.

Science.gov (United States)

Sung, Chang Ohk; Choi, Chel Hun; Ko, Young-Hyeh; Ju, Hyunjeong; Choi, Yoon-La; Kim, Nyunsu; Kang, So Young; Ha, Sang Yun; Choi, Kyusam; Bae, Duk-Soo; Lee, Jeong-Won; Kim, Tae-Joong; Song, Sang Yong; Kim, Byoung-Gie

2013-05-01

Ovarian clear cell adenocarcinoma (Ov-CCA) is a distinctive subtype of ovarian epithelial carcinoma. In this study, we performed array comparative genomic hybridization (aCGH) and paired gene expression microarray of 19 fresh-frozen samples and conducted integrative analysis. For the copy number alterations, significantly amplified regions (false discovery rate [FDR] q genes demonstrating frequent copy number alterations (>25% of samples) that correlated with gene expression (FDR genes were mainly located on 8p11.21, 8p21.2-p21.3, 8q22.1, 8q24.3, 17q23.2-q23.3, 19p13.3, and 19p13.11. Among the regions, 8q24.3 was found to contain the most genes (30 of 94 genes) including PTK2. The 8q24.3 region was indicated as the most significant region, as supported by copy number, GISTIC, and integrative analysis. Pathway analysis using differentially expressed genes on 8q24.3 revealed several major nodes, including PTK2. In conclusion, we identified a set of 94 candidate genes with frequent copy number alterations that correlated with gene expression. Specific chromosomal alterations, such as the 8q24.3 gain containing PTK2, could be a therapeutic target in a subset of Ov-CCAs. Copyright © 2013. Published by Elsevier Inc.

Engineering of highly ordered TiO2 nanopore arrays by anodization

Science.gov (United States)

Wang, Huijie; Huang, Zhennan; Zhang, Li; Ding, Jie; Ma, Zhaoxia; Liu, Yong; Kou, Shengzhong; Yang, Hangsheng

2016-07-01

Finite element analysis was used to simulate the current density distributions in the TiO2 barrier layer formed at the initial stage of Ti anodization. The morphology modification of the barrier layer was found to induce current density distribution change. By starting the anodization with proper TiO2 barrier layer morphology, the current density distribution can be adjusted to favor the formation of either nanotube arrays or nanopore arrays of anodic TiO2. We also found that the addition of sodium acetate into the electrolyte suppressed both the field-assisted chemical dissolution of TiO2 and the TiF62- hydrolysis induced TiO2 deposition during anodization, and thus further favored the nanopore formation. Accordingly, highly ordered anodic TiO2 nanopore arrays, similar to anodic aluminum oxide nanopore arrays, were successfully prepared.

Highly Uniform Epitaxial ZnO Nanorod Arrays for Nanopiezotronics

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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.

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.

Hard copies for digital medical images: an overview

Science.gov (United States)

Blume, Hartwig R.; Muka, Edward

1995-04-01

This paper is a condensed version of an invited overview on the technology of film hard-copies used in radiology. Because the overview was given to an essentially nonmedical audience, the reliance on film hard-copies in radiology is outlined in greater detail. The overview is concerned with laser image recorders generating monochrome prints on silver-halide films. The basic components of laser image recorders are sketched. The paper concentrates on the physical parameters - characteristic function, dynamic range, digitization resolution, modulation transfer function, and noise power spectrum - which define image quality and information transfer capability of the printed image. A preliminary approach is presented to compare the printed image quality with noise in the acquired image as well as with the noise of state-of- the-art cathode-ray-tube display systems. High-performance laser-image- recorder/silver-halide-film/light-box systems are well capable of reproducing acquired radiologic information. Most recently development was begun toward a display function standard for soft-copy display systems to facilitate similarity of image presentation between different soft-copy displays as well as between soft- and hard-copy displays. The standard display function is based on perceptional linearization. The standard is briefly reviewed to encourage the printer industry to adopt it, too.

Highly Sensitive Multi-Channel IDC Sensor Array for Low Concentration Taste Detection

Directory of Open Access Journals (Sweden)

Md. Rajibur Rahaman Khan

2015-06-01

Full Text Available In this study, we designed and developed an interdigitated capacitor (IDC-based taste sensor array to detect different taste substances. The designed taste sensing array has four IDC sensing elements. The four IDC taste sensing elements of the array are fabricated by incorporating four different types of lipids into the polymer, dioctyl phenylphosphonate (DOPP and tetrahydrofuran (THF to make the respective dielectric materials that are individually placed onto an interdigitated electrode (IDE via spin coating. When the dielectric material of an IDC sensing element comes into contact with a taste substance, its dielectric properties change with the capacitance of the IDC sensing element; this, in turn, changes the voltage across the IDC, as well as the output voltage of each channel of the system. In order to assess the effectiveness of the sensing system, four taste substances, namely sourness (HCl, saltiness (NaCl, sweetness (glucose and bitterness (quinine-HCl, were tested. The IDC taste sensor array had rapid response and recovery times of about 12.9 s and 13.39 s, respectively, with highly stable response properties. The response property of the proposed IDC taste sensor array was linear, and its correlation coefficient R2 was about 0.9958 over the dynamic range of the taste sensor array as the taste substance concentration was varied from 1 μM to 1 M. The proposed IDC taste sensor array has several other advantages, such as real-time monitoring capabilities, high sensitivity 45.78 mV/decade, good reproducibility with a standard deviation of about 0.029 and compactness, and the circuitry is based on readily available and inexpensive electronic components. The proposed IDC taste sensor array was compared with the potentiometric taste sensor with respect to sensitivity, dynamic range width, linearity and response time. We found that the proposed IDC sensor array has better performance. Finally, principal component analysis (PCA was applied

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

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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.

Array-based molecular karyotyping in 115 VATER/VACTERL and VATER/VACTERL-like patients identifies disease-causing copy number variations.

Science.gov (United States)

Zhang, Rong; Marsch, Florian; Kause, Franziska; Degenhardt, Franziska; Schmiedeke, Eeberhard; Märzheuser, Stefanie; Hoppe, Bernd; Bachour, Haitham; Boemers, Thomas M; Schäfer, Matthias; Spychalski, Nicole; Neser, Jörg; Leonhardt, Johannes; Kosch, Ferdinand; Ure, Benno; Gómez, Barbara; Lacher, Martin; Deffaa, Oliver J; Palta, Markus; Wittekindt, Boris; Kleine, Katharina; Schmedding, Andrea; Grasshoff-Derr, Sabine; Ven, Amelie van der; Heilmann-Heimbach, Stefanie; Zwink, Nadine; Jenetzky, Ekkehart; Ludwig, Michael; Reutter, Heiko

2017-07-17

The acronym VATER/VACTERL refers to the rare nonrandom association of the following component features (CF): vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia, renal malformations (R), and limb defects (L). Patients presenting with at least three CFs are diagnosed as having VATER/VACTERL association while patients presenting with only two CFs are diagnosed as having VATER/VACTERL-like phenotypes. Recently, rare causative copy number variations (CNVs) have been identified in patients with VATER/VACTERL association and VATER/VACTERL-like phenotypes. To detect further causative CNVs we performed array based molecular karyotyping in 75 VATER/VACTERL and 40 VATER/VACTERL-like patients. Following the application of stringent filter criteria, we identified 13 microdeletions and seven microduplications in 20 unrelated patients all of which were absent in 1,307 healthy inhouse controls (n microdeletion at 17q12 was confirmed to be de novo. Three microdeletions at 5q23.1, 16q23.3, 22q11.21, and one microduplication at 10q11.21 were all absent in the available parent. Microdeletion of chromosomal region 22q11.21 was previously found in VATER/VACTERL patients rendering it to be causative in our patient. The remaining 15 CNVs were inherited from a healthy parent. In two of 115 patients' causative CNVs were found (2%). The remaining identified rare CNVs represent candidates for further evaluation. Rare inherited CNVs may constitute modifiers of, or contributors to, multifactorial VATER/VACTERL or VATER/VACTERL-like phenotypes. Birth Defects Research 109:1063-1069, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Array comparative genomic hybridisation analysis of boys with X linked hypopituitarism identifies a 3.9 Mb duplicated critical region at Xq27 containing SOX3.

NARCIS (Netherlands)

Solomon, N.M.; Ross, S.; Morgan, T.; Belsky, J.L.; Hol, F.A.; Karnes, P.; Hopwood, N.J.; Myers, S.E.; Tan, A.; Warne, G.L.; Forrest, S.M.; Thomas, P.Q.

2004-01-01

INTRODUCTION: Array comparative genomic hybridisation (array CGH) is a powerful method that detects alteration of gene copy number with greater resolution and efficiency than traditional methods. However, its ability to detect disease causing duplications in constitutional genomic DNA has not been

Population-genetic properties of differentiated copy number variations in cattle.

Science.gov (United States)

Xu, Lingyang; Hou, Yali; Bickhart, Derek M; Zhou, Yang; Hay, El Hamidi Abdel; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Liu, George E

2016-03-23

While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.

Fabrication of combinatorial nm-planar electrode array for high throughput evaluation of organic semiconductors

International Nuclear Information System (INIS)

Haemori, M.; Edura, T.; Tsutsui, K.; Itaka, K.; Wada, Y.; Koinuma, H.

2006-01-01

We have fabricated a combinatorial nm-planar electrode array by using photolithography and chemical mechanical polishing processes for high throughput electrical evaluation of organic devices. Sub-nm precision was achieved with respect to the average level difference between each pair of electrodes and a dielectric layer. The insulating property between the electrodes is high enough to measure I-V characteristics of organic semiconductors. Bottom-contact field-effect-transistors (FETs) of pentacene were fabricated on this electrode array by use of molecular beam epitaxy. It was demonstrated that the array could be used as a pre-patterned device substrate for high throughput screening of the electrical properties of organic semiconductors

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.

HIGH-SPEED IMAGING AND WAVEFRONT SENSING WITH AN INFRARED AVALANCHE PHOTODIODE ARRAY

Energy Technology Data Exchange (ETDEWEB)

Baranec, Christoph; Atkinson, Dani; Hall, Donald; Jacobson, Shane; Chun, Mark [Institute for Astronomy, University of Hawai‘i at Mānoa, Hilo, HI 96720-2700 (United States); Riddle, Reed [Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Law, Nicholas M., E-mail: baranec@hawaii.edu [Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3255 (United States)

2015-08-10

Infrared avalanche photodiode (APD) 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 APD array that achieves a correlated double sampling read noise of 0.73 e{sup −} in the lab, and a total noise of 2.52 e{sup −} on sky, and supports simultaneous high-speed imaging and tip-tilt wavefront sensing with the Robo-AO visible-light laser adaptive optics (AO) system at the Palomar Observatory 1.5 m telescope. Here we report on the improved image quality simultaneously achieved at visible and infrared wavelengths by using the array as part of an image stabilization control loop with AO-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 AO and high-contrast imaging applications.

Local copying of orthogonal entangled quantum states

International Nuclear Information System (INIS)

Anselmi, Fabio; Chefles, Anthony; Plenio, Martin B

2004-01-01

In classical information theory one can, in principle, produce a perfect copy of any input state. In quantum information theory, the no cloning theorem prohibits exact copying of non-orthogonal states. Moreover, if we wish to copy multiparticle entangled states and can perform only local operations and classical communication (LOCC), then further restrictions apply. We investigate the problem of copying orthogonal, entangled quantum states with an entangled blank state under the restriction to LOCC. Throughout, the subsystems have finite dimension D. We show that if all of the states to be copied are non-maximally entangled, then novel LOCC copying procedures based on entanglement catalysis are possible. We then study in detail the LOCC copying problem where both the blank state and at least one of the states to be copied are maximally entangled. For this to be possible, we find that all the states to be copied must be maximally entangled. We obtain a necessary and sufficient condition for LOCC copying under these conditions. For two orthogonal, maximally entangled states, we provide the general solution to this condition. We use it to show that for D = 2, 3, any pair of orthogonal, maximally entangled states can be locally copied using a maximally entangled blank state. However, we also show that for any D which is not prime, one can construct pairs of such states for which this is impossible

Discussion paper for a highly parallel array processor-based machine

International Nuclear Information System (INIS)

Hagstrom, R.; Bolotin, G.; Dawson, J.

1984-01-01

The architectural plant for a quickly realizable implementation of a highly parallel special-purpose computer system with peak performance in the range of 6 billion floating point operations per second is discussed. The architecture is suitable to Lattice Gauge theoretical computations of fundamental physics interest and may be applicable to a range of other problems which deal with numerically intensive computational problems. The plan is quickly realizable because it employs a maximum of commercially available hardware subsystems and because the architecture is software-transparent to the individual processors, allowing straightforward re-use of whatever commercially available operating-systems and support software that is suitable to run on the commercially-produced processors. A tiny prototype instrument, designed along this architecture has already operated. A few elementary examples of programs which can run efficiently are presented. The large machine which the authors would propose to build would be based upon a highly competent array-processor, the ST-100 Array Processor, and specific design possibilities are discussed. The first step toward realizing this plan practically is to install a single ST-100 to allow algorithm development to proceed while a demonstration unit is built using two of the ST-100 Array Processors

Gene copy number variation throughout the Plasmodium falciparum genome

Directory of Open Access Journals (Sweden)

Stewart Lindsay B

2009-08-01

Full Text Available Abstract Background Gene copy number variation (CNV is responsible for several important phenotypes of the malaria parasite Plasmodium falciparum, including drug resistance, loss of infected erythrocyte cytoadherence and alteration of receptor usage for erythrocyte invasion. Despite the known effects of CNV, little is known about its extent throughout the genome. Results We performed a whole-genome survey of CNV genes in P. falciparum using comparative genome hybridisation of a diverse set of 16 laboratory culture-adapted isolates to a custom designed high density Affymetrix GeneChip array. Overall, 186 genes showed hybridisation signals consistent with deletion or amplification in one or more isolate. There is a strong association of CNV with gene length, genomic location, and low orthology to genes in other Plasmodium species. Sub-telomeric regions of all chromosomes are strongly associated with CNV genes independent from members of previously described multigene families. However, ~40% of CNV genes were located in more central regions of the chromosomes. Among the previously undescribed CNV genes, several that are of potential phenotypic relevance are identified. Conclusion CNV represents a major form of genetic variation within the P. falciparum genome; the distribution of gene features indicates the involvement of highly non-random mutational and selective processes. Additional studies should be directed at examining CNV in natural parasite populations to extend conclusions to clinical settings.

Improving Reliability of High Power Quasi-CW Laser Diode Arrays for Pumping Solid State Lasers

Science.gov (United States)

Amzajerdian, Farzin; Meadows, Byron L.; Baker, Nathaniel R.; Barnes, Bruce W.; Baggott, Renee S.; Lockard, George E.; Singh, Upendra N.; Kavaya, Michael J.

2005-01-01

Most Lidar applications rely on moderate to high power solid state lasers to generate the required transmitted pulses. However, the reliability of solid state lasers, which can operate autonomously over long periods, is constrained by their laser diode pump arrays. Thermal cycling of the active regions is considered the primary reason for rapid degradation of the quasi-CW high power laser diode arrays, and the excessive temperature rise is the leading suspect in premature failure. The thermal issues of laser diode arrays are even more drastic for 2-micron solid state lasers which require considerably longer pump pulses compared to the more commonly used pump arrays for 1-micron lasers. This paper describes several advanced packaging techniques being employed for more efficient heat removal from the active regions of the laser diode bars. Experimental results for several high power laser diode array devices will be reported and their performance when operated at long pulsewidths of about 1msec will be described.

Patterns, correlates, and reduction of homework copying

Directory of Open Access Journals (Sweden)

David J. Palazzo

2010-03-01

Full Text Available Submissions to an online homework tutor were analyzed to determine whether they were copied. The fraction of copied submissions increased rapidly over the semester, as each weekly deadline approached and for problems later in each assignment. The majority of students, who copied less than 10% of their problems, worked steadily over the three days prior to the deadline, whereas repetitive copiers (those who copied >30% of their submitted problems exerted little effort early. Importantly, copying homework problems that require an analytic answer correlates with a 2(σ decline over the semester in relative score for similar problems on exams but does not significantly correlate with the amount of conceptual learning as measured by pretesting and post-testing. An anonymous survey containing questions used in many previous studies of self-reported academic dishonesty showed ∼1/3 less copying than actually was detected. The observed patterns of copying, free response questions on the survey, and interview data suggest that time pressure on students who do not start their homework in a timely fashion is the proximate cause of copying. Several measures of initial ability in math or physics correlated with copying weakly or not at all. Changes in course format and instructional practices that previous self-reported academic dishonesty surveys and/or the observed copying patterns suggested would reduce copying have been accompanied by more than a factor of 4 reduction of copying from ∼11% of all electronic problems to less than 3%. As expected (since repetitive copiers have approximately three times the chance of failing, this was accompanied by a reduction in the overall course failure rate. Survey results indicate that students copy almost twice as much written homework as online homework and show that students nationally admit to more academic dishonesty than MIT students.

Genome Architecture and Its Roles in Human Copy Number Variation

Directory of Open Access Journals (Sweden)

Lu Chen

2014-12-01

Full Text Available Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs, are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

Monolithic array of 32 SPAD pixels for single-photon imaging at high frame rates

International Nuclear Information System (INIS)

Tisa, Simone; Guerrieri, Fabrizio; Zappa, Franco

2009-01-01

We present a single-chip monolithic array of 32 Single-Photon Avalanche Diodes (SPAD) and associated electronics for imaging at high frame rates and high sensitivity. Photodetectors, front-end circuitry and control electronics used to manage the array are monolithically integrated on the same chip in a standard 0.35 μm CMOS high-voltage technology. The array is composed of 32 'smart' pixels working in photon counting mode and functioning in a parallel fashion. Every cell comprises of an integrated SPAD photodetector, a novel quenching circuit named as Variable Load Quenching Circuit (VLQC), counting electronics and a buffer memory. Proper ancillary electronics that perform the arbitration of photon counts between two consecutive frames is integrated as well. Thanks to the presence of in-pixel memory registers, the inter-frame dead time between subsequent frames is limited to few nanoseconds. Since integration and download are performed simultaneously and the array can be addressed like a standard digital memory, the achievable maximum frame rate is very high in the order of hundreds of thousands of frame/s.

Phosphorization boosts the capacitance of mixed metal nanosheet arrays for high performance supercapacitor electrodes.

Science.gov (United States)

Lan, Yingying; Zhao, Hongyang; Zong, Yan; Li, Xinghua; Sun, Yong; Feng, Juan; Wang, Yan; Zheng, Xinliang; Du, Yaping

2018-05-01

Binary transition metal phosphides hold immense potential as innovative electrode materials for constructing high-performance energy storage devices. Herein, porous binary nickel-cobalt phosphide (NiCoP) nanosheet arrays anchored on nickel foam (NF) were rationally designed as self-supported binder-free electrodes with high supercapacitance performance. Taking the combined advantages of compositional features and array architectures, the nickel foam supported NiCoP nanosheet array (NiCoP@NF) electrode possesses superior electrochemical performance in comparison with Ni-Co LDH@NF and NiCoO2@NF electrodes. The NiCoP@NF electrode shows an ultrahigh specific capacitance of 2143 F g-1 at 1 A g-1 and retained 1615 F g-1 even at 20 A g-1, showing excellent rate performance. Furthermore, a binder-free all-solid-state asymmetric supercapacitor device is designed, which exhibits a high energy density of 27 W h kg-1 at a power density of 647 W kg-1. The hierarchical binary nickel-cobalt phosphide nanosheet arrays hold great promise as advanced electrode materials for supercapacitors with high electrochemical performance.

Breast tumor copy number aberration phenotypes and genomic instability

International Nuclear Information System (INIS)

Fridlyand, Jane; Jain, Ajay N; McLennan, Jane; Ziegler, John; Chin, Koei; Devries, Sandy; Feiler, Heidi; Gray, Joe W; Waldman, Frederic; Pinkel, Daniel; Albertson, Donna G; Snijders, Antoine M; Ylstra, Bauke; Li, Hua; Olshen, Adam; Segraves, Richard; Dairkee, Shanaz; Tokuyasu, Taku; Ljung, Britt Marie

2006-01-01

Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome

Array capabilities and future arrays

International Nuclear Information System (INIS)

Radford, D.

1993-01-01

Early results from the new third-generation instruments GAMMASPHERE and EUROGAM are confirming the expectation that such arrays will have a revolutionary effect on the field of high-spin nuclear structure. When completed, GAMMASHPERE will have a resolving power am order of magnitude greater that of the best second-generation arrays. When combined with other instruments such as particle-detector arrays and fragment mass analysers, the capabilites of the arrays for the study of more exotic nuclei will be further enhanced. In order to better understand the limitations of these instruments, and to design improved future detector systems, it is important to have some intelligible and reliable calculation for the relative resolving power of different instrument designs. The derivation of such a figure of merit will be briefly presented, and the relative sensitivities of arrays currently proposed or under construction presented. The design of TRIGAM, a new third-generation array proposed for Chalk River, will also be discussed. It is instructive to consider how far arrays of Compton-suppressed Ge detectors could be taken. For example, it will be shown that an idealised open-quote perfectclose quotes third-generation array of 1000 detectors has a sensitivity an order of magnitude higher again than that of GAMMASPHERE. Less conventional options for new arrays will also be explored

Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization.

Science.gov (United States)

Poorman, Kelsey; Borst, Luke; Moroff, Scott; Roy, Siddharth; Labelle, Philippe; Motsinger-Reif, Alison; Breen, Matthew

2015-06-01

Melanocytic lesions originating from the oral mucosa or cutaneous epithelium are common in the general dog population, with up to 100,000 diagnoses each year in the USA. Oral melanoma is the most frequent canine neoplasm of the oral cavity, exhibiting a highly aggressive course. Cutaneous melanocytomas occur frequently, but rarely develop into a malignant form. Despite the differential prognosis, it has been assumed that subtypes of melanocytic lesions represent the same disease. To address the relative paucity of information about their genomic status, molecular cytogenetic analysis was performed on the three recognized subtypes of canine melanocytic lesions. Using array comparative genomic hybridization (aCGH) analysis, highly aberrant distinct copy number status across the tumor genome for both of the malignant melanoma subtypes was revealed. The most frequent aberrations included gain of dog chromosome (CFA) 13 and 17 and loss of CFA 22. Melanocytomas possessed fewer genome wide aberrations, yet showed a recurrent gain of CFA 20q15.3-17. A distinctive copy number profile, evident only in oral melanomas, displayed a sigmoidal pattern of copy number loss followed immediately by a gain, around CFA 30q14. Moreover, when assessed by fluorescence in situ hybridization (FISH), copy number aberrations of targeted genes, such as gain of c-MYC (80 % of cases) and loss of CDKN2A (68 % of cases), were observed. This study suggests that in concordance with what is known for human melanomas, canine melanomas of the oral mucosa and cutaneous epithelium are discrete and initiated by different molecular pathways.

Copy number variation in the bovine genome

DEFF Research Database (Denmark)

Fadista, João; Thomsen, Bo; Holm, Lars-Erik

2010-01-01

to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation...... in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental...... duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences. Conclusions Together, this analysis provides a useful...

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations.

NARCIS (Netherlands)

van Houte, B.P.P.; Binsl, T.W.; Hettling, H.; Pirovano, W.A.; Heringa, J.

2009-01-01

Background: Array comparative genomic hybridization (aCGH) is a popular technique for detection of genomic copy number imbalances. These play a critical role in the onset of various types of cancer. In the analysis of aCGH data, normalization is deemed a critical pre-processing step. In general,

Reliability of spring interconnects for high channel-count polyimide electrode arrays

Science.gov (United States)

Khan, Sharif; Ordonez, Juan Sebastian; Stieglitz, Thomas

2018-05-01

Active neural implants with a high channel-count need robust and reliable operational assembly for the targeted environment in order to be classified as viable fully implantable systems. The discrete functionality of the electrode array and the implant electronics is vital for intact assembly. A critical interface exists at the interconnection sites between the electrode array and the implant electronics, especially in hybrid assemblies (e.g. retinal implants) where electrodes and electronics are not on the same substrate. Since the interconnects in such assemblies cannot be hermetically sealed, reliable protection against the physiological environment is essential for delivering high insulation resistance and low defusibility of salt ions, which are limited in complexity by current assembly techniques. This work reports on a combination of spring-type interconnects on a polyimide array with silicone rubber gasket insulation for chronically active implantable systems. The spring design of the interconnects on the backend of the electrode array compensates for the uniform thickness of the sandwiched gasket during bonding in assembly and relieves the propagation of extrinsic stresses to the bulk polyimide substrate. The contact resistance of the microflex-bonded spring interconnects with the underlying metallized ceramic test vehicles and insulation through the gasket between adjacent contacts was investigated against the MIL883 standard. The contact and insulation resistances remained stable in the exhausting environmental conditions.

High-performance ferroelectric and magnetoresistive materials for next-generation thermal detector arrays

Science.gov (United States)

Todd, Michael A.; Donohue, Paul P.; Watton, Rex; Williams, Dennis J.; Anthony, Carl J.; Blamire, Mark G.

2002-12-01

This paper discusses the potential thermal imaging performance achievable from thermal detector arrays and concludes that the current generation of thin-film ferroelectric and resistance bolometer based detector arrays are limited by the detector materials used. It is proposed that the next generation of large uncooled focal plane arrays will need to look towards higher performance detector materials - particularly if they aim to approach the fundamental performance limits and compete with cooled photon detector arrays. Two examples of bolometer thin-film materials are described that achieve high performance from operating around phase transitions. The material Lead Scandium Tantalate (PST) has a paraelectric-to-ferroelectric phase transition around room temperature and is used with an applied field in the dielectric bolometer mode for thermal imaging. PST films grown by sputtering and liquid-source CVD have shown merit figures for thermal imaging a factor of 2 to 3 times higher than PZT-based pyroelectric thin films. The material Lanthanum Calcium Manganite (LCMO) has a paramagnetic to ferromagnetic phase transition around -20oC. This paper describes recent measurements of TCR and 1/f noise in pulsed laser-deposited LCMO films on Neodymium Gallate substrates. These results show that LCMO not only has high TCR's - up to 30%/K - but also low 1/f excess noise, with bolometer merit figures at least an order of magnitude higher than Vanadium Oxide, making it ideal for the next generation of microbolometer arrays. These high performance properties come at the expense of processing complexities and novel device designs will need to be introduced to realize the potential of these materials in the next generation of thermal detectors.

Timed arrays wideband and time varying antenna arrays

CERN Document Server

Haupt, Randy L

2015-01-01

Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

Highly selective gas sensor arrays based on thermally reduced graphene oxide.

Science.gov (United States)

Lipatov, Alexey; Varezhnikov, Alexey; Wilson, Peter; Sysoev, Victor; Kolmakov, Andrei; Sinitskii, Alexander

2013-06-21

The electrical properties of reduced graphene oxide (rGO) have been previously shown to be very sensitive to surface adsorbates, thus making rGO a very promising platform for highly sensitive gas sensors. However, poor selectivity of rGO-based gas sensors remains a major problem for their practical use. In this paper, we address the selectivity problem by employing an array of rGO-based integrated sensors instead of focusing on the performance of a single sensing element. Each rGO-based device in such an array has a unique sensor response due to the irregular structure of rGO films at different levels of organization, ranging from nanoscale to macroscale. The resulting rGO-based gas sensing system could reliably recognize analytes of nearly the same chemical nature. In our experiments rGO-based sensor arrays demonstrated a high selectivity that was sufficient to discriminate between different alcohols, such as methanol, ethanol and isopropanol, at a 100% success rate. We also discuss a possible sensing mechanism that provides the basis for analyte differentiation.

High Dynamic Range adaptive ΔΣ-based Focal Plane Array architecture

KAUST Repository

Yao, Shun; Kavusi, Sam; Salama, Khaled N.

2012-01-01

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

High-resolution 3D laser imaging based on tunable fiber array link

Science.gov (United States)

Zhao, Sisi; Ruan, Ningjuan; Yang, Song

2017-10-01

Airborne photoelectric reconnaissance system with the bore sight down to the ground is an important battlefield situational awareness system, which can be used for reconnaissance and surveillance of complex ground scene. Airborne 3D imaging Lidar system is recognized as the most potential candidates for target detection under the complex background, and is progressing in the directions of high resolution, long distance detection, high sensitivity, low power consumption, high reliability, eye safe and multi-functional. However, the traditional 3D laser imaging system has the disadvantages of lower imaging resolutions because of the small size of the existing detector, and large volume. This paper proposes a high resolution laser 3D imaging technology based on the tunable optical fiber array link. The echo signal is modulated by a tunable optical fiber array link and then transmitted to the focal plane detector. The detector converts the optical signal into electrical signals which is given to the computer. Then, the computer accomplishes the signal calculation and image restoration based on modulation information, and then reconstructs the target image. This paper establishes the mathematical model of tunable optical fiber array signal receiving link, and proposes the simulation and analysis of the affect factors on high density multidimensional point cloud reconstruction.

Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.

Science.gov (United States)

Khan, Fayeza F; Carpenter, Danielle; Mitchell, Laura; Mansouri, Omniah; Black, Holly A; Tyson, Jess; Armour, John A L

2013-10-20

Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing. In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples. We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn's disease, type I diabetes, HIV progression and multiple sclerosis.

Development of HgCdTe large format MBE arrays and noise-free high speed MOVPE EAPD arrays for ground based NIR astronomy

Science.gov (United States)

Finger, G.; Baker, I.; Downing, M.; Alvarez, D.; Ives, D.; Mehrgan, L.; Meyer, M.; Stegmeier, J.; Weller, H. J.

2017-11-01

Large format near infrared HgCdTe 2Kx2K and 4Kx4K MBE arrays have reached a level of maturity which meets most of the specifications required for near infrared (NIR) astronomy. The only remaining problem is the persistence effect which is device specific and not yet fully under control. For ground based multi-object spectroscopy on 40 meter class telescopes larger pixels would be advantageous. For high speed near infrared fringe tracking and wavefront sensing the only way to overcome the CMOS noise barrier is the amplification of the photoelectron signal inside the infrared pixel by means of the avalanche gain. A readout chip for a 320x256 pixel HgCdTe eAPD array will be presented which has 32 parallel video outputs being arranged in such a way that the full multiplex advantage is also available for small sub-windows. In combination with the high APD gain this allows reducing the readout noise to the subelectron level by applying nondestructive readout schemes with subpixel sampling. Arrays grown by MOVPE achieve subelectron readout noise and operate with superb cosmetic quality at high APD gain. Efforts are made to reduce the dark current of those arrays to make this technology also available for large format focal planes of NIR instruments offering noise free detectors for deep exposures. The dark current of the latest MOVPE eAPD arrays is already at a level adequate for noiseless broad and narrow band imaging in scientific instruments.

High Frequency of Copy-Neutral Loss of Heterozygosity in Patients with Myelofibrosis.

Science.gov (United States)

Rego de Paula Junior, Milton; Nonino, Alexandre; Minuncio Nascimento, Juliana; Bonadio, Raphael S; Pic-Taylor, Aline; de Oliveira, Silviene F; Wellerson Pereira, Rinaldo; do Couto Mascarenhas, Cintia; Forte Mazzeu, Juliana

2018-01-01

Myelofibrosis is the rarest and most severe type of Philadelphia-negative classical myeloproliferative neoplasms. Although mutually exclusive driver mutations in JAK2, MPL, or CALR that activate JAK-STAT pathway have been related to the pathogenesis of the disease, chromosome abnormalities have also been associated with the phenotype and prognosis of the disease. Here, we report the use of a chromosomal microarray platform consisting of both oligo and SNP probes to improve the detection of chromosome abnormalities in patients with myelofibrosis. Sixteen patients with myelofibrosis were tested, and the results were compared to karyotype analysis. Driver mutations in JAK2, MPL, or CALR were investigated by PCR and MLPA. Conventional cytogenetics revealed chromosome abnormalities in 3 out of 16 cases (18.7%), while chromosomal microarray analysis detected copy-number variations (CNV) or copy-neutral loss of heterozygosity (CN-LOH) alterations in 11 out of 16 (68.7%) patients. These included 43 CN-LOH, 14 deletions, 1 trisomy, and 1 duplication. Ten patients showed multiple chromosomal abnormalities, varying from 2 to 13 CNVs or CN-LOHs. Mutational status for JAK2, CALR, and MPL by MLPA revealed a total of 3/16 (18.7%) patients positive for the JAK2 V617F mutation, 9 with CALR deletion or insertion and 1 positive for MPL mutation. Considering that most of the CNVs identified were smaller than the karyotype resolution and the high frequency of CN-LOHs in our study, we propose that chromosomal microarray platforms that combine oligos and SNP should be used as a first-tier genetic test in patients with myelofibrosis. © 2018 S. Karger AG, Basel.

Evaluation of electrical crosstalk in high-density photodiode arrays for X-ray imaging applications

International Nuclear Information System (INIS)

Ji Fan; Juntunen, Mikko; Hietanen, Iiro

2009-01-01

Electrical crosstalk is one of the important parameters in the photodiode array detector for X-ray imaging applications, and it becomes more important when the density of the photodiode array becomes higher. This paper presents the design of the high-density photodiode array with 250 μm pitch and 50 μm gap. The electrical crosstalk of the demonstrated samples is evaluated and compared with different electrode configurations: cathode bias mode and anode bias mode. The measurement results show good electrical crosstalk, ∼0.23%, in cathode bias mode regardless of the bias voltage, and slightly decreased or increased electrical crosstalk in anode bias mode. Moreover, the quantum efficiency is also evaluated from the same samples, and it behaves similar to the electrical crosstalk. Finally, some design guidance of the high-density photodiode array is given based on the discussion.

Multiple-copy entanglement transformation and entanglement catalysis

International Nuclear Information System (INIS)

Duan Runyao; Feng Yuan; Li Xin; Ying Mingsheng

2005-01-01

We prove that any multiple-copy entanglement transformation [S. Bandyopadhyay, V. Roychowdhury, and U. Sen, Phys. Rev. A 65, 052315 (2002)] can be implemented by a suitable entanglement-assisted local transformation [D. Jonathan and M. B. Plenio, Phys. Rev. Lett. 83, 3566 (1999)]. Furthermore, we show that the combination of multiple-copy entanglement transformation and the entanglement-assisted one is still equivalent to the pure entanglement-assisted one. The mathematical structure of multiple-copy entanglement transformations then is carefully investigated. Many interesting properties of multiple-copy entanglement transformations are presented, which exactly coincide with those satisfied by the entanglement-assisted ones. Most interestingly, we show that an arbitrarily large number of copies of state should be considered in multiple-copy entanglement transformations

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.

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...

RAID Disk Arrays for High Bandwidth Applications

Science.gov (United States)

Moren, Bill

1996-01-01

High bandwidth applications require large amounts of data transferred to/from storage devices at extremely high data rates. Further, these applications often are 'real time' in which access to the storage device must take place on the schedule of the data source, not the storage. A good example is a satellite downlink - the volume of data is quite large and the data rates quite high (dozens of MB/sec). Further, a telemetry downlink must take place while the satellite is overhead. A storage technology which is ideally suited to these types of applications is redundant arrays of independent discs (RAID). Raid storage technology, while offering differing methodologies for a variety of applications, supports the performance and redundancy required in real-time applications. Of the various RAID levels, RAID-3 is the only one which provides high data transfer rates under all operating conditions, including after a drive failure.

Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

Science.gov (United States)

Bickhart, Derek M.; Xu, Lingyang; Hutchison, Jana L.; Cole, John B.; Null, Daniel J.; Schroeder, Steven G.; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S.; Van Tassell, Curtis P.; Schnabel, Robert D.; Taylor, Jeremy F.; Lewin, Harris A.; Liu, George E.

2016-01-01

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

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.

A review of array radars

Science.gov (United States)

Brookner, E.

1981-10-01

Achievements in the area of array radars are illustrated by such activities as the operational deployment of the large high-power, high-range-resolution Cobra Dane; the operational deployment of two all-solid-state high-power, large UHF Pave Paws radars; and the development of the SAM multifunction Patriot radar. This paper reviews the following topics: array radars steered in azimuth and elevation by phase shifting (phase-phase steered arrays); arrays steered + or - 60 deg, limited scan arrays, hemispherical coverage, and omnidirectional coverage arrays; array radars steering electronically in only one dimension, either by frequency or by phase steering; and array radar antennas which use no electronic scanning but instead use array antennas for achieving low antenna sidelobes.

Copy Number Variation in Hereditary Non-Polyposis Colorectal Cancer

Directory of Open Access Journals (Sweden)

Garry N. Hannan

2013-09-01

Full Text Available Hereditary non-polyposis colorectal cancer (HNPCC is the commonest form of inherited colorectal cancer (CRC predisposition and by definition describes families which conform to the Amsterdam Criteria or reiterations thereof. In ~50% of patients adhering to the Amsterdam criteria germline variants are identified in one of four DNA Mismatch repair (MMR genes MLH1, MSH2, MSH6 and PMS2. Loss of function of any one of these genes results in a failure to repair DNA errors occurring during replication which can be most easily observed as DNA microsatellite instability (MSI—a hallmark feature of this disease. The remaining 50% of patients without a genetic diagnosis of disease may harbour more cryptic changes within or adjacent to MLH1, MSH2, MSH6 or PMS2 or elsewhere in the genome. We used a high density cytogenetic array to screen for deletions or duplications in a series of patients, all of whom adhered to the Amsterdam/Bethesda criteria, to determine if genomic re-arrangements could account for a proportion of patients that had been shown not to harbour causative mutations as assessed by standard diagnostic techniques. The study has revealed some associations between copy number variants (CNVs and HNPCC mutation negative cases and further highlights difficulties associated with CNV analysis.

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).

High operating temperature interband cascade focal plane arrays

Energy Technology Data Exchange (ETDEWEB)

Tian, Z.-B.; Godoy, S. E.; Kim, H. S.; Schuler-Sandy, T.; Montoya, J. A.; Krishna, S. [Center for High Technology Materials, Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, New Mexico 87106 (United States)

2014-08-04

In this paper, we report the initial demonstration of mid-infrared interband cascade (IC) photodetector focal plane arrays with multiple-stage/junction design. The merits of IC photodetectors include low noise and efficient photocarrier extraction, even for zero-bias operation. By adopting enhanced electron barrier design and a total absorber thickness of 0.7 μm, the 5-stage IC detectors show very low dark current (1.10 × 10{sup −7} A/cm{sup 2} at −5 mV and 150 K). Even with un-optimized fabrication and standard commercial (mis-matched) read-out circuit technology, infrared images are obtained by the 320 × 256 IC focal plane array up to 180 K with f/2.3 optics. The minimum noise equivalent temperature difference of 28 mK is obtained at 120 K. These initial results indicate great potential of IC photodetectors, particularly for high operating temperature applications.

High operating temperature interband cascade focal plane arrays

International Nuclear Information System (INIS)

Tian, Z.-B.; Godoy, S. E.; Kim, H. S.; Schuler-Sandy, T.; Montoya, J. A.; Krishna, S.

2014-01-01

In this paper, we report the initial demonstration of mid-infrared interband cascade (IC) photodetector focal plane arrays with multiple-stage/junction design. The merits of IC photodetectors include low noise and efficient photocarrier extraction, even for zero-bias operation. By adopting enhanced electron barrier design and a total absorber thickness of 0.7 μm, the 5-stage IC detectors show very low dark current (1.10 × 10 −7 A/cm 2 at −5 mV and 150 K). Even with un-optimized fabrication and standard commercial (mis-matched) read-out circuit technology, infrared images are obtained by the 320 × 256 IC focal plane array up to 180 K with f/2.3 optics. The minimum noise equivalent temperature difference of 28 mK is obtained at 120 K. These initial results indicate great potential of IC photodetectors, particularly for high operating temperature applications

A novel method for the fabrication of a high-density carbon nanotube microelectrode array

Directory of Open Access Journals (Sweden)

Adam Khalifa

2015-09-01

Full Text Available We present a novel method for fabricating a high-density carbon nanotube microelectrode array (MEA chip. Vertically aligned carbon nanotubes (VACNTs were synthesized by microwave plasma-enhanced chemical vapor deposition and thermal chemical vapor deposition. The device was characterized using electrochemical experiments such as cyclic voltammetry, impedance spectroscopy and potential transient measurements. Through-silicon vias (TSVs were fabricated and partially filled with polycrystalline silicon to allow electrical connection from the high-density electrodes to a stimulator microchip. In response to the demand for higher resolution implants, we have developed a unique process to obtain a high-density electrode array by making the microelectrodes smaller in size and designing new ways of routing the electrodes to current sources. Keywords: Microelectrode array, Neural implant, Carbon nanotubes, Through-silicon via interconnects, Microfabrication

High Sensitivity Indium Phosphide Based Avalanche Photodiode Focal Plane Arrays, Phase II

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...

Synthesis of highly-ordered TiO2 nanotube arrays with tunable sizes

Science.gov (United States)

Wang, Xian; Zha, Chenyang; Ji, Cheng; Zhang, Xiaoyan; Shen, Liming; Wang, Yifeng; Gupta, Arunava; Yoriya, Sorachon; Bao, Ningzhong

2014-09-01

Vertically-oriented one-dimensional TiO2 nanotube (TNT) arrays have been fabricated by anodic oxidation using different electrolyte solvents, including ethylene glycol (EG), diethylene glycol (DEG), and dimethyl sulfoxide (DMSO), in the presence of hydrofluoric acid (HF) or ammonium fluoride (NH4F). The influence of synthetic conditions, including the nature of the electrolyte and anodization voltage, on nanotube microstructure has been systematically investigated. Highly-ordered TNTs with tube length of ˜0.5-26.7 μm, inner diameter of ˜13-201 nm, and outer diameter of ˜28-250 nm have been obtained. The conversion of as-prepared TNT arrays from amorphous phase to crystalline structure has been achieved by a post-synthetic annealing at 500 °C for 3 h in oxygen ambient. The TNT arrays with tunable sizes and structures are attractive for use as electrode materials in fabrication of thin film solar cells and highly active photocatalysts.

Synthesis of highly-ordered TiO2 nanotube arrays with tunable sizes

International Nuclear Information System (INIS)

Wang, Xian; Zha, Chenyang; Ji, Cheng; Zhang, Xiaoyan; Shen, Liming; Wang, Yifeng; Bao, Ningzhong; Gupta, Arunava; Yoriya, Sorachon

2014-01-01

Vertically-oriented one-dimensional TiO 2 nanotube (TNT) arrays have been fabricated by anodic oxidation using different electrolyte solvents, including ethylene glycol (EG), diethylene glycol (DEG), and dimethyl sulfoxide (DMSO), in the presence of hydrofluoric acid (HF) or ammonium fluoride (NH 4 F). The influence of synthetic conditions, including the nature of the electrolyte and anodization voltage, on nanotube microstructure has been systematically investigated. Highly-ordered TNTs with tube length of ∼0.5–26.7 μm, inner diameter of ∼13–201 nm, and outer diameter of ∼28–250 nm have been obtained. The conversion of as-prepared TNT arrays from amorphous phase to crystalline structure has been achieved by a post-synthetic annealing at 500 °C for 3 h in oxygen ambient. The TNT arrays with tunable sizes and structures are attractive for use as electrode materials in fabrication of thin film solar cells and highly active photocatalysts. (paper)

FDM-HAWK, A High Performance Compact Modular Solar Array, Phase I

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...

Hard Copy Market Overview

Science.gov (United States)

Testan, Peter R.

1987-04-01

A number of Color Hard Copy (CHC) market drivers are currently indicating strong growth in the use of CHC technologies for the business graphics marketplace. These market drivers relate to product, software, color monitors and color copiers. The use of color in business graphics allows more information to be relayed than is normally the case in a monochrome format. The communicative powers of full-color computer generated output in the business graphics application area will continue to induce end users to desire and require color in their future applications. A number of color hard copy technologies will be utilized in the presentation graphics arena. Thermal transfer, ink jet, photographic and electrophotographic technologies are all expected to be utilized in the business graphics presentation application area in the future. Since the end of 1984, the availability of color application software packages has grown significantly. Sales revenue generated by business graphics software is expected to grow at a compound annual growth rate of just over 40 percent to 1990. Increased availability of packages to allow the integration of text and graphics is expected. Currently, the latest versions of page description languages such as Postscript, Interpress and DDL all support color output. The use of color monitors will also drive the demand for color hard copy in the business graphics market place. The availability of higher resolution screens is allowing color monitors to be easily used for both text and graphics applications in the office environment. During 1987, the sales of color monitors are expected to surpass the sales of monochrome monitors. Another major color hard copy market driver will be the color copier. In order to take advantage of the communications power of computer generated color output, multiple copies are required for distribution. Product introductions of a new generation of color copiers is now underway with additional introductions expected

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.

Application of high resolution SNP arrays in patients with congenital ...

Indian Academy of Sciences (India)

clinical experience in implementing whole-genome high-resolution SNP arrays to investigate 33 patients with syndromic and .... Online Mendelian Inheritance in Man database (OMIM, ..... of damaged mitochondria through either autophagy or mito- ..... malformations: associations with maternal and infant character- istics in a ...

Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines

International Nuclear Information System (INIS)

Junnila, Siina; Kokkola, Arto; Karjalainen-Lindsberg, Marja-Liisa; Puolakkainen, Pauli; Monni, Outi

2010-01-01

Gastric cancer is one of the most common malignancies worldwide and the second most common cause of cancer related death. Gene copy number alterations play an important role in the development of gastric cancer and a change in gene copy number is one of the main mechanisms for a cancer cell to control the expression of potential oncogenes and tumor suppressor genes. To highlight genes of potential biological and clinical relevance in gastric cancer, we carried out a systematic array-based survey of gene expression and copy number levels in primary gastric tumors and gastric cancer cell lines and validated the results using an affinity capture based transcript analysis (TRAC assay) and real-time qRT-PCR. Integrated microarray analysis revealed altogether 256 genes that were located in recurrent regions of gains or losses and had at least a 2-fold copy number- associated change in their gene expression. The expression levels of 13 of these genes, ALPK2, ASAP1, CEACAM5, CYP3A4, ENAH, ERBB2, HHIPL2, LTB4R, MMP9, PERLD1, PNMT, PTPRA, and OSMR, were validated in a total of 118 gastric samples using either the qRT-PCR or TRAC assay. All of these 13 genes were differentially expressed between cancerous samples and nonmalignant tissues (p < 0.05) and the association between copy number and gene expression changes was validated for nine (69.2%) of these genes (p < 0.05). In conclusion, integrated gene expression and copy number microarray analysis highlighted genes that may be critically important for gastric carcinogenesis. TRAC and qRT-PCR analyses validated the microarray results and therefore the role of these genes as potential biomarkers for gastric cancer

Foldable Compactly Stowable Extremely High Power Solar Array System, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Deployable Space Systems, Inc. (DSS) has developed a high performance solar array system that has game-changing performance metrics in terms of ultra-compact stowage...

Copy-Move Forgery Detection Technique for Forensic Analysis in Digital Images

Directory of Open Access Journals (Sweden)

Toqeer Mahmood

2016-01-01

Full Text Available Due to the powerful image editing tools images are open to several manipulations; therefore, their authenticity is becoming questionable especially when images have influential power, for example, in a court of law, news reports, and insurance claims. Image forensic techniques determine the integrity of images by applying various high-tech mechanisms developed in the literature. In this paper, the images are analyzed for a particular type of forgery where a region of an image is copied and pasted onto the same image to create a duplication or to conceal some existing objects. To detect the copy-move forgery attack, images are first divided into overlapping square blocks and DCT components are adopted as the block representations. Due to the high dimensional nature of the feature space, Gaussian RBF kernel PCA is applied to achieve the reduced dimensional feature vector representation that also improved the efficiency during the feature matching. Extensive experiments are performed to evaluate the proposed method in comparison to state of the art. The experimental results reveal that the proposed technique precisely determines the copy-move forgery even when the images are contaminated with blurring, noise, and compression and can effectively detect multiple copy-move forgeries. Hence, the proposed technique provides a computationally efficient and reliable way of copy-move forgery detection that increases the credibility of images in evidence centered applications.

An Ultra-High Element Density pMUT Array with Low Crosstalk for 3-D Medical Imaging

Directory of Open Access Journals (Sweden)

Tian-Ling Ren

2013-07-01

Full Text Available A ~1 MHz piezoelectric micromachined ultrasonic transducer (pMUT array with ultra-high element density and low crosstalk is proposed for the first time. This novel pMUT array is based on a nano-layer spin-coating lead zirconium titanium film technique and can be fabricated with high element density using a relatively simple process. Accordingly, key fabrication processes such as thick piezoelectric film deposition, low-stress Si-SOI bonding and bulk silicon removal have been successfully developed. The novel fine-pitch 6 × 6 pMUT arrays can all work at the desired frequency (~1 MHz with good uniformity, high performance and potential IC integration compatibility. The minimum interspace is ~20 μm, the smallest that has ever been achieved to the best of our knowledge. These arrays can be potentially used to steer ultrasound beams and implement high quality 3-D medical imaging applications.

High-power, format-flexible, 885-nm vertical-cavity surface-emitting laser arrays

Science.gov (United States)

Wang, Chad; Talantov, Fedor; Garrett, Henry; Berdin, Glen; Cardellino, Terri; Millenheft, David; Geske, Jonathan

2013-03-01

High-power, format flexible, 885 nm vertical-cavity surface-emitting laser (VCSEL) arrays have been developed for solid-state pumping and illumination applications. In this approach, a common VCSEL size format was designed to enable tiling into flexible formats and operating configurations. The fabrication of a common chip size on ceramic submount enables low-cost volume manufacturing of high-power VCSEL arrays. This base VCSEL chip was designed to be 5x3.33 mm2, and produced up to 50 Watts of peak continuous wave (CW) power. To scale to higher powers, multiple chips can be tiled into a combination of series or parallel configurations tailored to the application driver conditions. In actively cooled CW operation, the VCSEL array chips were packaged onto a single water channel cooler, and we have demonstrated 0.5x1, 1x1, and 1x3 cm2 formats, producing 150, 250, and 500 Watts of peak power, respectively, in under 130 A operating current. In QCW operation, the 1x3 cm2 VCSEL module, which contains 18 VCSEL array chips packaged on a single water cooler, produced over 1.3 kW of peak power. In passively cooled packages, multiple chip configurations have been developed for illumination applications, producing over 300 Watts of peak power in QCW operating conditions. These VCSEL chips use a substrate-removed structure to allow for efficient thermal heatsinking to enable high-power operation. This scalable, format flexible VCSEL architecture can be applied to wavelengths ranging from 800 to 1100 nm, and can be used to tailor emission spectral widths and build high-power hyperspectral sources.

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....

Practical method for appearance match between soft copy and hard copy

Science.gov (United States)

Katoh, Naoya

1994-04-01

CRT monitors are often used as a soft proofing device for the hard copy image output. However, what the user sees on the monitor does not match its output, even if the monitor and the output device are calibrated with CIE/XYZ or CIE/Lab. This is especially obvious when correlated color temperature (CCT) of CRT monitor's white point significantly differs from ambient light. In a typical office environment, one uses a computer graphic monitor having a CCT of 9300K in a room of white fluorescent light of 4150K CCT. In such a case, human visual system is partially adapted to the CRT monitor's white point and partially to the ambient light. The visual experiments were performed on the effect of the ambient lighting. Practical method for soft copy color reproduction that matches the hard copy image in appearance is presented in this paper. This method is fundamentally based on a simple von Kries' adaptation model and takes into account the human visual system's partial adaptation and contrast matching.

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

Science.gov (United States)

2014-01-01

Background Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in

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.

Carcinoma ex-pleomorphic adenoma derived from recurrent pleomorphic adenoma shows important difference by array CGH compared to recurrent pleomorphic adenoma without malignant transformation

Directory of Open Access Journals (Sweden)

Fernanda Viviane Mariano

Full Text Available Abstract Introduction: A key step of cancer development is the progressive accumulation of genomic changes resulting in disruption of several biological mechanisms. Carcinoma ex-pleomorphic adenoma (CXPA is an aggressive neoplasm that arises from a pleomorphic adenoma. CXPA derived from a recurrent PA (RPA has been rarely reported, and the genomic changes associated with these tumors have not yet been studied. Objective: We analyzed CXPA from RPAs and RPAs without malignant transformation using array-comparative genomic hybridization (array-CGH to identify somatic copy number alterations and affected genes. Methods: DNA samples extracted from FFPE tumors were submitted to array-CGH investigation, and data was analyzed by Nexus Copy Number Discovery Edition v.7. Results: No somatic copy number alterations were found in RPAs without malignant transformation. As for CXPA from RPA, although genomic profiles were unique for each case, we detected some chromosomal regions that appear to be preferentially affected by copy number alterations. The first case of CXPA-RPA (frankly invasive myoepithelial carcinoma showed copy number alterations affecting 1p36.33p13, 5p and chromosomes 3 and 8. The second case of CXPA-RPA (frankly invasive epithelial-myoepithelial carcinoma showed several alterations at chromosomes 3, 8, and 16, with two amplifications at 8p12p11.21 and 12q14.3q21.2. The third case of CXPA-RPA (minimally invasive epithelial-myoepithelial carcinoma exhibited amplifications at 12q13.3q14.1, 12q14.3, and 12q15. Conclusion: The occurrence of gains at chromosomes 3 and 8 and genomic amplifications at 8p and 12q, mainly those encompassing the HMGA2, MDM2, WIF1, WHSC1L1, LIRG3, CDK4 in CXAP from RPA can be a significant promotional factor in malignant transformation.

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.

Identification of chromosome aberrations in sporadic microsatellite stable and unstable colorectal cancers using array comparative genomic hybridization

DEFF Research Database (Denmark)

Jensen, Thomas Dyrsø; Li, Jian; Wang, Kai

2011-01-01

cancers constitute approximately 85% of sporadic cases, whereas microsatellite unstable (MSI) cases constitute the remaining 15%. In this study, we used array comparative genomic hybridization (aCGH) to identify genomic hotspot regions that harbor recurrent copy number changes. The study material...

Intracavitary ultrasound phased arrays for thermal therapies

Science.gov (United States)

Hutchinson, Erin

that the heating capabilities of the constructed phased arrays were adequate for hyperthermia and thermal surgery treatments. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253- 1690.)

An integrated analysis of miRNA and gene copy numbers in xenografts of Ewing's sarcoma

Directory of Open Access Journals (Sweden)

Mosakhani Neda

2012-03-01

Full Text Available Abstract Background Xenografts have been shown to provide a suitable source of tumor tissue for molecular analysis in the absence of primary tumor material. We utilized ES xenograft series for integrated microarray analyses to identify novel biomarkers. Method Microarray technology (array comparative genomic hybridization (aCGH and micro RNA arrays was used to screen and identify copy number changes and differentially expressed miRNAs of 34 and 14 passages, respectively. Incubated cells used for xenografting (Passage 0 were considered to represent the primary tumor. Four important differentially expressed miRNAs (miR-31, miR-31*, miR-145, miR-106 were selected for further validation by real time polymerase chain reaction (RT-PCR. Integrated analysis of aCGH and miRNA data was performed on 14 xenograft passages by bioinformatic methods. Results The most frequent losses and gains of DNA copy number were detected at 9p21.3, 16q and at 8, 15, 17q21.32-qter, 1q21.1-qter, respectively. The presence of these alterations was consistent in all tumor passages. aCGH profiles of xenograft passages of each series resembled their corresponding primary tumors (passage 0. MiR-21, miR-31, miR-31*, miR-106b, miR-145, miR-150*, miR-371-5p, miR-557 and miR-598 showed recurrently altered expression. These miRNAS were predicted to regulate many ES-associated genes, such as genes of the IGF1 pathway, EWSR1, FLI1 and their fusion gene (EWS-FLI1. Twenty differentially expressed miRNAs were pinpointed in regions carrying altered copy numbers. Conclusion In the present study, ES xenografts were successfully applied for integrated microarray analyses. Our findings showed expression changes of miRNAs that were predicted to regulate many ES associated genes, such as IGF1 pathway genes, FLI1, EWSR1, and the EWS-FLI1 fusion genes.

The acceptance of surface detector arrays for high energy cosmological muon neutrinos

International Nuclear Information System (INIS)

Vo Van Thuan; Hoang Van Khanh

2011-01-01

In order to search for ultra-high energy cosmological earth-skimming muon neutrinos by the surface detector array (SD) similar to one of the Pierre Auger Observatory (PAO), we propose to use the transition electromagnetic radiation at the medium interface induced by earth-skimming muons for triggering a few of aligned neighboring Cherenkov SD stations. Simulations of the acceptance of a modeling SD array have been done to estimate the detection probability of earth-skimming muon neutrinos.

Novel iron oxide nanotube arrays as high-performance anodes for lithium ion batteries

Science.gov (United States)

Zhong, Yuan; Fan, Huiqing; Chang, Ling; Shao, Haibo; Wang, Jianming; Zhang, Jianqing; Cao, Chu-nan

2015-11-01

Nanostructured iron oxides can be promising anode materials for lithium ion batteries (LIBs). However, improvement on the rate capability and/or electrochemical cycling stability of iron oxide anode materials remains a key challenge because of their poor electrical conductivities and large volume expansion during cycling. Herein, the vertically aligned arrays of one-dimensional (1D) iron oxide nanotubes with 5.8 wt% carbon have been fabricated by a novel surfactant-free self-corrosion process and subsequent thermal treatment. The as-fabricated nanotube array electrode delivers a reversible capacity of 932 mAh g-1 after 50 charge-discharge cycles at a current of 0.6 A g-1. The electrode still shows a reversible capacity of 610 mAh g-1 even at a very high rate (8.0 A g-1), demonstrating its prominent rate capability. Furthermore, the nanotube array electrode also exhibits the excellent electrochemical cycling stability with a reversible capacity of 880 mAh g-1 after 500 cycles at a current of 4 A g-1. The nanotube array electrode with superior lithium storage performance reveals the promising potential as a high-performance anode for LIBs.

Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome.

Directory of Open Access Journals (Sweden)

Maribel Forero-Castro

Full Text Available Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL is still a challenge.To characterize the presence of additional DNA copy number alterations (CNAs in children and adults with ALL by whole-genome oligonucleotide array (aCGH analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults. The NimbleGen CGH 12x135K array (Roche was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q. CNAs were associated with age, phenotype, genetic subtype and overall survival (OS. In the whole cohort of children, the losses on 14q32.33 (p = 0.019 and 15q13.2 (p = 0.04 were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001 and Xp21.1 (p = 0.029, and the loss of 17p (p = 0.014 were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.

Optimal design of a double-sided linear motor with a multi-segmented trapezoidal magnet array for a high precision positioning system

International Nuclear Information System (INIS)

Lee, Moon G.; Gweon, Dae-Gab

2004-01-01

A comparative analysis is performed for linear motors adopting conventional and multi-segmented trapezoidal (MST) magnet arrays, respectively, for a high-precision positioning system. The proposed MST magnet array is a modified version of a Halbach magnet array. The MST array has trapezoidal magnets with variable shape and dimensions while the Halbach magnet array generally has a rectangular magnet with identical dimensions. We propose a new model that can describe the magnetic field resulting from the complex-shaped magnets. The model can be applied to both MST and conventional magnet arrays. Using the model, a design optimization of the two types of linear motors is performed and compared. The magnet array with trapezoidal magnets can produce more force than one with rectangular magnets when they are arrayed in a linear motor where there is a yoke with high permeability. After the optimization and comparison, we conclude that the linear motor with the MST magnet array can generate more actuating force per volume than the motor with the conventional array. In order to satisfy the requirements of next generation systems such as high resolution, high speed, and long stroke, the use of a linear motor with a MST array as an actuator in a high precision positioning system is recommended from the results obtained here

Optimum concentric circular array antenna with high gain and side lobe reduction at 5.8 GHz

Science.gov (United States)

Zaid, Mohammed; Rafiqul Islam, Md; Habaebi, Mohamed H.; Zahirul Alam, AHM; Abdullah, Khaizuran

2017-11-01

The significance of high gain directional antennas stems from the need to cope up with the everyday progressing wireless communication systems. Due to low gain of the widely used microstrip antenna, combining multiple antennas in proper geometry increases the gain with good directive property. Over other array forms, this paper uses concentric circular array configuration for its compact structure and inherent symmetry in azimuth. This proposed array is composed of 9 elements on FR-4 substrate, which is designed for WLAN applications at 5.8GHz. Antenna Magus software is used for synthesis, while CST software is used for optimization. The proposed array is designed with optimum inter-element spacing and number of elements achieving a high directional gain of 15.7 dB compared to 14.2 dB of available literature, with a high reduction in side lobe level of -17.6 dB.

Virtual electrodes for high-density electrode arrays

Science.gov (United States)

Cela, Carlos J.; Lazzi, Gianluca

2015-10-13

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.

36 CFR 1290.6 - Originals and copies.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Originals and copies. 1290.6... ASSASSINATION RECORDS COLLECTION ACT OF 1992 (JFK ACT) § 1290.6 Originals and copies. (a) For purposes of determining whether originals or copies of assassination records will be made part of the President John F...

Preservation Copying Endangered Historic Negative Collections

DEFF Research Database (Denmark)

Kejser, Ulla Bøgvad

2008-01-01

This article discusses preservation copying of unstable B&W nitrate and acetate still photographic negatives. It focuses on evaluating two different strategies for preserving the copies from a point of view of quality and cost-effectiveness. The evaluated strategies are preservation of the master...... by describing essential characteristics of negatives, which must be passed on to the copies, and the required metadata and technical imaging specifications. Next the paper discusses strategies for preservation and makes an analysis with the LIFE2 Costing Model. The paper concludes that the most beneficial...... and cost-effective preservation solution for large format negatives is to keep the preservation copies as digital files. However, it also acknowledges that it is important to revisit such strategies regularly to monitor changes in user expectations, technologies and costs....

COPI is required for enterovirus 71 replication.

Directory of Open Access Journals (Sweden)

Jianmin Wang

Full Text Available Enterovirus 71 (EV71, a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11, is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies.

Human Y chromosome copy number variation in the next generation sequencing era and beyond.

Science.gov (United States)

Massaia, Andrea; Xue, Yali

2017-05-01

The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.

Copy-Editing: The Cambridge Handbook.

Science.gov (United States)

Butcher, Judith

This handbook is designed as a reference manual for copy editors who prepare typescript for printing. It deals with the following topics: the copy editor's function; the work to be done at each stage in the production process; some difficult points of spelling, capitalization, and other features collectively known as "house style"; the parts of a…

Advancement of High Power Quasi-CW Laser Diode Arrays For Space-based Laser Instruments

Science.gov (United States)

Amzajerdian, Farzin; Meadows, Byron L.; Baker, nathaniel R.; Baggott, Renee S.; Singh, Upendra N.; Kavaya, Michael J.

2004-01-01

Space-based laser and lidar instruments play an important role in NASA s plans for meeting its objectives in both Earth Science and Space Exploration areas. Almost all the lidar instrument concepts being considered by NASA scientist utilize moderate to high power diode-pumped solid state lasers as their transmitter source. Perhaps the most critical component of any solid state laser system is its pump laser diode array which essentially dictates instrument efficiency, reliability and lifetime. For this reason, premature failures and rapid degradation of high power laser diode arrays that have been experienced by laser system designers are of major concern to NASA. This work addresses these reliability and lifetime issues by attempting to eliminate the causes of failures and developing methods for screening laser diode arrays and qualifying them for operation in space.

Hierarchically Structured Co3O4@Pt@MnO2 Nanowire Arrays for High-Performance Supercapacitors

Science.gov (United States)

Xia, Hui; Zhu, Dongdong; Luo, Zhentao; Yu, Yue; Shi, Xiaoqin; Yuan, Guoliang; Xie, Jianping

2013-10-01

Here we proposed a novel architectural design of a ternary MnO2-based electrode - a hierarchical Co3O4@Pt@MnO2 core-shell-shell structure, where the complemental features of the three key components (a well-defined Co3O4 nanowire array on the conductive Ti substrate, an ultrathin layer of small Pt nanoparticles, and a thin layer of MnO2 nanoflakes) are strategically combined into a single entity to synergize and construct a high-performance electrode for supercapacitors. Owing to the high conductivity of the well-defined Co3O4 nanowire arrays, in which the conductivity was further enhanced by a thin metal (Pt) coating layer, in combination with the large surface area provided by the small MnO2 nanoflakes, the as-fabricated Co3O4@Pt@MnO2 nanowire arrays have exhibited high specific capacitances, good rate capability, and excellent cycling stability. The architectural design demonstrated in this study provides a new approach to fabricate high-performance MnO2-based nanowire arrays for constructing next-generation supercapacitors.

Affordable, Lightweight, Compactly Stowable, High Strength / Stiffness Lander Solar Array, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Deployable Space Systems, Inc. (DSS) has developed a next-generation high performance solar array system specifically for NASA's future Lander and sample return...

Affordable, Lightweight, Compactly Stowable, High Strength / Stiffness Lander Solar Array, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Deployable Space Systems, Inc. (DSS) has developed a next-generation high performance solar array system specifically for NASA's future Lander and sample return...

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.

. This geometry is tested using the Bartlett method for varying arc and linear arrays of 30 - elements. We also examine `high resolution techniques' such as the Maximum LIkelihood (ML) method and the Maximum Entropy (ME) methods (different orders), for 16-element...

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...

Single-copy insertion of transgenes in Caenorhabditis elegans

DEFF Research Database (Denmark)

Frøkjaer-Jensen, Christian; Davis, M Wayne; Hopkins, Christopher E

2008-01-01

developed a method that inserts a single copy of a transgene into a defined site. Mobilization of a Mos1 transposon generates a double-strand break in noncoding DNA. The break is repaired by copying DNA from an extrachromosomal template into the chromosomal site. Homozygous single-copy insertions can...... be obtained in less than 2 weeks by injecting approximately 20 worms. We have successfully inserted transgenes as long as 9 kb and verified that single copies are inserted at the targeted site. Single-copy transgenes are expressed at endogenous levels and can be expressed in the female and male germlines....

Beyond KRAS mutation status: influence of KRAS copy number status and microRNAs on clinical outcome to cetuximab in metastatic colorectal cancer patients

Directory of Open Access Journals (Sweden)

Mekenkamp Leonie JM

2012-07-01

Full Text Available Abstract Background KRAS mutation is a negative predictive factor for treatment with anti-epidermal growth factor receptor (EGFR antibodies in metastatic colorectal cancer (mCRC. Novel predictive markers are required to further improve the selection of patients for this treatment. We assessed the influence of modification of KRAS by gene copy number aberration (CNA and microRNAs (miRNAs in correlation to clinical outcome in mCRC patients treated with cetuximab in combination with chemotherapy and bevacizumab. Methods Formalin-fixed paraffin-embedded primary tumour tissue was used from 34 mCRC patients in a phase III trial, who were selected based upon their good (n = 17 or poor (n = 17 progression-free survival (PFS upon treatment with cetuximab in combination with capecitabine, oxaliplatin, and bevacizumab. Gene copy number at the KRAS locus was assessed using high resolution genome-wide array CGH and the expression levels of 17 miRNAs targeting KRAS were determined by real-time PCR. Results Copy number loss of the KRAS locus was observed in the tumour of 5 patients who were all good responders including patients with a KRAS mutation. Copy number gains in two wild-type KRAS tumours were associated with a poor PFS. In KRAS mutated tumours increased miR-200b and decreased miR-143 expression were associated with a good PFS. In wild-type KRAS patients, miRNA expression did not correlate with PFS in a multivariate model. Conclusions Our results indicate that the assessment of KRAS CNA and miRNAs targeting KRAS might further optimize the selection of mCRC eligible for anti-EGFR therapy.

Josephson junction arrays

International Nuclear Information System (INIS)

Bindslev Hansen, J.; Lindelof, P.E.

1985-01-01

In this review we intend to cover recent work involving arrays of Josephson junctions. The work on such arrays falls naturally into three main areas of interest: 1. Technical applications of Josephson junction arrays for high-frequency devices. 2. Experimental studies of 2-D model systems (Kosterlitz-Thouless phase transition, commensurate-incommensurate transition in frustrated (flux) lattices). 3. Investigations of phenomena associated with non-equilibrium superconductivity in and around Josephson junctions (with high current density). (orig./BUD)

High-Resolution Spin-on-Patterning of Perovskite Thin Films for a Multiplexed Image Sensor Array.

Science.gov (United States)

Lee, Woongchan; Lee, Jongha; Yun, Huiwon; Kim, Joonsoo; Park, Jinhong; Choi, Changsoon; Kim, Dong Chan; Seo, Hyunseon; Lee, Hakyong; Yu, Ji Woong; Lee, Won Bo; Kim, Dae-Hyeong

2017-10-01

Inorganic-organic hybrid perovskite thin films have attracted significant attention as an alternative to silicon in photon-absorbing devices mainly because of their superb optoelectronic properties. However, high-definition patterning of perovskite thin films, which is important for fabrication of the image sensor array, is hardly accomplished owing to their extreme instability in general photolithographic solvents. Here, a novel patterning process for perovskite thin films is described: the high-resolution spin-on-patterning (SoP) process. This fast and facile process is compatible with a variety of spin-coated perovskite materials and perovskite deposition techniques. The SoP process is successfully applied to develop a high-performance, ultrathin, and deformable perovskite-on-silicon multiplexed image sensor array, paving the road toward next-generation image sensor arrays. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High Voltage Solar Array Arc Testing for a Direct Drive Hall Effect Thruster System

Science.gov (United States)

Schneider, Todd; Carruth, M. R., Jr.; Vaughn, J. A.; Jongeward, G. A.; Mikellides, I. G.; Ferguson, D.; Kerslake, T. W.; Peterson, T.; Snyder, D.; Hoskins, A.

2004-01-01

The deleterious effects of spacecraft charging are well known, particularly when the charging leads to arc events. The damage that results from arcing can severely reduce system lifetime and even cause critical system failures. On a primary spacecraft system such as a solar array, there is very little tolerance for arcing. Motivated by these concerns, an experimental investigation was undertaken to determine arc thresholds for a high voltage (200-500 V) solar array in a plasma environment. The investigation was in support of a NASA program to develop a Direct Drive Hall-Effect Thruster (D2HET) system. By directly coupling the solar array to a Hall-effect thruster, the D2HET program seeks to reduce mass, cost and complexity commonly associated with the power processing in conventional power systems. In the investigation, multiple solar array technologies and configurations were tested. The cell samples were biased to a negative voltage, with an applied potential difference between them, to imitate possible scenarios in solar array strings that could lead to damaging arcs. The samples were tested in an environment that emulated a low-energy, HET-induced plasma. Short duration trigger arcs as well as long duration sustained arcs were generated. Typical current and voltage waveforms associated with the arc events are presented. Arc thresholds are also defined in terms of voltage, current and power. The data will be used to propose a new, high-voltage (greater than 300 V) solar array design for which the likelihood of damage from arcing is minimal.

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

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.

Rapid Integration of Multi-copy Transgenes Using Optogenetic Mutagenesis in Caenorhabditis elegans

Directory of Open Access Journals (Sweden)

Kentaro Noma

2018-06-01

Full Text Available Stably transmitted transgenes are indispensable for labeling cellular components and manipulating cellular functions. In Caenorhabditis elegans, transgenes are generally generated as inheritable multi-copy extrachromosomal arrays, which can be stabilized in the genome through a mutagenesis-mediated integration process. Standard methods to integrate extrachromosomal arrays primarily use protocols involving ultraviolet light plus trimethylpsoralen or gamma- or X-ray irradiation, which are laborious and time-consuming. Here, we describe a one-step integration method, following germline-mutagenesis induced by mini Singlet Oxygen Generator (miniSOG. Upon blue light treatment, miniSOG tagged to histone (Histone-miniSOG generates reactive oxygen species (ROS and induces heritable mutations, including DNA double-stranded breaks. We demonstrate that we can bypass the need to first establish extrachromosomal transgenic lines by coupling microinjection of desired plasmids with blue light illumination on Histone-miniSOG worms to obtain integrants in the F3 progeny. We consistently obtained more than one integrant from 12 injected animals in two weeks. This optogenetic approach significantly reduces the amount of time and labor for transgene integration. Moreover, it enables to generate stably expressed transgenes that cause toxicity in animal growth.

High Performance Systolic Array Core Architecture Design for DNA Sequencer

Directory of Open Access Journals (Sweden)

Saiful Nurdin Dayana

2018-01-01

Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples

Directory of Open Access Journals (Sweden)

LaFramboise William A

2011-01-01

Full Text Available Abstract Background Genomic instability in cancer leads to abnormal genome copy number alterations (CNA as a mechanism underlying tumorigenesis. Using microarrays and other technologies, tumor CNA are detected by comparing tumor sample CN to normal reference sample CN. While advances in microarray technology have improved detection of copy number alterations, the increase in the number of measured signals, noise from array probes, variations in signal-to-noise ratio across batches and disparity across laboratories leads to significant limitations for the accurate identification of CNA regions when comparing tumor and normal samples. Methods To address these limitations, we designed a novel "Virtual Normal" algorithm (VN, which allowed for construction of an unbiased reference signal directly from test samples within an experiment using any publicly available normal reference set as a baseline thus eliminating the need for an in-lab normal reference set. Results The algorithm was tested using an optimal, paired tumor/normal data set as well as previously uncharacterized pediatric malignant gliomas for which a normal reference set was not available. Using Affymetrix 250K Sty microarrays, we demonstrated improved signal-to-noise ratio and detected significant copy number alterations using the VN algorithm that were validated by independent PCR analysis of the target CNA regions. Conclusions We developed and validated an algorithm to provide a virtual normal reference signal directly from tumor samples and minimize noise in the derivation of the raw CN signal. The algorithm reduces the variability of assays performed across different reagent and array batches, methods of sample preservation, multiple personnel, and among different laboratories. This approach may be valuable when matched normal samples are unavailable or the paired normal specimens have been subjected to variations in methods of preservation.

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.

High-resolution imaging using a wideband MIMO radar system with two distributed arrays.

Science.gov (United States)

Wang, Dang-wei; Ma, Xiao-yan; Chen, A-Lei; Su, Yi

2010-05-01

Imaging a fast maneuvering target has been an active research area in past decades. Usually, an array antenna with multiple elements is implemented to avoid the motion compensations involved in the inverse synthetic aperture radar (ISAR) imaging. Nevertheless, there is a price dilemma due to the high level of hardware complexity compared to complex algorithm implemented in the ISAR imaging system with only one antenna. In this paper, a wideband multiple-input multiple-output (MIMO) radar system with two distributed arrays is proposed to reduce the hardware complexity of the system. Furthermore, the system model, the equivalent array production method and the imaging procedure are presented. As compared with the classical real aperture radar (RAR) imaging system, there is a very important contribution in our method that the lower hardware complexity can be involved in the imaging system since many additive virtual array elements can be obtained. Numerical simulations are provided for testing our system and imaging method.

Modeling of a VMJ PV array under Gaussian high intensity laser power beam condition

Science.gov (United States)

Eom, Jeongsook; Kim, Gunzung; Park, Yongwan

2018-02-01

The high intensity laser power beaming (HILPB) system is one of the most promising systems in the long-rang wireless power transfer field. The vertical multi-junction photovoltaic (VMJ PV) array converts the HILPB into electricity to power the load or charges a battery. The output power of a VMJ PV array depends mainly on irradiance values of each VMJ PV cells. For simulating an entire VMJ PV array, the irradiance profile of the Gaussian HILPB and the irradiance level of the VMJ PV cell are mathematically modeled first. The VMJ PV array is modeled as a network with dimension m*n, where m represents the number of VMJ PV cells in a column, and n represents the number of VMJ PV cells in a row. In order to validate the results obtained in modeling and simulation, a laboratory setup was developed using 55 VMJ PV array. By using the output power model of VMJ PV array, we can establish an optimal power transmission path by the receiver based on the received signal strength. When the laser beam from multiple transmitters aimed at a VMJ PV array at the same time, the received power is the sum of all energy at a VMJ PV array. The transmitter sends its power characteristics as optically coded laser pulses and powers as HILPB. Using the attenuated power model and output power model of VMJ PV array, the receiver can estimate the maximum receivable powers from the transmitters and select optimal transmitters.

Nano-engineering of three-dimensional core/shell nanotube arrays for high performance supercapacitors

Science.gov (United States)

Grote, Fabian; Wen, Liaoyong; Lei, Yong

2014-06-01

Large-scale arrays of core/shell nanostructures are highly desirable to enhance the performance of supercapacitors. Here we demonstrate an innovative template-based fabrication technique with high structural controllability, which is capable of synthesizing well-ordered three-dimensional arrays of SnO2/MnO2 core/shell nanotubes for electrochemical energy storage in supercapacitor applications. The SnO2 core is fabricated by atomic layer deposition and provides a highly electrical conductive matrix. Subsequently a thin MnO2 shell is coated by electrochemical deposition onto the SnO2 core, which guarantees a short ion diffusion length within the shell. The core/shell structure shows an excellent electrochemical performance with a high specific capacitance of 910 F g-1 at 1 A g-1 and a good rate capability of remaining 217 F g-1 at 50 A g-1. These results shall pave the way to realize aqueous based asymmetric supercapacitors with high specific power and high specific energy.

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).

The Applicability of Incoherent Array Processing to IMS Seismic Array Stations

Science.gov (United States)

Gibbons, S. J.

2012-04-01

The seismic arrays of the International Monitoring System for the CTBT differ greatly in size and geometry, with apertures ranging from below 1 km to over 60 km. Large and medium aperture arrays with large inter-site spacings complicate the detection and estimation of high frequency phases since signals are often incoherent between sensors. Many such phases, typically from events at regional distances, remain undetected since pipeline algorithms often consider only frequencies low enough to allow coherent array processing. High frequency phases that are detected are frequently attributed qualitatively incorrect backazimuth and slowness estimates and are consequently not associated with the correct event hypotheses. This can lead to missed events both due to a lack of contributing phase detections and by corruption of event hypotheses by spurious detections. Continuous spectral estimation can be used for phase detection and parameter estimation on the largest aperture arrays, with phase arrivals identified as local maxima on beams of transformed spectrograms. The estimation procedure in effect measures group velocity rather than phase velocity and the ability to estimate backazimuth and slowness requires that the spatial extent of the array is large enough to resolve time-delays between envelopes with a period of approximately 4 or 5 seconds. The NOA, AKASG, YKA, WRA, and KURK arrays have apertures in excess of 20 km and spectrogram beamforming on these stations provides high quality slowness estimates for regional phases without additional post-processing. Seven arrays with aperture between 10 and 20 km (MJAR, ESDC, ILAR, KSRS, CMAR, ASAR, and EKA) can provide robust parameter estimates subject to a smoothing of the resulting slowness grids, most effectively achieved by convolving the measured slowness grids with the array response function for a 4 or 5 second period signal. The MJAR array in Japan recorded high SNR Pn signals for both the 2006 and 2009 North Korea

Servo scanning 3D micro EDM for array micro cavities using on-machine fabricated tool electrodes

Science.gov (United States)

Tong, Hao; Li, Yong; Zhang, Long

2018-02-01

Array micro cavities are useful in many fields including in micro molds, optical devices, biochips and so on. Array servo scanning micro electro discharge machining (EDM), using array micro electrodes with simple cross-sectional shape, has the advantage of machining complex 3D micro cavities in batches. In this paper, the machining errors caused by offline-fabricated array micro electrodes are analyzed in particular, and then a machining process of array servo scanning micro EDM is proposed by using on-machine fabricated array micro electrodes. The array micro electrodes are fabricated on-machine by combined procedures including wire electro discharge grinding, array reverse copying and electrode end trimming. Nine-array tool electrodes with Φ80 µm diameter and 600 µm length are obtained. Furthermore, the proposed process is verified by several machining experiments for achieving nine-array hexagonal micro cavities with top side length of 300 µm, bottom side length of 150 µm, and depth of 112 µm or 120 µm. In the experiments, a chip hump accumulates on the electrode tips like the built-up edge in mechanical machining under the conditions of brass workpieces, copper electrodes and the dielectric of deionized water. The accumulated hump can be avoided by replacing the water dielectric by an oil dielectric.

Extending the scope of diagnostic chromosome analysis: detection of single gene defects using high-resolution SNP microarrays.

Science.gov (United States)

Bruno, Damien L; Stark, Zornitza; Amor, David J; Burgess, Trent; Butler, Kathy; Corrie, Sylvea; Francis, David; Ganesamoorthy, Devika; Hills, Louise; James, Paul A; O'Rielly, Darren; Oertel, Ralph; Savarirayan, Ravi; Prabhakara, Krishnamurthy; Salce, Nicholas; Slater, Howard R

2011-12-01

Microarray analysis has provided significant advances in the diagnosis of conditions resulting from submicroscopic chromosome abnormalities. It has been recommended that array testing should be a "first tier" test in the evaluation of individuals with intellectual disability, developmental delay, congenital anomalies, and autism. The availability of arrays with increasingly high probe coverage and resolution has increased the detection of decreasingly small copy number changes (CNCs) down to the intragenic or even exon level. Importantly, arrays that genotype SNPs also detect extended regions of homozygosity. We describe 14 examples of single gene disorders caused by intragenic changes from a consecutive set of 6,500 tests using high-resolution SNP microarrays. These cases illustrate the increased scope of cytogenetic testing beyond dominant chromosome rearrangements that typically contain many genes. Nine of the cases confirmed the clinical diagnosis, that is, followed a "phenotype to genotype" approach. Five were diagnosed by the laboratory analysis in the absence of a specific clinical diagnosis, that is, followed a "genotype to phenotype" approach. Two were clinically significant, incidental findings. The importance of astute clinical assessment and laboratory-clinician consultation is emphasized to optimize the value of microarrays in the diagnosis of disorders caused by single gene copy number and sequence mutations. © 2011 Wiley-Liss, Inc.

Clinical utility of the X-chromosome array.

Science.gov (United States)

Zarate, Yuri A; Dwivedi, Alka; Bartel, Frank O; Bellomo, M Allison; Cathey, Sara S; Champaigne, Neena L; Clarkson, L Kate; Dupont, Barbara R; Everman, David B; Geer, Joseph S; Gordon, Barbara C; Lichty, Angie W; Lyons, Michael J; Rogers, R Curtis; Saul, Robert A; Schroer, Richard J; Skinner, Steven A; Stevenson, Roger E

2013-01-01

Previous studies have limited the use of specific X-chromosome array designed platforms to the evaluation of patients with intellectual disability. In this retrospective analysis, we reviewed the clinical utility of an X-chromosome array in a variety of scenarios. We divided patients according to the indication for the test into four defined categories: (1) autism spectrum disorders and/or developmental delay and/or intellectual disability (ASDs/DD/ID) with known family history of neurocognitive disorders; (2) ASDs/DD/ID without known family history of neurocognitive disorders; (3) breakpoint definition of an abnormality detected by a different cytogenetic test; and (4) evaluation of suspected or known X-linked conditions. A total of 59 studies were ordered with 27 copy number variants detected in 25 patients (25/59 = 42%). The findings were deemed pathogenic/likely pathogenic (16/59 = 27%), benign (4/59 = 7%) or uncertain (7/59 = 12%). We place particular emphasis on the utility of this test for the diagnostic evaluation of families affected with X-linked conditions and how it compares to whole genome arrays in this setting. In conclusion, the X-chromosome array frequently detects genomic alterations of the X chromosome and it has advantages when evaluating some specific X-linked conditions. However, careful interpretation and correlation with clinical findings is needed to determine the significance of such changes. When the X-chromosome array was used to confirm a suspected X-linked condition, it had a yield of 63% (12/19) and was useful in the evaluation and risk assessment of patients and families. Copyright © 2012 Wiley Periodicals, Inc.

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio).

Science.gov (United States)

Xu, Jian; Zhao, Zixia; Zhang, Xiaofeng; Zheng, Xianhu; Li, Jiongtang; Jiang, Yanliang; Kuang, Youyi; Zhang, Yan; Feng, Jianxin; Li, Chuangju; Yu, Juhua; Li, Qiang; Zhu, Yuanyuan; Liu, Yuanyuan; Xu, Peng; Sun, Xiaowen

2014-04-24

A large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio. The SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster. The Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

Fast fabrication of long TiO2 nanotube array with high photoelectrochemical property on flexible stainless steel.

Science.gov (United States)

Tao, Jie; Wu, Tao; Gao, Peng

2012-03-01

Oriented highly ordered long TiO2 nanotube array films with nanopore structure and high photoelectrochemical property were fabricated on flexible stainless steel substrate (50 microm) by anodization treatment of titanium thin films in a short time. The samples were characterized by means of field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD) and photoelectrochemical methods, respectively. The results showed that Ti films deposited at the condition of 0.7 Pa Ar pressure and 96 W sputtering power at room temperature was uniform and dense with good homogeneity and high crystallinity. The voltage and the anodization time both played significant roles in the formation of TiO2 nanopore-nanotube array film. The optimal voltage was 60 V and the anodization time is less than 30 min by anodizing Ti films in ethylene glycerol containing 0.5% (w) NH4F and 3% (w) H2O. The growth rate of TiO2 nanotube array was as high as 340 nm/min. Moreover, the photocurrent-potential curves, photocurrent response curves and electrochemical impedance spectra results indicated that the TiO2 nanotube array film with the nanoporous structure exhibited a better photo-response ability and photoelectrochemical performance than the ordinary TiO2 nanotube array film. The reason is that the nanoporous structure on the surface of the nanotube array can separate the photo electron-hole pairs more efficiently and completely than the tubular structure.

Highly reproducible and sensitive silver nanorod array for the rapid detection of Allura Red in candy

Science.gov (United States)

Yao, Yue; Wang, Wen; Tian, Kangzhen; Ingram, Whitney Marvella; Cheng, Jie; Qu, Lulu; Li, Haitao; Han, Caiqin

2018-04-01

Allura Red (AR) is a highly stable synthetic red azo dye, which is widely used in the food industry to dye food and increase its attraction to consumers. However, the excessive consumption of AR can result in adverse health effects to humans. Therefore, a highly reproducible silver nanorod (AgNR) array was developed for surface enhanced Raman scattering (SERS) detection of AR in candy. The relative standard deviation (RSD) of AgNR substrate obtained from the same batch and different batches were 5.7% and 11.0%, respectively, demonstrating the high reproducibility. Using these highly reproducible AgNR arrays as the SERS substrates, AR was detected successfully, and its characteristic peaks were assigned by the density function theory (DFT) calculation. The limit of detection (LOD) of AR was determined to be 0.05 mg/L with a wide linear range of 0.8-100 mg/L. Furthermore, the AgNR SERS arrays can detect AR directly in different candy samples within 3 min without any complicated pretreatment. These results suggest the AgNR array can be used for rapid and qualitative SERS detection of AR, holding a great promise for expanding SERS application in food safety control field.

Copies, Concepts and Time

Directory of Open Access Journals (Sweden)

Anne Eriksen

2017-09-01

Full Text Available Copies are defined by their relation to an original. The understanding and evaluation of this relationship has been changing over time. A main argument of this article is that originals and copies are phenomena with no "natural" or essential meaning outside of their specific historical settings. The idea to be explored is how changing historicity regimes have transformed notions of originals and copies over time and how these differences also are reflected in the intrinsically temporal relation between the two concepts. The discussion will be framed by two theory sets. The first is Alexander Nagel and Christopher Woods investigation of two kinds of temporality that vied for dominance in works of art in the late Middle Ages and the Renaissance. The second is Walter Benjamins discussion of artwork in the "age of mechanical reproduction", i.e. the twentieth century. The second half of the article seeks to add to the historical complexity described by both theory sets by introducing a concept of tradition and discussing the early modern ideals of exemplarity, emulation and copiousness.

Single-nucleotide polymorphism array-based karyotyping of acute promyelocytic leukemia.

Science.gov (United States)

Gómez-Seguí, Inés; Sánchez-Izquierdo, Dolors; Barragán, Eva; Such, Esperanza; Luna, Irene; López-Pavía, María; Ibáñez, Mariam; Villamón, Eva; Alonso, Carmen; Martín, Iván; Llop, Marta; Dolz, Sandra; Fuster, Oscar; Montesinos, Pau; Cañigral, Carolina; Boluda, Blanca; Salazar, Claudia; Cervera, Jose; Sanz, Miguel A

2014-01-01

Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (6%) the most frequent copy-number abnormalities (CNA). Four patients (8%) showed CNAs adjacent to the breakpoints of the translocation. We compared our results with other APL series and found that, except for dup(8q24) and del(7q33-qter), ACA were infrequent (≤3%) but most of them recurrent (70%). Interestingly, having CNA or FLT3 mutation were mutually exclusive events. Neither the number of CNA, nor any specific CNA was associated significantly with prognosis. This study has delineated recurrent abnormalities in addition to t(15;17) that may act as secondary events and could explain leukemogenesis in up to 40% of APL cases with no ACA by conventional cytogenetics.

Synthesis and high catalytic properties of mesoporous Pt nanowire array by novel conjunct template method

Science.gov (United States)

Zhong, Yi; Xu, Cai-Ling; Kong, Ling-Bin; Li, Hu-Lin

2008-12-01

A novel conjunct template method for fabricating mesoporous Pt nanowire array through direct current (DC) electrodeposition of Pt into the pores of anodic aluminum oxide (AAO) template on Ti/Si substrate from hexagonal structured lyotropic liquid crystalline phase is demonstrated in this paper. The morphology and structure of as-prepared Pt nanowire array are characterized by field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD). The electrocatalytic properties of Pt nanowire array for methanol are also investigated in detail. The results indicate that Pt nanowire array has the unique mesoporous structure of approximate 40-50 nm in diameter, which resulted in the high surface area and greatly improved electrocatalytic activity for methanol. The mesoporous Pt nanowire array synthesized by the new conjunct template method has a very promising application in portable fuel cell power sources.

High thermoelectric properties of (Sb, Bi)2Te3 nanowire arrays by tilt-structure engineering

Science.gov (United States)

Tan, Ming; Hao, Yanming; Deng, Yuan; Chen, Jingyi

2018-06-01

In this paper, we present an innovative tilt-structure design concept for (Sb, Bi)2Te3 nanowire array assembled by high-quality nanowires with well oriented growth, utilizing a simple vacuum thermal evaporation technique. The unusual tilt-structure (Sb, Bi)2Te3 nanowire array with a tilted angle of 45° exhibits a high thermoelectric dimensionless figure-of-merit ZT = 1.72 at room temperature. The relatively high ZT value in contrast to that of previously reported (Sb, Bi)2Te3 materials and the vertical (Sb, Bi)2Te3 nanowire arrays evidently reveals the crucial role of the unique tilt-structure in favorably influencing carrier and phonon transport properties, resulting in a significantly improved ZT value. The transport mechanism of such tilt-structure is proposed and investigated. This method opens a new approach to optimize nano-structure in thin films for next-generation thermoelectric materials and devices.

Autism-specific copy number variants further implicate the phosphatidylinositol signaling pathway and the glutamatergic synapse in the etiology of the disorder.

Science.gov (United States)

Cuscó, Ivon; Medrano, Andrés; Gener, Blanca; Vilardell, Mireia; Gallastegui, Fátima; Villa, Olaya; González, Eva; Rodríguez-Santiago, Benjamín; Vilella, Elisabet; Del Campo, Miguel; Pérez-Jurado, Luis A

2009-05-15

Autism spectrum disorders (ASDs) constitute a group of severe neurodevelopmental conditions with complex multifactorial etiology. In order to explore the hypothesis that submicroscopic genomic rearrangements underlie some ASD cases, we have analyzed 96 Spanish patients with idiopathic ASD after extensive clinical and laboratory screening, by array comparative genomic hybridization (aCGH) using a homemade bacterial artificial chromosome (BAC) array. Only 13 of the 238 detected copy number alterations, ranging in size from 89 kb to 2.4 Mb, were present specifically in the autistic population (12 out of 96 individuals, 12.5%). Following validation by additional molecular techniques, we have characterized these novel candidate regions containing 24 different genes including alterations in two previously reported regions of chromosome 7 associated with the ASD phenotype. Some of the genes located in ASD-specific copy number variants act in common pathways, most notably the phosphatidylinositol signaling and the glutamatergic synapse, both known to be affected in several genetic syndromes related with autism and previously associated with ASD. Our work supports the idea that the functional alteration of genes in related neuronal networks is involved in the etiology of the ASD phenotype and confirms a significant diagnostic yield for aCGH, which should probably be included in the diagnostic workup of idiopathic ASD.

Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP Array

Directory of Open Access Journals (Sweden)

Qian You

2018-02-01

Full Text Available Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1 discussed the pros and cons of SNP array in general for high throughput genotyping, (2 presented the challenges of and solutions to SNP calling in polyploid species, (3 summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4 illustrated SNP array applications in several different polyploid crop species, then (5 discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6 provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.

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.

Telescope Array Radar (TARA) observatory for Ultra-High Energy Cosmic Rays

International Nuclear Information System (INIS)

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.

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. In this report, we describe the design and performance of the TARA transmitter and receiver systems

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.

Simulating pad-electrodes with high-definition arrays in transcranial electric stimulation

Science.gov (United States)

Kempe, René; Huang, Yu; Parra, Lucas C.

2014-04-01

Objective. Research studies on transcranial electric stimulation, including direct current, often use a computational model to provide guidance on the placing of sponge-electrode pads. However, the expertise and computational resources needed for finite element modeling (FEM) make modeling impractical in a clinical setting. Our objective is to make the exploration of different electrode configurations accessible to practitioners. We provide an efficient tool to estimate current distributions for arbitrary pad configurations while obviating the need for complex simulation software. Approach. To efficiently estimate current distributions for arbitrary pad configurations we propose to simulate pads with an array of high-definition (HD) electrodes and use an efficient linear superposition to then quickly evaluate different electrode configurations. Main results. Numerical results on ten different pad configurations on a normal individual show that electric field intensity simulated with the sampled array deviates from the solutions with pads by only 5% and the locations of peak magnitude fields have a 94% overlap when using a dense array of 336 electrodes. Significance. Computationally intensive FEM modeling of the HD array needs to be performed only once, perhaps on a set of standard heads that can be made available to multiple users. The present results confirm that by using these models one can now quickly and accurately explore and select pad-electrode montages to match a particular clinical need.

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

Directory of Open Access Journals (Sweden)

Lo Fang-Yi

2012-06-01

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

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

International Nuclear Information System (INIS)

Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

2012-01-01

Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

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...

In-situ preparation of Fe2O3 hierarchical arrays on stainless steel substrate for high efficient catalysis

International Nuclear Information System (INIS)

Yang, Zeheng; Wang, Kun; Shao, Zongming; Tian, Yuan; Chen, Gongde; Wang, Kai; Chen, Zhangxian; Dou, Yan; Zhang, Weixin

2017-01-01

Hierarchical array catalysts with micro/nano structures on substrates not only possess high reactivity from large surface area and suitable interface, but intensify mass transfer through shortening the diffusion paths of both reactants and products for high catalytic efficiency. Herein, we first demonstrate fabrication of Fe 2 O 3 hierarchical arrays grown on stainless-steel substrates via in-situ hydrothermal chemical oxidation followed by heat treatment in N 2 atmosphere. As a Fenton-like catalyst, Fe 2 O 3 hierarchical arrays exhibit excellent catalytic activity and life cycle performance for methylene blue (MB) dye degradation in aqueous solution in the presence of H 2 O 2 . The Fe 2 O 3 catalyst with unique hierarchical structures and efficient transport channels, effectively activates H 2 O 2 to generate large quantity of • OH radicals and highly promotes reaction kinetics between MB and • OH radicals. Immobilization of hierarchical array catalysts on stainless-steel can prevent particles agglomeration, facilitate the recovery and reuse of the catalysts, which is expected promising applications in wastewater remediation. - Graphical abstract: The in-situ synthesis of Fe 2 O 3 hierarchical arrays on stainless-steel substrates was reported for the first time, which exhibit excellent catalytic activity performance for methylene blue (MB) dye degradation in aqueous solution in the presence of H 2 O 2 . - Highlights: • Fe 2 O 3 hierarchical arrays was prepared by in-situ hydrothermal chemical oxidation. • F − ions play an important role in the formation of the Fe 2 O 3 hierarchical arrays. • Fe 2 O 3 hierarchical arrays show high catalytic activity to methylene blue degradation.

Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome

Science.gov (United States)

2013-01-01

Background Miniature inverted-repeat transposable elements (MITEs) are expected to play important roles in evolution of genes and genome in plants, especially in the highly duplicated plant genomes. Various MITE families and their roles in plants have been characterized. However, there have been fewer studies of MITE families and their potential roles in evolution of the recently triplicated Brassica genome. Results We identified a new MITE family, BRAMI-1, belonging to the Stowaway super-family in the Brassica genome. In silico mapping revealed that 697 members are dispersed throughout the euchromatic regions of the B. rapa pseudo-chromosomes. Among them, 548 members (78.6%) are located in gene-rich regions, less than 3 kb from genes. In addition, we identified 516 and 15 members in the 470 Mb and 15 Mb genomic shotgun sequences currently available for B. oleracea and B. napus, respectively. The resulting estimated copy numbers for the entire genomes were 1440, 1464 and 2490 in B. rapa, B. oleracea and B. napus, respectively. Concurrently, only 70 members of the related Arabidopsis ATTIRTA-1 MITE family were identified in the Arabidopsis genome. Phylogenetic analysis revealed that BRAMI-1 elements proliferated in the Brassica genus after divergence from the Arabidopsis lineage. MITE insertion polymorphism (MIP) was inspected for 50 BRAMI-1 members, revealing high levels of insertion polymorphism between and within species of Brassica that clarify BRAMI-1 activation periods up to the present. Comparative analysis of the 71 genes harbouring the BRAMI-1 elements with their non-insertion paralogs (NIPs) showed that the BRAMI-1 insertions mainly reside in non-coding sequences and that the expression levels of genes with the elements differ from those of their NIPs. Conclusion A Stowaway family MITE, named as BRAMI-1, was gradually amplified and remained present in over than 1400 copies in each of three Brassica species. Overall, 78% of the members were identified in

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...

The Hegemony of the Copy

DEFF Research Database (Denmark)

Graulund, Rune

2017-01-01

This essay questions when the creative process leading tothe original can be said to be complete. When does the series of a pupil’sbotched attempts at perfection leading to “the” singular and unique object,text, tool, or artwork we recognise as the original expression of themaster craftsman stop......? Where is the cut-off point between the differentversions (copies) of earlier inferior iterations in the gestation process thatlead to the original, and final, superior original? This essay chiefly examinesthe manner in which text has been copied and stored in one particulartype of object, namely...... that of the book, in order to provide some fairlywell-known arguments regarding pre-mechanical as well as mechanical reproduction.In particular, it examines the differences between manuscriptculture and print culture as we see them expressed in the production (andreproduction) of master copies and subsequent...

Left ventricular hypertrabeculation/noncompaction with epilepsy, other heart defects, minor facial anomalies and new copy number variants

Directory of Open Access Journals (Sweden)

Nagel Bert

2012-07-01

Full Text Available Abstract Background Left ventricular hypertrabeculation/noncompaction (LVHT is a cardiac abnormality of unknown etiology which has been described in children as well as in adults with and without chromosomal aberrations. LVHT has been reported in association with various cardiac and extracardiac abnormalities like epilepsy and facial dysmorphism. Case presentation A unique combination of LVHT, atrial septal defect, pulmonary valve stenosis, aortic stenosis, epilepsy and minor facial anomalies is presented in a 5.5 years old girl. Microarray-based genomic hybridization (array-CGH detected six previously not described copy number variants (CNVs inherited from a clinically unaffected father and minimally affected mother, thus, most likely, not clinically significant but rare benign variants. Conclusions Despite this complex phenotype de novo microdeletions or microduplications were not detected by array CGH. Further investigations, such as whole exome sequencing, could reveal point mutations and small indels as the possible cause.

40 CFR 264.53 - Copies of contingency plan.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Copies of contingency plan. 264.53... Contingency Plan and Emergency Procedures § 264.53 Copies of contingency plan. A copy of the contingency plan... called upon to provide emergency services. [Comment: The contingency plan must be submitted to the...

Measurement of locus copy number by hybridisation with amplifiable probes

Science.gov (United States)

Armour, John A. L.; Sismani, Carolina; Patsalis, Philippos C.; Cross, Gareth

2000-01-01

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicroscopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader–Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications. PMID:10606661

Measurement of locus copy number by hybridisation with amplifiable probes.

Science.gov (United States)

Armour, J A; Sismani, C; Patsalis, P C; Cross, G

2000-01-15

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicro-scopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader-Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications.

Nanoliter Centrifugal Liquid Dispenser Coupled with Superhydrophobic Microwell Array Chips for High-Throughput Cell Assays

Directory of Open Access Journals (Sweden)

Yuyi Wang

2018-06-01

Full Text Available Microfluidic systems have been regarded as a potential platform for high-throughput screening technology in drug discovery due to their low sample consumption, high integration, and easy operation. The handling of small-volume liquid is an essential operation in microfluidic systems, especially in investigating large-scale combination conditions. Here, we develop a nanoliter centrifugal liquid dispenser (NanoCLD coupled with superhydrophobic microwell array chips for high-throughput cell-based assays in the nanoliter scale. The NanoCLD consists of a plastic stock block with an array of drilled through holes, a reagent microwell array chip (reagent chip, and an alignment bottom assembled together in a fixture. A simple centrifugation at 800 rpm can dispense ~160 nL reagents into microwells in 5 min. The dispensed reagents are then delivered to cells by sandwiching the reagent chip upside down with another microwell array chip (cell chip on which cells are cultured. A gradient of doxorubicin is then dispensed to the cell chip using the NanoCLD for validating the feasibility of performing drug tests on our microchip platform. This novel nanoliter-volume liquid dispensing method is simple, easy to operate, and especially suitable for repeatedly dispensing many different reagents simultaneously to microwells.

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.

Diversity arrays technology (DArT) markers in apple for genetic linkage maps.

Science.gov (United States)

Schouten, Henk J; van de Weg, W Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J; van Kaauwen, Martijn P W; Wittenberg, Alexander H J; Koehorst-van Putten, Herma J J; Noordijk, Yolanda; Gao, Zhongshan; Rees, D Jasper G; Van Dyk, Maria M; Jaccoud, Damian; Considine, Michael J; Kilian, Andrzej

2012-03-01

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

Frontend Receiver Electronics for High Frequency Monolithic CMUT-on-CMOS Imaging Arrays

Science.gov (United States)

Gurun, Gokce; Hasler, Paul; Degertekin, F. Levent

2012-01-01

This paper describes the design of CMOS receiver electronics for monolithic integration with capacitive micromachined ultrasonic transducer (CMUT) arrays for high-frequency intravascular ultrasound imaging. A custom 8-inch 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 pulse-echo 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 MHz to 20 MHz. PMID:21859585

The cost of copy number in a selfish genetic element: the 2-μm plasmid of Saccharomyces cerevisiae.

Science.gov (United States)

Harrison, Ellie; Koufopanou, V; Burt, A; MacLean, R C

2012-11-01

Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2 μm is a multicopy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2 μm is that plasmid copy number evolves as a trade-off between selection for increased vertical transmission, favouring high copy number, and selection for decreased virulence, favouring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2 μm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (± 0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast per 2 μm associations and pave the way for future studies examining how selection can shape the cost of multicopy elements. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Improved Ordinary Measure and Image Entropy Theory based intelligent Copy Detection Method

Directory of Open Access Journals (Sweden)

Dengpan Ye

2011-10-01

Full Text Available Nowadays, more and more multimedia websites appear in social network. It brings some security problems, such as privacy, piracy, disclosure of sensitive contents and so on. Aiming at copyright protection, the copy detection technology of multimedia contents becomes a hot topic. In our previous work, a new computer-based copyright control system used to detect the media has been proposed. Based on this system, this paper proposes an improved media feature matching measure and an entropy based copy detection method. The Levenshtein Distance was used to enhance the matching degree when using for feature matching measure in copy detection. For entropy based copy detection, we make a fusion of the two features of entropy matrix of the entropy feature we extracted. Firstly,we extract the entropy matrix of the image and normalize it. Then, we make a fusion of the eigenvalue feature and the transfer matrix feature of the entropy matrix. The fused features will be used for image copy detection. The experiments show that compared to use these two kinds of features for image detection singly, using feature fusion matching method is apparent robustness and effectiveness. The fused feature has a high detection for copy images which have been received some attacks such as noise, compression, zoom, rotation and so on. Comparing with referred methods, the method proposed is more intelligent and can be achieved good performance.

40 CFR 265.53 - Copies of contingency plan.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Copies of contingency plan. 265.53... DISPOSAL FACILITIES Contingency Plan and Emergency Procedures § 265.53 Copies of contingency plan. A copy of the contingency plan and all revisions to the plan must be: (a) Maintained at the facility; and (b...

Gauge and non-gauge curvature tensor copies

International Nuclear Information System (INIS)

Srivastava, P.P.

1982-10-01

A procedure for constructing curvature tensor copies is discussed using the anholonomic geometrical framework. The corresponding geometries are compared and the notion of gauge copy is elucidated. An explicit calculation is also made. (author)

A random phased array device for delivery of high intensity focused ultrasound.

Science.gov (United States)

Hand, J W; Shaw, A; Sadhoo, N; Rajagopal, S; Dickinson, R J; Gavrilov, L R

2009-10-07

Randomized phased arrays can offer electronic steering of a single focus and simultaneous multiple foci concomitant with low levels of secondary maxima and are potentially useful as sources of high intensity focused ultrasound (HIFU). This work describes laboratory testing of a 1 MHz random phased array consisting of 254 elements on a spherical shell of radius of curvature 130 mm and diameter 170 mm. Acoustic output power and efficiency are measured for a range of input electrical powers, and field distributions for various single- and multiple-focus conditions are evaluated by a novel technique using an infrared camera to provide rapid imaging of temperature changes on the surface of an absorbing target. Experimental results show that the array can steer a single focus laterally to at least +/-15 mm off axis and axially to more than +/-15 mm from the centre of curvature of the array and patterns of four and five simultaneous foci +/-10 mm laterally and axially whilst maintaining low intensity levels in secondary maxima away from the targeted area in good agreement with linear theoretical predictions. Experiments in which pork meat was thermally ablated indicate that contiguous lesions several cm(3) in volume can be produced using the patterns of multiple foci.

A random phased array device for delivery of high intensity focused ultrasound

International Nuclear Information System (INIS)

Hand, J W; Shaw, A; Sadhoo, N; Rajagopal, S; Dickinson, R J; Gavrilov, L R

2009-01-01

Randomized phased arrays can offer electronic steering of a single focus and simultaneous multiple foci concomitant with low levels of secondary maxima and are potentially useful as sources of high intensity focused ultrasound (HIFU). This work describes laboratory testing of a 1 MHz random phased array consisting of 254 elements on a spherical shell of radius of curvature 130 mm and diameter 170 mm. Acoustic output power and efficiency are measured for a range of input electrical powers, and field distributions for various single- and multiple-focus conditions are evaluated by a novel technique using an infrared camera to provide rapid imaging of temperature changes on the surface of an absorbing target. Experimental results show that the array can steer a single focus laterally to at least ±15 mm off axis and axially to more than ±15 mm from the centre of curvature of the array and patterns of four and five simultaneous foci ±10 mm laterally and axially whilst maintaining low intensity levels in secondary maxima away from the targeted area in good agreement with linear theoretical predictions. Experiments in which pork meat was thermally ablated indicate that contiguous lesions several cm 3 in volume can be produced using the patterns of multiple foci.

Compression and radiation of high-power short rf pulses. II. A novel antenna array design with combined compressor/radiator elements

KAUST Repository

Sirenko, Kostyantyn

2011-01-01

The paper discusses the radiation of compressed high power short RF pulses using two different types of antennas: (i) A simple monopole antenna and (ii) a novel array design, where each of the elements is constructed by combining a compressor and a radiator. The studies on the monopole antenna demonstrate the possibility of a high power short RF pulse\\'s efficient radiation even using simple antennas. The studies on the novel array design demonstrate that a reduced size array with lower pulse distortion and power decay can be constructed by assembling the array from elements each of which integrates a compressor and a radiator. This design idea can be used with any type of antenna array; in this work it is applied to a phased array.

High-speed growth of TiO2 nanotube arrays with gradient pore diameter and ultrathin tube wall under high-field anodization

Science.gov (United States)

Yuan, Xiaoliang; Zheng, Maojun; Ma, Li; Shen, Wenzhong

2010-10-01

Highly ordered TiO2 nanotubular arrays have been prepared by two-step anodization under high field. The high anodizing current densities lead to a high-speed film growth (0.40-1.00 µm min - 1), which is nearly 16 times faster than traditional fabrication of TiO2 at low field. It was found that an annealing process of Ti foil is an effective approach to get a monodisperse and double-pass TiO2 nanotubular layer with a gradient pore diameter and ultrathin tube wall (nearly 10 nm). A higher anodic voltage and longer anodization time are beneficial to the formation of ultrathin tube walls. This approach is simple and cost-effective in fabricating high-quality ordered TiO2 nanotubular arrays for practical applications.

Gauge field copies and Higgs mechanism

International Nuclear Information System (INIS)

Gleiser, M.

1982-07-01

From the algebric classification of the possible solutions of the necessary and sufficient condition for the existence of gauge field copies in two possible classes the Higgs mechanism for the potential obtained from the difference between two copied potentials is applied. It is shown that for class I 'electric type' it is possible to construct a vector field that satisfies an electromagnetic wave equation. For class I 'magnetic type', a vector field that satisfies a non-linear equation as a consequence of the non-abelianity of the theory, is obtained. It is shown that for class II it's not possible to apply the Higgs mechanism. A possible physical interpretation for the 'gauge field copies' phenomenon, is obtained. (author) [pt

Understanding the impact of 1q21.1 copy number variant

Directory of Open Access Journals (Sweden)

Harvard Chansonette

2011-08-01

Full Text Available Abstract Background 1q21.1 Copy Number Variant (CNV is associated with a highly variable phenotype ranging from congenital anomalies, learning deficits/intellectual disability (ID, to a normal phenotype. Hence, the clinical significance of this CNV can be difficult to evaluate. Here we described the consequences of the 1q21.1 CNV on genome-wide gene expression and function of selected candidate genes within 1q21.1 using cell lines from clinically well described subjects. Methods and Results Eight subjects from 3 families were included in the study: six with a 1q21.1 deletion and two with a 1q21.1 duplication. High resolution Affymetrix 2.7M array was used to refine the 1q21.1 CNV breakpoints and exclude the presence of secondary CNVs of pathogenic relevance. Whole genome expression profiling, studied in lymphoblast cell lines (LBCs from 5 subjects, showed enrichment of genes from 1q21.1 in the top 100 genes ranked based on correlation of expression with 1q21.1 copy number. The function of two top genes from 1q21.1, CHD1L/ALC1 and PRKAB2, was studied in detail in LBCs from a deletion and a duplication carrier. CHD1L/ALC1 is an enzyme with a role in chromatin modification and DNA damage response while PRKAB2 is a member of the AMP kinase complex, which senses and maintains systemic and cellular energy balance. The protein levels for CHD1L/ALC1 and PRKAB2 were changed in concordance with their copy number in both LBCs. A defect in chromatin remodeling was documented based on impaired decatenation (chromatid untangling checkpoint (DCC in both LBCs. This defect, reproduced by CHD1L/ALC1 siRNA, identifies a new role of CHD1L/ALC1 in DCC. Both LBCs also showed elevated levels of micronuclei following treatment with a Topoisomerase II inhibitor suggesting increased DNA breaks. AMP kinase function, specifically in the deletion containing LBCs, was attenuated. Conclusion Our studies are unique as they show for the first time that the 1q21.1 CNV not only

High Density Nano-Electrode Array for Radiation Detection

International Nuclear Information System (INIS)

Misra, Mano

2010-01-01

Bulk single crystals of Cd 1-x Zn x Te (x=0.04 to x=0.2) compound semiconductor is used for room temperature radiation detection. The production of large volume of Cd 1-x Zn x Te with low defect density is expensive. As a result there is a growing research interest in the production of nanostructured compound semiconductors such as Cd 1-x Zn x Te in an electrochemical route. In this investigation, Cd 1-x Zn x Te ternary compound semiconductor, referred as CZT, was electrodeposited in the form of nanowires onto a TiO 2 nanotubular template from propylene carbonate as the non-aqueous electrolyte, using a pulse-reverse electrodeposition process at 130 C. 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 Cd 0.9 Zn 0.1 Te nanowires were 4.29 x 10 13 cm -3 , 1.56 eV and 2.76 x 10 11 (Omega)-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 (micro)Ci), the stacked CZT nanowires arrays showed sensing behavior. The sensitivity of the nanowire arrays increased as the number of stacks increased. The

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

Detection of Answer Copying Based on the Structure of a High-Stakes Test

Science.gov (United States)

Belov, Dmitry I.

2011-01-01

This article presents the Variable Match Index (VM-Index), a new statistic for detecting answer copying. The power of the VM-Index relies on two-dimensional conditioning as well as the structure of the test. The asymptotic distribution of the VM-Index is analyzed by reduction to Poisson trials. A computational study comparing the VM-Index with the…

Solar array experiments on the SPHINX satellite. [Space Plasma High voltage INteraction eXperiment satellite

Science.gov (United States)

Stevens, N. J.

1974-01-01

The Space Plasma, High Voltage Interaction Experiment (SPHINX) is the name given to an auxiliary payload satellite scheduled to be launched in January 1974. The principal experiments carried on this satellite are specifically designed to obtain the engineering data on the interaction of high voltage systems with the space plasma. The classes of experiments are solar array segments, insulators, insulators with pin holes and conductors. The satellite is also carrying experiments to obtain flight data on three new solar array configurations: the edge illuminated-multijunction cells, the teflon encased cells, and the violet cells.

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.

High-performance asymmetric supercapacitors based on core/shell cobalt oxide/carbon nanowire arrays with enhanced electrochemical energy storage

International Nuclear Information System (INIS)

Pan, G.X.; Xia, X.H.; Cao, F.; Chen, J.; Tang, P.S.; Zhang, Y.J.; Chen, H.F.

2014-01-01

Graphical abstract: - Highlights: • We prepared a self-supported porous Co 3 O 4 /C core/shell nanowire array. • Core/shell nanowire array showed high pseudo-capacitive properties. • Core/shell array structure was favorable for fast ion and electron transfer. - Abstract: High-reactivity electrode materials are indispensible for developing high-performance electrochemical energy storage devices. Herein, we report self-supported core/shell Co 3 O 4 /C nanowire arrays by using hydrothermal synthesis and chemical vapor deposition methods. A uniform and thin carbon shell is coated on the surface of Co 3 O 4 nanowire forming core/shell nanowires with diameters of ∼100 nm. Asymmetric supercapacitors have been assembled with the core/shell Co 3 O 4 /C nanowire arrays as the positive electrode and activated carbon (AC) as the negative electrode. The core/shell Co 3 O 4 /C nanowire arrays exhibit a specific capacity of 116 mAh g −1 at the working current of 100 mA (4 A g −1 ), and a long cycle life along with ∼ 92% retention after 8000 cycles at 4 A g −1 , higher than the unmodified Co 3 O 4 nanowire arrays (81 mAh g −1 at 4 A g −1 ). The introduction of uniform carbon layer into the core/shell structure is favorable for the enhancement of supercapacitor due to the improved electrical conductivity and reaction kinetics

Clinical Omics Analysis of Colorectal Cancer Incorporating Copy Number Aberrations and Gene Expression Data

Directory of Open Access Journals (Sweden)

Tsuyoshi Yoshida

2010-07-01

Full Text Available Background: Colorectal cancer (CRC is one of the most frequently occurring cancers in Japan, and thus a wide range of methods have been deployed to study the molecular mechanisms of CRC. In this study, we performed a comprehensive analysis of CRC, incorporating copy number aberration (CRC and gene expression data. For the last four years, we have been collecting data from CRC cases and organizing the information as an “omics” study by integrating many kinds of analysis into a single comprehensive investigation. In our previous studies, we had experienced difficulty in finding genes related to CRC, as we observed higher noise levels in the expression data than in the data for other cancers. Because chromosomal aberrations are often observed in CRC, here, we have performed a combination of CNA analysis and expression analysis in order to identify some new genes responsible for CRC. This study was performed as part of the Clinical Omics Database Project at Tokyo Medical and Dental University. The purpose of this study was to investigate the mechanism of genetic instability in CRC by this combination of expression analysis and CNA, and to establish a new method for the diagnosis and treatment of CRC. Materials and methods: Comprehensive gene expression analysis was performed on 79 CRC cases using an Affymetrix Gene Chip, and comprehensive CNA analysis was performed using an Affymetrix DNA Sty array. To avoid the contamination of cancer tissue with normal cells, laser micro-dissection was performed before DNA/RNA extraction. Data analysis was performed using original software written in the R language. Result: We observed a high percentage of CNA in colorectal cancer, including copy number gains at 7, 8q, 13 and 20q, and copy number losses at 8p, 17p and 18. Gene expression analysis provided many candidates for CRC-related genes, but their association with CRC did not reach the level of statistical significance. The combination of CNA and gene

A novel high electrode count spike recording array using an 81,920 pixel transimpedance amplifier-based imaging chip.

Science.gov (United States)

Johnson, Lee J; Cohen, Ethan; Ilg, Doug; Klein, Richard; Skeath, Perry; Scribner, Dean A

2012-04-15

Microelectrode recording arrays of 60-100 electrodes are commonly used to record neuronal biopotentials, and these have aided our understanding of brain function, development and pathology. However, higher density microelectrode recording arrays of larger area are needed to study neuronal function over broader brain regions such as in cerebral cortex or hippocampal slices. Here, we present a novel design of a high electrode count picocurrent imaging array (PIA), based on an 81,920 pixel Indigo ISC9809 readout integrated circuit camera chip. While originally developed for interfacing to infrared photodetector arrays, we have adapted the chip for neuron recording by bonding it to microwire glass resulting in an array with an inter-electrode pixel spacing of 30 μm. In a high density electrode array, the ability to selectively record neural regions at high speed and with good signal to noise ratio are both functionally important. A critical feature of our PIA is that each pixel contains a dedicated low noise transimpedance amplifier (∼0.32 pA rms) which allows recording high signal to noise ratio biocurrents comparable to single electrode voltage amplifier recordings. Using selective sampling of 256 pixel subarray regions, we recorded the extracellular biocurrents of rabbit retinal ganglion cell spikes at sampling rates up to 7.2 kHz. Full array local electroretinogram currents could also be recorded at frame rates up to 100 Hz. A PIA with a full complement of 4 readout circuits would span 1cm and could acquire simultaneous data from selected regions of 1024 electrodes at sampling rates up to 9.3 kHz. Published by Elsevier B.V.

A dual-directional light-control film with a high-sag and high-asymmetrical-shape microlens array fabricated by a UV imprinting process

International Nuclear Information System (INIS)

Lin, Ta-Wei; Liao, Yunn-Shiuan; Chen, Chi-Feng; Yang, Jauh-Jung

2008-01-01

A dual-directional light-control film with a high-sag and high-asymmetric-shape long gapless hexagonal microlens array fabricated by an ultra-violent (UV) imprinting process is presented. Such a lens array is designed by ray-tracing simulation and fabricated by a micro-replication process including gray-scale lithography, electroplating process and UV curing. The shape of the designed lens array is similar to that of a near half-cylindrical lens array with a periodical ripple. The measurement results of a prototype show that the incident lights using a collimated LED with the FWHM of dispersion angle, 12°, are diversified differently in short and long axes. The numerical and experimental results show that the FWHMs of the view angle for angular brightness in long and short axis directions through the long hexagonal lens are about 34.3° and 18.1° and 31° and 13°, respectively. Compared with the simulation result, the errors in long and short axes are about 5% and 16%, respectively. Obviously, the asymmetric gapless microlens array can realize the aim of the controlled asymmetric angular brightness. Such a light-control film can be used as a power saving screen compared with convention diffusing film for the application of a rear projection display

A BaF2 crystal array for high energy-ray measurements

Indian Academy of Sciences (India)

Abstract. 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 ...

The hyperion particle-γ detector array

Energy Technology Data Exchange (ETDEWEB)

Hughes, R.O.; Burke, J.T.; Casperson, R.J.; Ota, S. [Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Fisher, S.; Parker, J. [Science, Technology and Engineering Division, Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Beausang, C.W. [Department of Physics, University of Richmond, 28 Westhampton Way, Richmond, VA 23173 (United States); Dag, M. [Cyclotron Institute, Texas A& M University, College Station, TX 77840 (United States); Humby, P. [Department of Physics, University of Richmond, 28 Westhampton Way, Richmond, VA 23173 (United States); Department of Physics, University of Surrey, Surrey GU27XH (United Kingdom); Koglin, J. [Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); McCleskey, E.; McIntosh, A.B.; Saastamoinen, A. [Cyclotron Institute, Texas A& M University, College Station, TX 77840 (United States); Tamashiro, A.S. [Department of Nuclear Science and Engineering, Oregon State University, Corvallis, OR 97331 (United States); Wilson, E. [Department of Physics, University of Richmond, 28 Westhampton Way, Richmond, VA 23173 (United States); Wu, T.C. [Department of Physics and Astronomy, University of Utah, Salt Lake City UT 84112-0830 (United States)

2017-06-01

Hyperion is a new high-efficiency charged-particle γ-ray detector array which consists of a segmented silicon telescope for charged-particle detection and up to fourteen high-purity germanium clover detectors for the detection of coincident γ rays. The array will be used in nuclear physics measurements and Stockpile Stewardship studies and replaces the STARLiTeR array. This article discusses the features of the array and presents data collected with the array in the commissioning experiment.

A method of incident angle estimation for high resolution spectral recovery in filter-array-based spectrometers

Science.gov (United States)

Kim, Cheolsun; Lee, Woong-Bi; Ju, Gun Wu; Cho, Jeonghoon; Kim, Seongmin; Oh, Jinkyung; Lim, Dongsung; Lee, Yong Tak; Lee, Heung-No

2017-02-01

In recent years, there has been an increasing interest in miniature spectrometers for research and development. Especially, filter-array-based spectrometers have advantages of low cost and portability, and can be applied in various fields such as biology, chemistry and food industry. Miniaturization in optical filters causes degradation of spectral resolution due to limitations on spectral responses and the number of filters. Nowadays, many studies have been reported that the filter-array-based spectrometers have achieved resolution improvements by using digital signal processing (DSP) techniques. The performance of the DSP-based spectral recovery highly depends on the prior information of transmission functions (TFs) of the filters. The TFs vary with respect to an incident angle of light onto the filter-array. Conventionally, it is assumed that the incident angle of light on the filters is fixed and the TFs are known to the DSP. However, the incident angle is inconstant according to various environments and applications, and thus TFs also vary, which leads to performance degradation of spectral recovery. In this paper, we propose a method of incident angle estimation (IAE) for high resolution spectral recovery in the filter-array-based spectrometers. By exploiting sparse signal reconstruction of the L1- norm minimization, IAE estimates an incident angle among all possible incident angles which minimizes the error of the reconstructed signal. Based on IAE, DSP effectively provides a high resolution spectral recovery in the filter-array-based spectrometers.

Ultra-high-aspect-orthogonal and tunable three dimensional polymeric nanochannel stack array for BioMEMS applications

Science.gov (United States)

Heo, Joonseong; Kwon, Hyukjin J.; Jeon, Hyungkook; Kim, Bumjoo; Kim, Sung Jae; Lim, Geunbae

2014-07-01

Nanofabrication technologies have been a strong advocator for new scientific fundamentals that have never been described by traditional theory, and have played a seed role in ground-breaking nano-engineering applications. In this study, we fabricated ultra-high-aspect (~106 with O(100) nm nanochannel opening and O(100) mm length) orthogonal nanochannel array using only polymeric materials. Vertically aligned nanochannel arrays in parallel can be stacked to form a dense nano-structure. Due to the flexibility and stretchability of the material, one can tune the size and shape of the nanochannel using elongation and even roll the stack array to form a radial-uniformly distributed nanochannel array. The roll can be cut at discretionary lengths for incorporation with a micro/nanofluidic device. As examples, we demonstrated ion concentration polarization with the device for Ohmic-limiting/overlimiting current-voltage characteristics and preconcentrated charged species. The density of the nanochannel array was lower than conventional nanoporous membranes, such as anodic aluminum oxide membranes (AAO). However, accurate controllability over the nanochannel array dimensions enabled multiplexed one microstructure-on-one nanostructure interfacing for valuable biological/biomedical microelectromechanical system (BioMEMS) platforms, such as nano-electroporation.Nanofabrication technologies have been a strong advocator for new scientific fundamentals that have never been described by traditional theory, and have played a seed role in ground-breaking nano-engineering applications. In this study, we fabricated ultra-high-aspect (~106 with O(100) nm nanochannel opening and O(100) mm length) orthogonal nanochannel array using only polymeric materials. Vertically aligned nanochannel arrays in parallel can be stacked to form a dense nano-structure. Due to the flexibility and stretchability of the material, one can tune the size and shape of the nanochannel using elongation and even

The double copy: Bremsstrahlung and accelerating black holes

CERN Document Server

Luna, Andres; Nicholson, Isobel; O'Connell, Donal; White, Chris D

2016-01-01

Advances in our understanding of perturbation theory suggest the existence of a correspondence between classical general relativity and Yang-Mills theory. A concrete example of this correspondence, which is known as the double copy, was recently introduced for the case of stationary Kerr-Schild spacetimes. Building on this foundation, we examine the simple time-dependent case of an accelerating, radiating point source. The gravitational solution, which generalises the Schwarzschild solution, includes a non-trivial stress-energy tensor. This stress-energy tensor corresponds to a gauge theoretic current in the double copy. We interpret both of these sources as representing the radiative part of the field. Furthermore, in the simple example of Bremsstrahlung, we determine a scattering amplitude describing the radiation, maintaining the double copy throughout. Our results provide the strongest evidence yet that the classical double copy is directly related to the BCJ double copy for scattering amplitudes.

The λ transformation and gravitational copies

International Nuclear Information System (INIS)

Silva, M.R. da.

1984-01-01

An Abelian symmetry already considered by Einstein with respect to his asymmetrical field theories is related to the gravitational and gauge field copy phenomenon. It is shown that gauge field copies arise out of a straightforward generalization of the λ - map. The connection between Einstein's work on the λ-transformation and the copy phenomenon is obtained with the help of the Frobenius Theorem on the existence of foliations on a differentiable manifold. A problem like the one above is usually treated within the language of (intrinsic) Differential Geometry; General Relativity and classical unified field theories are traditionally developed in a classical style, that gap, a long introduction is prepared where the same structures are studied from the traditional and from the more recent point of view. (author)

Demonstration of radiation pulse shaping with nested-tungsten-wire-array pinches for high-yield inertial confinement fusion.

Science.gov (United States)

Cuneo, M E; Vesey, R A; Sinars, D B; Chittenden, J P; Waisman, E M; Lemke, R W; Lebedev, S V; Bliss, D E; Stygar, W A; Porter, J L; Schroen, D G; Mazarakis, M G; Chandler, G A; Mehlhorn, T A

2005-10-28

Nested wire-array pinches are shown to generate soft x-ray radiation pulse shapes required for three-shock isentropic compression and hot-spot ignition of high-yield inertial confinement fusion capsules. We demonstrate a reproducible and tunable foot pulse (first shock) produced by interaction of the outer and inner arrays. A first-step pulse (second shock) is produced by inner array collision with a central CH2 foam target. Stagnation of the inner array at the axis produces the third shock. Capsules optimized for several of these shapes produce 290-900 MJ fusion yields in 1D simulations.

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.

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.

Science.gov (United States)

Black, Holly A; Khan, Fayeza F; Tyson, Jess; Al Armour, John

2014-07-21

The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3-16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

Single-nucleotide polymorphism array-based karyotyping of acute promyelocytic leukemia.

Directory of Open Access Journals (Sweden)

Inés Gómez-Seguí

Full Text Available Acute promyelocytic leukemia (APL is characterized by the t(15;17(q22;q21, but additional chromosomal abnormalities (ACA and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A 6.0 (Affymetrix in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%: 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH, being a duplication of 8(q24 (23% and a deletion of 7(q33-qter (6% the most frequent copy-number abnormalities (CNA. Four patients (8% showed CNAs adjacent to the breakpoints of the translocation. We compared our results with other APL series and found that, except for dup(8q24 and del(7q33-qter, ACA were infrequent (≤3% but most of them recurrent (70%. Interestingly, having CNA or FLT3 mutation were mutually exclusive events. Neither the number of CNA, nor any specific CNA was associated significantly with prognosis. This study has delineated recurrent abnormalities in addition to t(15;17 that may act as secondary events and could explain leukemogenesis in up to 40% of APL cases with no ACA by conventional cytogenetics.

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

Directory of Open Access Journals (Sweden)

Wojciech Szmyt

2017-01-01

Full Text Available 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.

Combinatorial electrochemical cell array for high throughput screening of micro-fuel-cells and metal/air batteries.

Science.gov (United States)

Jiang, Rongzhong

2007-07-01

An electrochemical cell array was designed that contains a common air electrode and 16 microanodes for high throughput screening of both fuel cells (based on polymer electrolyte membrane) and metal/air batteries (based on liquid electrolyte). Electrode materials can easily be coated on the anodes of the electrochemical cell array and screened by switching a graphite probe from one cell to the others. The electrochemical cell array was used to study direct methanol fuel cells (DMFCs), including high throughput screening of electrode catalysts and determination of optimum operating conditions. For screening of DMFCs, there is about 6% relative standard deviation (percentage of standard deviation versus mean value) for discharge current from 10 to 20 mAcm(2). The electrochemical cell array was also used to study tin/air batteries. The effect of Cu content in the anode electrode on the discharge performance of the tin/air battery was investigated. The relative standard deviations for screening of metal/air battery (based on zinc/air) are 2.4%, 3.6%, and 5.1% for discharge current at 50, 100, and 150 mAcm(2), respectively.

Hacking DNA copy number for circuit engineering.

Science.gov (United States)

Wu, Feilun; You, Lingchong

2017-07-27

DNA copy number represents an essential parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered. A new study demonstrates how dynamic control of DNA copy number can serve as an effective strategy to program robust oscillations in gene expression circuits.

A switched capacitor array based system for high-speed calorimetry

International Nuclear Information System (INIS)

Levi, M.; Bebek, C.; Ely, R.; Jared, R.; Kipnis, I.; Kirsten, F.; Kleinfelder, S.; Merrick, T.; Milgrome, O.

1991-12-01

A sixteen channel analog transient recorder with 256 cells per channel has been fabricated as an integrated circuit. The circuit uses switched capacitor array technology to achieve simultaneous read/write capability and twelve bit dynamic range. Combined with highly parallel analog-to-digital converter and readout control circuitry being developed this system should satisfy the demanding electronics requirements for calorimeter detectors at the SSC. The system design and test results are presented

Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation.

Science.gov (United States)

Narang, Ankita; Jha, Pankaj; Kumar, Dhirendra; Kutum, Rintu; Mondal, Anupam Kumar; Dash, Debasis; Mukerji, Mitali

2014-11-13

Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Copy number variation in salivary amylase: A participant-based study on genetic variation.

Directory of Open Access Journals (Sweden)

Phillips, E.

2017-07-01

Full Text Available Amylase (AMY1 is an enzyme found in the mouth that is used to help digest carbohydrates. It has been found that the copy number of AMY1 has been positively associated with protein levels within an individual and also that individual’s population. This information can correspond to the positive ancestral linkage of high starch consumption within agricultural and hunter-gatherer societies. A high starch consumption means that the AMY1 enzyme will be more prevalent within their bodies, and the presence of AMY1 could both help bodies process starches better and prevent future conditions or intestinal diseases. The amylase gene is conclusively connected to the AMY1 copy number production. I hypothesized that individuals within a population will have a similar copy number of the AMY1 gene to each other. Twenty-five high school students located in Norman, Oklahoma were asked to retrieve buccal swabs from the inside of their cheek. DNA then was abstracted from these samples, and a quantitative polymerase chain reaction (qPCR, a machine used to detect the amount of genetic material found in the DNA, was completed in order to determine the copy number within each salivary sample. The qPCR was completed two different times in order to ensure correct results when the data was presented. Results indicated that the copy number within the population were similar to each other, and ranged from 1-12. This means that individuals located in this population have a lower production of amylase, and this provides indication that they are more likely to become obese than in previous research papers located in Arizona. Research shows that a smaller production of AMY1 may contribute to the chances of obesity in the future.

New fabrication of high-frequency (100-MHz) ultrasound PZT film kerfless linear array.

Science.gov (United States)

Zhu, Benpeng; Chan, Ngai Yui; Dai, Jiyan; Shung, K Kirk; Takeuchi, Shinichi; Zhou, Qifa

2013-04-01

The paper describes the design, fabrication, and measurements of a high-frequency ultrasound kerfless linear array prepared from hydrothermal lead zirconate titanate (PZT) thick film. The 15-μm hydrothermal PZT thick film with an area of 1 × 1 cm, obtained through a self-separation process from Ti substrate, was used to fabricate a 32-element 100-MHz kerfless linear array with photolithography. The bandwidth at -6 dB without matching layer, insertion loss around center frequency, and crosstalk between adjacent elements were measured to be 39%, -30 dB, and -15 dB, respectively.

Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

Directory of Open Access Journals (Sweden)

Verena Jabs

Full Text Available Non-small cell lung cancer (NSCLC represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190 and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes, high correlations, with a correlation coefficient >0.7, were obtained only in a subset of 301 genes (1.6%, including KRAS, EGFR and MDM2. Higher correlation coefficients were associated with higher copy number and expression levels. Strong correlations were frequently based on few tumors with high copy number gains and correspondingly increased mRNA expression. Among the highly correlating genes, GO groups associated with posttranslational protein modifications were particularly frequent, including ubiquitination and neddylation. In a meta-analysis including 1,779 patients we found that survival associated genes were overrepresented among highly correlating genes (61 of the 301 highly correlating genes, FDR adjusted p<0.05. Among them are the chaperone CCT2, the core complex protein NUP107 and the ubiquitination and neddylation associated protein CAND1. In conclusion, in a comprehensive analysis we described a distinct set of highly correlating genes. These genes were found to be overrepresented among survival-associated genes based on gene expression in a large collection of publicly available datasets.

A flexible coil array for high resolution magnetic resonance imaging at 7 Tesla

International Nuclear Information System (INIS)

Kriegl, R.

2015-01-01

Magnetic resonance imaging (MRI), among other imaging techniques, has become a major backbone of modern medical diagnostics. MRI enables the non-invasive combined, identification of anatomical structures, functional and chemical properties, especially in soft tissues. Nonetheless, applications requiring very high spatial and/or temporal resolution are often limited by the available signal-to-noise ratio (SNR) in MR experiments. Since first clinical applications, image quality in MRI has been constantly improved by applying one or several of the following strategies: increasing the static magnetic field strength, improvement of the radiofrequency (RF) detection system, development of specialized acquisition sequences and optimization of image reconstruction techniques. This work is concerned with the development of highly sensitive RF detection systems for biomedical ultra-high field MRI. In particular, auto-resonant RF coils based on transmission line technology are investigated. These resonators may be fabricated on flexible substrate which enables form-fitting of the RF detector to the target anatomy, leading to a significant SNR gain. The main objective of this work is the development of a flexible RF coil array for high-resolution MRI on a human whole-body 7 T MR scanner. With coil arrays, the intrinsically high SNR of small surface coils may be exploited for an extended field of view. Further, parallel imaging techniques are accessible with RF array technology, allowing acceleration of the image acquisition. Secondly, in this PhD project a novel design for transmission line resonators is developed, that brings an additional degree of freedom in geometric design and enables the fabrication of large multi-turn resonators for high field MR applications. This thesis describes the development, successful implementation and evaluation of novel, mechanically flexible RF devices by analytical and 3D electromagnetic simulations, in bench measurements and in MRI

Highly Deformable Origami Paper Photodetector Arrays

KAUST Repository

Lin, Chun-Ho

2017-09-25

Flexible electronics will form the basis of many next-generation technologies, such as wearable devices, biomedical sensors, the Internet of things, and more. However, most flexible devices can bear strains of less than 300% as a result of stretching. In this work, we demonstrate a simple and low-cost paper-based photodetector array featuring superior deformability using printable ZnO nanowires, carbon electrodes, and origami-based techniques. With a folded Miura structure, the paper photodetector array can be oriented in four different directions via tessellated parallelograms to provide the device with excellent omnidirectional light harvesting capabilities. Additionally, we demonstrate that the device can be repeatedly stretched (up to 1000% strain), bent (bending angle ±30°), and twisted (up to 360°) without degrading performance as a result of the paper folding technique, which enables the ZnO nanowire layers to remain rigid even as the device is deformed. The origami-based strategy described herein suggests avenues for the development of next-generation deformable optoelectronic applications.

One-step electrodeposited nickel cobalt sulfide nanosheet arrays for high-performance asymmetric supercapacitors.

Science.gov (United States)

Chen, Wei; Xia, Chuan; Alshareef, Husam N

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.

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.

One-Step Electrodeposited Nickel Cobalt Sulfide Nanosheet Arrays for High-Performance Asymmetric Supercapacitors

KAUST Repository

Chen, Wei; Xia, Chuan; Alshareef, Husam N.

2014-01-01

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.

Electrodeposited highly-ordered manganese oxide nanowire arrays for supercapacitors

Science.gov (United States)

Liu, Haifeng; Lu, Bingqiang; Wei, Shuiqiang; Bao, Mi; Wen, Yanxuan; Wang, Fan

2012-07-01

Large arrays of well-aligned Mn oxide nanowires were prepared by electrodeposition using anodic aluminum oxide templates. The sizes of nanowires were tuned by varying the electrotype solution involved and the MnO2 nanowires with 10 μm in length were obtained in a neutral KMnO4 bath for 1 h. MnO2 nanowire arrays grown on conductor substance save the tedious electrode-making process, and electrochemical characterization demonstrates that the MnO2 nanowire arrays electrode has good capacitive behavior. Due to the limited mass transportation in narrow spacing, the spacing effects between the neighbor nanowires have show great influence to the electrochemical performance.

Mutation mechanisms that underlie turnover of a human telomere-adjacent segmental duplication containing an unstable minisatellite.

Science.gov (United States)

Hills, Mark; Jeyapalan, Jennie N; Foxon, Jennifer L; Royle, Nicola J

2007-04-01

Subterminal regions, juxtaposed to telomeres on human chromosomes, contain a high density of segmental duplications, but relatively little is known about the evolutionary processes that underlie sequence turnover in these regions. We have characterized a segmental duplication adjacent to the Xp/Yp telomere, each copy containing a hypervariable array of the DXYS14 minisatellite. Both DXYS14 repeat arrays mutate at a high rate (0.3 and 0.2% per gamete) but linkage disequilibrium analysis across 27 SNPs and a direct crossover assay show that recombination during meiosis is suppressed. Therefore instability at DXYS14a and b is dominated by intra-allelic processes or possibly conversion limited to the repeat arrays. Furthermore some chromosomes (14%) carry only one copy of the duplicon, including one DXYS14 repeat array that is also highly mutable (1.2% per gamete). To explain these and other observations, we propose there is another low-rate mutation process that causes copy number change in part or all of the duplicon.

Readability as a Factor in Magazine Ad Copy Recall.

Science.gov (United States)

Wesson, David A.

1989-01-01

Examines the relationship between advertising copy readability and advertising effectiveness. Finds that recall is improved when the copy style is either fairly easy or fairly hard to read. Suggests the value of considering copy readability as a potential contributor, though a minor one, to the success of magazine advertising. (RS)

Population-genetic nature of copy number variations in the human genome.

Science.gov (United States)

Kato, Mamoru; Kawaguchi, Takahisa; Ishikawa, Shumpei; Umeda, Takayoshi; Nakamichi, Reiichiro; Shapero, Michael H; Jones, Keith W; Nakamura, Yusuke; Aburatani, Hiroyuki; Tsunoda, Tatsuhiko

2010-03-01

Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000-4000 CNVs (4-6% of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV-SNP haplotypes. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV-SNP linkage disequilibrium (LD) for 500-900 bi- and multi-allelic CNVs per population revealed that previous conflicting reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP-SNP LD, whereas the multi-allelic LD was somewhat stronger than the bi-allelic LD. After further investigation of tag SNPs for CNVs, we conclude that the customary tagging strategy for disease association studies can be applicable for common deletion CNVs, but direct interrogation is needed for other types of CNVs.

High-efficient light absorption of monolayer graphene via cylindrical dielectric arrays and the sensing application

Science.gov (United States)

Zhou, Peng; Zheng, Gaige

2018-04-01

The efficiency of graphene-based optoelectronic devices is typically limited by the poor absolute absorption of light. A hybrid structure of monolayer graphene with cylindrical titanium dioxide (TiO2) array and aluminum oxide (Al2O3) spacer layer on aluminum (Al) substrate has been proposed to enhance the absorption for two-dimensional (2D) materials. By combining dielectric array with metal substrate, the structure achieves multiple absorption peaks with near unity absorbance at near-infrared wavelengths due to the resonant effect of dielectric array. Completed monolayer graphene is utilized in the design without any demand of manufacture process to form the periodic patterns. Further analysis indicates that the near-field enhancement induced by surface modes gives rise to the high absorption. This favorable field enhancement and tunability of absorption not only open up new approaches to accelerate the light-graphene interaction, but also show great potential for practical applications in high-performance optoelectronic devices, such as modulators and sensors.

TRUSSELATOR - On-Orbit Fabrication of High Performance Support Structures for Solar Arrays, Phase II

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...

Elimination of Parallel Copies using Code Motion on Data Dependence Graphs

DEFF Research Database (Denmark)

Brandner, Florian; Colombet, Quentin

2013-01-01

, while at the same time a valid register assignment is preserved. Our results show that even after traditional register allocation with coalescing our technique is able to eliminate an additional 3% (up to 9%) of the remaining copies and reduce the weighted costs of register copies by up to 25......Register allocation regained much interest in recent years due to the development of decoupled strategies that split the problem into separate phases: spilling, register assignment, and copy elimination. Traditional approaches to copy elimination during register allocation are based on interference......% for the SPECINT 2000 benchmarks. In comparison to Parallel Copy Motion, our technique removes 11% (up to 20%) more copies and up to 39% more of the copy costs....

High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays

Directory of Open Access Journals (Sweden)

Crenshaw Andrew

2009-01-01

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

A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans.

Science.gov (United States)

Jeon, Jae Pil; Shim, Sung Mi; Jung, Jong Sun; Nam, Hye Young; Lee, Hye Jin; Oh, Berm Seok; Kim, Kuchan; Kim, Hyung Lae; Han, Bok Ghee

2009-09-30

To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (Por= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (Por=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.

High-speed growth of TiO{sub 2} nanotube arrays with gradient pore diameter and ultrathin tube wall under high-field anodization

Energy Technology Data Exchange (ETDEWEB)

Yuan Xiaoliang; Zheng Maojun; Shen Wenzhong [Key Laboratory of Artificial Structures and Quantum Control, Ministry of Education, Department of Physics, Shanghai Jiao Tong University, Shanghai 200240 (China); Ma Li, E-mail: mjzheng@sjtu.edu.cn [School of Chemistry and Chemical Technology, Shanghai Jiao Tong University, Shanghai 200240 (China)

2010-10-08

Highly ordered TiO{sub 2} nanotubular arrays have been prepared by two-step anodization under high field. The high anodizing current densities lead to a high-speed film growth (0.40-1.00 {mu}m min{sup -1}), which is nearly 16 times faster than traditional fabrication of TiO{sub 2} at low field. It was found that an annealing process of Ti foil is an effective approach to get a monodisperse and double-pass TiO{sub 2} nanotubular layer with a gradient pore diameter and ultrathin tube wall (nearly 10 nm). A higher anodic voltage and longer anodization time are beneficial to the formation of ultrathin tube walls. This approach is simple and cost-effective in fabricating high-quality ordered TiO{sub 2} nanotubular arrays for practical applications.

DNA suspension arrays: silencing discrete artifacts for high-sensitivity applications.

Directory of Open Access Journals (Sweden)

Matthew S Lalonde

2010-11-01

Full Text Available Detection of low frequency single nucleotide polymorphisms (SNPs has important implications in early screening for tumorgenesis, genetic disorders and pathogen drug resistance. Nucleic acid arrays are a powerful tool for genome-scale SNP analysis, but detection of low-frequency SNPs in a mixed population on an array is problematic. We demonstrate a model assay for HIV-1 drug resistance mutations, wherein ligase discrimination products are collected on a suspension array. In developing this system, we discovered that signal from multiple polymorphisms was obscured by two discrete hybridization artifacts. Specifically: 1 tethering of unligated probes on the template DNA elicited false signal and 2 unpredictable probe secondary structures impaired probe capture and suppressed legitimate signal from the array. Two sets of oligonucleotides were used to disrupt these structures; one to displace unligated reporter labels from the bead-bound species and another to occupy sequences which interfered with array hybridization. This artifact silencing system resulted in a mean 21-fold increased sensitivity for 29 minority variants of 17 codons in our model assay for mutations most commonly associated with HIV-1 drug resistance. Furthermore, since the artifacts we characterized are not unique to our system, their specific inhibition might improve the quality of data from solid-state microarrays as well as from the growing number of multiple analyte suspension arrays relying on sequence-specific nucleic acid target capture.

Chromosomal abnormalities and copy number variations in fetal left-sided congenital heart defects.

Science.gov (United States)

Jansen, Fenna A R; Hoffer, Mariette J V; van Velzen, Christine L; Plati, Stephani Klingeman; Rijlaarsdam, Marry E B; Clur, Sally-Ann B; Blom, Nico A; Pajkrt, Eva; Bhola, Shama L; Knegt, Alida C; de Boer, Marion A; Haak, Monique C

2016-02-01

To demonstrate the spectrum of copy number variants (CNVs) in fetuses with isolated left-sided congenital heart defects (CHDs), and analyse genetic content. Between 2003 and 2012, 200 fetuses were identified with left-sided CHD. Exclusion criteria were chromosomal rearrangements, 22q11.2 microdeletion and/or extra-cardiac malformations (n = 64). We included cases with additional minor anomalies (n = 39), such as single umbilical artery. In 54 of 136 eligible cases, stored material was available for array analysis. CNVs were categorized as either (likely) benign, (likely) pathogenic or of unknown significance. In 18 of the 54 isolated left-sided CHDs we found 28 rare CNVs (prevalence 33%, average 1.6 CNV per person, size 10.6 kb-2.2 Mb). Our interpretation yielded clinically significant CNVs in two of 54 cases (4%) and variants of unknown significance in three other cases (6%). In left-sided CHDs that appear isolated, with normal chromosome analysis and 22q11.2 FISH analysis, array analysis detects clinically significant CNVs. When counselling parents of a fetus with a left-sided CHD it must be taken into consideration that aside from the cardiac characteristics, the presence of extra-cardiac malformations and chromosomal abnormalities influence the treatment plan and prognosis. © 2015 John Wiley & Sons, Ltd.

Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. | Office of Cancer Genomics

Science.gov (United States)

Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent.

Final Technical Report Radiation Hard Tight Pitch GaInP SPAD Arrays for High Energy Physics

Energy Technology Data Exchange (ETDEWEB)

Harmon, Eric

2018-01-26

The specialized photodetectors used in high energy physics experiments often need to remain extremely sensitive for years despite radiation induced damage caused by the constant bombardment of high energy particles. To solve this problem, LightSpin Technologies, Inc. in collaboration with Prof. Bradley Cox and the University of Virginia is developing radiation-hard GaInP photodetectors which are projected to be extraordinarily radiation hard, theoretically capable of withstanding a 100,000-fold higher radiation dose than silicon. In this Phase I SBIR project, LightSpin investigated the performance and radiation hardness of fifth generation GaInP SPAD arrays. These fifth generation devices used a new planar processing approach that enables very tight pitch arrays to be produced. High performance devices with SPAD pitches of 11, 15, and 25 μm were successfully demonstrated, which greatly increased the dynamic range and maximum count rate of the devices. High maximum count rates are critical when considering radiation hardness, since radiation damage causes a proportional increase in the dark count rate, causing SPAD arrays with low maximum count rates (large SPAD pitches) to fail. These GaInP SPAD array Photomultiplier Chips™ were irradiated with protons, electrons, and neutrons. Initial irradiation results were disappointing, with the post-irradiation devices exhibiting excessively high dark currents. The degradation was traced to surface leakage currents that were largely eliminated through the use of trenches etched around the exterior of the Photomultiplier Chip™ (not between SPAD elements). A second round of irradiations on Photomultiplier Chips™ with trenches proved substantially more successful, with post-irradiation dark currents remaining relatively low, though dark count rates were observed to increase at the highest doses. Preliminary analysis of the post-irradiation devices is promising … many of the irradiated Photomultiplier Chips™ still

Development of high-performance phased-array UT system 'DYNARAY' and its application examples

International Nuclear Information System (INIS)

Ehara, Eiji

2011-01-01

This article outlined the history leading to develop high-performance phased-array (PA) UT system called DYNARAY, with up to 256 phased-array active channels and maximum 4096 focal laws, lowering the inspection time. As examples it was applied to in-service inspection of reactor pressure vessel welded joints using module of PA-UT probe or eddy-current probe, inspection of seal welds of dry storage containers using scanner of PA-UT, crack detection of end ring of generators using PA-UT probe and UT inspection of cast austenitic stainless steel using 500 kHz probe. Advanced data acquisition and analysis functions for PA-UT system had been developed. (T. Tanaka)

ESPRIT And Uniform Linear Arrays

Science.gov (United States)

Roy, R. H.; Goldburg, M.; Ottersten, B. E.; Swindlehurst, A. L.; Viberg, M.; Kailath, T.

1989-11-01

Abstract ¬â€?ESPRIT is a recently developed and patented technique for high-resolution estimation of signal parameters. It exploits an invariance structure designed into the sensor array to achieve a reduction in computational requirements of many orders of magnitude over previous techniques such as MUSIC, Burg's MEM, and Capon's ML, and in addition achieves performance improvement as measured by parameter estimate error variance. It is also manifestly more robust with respect to sensor errors (e.g. gain, phase, and location errors) than other methods as well. Whereas ESPRIT only requires that the sensor array possess a single invariance best visualized by considering two identical but other-wise arbitrary arrays of sensors displaced (but not rotated) with respect to each other, many arrays currently in use in various applications are uniform linear arrays of identical sensor elements. Phased array radars are commonplace in high-resolution direction finding systems, and uniform tapped delay lines (i.e., constant rate A/D converters) are the rule rather than the exception in digital signal processing systems. Such arrays possess many invariances, and are amenable to other types of analysis, which is one of the main reasons such structures are so prevalent. Recent developments in high-resolution algorithms of the signal/noise subspace genre including total least squares (TLS) ESPRIT applied to uniform linear arrays are summarized. ESPRIT is also shown to be a generalization of the root-MUSIC algorithm (applicable only to the case of uniform linear arrays of omni-directional sensors and unimodular cisoids). Comparisons with various estimator bounds, including CramerRao bounds, are presented.

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...

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.

High-Frequency Antenna Arrays and Coupling Structures

Data.gov (United States)

National Aeronautics and Space Administration — We are fabricating antenna arrays and coupling structure for frequencies in the 200-300 GHz frequency bands. The primary motivation of this work is to develop...

Vocal copying of individually distinctive signature whistles in bottlenose dolphins

Science.gov (United States)

King, Stephanie L.; Sayigh, Laela S.; Wells, Randall S.; Fellner, Wendi; Janik, Vincent M.

2013-01-01

Vocal learning is relatively common in birds but less so in mammals. Sexual selection and individual or group recognition have been identified as major forces in its evolution. While important in the development of vocal displays, vocal learning also allows signal copying in social interactions. Such copying can function in addressing or labelling selected conspecifics. Most examples of addressing in non-humans come from bird song, where matching occurs in an aggressive context. However, in other animals, addressing with learned signals is very much an affiliative signal. We studied the function of vocal copying in a mammal that shows vocal learning as well as complex cognitive and social behaviour, the bottlenose dolphin (Tursiops truncatus). Copying occurred almost exclusively between close associates such as mother–calf pairs and male alliances during separation and was not followed by aggression. All copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it. We found no evidence for the use of copying in aggression or deception. This use of vocal copying is similar to its use in human language, where the maintenance of social bonds appears to be more important than the immediate defence of resources. PMID:23427174

High-Performance Carbon Dioxide Electrocatalytic Reduction by Easily Fabricated Large-Scale Silver Nanowire Arrays.

Science.gov (United States)

Luan, Chuhao; Shao, Yang; Lu, Qi; Gao, Shenghan; Huang, Kai; Wu, Hui; Yao, Kefu

2018-05-17

An efficient and selective catalyst is in urgent need for carbon dioxide electroreduction and silver is one of the promising candidates with affordable costs. Here we fabricated large-scale vertically standing Ag nanowire arrays with high crystallinity and electrical conductivity as carbon dioxide electroreduction catalysts by a simple nanomolding method that was usually considered not feasible for metallic crystalline materials. A great enhancement of current densities and selectivity for CO at moderate potentials was achieved. The current density for CO ( j co ) of Ag nanowire array with 200 nm in diameter was more than 2500 times larger than that of Ag foil at an overpotential of 0.49 V with an efficiency over 90%. The origin of enhanced performances are attributed to greatly increased electrochemically active surface area (ECSA) and higher intrinsic activity compared to those of polycrystalline Ag foil. More low-coordinated sites on the nanowires which can stabilize the CO 2 intermediate better are responsible for the high intrinsic activity. In addition, the impact of surface morphology that induces limited mass transportation on reaction selectivity and efficiency of nanowire arrays with different diameters was also discussed.

Cyclotron-Resonance-Maser Arrays

International Nuclear Information System (INIS)

Kesar, A.; Lei, L.; Dikhtyar, V.; Korol, M.; Jerby, E.

1999-01-01

The cyclotron-resonance-maser (CRM) array [1] is a radiation source which consists of CRM elements coupled together under a common magnetic field. Each CRM-element employs a low-energy electron-beam which performs a cyclotron interaction with the local electromagnetic wave. These waves can be coupled together among the CRM elements, hence the interaction is coherently synchronized in the entire array. The implementation of the CRM-array approach may alleviate several technological difficulties which impede the development of single-beam gyro-devices. Furthermore, it proposes new features, such as the phased-array antenna incorporated in the CRM-array itself. The CRM-array studies may lead to the development of compact, high-power radiation sources operating at low-voltages. This paper introduces new conceptual schemes of CRM-arrays, and presents the progress in related theoretical and experimental studies in our laboratory. These include a multi-mode analysis of a CRM-array, and a first operation of this device with five carbon-fiber cathodes

Pathway-engineering for highly-aligned block copolymer arrays.

Science.gov (United States)

Choo, Youngwoo; Majewski, Paweł W; Fukuto, Masafumi; Osuji, Chinedum O; Yager, Kevin G

2017-12-21

While the ultimate driving force in self-assembly is energy minimization and the corresponding evolution towards equilibrium, kinetic effects can also play a very strong role. These kinetic effects, such as trapping in metastable states, slow coarsening kinetics, and pathway-dependent assembly, are often viewed as complications to be overcome. Here, we instead exploit these effects to engineer a desired final nano-structure in a block copolymer thin film, by selecting a particular ordering pathway through the self-assembly energy landscape. In particular, we combine photothermal shearing with high-temperature annealing to yield hexagonal arrays of block copolymer cylinders that are aligned in a single prescribed direction over macroscopic sample dimensions. Photothermal shearing is first used to generate a highly-aligned horizontal cylinder state, with subsequent thermal processing used to reorient the morphology to the vertical cylinder state in a templated manner. Finally, we demonstrate the successful transfer of engineered morphologies into inorganic replicas.

Improvements on Fresnel arrays for high contrast imaging

Science.gov (United States)

Wilhem, Roux; Laurent, Koechlin

2018-03-01

The Fresnel Diffractive Array Imager (FDAI) is based on a new optical concept for space telescopes, developed at Institut de Recherche en Astrophysique et Planétologie (IRAP), Toulouse, France. For the visible and near-infrared it has already proven its performances in resolution and dynamic range. We propose it now for astrophysical applications in the ultraviolet with apertures from 6 to 30 meters, aimed at imaging in UV faint astrophysical sources close to bright ones, as well as other applications requiring high dynamic range. Of course the project needs first a probatory mission at small aperture to validate the concept in space. In collaboration with institutes in Spain and Russia, we will propose to board a small prototype of Fresnel imager on the International Space Station (ISS), with a program combining technical tests and astrophysical targets. The spectral domain should contain the Lyman- α line ( λ = 121 nm). As part of its preparation, we improve the Fresnel array design for a better Point Spread Function in UV, presently on a small laboratory prototype working at 260 nm. Moreover, we plan to validate a new optical design and chromatic correction adapted to UV. In this article we present the results of numerical propagations showing the improvement in dynamic range obtained by combining and adapting three methods : central obturation, optimization of the bars mesh holding the Fresnel rings, and orthogonal apodization. We briefly present the proposed astrophysical program of a probatory mission with such UV optics.

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.

Advancements of ultra-high peak power laser diode arrays

Science.gov (United States)

Crawford, D.; Thiagarajan, P.; Goings, J.; Caliva, B.; Smith, S.; Walker, R.

2018-02-01

Enhancements of laser diode epitaxy in conjunction with process and packaging improvements have led to the availability of 1cm bars capable of over 500W peak power at near-infrared wavelengths (770nm to 1100nm). Advances in cooler design allow for multi-bar stacks with bar-to-bar pitches as low as 350μm and a scalable package architecture enabled a single diode assembly with total peak powers of over 1MegaWatt of peak power. With the addition of micro-optics, overall array brightness greater than 10kW/cm2 was achieved. Performance metrics of barbased diode lasers specifically engineered for high peak power and high brightness at wavelengths and pulse conditions commonly used to pump a variety of fiber and solid-state materials are presented.

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......RNAs with known killing effects as a model system to demonstrate that RPPA-based protein quantification can serve as substitute readout of cell viability, hereby reliably reflecting toxicity. In terms of automation, cell exposure, protein harvest, serial dilution and sample reformatting were performed using...

Integration of a highly ordered gold nanowires array with glucose oxidase for ultra-sensitive glucose detection

Energy Technology Data Exchange (ETDEWEB)

Cui, Jiewu [NanoScience and Sensor Technology Research Group, School of Applied Sciences and Engineering, Monash University, Gippsland Campus, Churchill 3842, VIC Australia (Australia); Laboratory of Functional Nanomaterials and Devices, School of Materials Science and Engineering, Hefei University of Technology, Hefei 230009, Anhui (China); Adeloju, Samuel B., E-mail: sam.adeloju@monash.edu [NanoScience and Sensor Technology Research Group, School of Applied Sciences and Engineering, Monash University, Gippsland Campus, Churchill 3842, VIC Australia (Australia); Wu, Yucheng, E-mail: ycwu@hfut.edu.cn [Laboratory of Functional Nanomaterials and Devices, School of Materials Science and Engineering, Hefei University of Technology, Hefei 230009, Anhui (China)

2014-01-27

Graphical abstract: -- Highlights: •Successfully synthesised highly-ordered gold nanowires array with an AAO template. •Fabricated an ultra-sensitive glucose nanobiosensor with the gold nanowires array. •Achieved sensitivity as high as 379.0 μA cm{sup −2} mM{sup −1} and detection limit as low as 50 nM. •Achieved excellent anti-interference with aid of Nafion membrane towards UA and AA. •Enabled successful detection and quantification of glucose in human blood serum. -- Abstract: A highly sensitive amperometric nanobiosensor has been developed by integration of glucose oxidase (GO{sub x}) with a gold nanowires array (AuNWA) by cross-linking with a mixture of glutaraldehyde (GLA) and bovine serum albumin (BSA). An initial investigation of the morphology of the synthesized AuNWA by field emission scanning electron microscopy (FESEM) and field emission transmission electron microscopy (FETEM) revealed that the nanowires array was highly ordered with rough surface, and the electrochemical features of the AuNWA with/without modification were also investigated. The integrated AuNWA–BSA–GLA–GO{sub x} nanobiosensor with Nafion membrane gave a very high sensitivity of 298.2 μA cm{sup −2} mM{sup −1} for amperometric detection of glucose, while also achieving a low detection limit of 0.1 μM, and a wide linear range of 5–6000 μM. Furthermore, the nanobiosensor exhibited excellent anti-interference ability towards uric acid (UA) and ascorbic acid (AA) with the aid of Nafion membrane, and the results obtained for the analysis of human blood serum indicated that the device is capable of glucose detection in real samples.

Homogeneous vertical ZnO nanorod arrays with high conductivity on an in situ Gd nanolayer

KAUST Repository

Flemban, Tahani H.; Singaravelu, Venkatesh; Devi, Assa Aravindh Sasikala; Roqan, Iman S.

2015-01-01

We demonstrate a novel, one-step, catalyst-free method for the production of size-controlled vertical highly conductive ZnO nanorod (NR) arrays with highly desirable characteristics by pulsed laser deposition using a Gd-doped ZnO target. Our study

In-situ preparation of Fe{sub 2}O{sub 3} hierarchical arrays on stainless steel substrate for high efficient catalysis

Energy Technology Data Exchange (ETDEWEB)

Yang, Zeheng, E-mail: zehengyang@hfut.edu.cn [School of Chemistry and Chemical Engineering, Anhui Key Laboratory of Controllable Chemical Reaction & Material Chemical Engineering, Hefei University of Technology, Hefei, Anhui 230009 (China); Wang, Kun; Shao, Zongming; Tian, Yuan [School of Chemistry and Chemical Engineering, Anhui Key Laboratory of Controllable Chemical Reaction & Material Chemical Engineering, Hefei University of Technology, Hefei, Anhui 230009 (China); Chen, Gongde [Department of Chemical and Environmental Engineering, University of California at Riverside, Riverside, CA 92521 (United States); Wang, Kai; Chen, Zhangxian; Dou, Yan [School of Chemistry and Chemical Engineering, Anhui Key Laboratory of Controllable Chemical Reaction & Material Chemical Engineering, Hefei University of Technology, Hefei, Anhui 230009 (China); Zhang, Weixin, E-mail: wxzhang@hfut.edu.cn [School of Chemistry and Chemical Engineering, Anhui Key Laboratory of Controllable Chemical Reaction & Material Chemical Engineering, Hefei University of Technology, Hefei, Anhui 230009 (China)

2017-02-15

Hierarchical array catalysts with micro/nano structures on substrates not only possess high reactivity from large surface area and suitable interface, but intensify mass transfer through shortening the diffusion paths of both reactants and products for high catalytic efficiency. Herein, we first demonstrate fabrication of Fe{sub 2}O{sub 3} hierarchical arrays grown on stainless-steel substrates via in-situ hydrothermal chemical oxidation followed by heat treatment in N{sub 2} atmosphere. As a Fenton-like catalyst, Fe{sub 2}O{sub 3} hierarchical arrays exhibit excellent catalytic activity and life cycle performance for methylene blue (MB) dye degradation in aqueous solution in the presence of H{sub 2}O{sub 2}. The Fe{sub 2}O{sub 3} catalyst with unique hierarchical structures and efficient transport channels, effectively activates H{sub 2}O{sub 2} to generate large quantity of • OH radicals and highly promotes reaction kinetics between MB and • OH radicals. Immobilization of hierarchical array catalysts on stainless-steel can prevent particles agglomeration, facilitate the recovery and reuse of the catalysts, which is expected promising applications in wastewater remediation. - Graphical abstract: The in-situ synthesis of Fe{sub 2}O{sub 3} hierarchical arrays on stainless-steel substrates was reported for the first time, which exhibit excellent catalytic activity performance for methylene blue (MB) dye degradation in aqueous solution in the presence of H{sub 2}O{sub 2}. - Highlights: • Fe{sub 2}O{sub 3} hierarchical arrays was prepared by in-situ hydrothermal chemical oxidation. • F{sup −} ions play an important role in the formation of the Fe{sub 2}O{sub 3} hierarchical arrays. • Fe{sub 2}O{sub 3} hierarchical arrays show high catalytic activity to methylene blue degradation.

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. Copyright © 2014 Elsevier Inc. All rights reserved.

Medipix3 array high performance read-out board for synchrotron research

International Nuclear Information System (INIS)

Tartoni, N.; Horswell, I. C.; Marchal, J.; Gimenez, E. N.; Fearn, R. D.; Silfhout, R. G. van

2010-01-01

The Medipix3 ASIC is one of the most advanced chip that is presently available to build photon counting area detectors. The capabilities of the chip include adjacent pixels charge summing circuitry to sort out the distortion due to charge sharing, simultaneous counting and read-out that enables frames to be acquired without dead time, the colour mode of operation that enables up to eight energy bands to be acquired. In order to fully exploit the capabilities of the Medipix3 chip in synchrotron research, a high performance electronic board capable of driving large arrays of chips is necessary. We propose a parallel read-out board of Medipix3 chip arrays with a scalable architecture that allows driving the Medipix3 chip in all of its modes of operation. The board functions include the control of the chip arrays, data formatting and data compression, the management of the communications with the data storage devices, and operation in various trigger modes. In addition to this the board will have some 'intelligence' embedded. This will add some very important features to the final detector such as pattern recognition, capability of variable frame duration as a function of the photon flux, feedback to other equipment and real time calculations of data relevant to experiments such as the autocorrelation function.

Integrated genomic classification of melanocytic tumors of the central nervous system using mutation analysis, copy number alterations and DNA methylation profiling.

Science.gov (United States)

Griewank, Klaus; Koelsche, Christian; van de Nes, Johannes A P; Schrimpf, Daniel; Gessi, Marco; Möller, Inga; Sucker, Antje; Scolyer, Richard A; Buckland, Michael E; Murali, Rajmohan; Pietsch, Torsten; von Deimling, Andreas; Schadendorf, Dirk

2018-06-11

In the central nervous system, distinguishing primary leptomeningeal melanocytic tumors from melanoma metastases and predicting their biological behavior solely using histopathologic criteria can be challenging. We aimed to assess the diagnostic and prognostic value of integrated molecular analysis. Targeted next-generation-sequencing, array-based genome-wide methylation analysis and BAP1 immunohistochemistry was performed on the largest cohort of central nervous system melanocytic tumors analyzed to date, incl. 47 primary tumors of the central nervous system, 16 uveal melanomas. 13 cutaneous melanoma metastasis and 2 blue nevus-like melanomas. Gene mutation, DNA-methylation and copy-number profiles were correlated with clinicopathological features. Combining mutation, copy-number and DNA-methylation profiles clearly distinguished cutaneous melanoma metastases from other melanocytic tumors. Primary leptomeningeal melanocytic tumors, uveal melanomas and blue nevus-like melanoma showed common DNA-methylation, copy-number alteration and gene mutation signatures. Notably, tumors demonstrating chromosome 3 monosomy and BAP1 alterations formed a homogeneous subset within this group. Integrated molecular profiling aids in distinguishing primary from metastatic melanocytic tumors of the central nervous system. Primary leptomeningeal melanocytic tumors, uveal melanoma and blue nevus-like melanoma share molecular similarity with chromosome 3 and BAP1 alterations markers of poor prognosis. Copyright ©2018, American Association for Cancer Research.

"Dear Teacher, Johnny Copied."

Science.gov (United States)

Jackson, Louise A.; And Others

1987-01-01

Presents the problem of intentional or unintentional plagiarism on the part of young students, several possible causes for it, and offers ways teachers can help students avoid copying and understand the value of owning one's writing. (JC)

38 CFR 1.526 - Copies of records and papers.

Science.gov (United States)

2010-07-01

... papers. 1.526 Section 1.526 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS... Copies of records and papers. (a) Any person desiring a copy of any record or document in the custody of... plain one-sided paper copies of a standard size (81/2″ × 11″; 81/2″ × 14″; 11″ × 14″) $0.15 per page...

The classical double copy for Taub–NUT spacetime

Energy Technology Data Exchange (ETDEWEB)

Luna, Andrés, E-mail: a.luna-godoy.1@research.gla.ac.uk [School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Monteiro, Ricardo, E-mail: monteiro@maths.ox.ac.uk [Mathematical Institute, University of Oxford, Oxford OX2 6GG, England (United Kingdom); O' Connell, Donal, E-mail: donal@staffmail.ed.ac.uk [Higgs Centre for Theoretical Physics, School of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106-4030 (United States); White, Chris D., E-mail: Christopher.White@glasgow.ac.uk [School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom)

2015-11-12

The double copy is a much-studied relationship between gauge theory and gravity amplitudes. Recently, this was generalised to an infinite family of classical solutions to Einstein's equations, namely stationary Kerr–Schild geometries. In this paper, we extend this to the Taub–NUT solution in gravity, which has a double Kerr–Schild form. The single copy of this solution is a dyon, whose electric and magnetic charges are related to the mass and NUT charge in the gravity theory. Finally, we find hints that the classical double copy extends to curved background geometries.

Shielding in ungated field emitter arrays

Energy Technology Data Exchange (ETDEWEB)

Harris, J. R. [U.S. Navy Reserve, Navy Operational Support Center New Orleans, New Orleans, Louisiana 70143 (United States); Jensen, K. L. [Code 6854, Naval Research Laboratory, Washington, D.C. 20375 (United States); Shiffler, D. A. [Directed Energy Directorate, Air Force Research Laboratory, Albuquerque, New Mexico 87117 (United States); Petillo, J. J. [Leidos, Billerica, Massachusetts 01821 (United States)

2015-05-18

Cathodes consisting of arrays of high aspect ratio field emitters are of great interest as sources of electron beams for vacuum electronic devices. The desire for high currents and current densities drives the cathode designer towards a denser array, but for ungated emitters, denser arrays also lead to increased shielding, in which the field enhancement factor β of each emitter is reduced due to the presence of the other emitters in the array. To facilitate the study of these arrays, we have developed a method for modeling high aspect ratio emitters using tapered dipole line charges. This method can be used to investigate proximity effects from similar emitters an arbitrary distance away and is much less computationally demanding than competing simulation approaches. Here, we introduce this method and use it to study shielding as a function of array geometry. Emitters with aspect ratios of 10{sup 2}–10{sup 4} are modeled, and the shielding-induced reduction in β is considered as a function of tip-to-tip spacing for emitter pairs and for large arrays with triangular and square unit cells. Shielding is found to be negligible when the emitter spacing is greater than the emitter height for the two-emitter array, or about 2.5 times the emitter height in the large arrays, in agreement with previously published results. Because the onset of shielding occurs at virtually the same emitter spacing in the square and triangular arrays, the triangular array is preferred for its higher emitter density at a given emitter spacing. The primary contribution to shielding in large arrays is found to come from emitters within a distance of three times the unit cell spacing for both square and triangular arrays.

29 CFR 1956.84 - Location of plan for inspection and copying.

Science.gov (United States)

2010-07-01

... 29 Labor 9 2010-07-01 2010-07-01 false Location of plan for inspection and copying. 1956.84... PLANS Illinois § 1956.84 Location of plan for inspection and copying. A copy of the plan may be inspected and copied during normal business hours at the following locations: Office of State Programs, U.S...

Isolation and characterization of novel mutations in the pSC101 origin that increase copy number

DEFF Research Database (Denmark)

Thompson, Mitchell G.; Sedaghatian, Nima; Barajas, Jesus F.

2018-01-01

/cell) based plasmids, respectively. The mutant copy number variants retained compatibility with p15a, pBBR, and ColE1 origins of replication. These pSC101 variants may be useful in future metabolic engineering efforts that require medium or high-copy vectors compatible with p15a- and ColE1-based plasmids....

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

29 CFR 1956.64 - Location of plan for inspection and copying.

Science.gov (United States)

2010-07-01

... 29 Labor 9 2010-07-01 2010-07-01 false Location of plan for inspection and copying. 1956.64... PLANS New Jersey § 1956.64 Location of plan for inspection and copying. A copy of the plan may be inspected and copied during normal business hours at the following locations: Office of State Programs, U.S...

High-efficiency VCSEL arrays for illumination and sensing in consumer applications

Science.gov (United States)

Seurin, Jean-Francois; Zhou, Delai; Xu, Guoyang; Miglo, Alexander; Li, Daizong; Chen, Tong; Guo, Baiming; Ghosh, Chuni

2016-03-01

There has been increased interest in vertical-cavity surface-emitting lasers (VCSELs) for illumination and sensing in the consumer market, especially for 3D sensing ("gesture recognition") and 3D image capture. For these applications, the typical wavelength range of interest is 830~950nm and power levels vary from a few milli-Watts to several Watts. The devices are operated in short pulse mode (a few nano-seconds) with fast rise and fall times for time-of-flight applications (ToF), or in CW/quasi-CW for structured light applications. In VCSELs, the narrow spectrum and its low temperature dependence allows the use of narrower filters and therefore better signal-to-noise performance, especially for outdoor applications. In portable devices (mobile devices, wearable devices, laptops etc.) the size of the illumination module (VCSEL and optics) is a primary consideration. VCSELs offer a unique benefit compared to other laser sources in that they are "surface-mountable" and can be easily integrated along with other electronics components on a printed circuit board (PCB). A critical concern is the power-conversion efficiency (PCE) of the illumination source operating at high temperatures (>50 deg C). We report on various VCSEL based devices and diffuser-integrated modules with high efficiency at high temperatures. Over 40% PCE was achieved in broad temperature range of 0-70 °C for either low power single devices or high power VCSEL arrays, with sub- nano-second rise and fall time. These high power VCSEL arrays show excellent reliability, with extracted mean-time-to-failure (MTTF) of over 500 years at 60 °C ambient temperature and 8W peak output.

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma

Science.gov (United States)

Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-01-01

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations. PMID:28533481

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma.

Science.gov (United States)

Wu, Ren-Chin; Chao, An-Shine; Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-07-18

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations.

Quantum copying and simplification of the quantum Fourier transform

Science.gov (United States)

Niu, Chi-Sheng

Theoretical studies of quantum computation and quantum information theory are presented in this thesis. Three topics are considered: simplification of the quantum Fourier transform in Shor's algorithm, optimal eavesdropping in the BB84 quantum cryptographic protocol, and quantum copying of one qubit. The quantum Fourier transform preceding the final measurement in Shor's algorithm is simplified by replacing a network of quantum gates with one that has fewer and simpler gates controlled by classical signals. This simplification results from an analysis of the network using the consistent history approach to quantum mechanics. The optimal amount of information which an eavesdropper can gain, for a given level of noise in the communication channel, is worked out for the BB84 quantum cryptographic protocol. The optimal eavesdropping strategy is expressed in terms of various quantum networks. A consistent history analysis of these networks using two conjugate quantum bases shows how the information gain in one basis influences the noise level in the conjugate basis. The no-cloning property of quantum systems, which is the physics behind quantum cryptography, is studied by considering copying machines that generate two imperfect copies of one qubit. The best qualities these copies can have are worked out with the help of the Bloch sphere representation for one qubit, and a quantum network is worked out for an optimal copying machine. If the copying machine does not have additional ancillary qubits, the copying process can be viewed using a 2-dimensional subspace in a product space of two qubits. A special representation of such a two-dimensional subspace makes possible a complete characterization of this type of copying. This characterization in turn leads to simplified eavesdropping strategies in the BB84 and the B92 quantum cryptographic protocols.

Assessment of High-Voltage Photovoltaic Technologies for the Design of a Direct Drive Hall Effect Thruster Solar Array

Science.gov (United States)

Mikellides, I. G.; Jongeward, G. A.; Schneider, T.; Carruth, M. R.; Peterson, T.; Kerslake, T. W.; Snyder, D.; Ferguson, D.; Hoskins, A.

2004-01-01

A three-year program to develop a Direct Drive Hall-Effect Thruster system (D2HET) begun in 2001 as part of the NASA Advanced Cross-Enterprise Technology Development initiative. The system, which is expected to reduce significantly the power processing, complexity, weight, and cost over conventional low-voltage systems, will employ solar arrays that operate at voltages higher than (or equal to) 300 V. The lessons learned from the development of the technology also promise to become a stepping-stone for the production of the next generation of power systems employing high voltage solar arrays. This paper summarizes the results from experiments conducted mainly at the NASA Marshal Space Flight Center with two main solar array technologies. The experiments focused on electron collection and arcing studies, when the solar cells operated at high voltages. The tests utilized small coupons representative of each solar array technology. A hollow cathode was used to emulate parts of the induced environment on the solar arrays, mostly the low-energy charge-exchange plasma (1012-1013 m-3 and 0.5-1 eV). Results and conclusions from modeling of electron collection are also summarized. The observations from the total effort are used to propose a preliminary, new solar array design for 2 kW and 30-40 kW class, deep space missions that may employ a single or a cluster of Hall- Effect thrusters.

Hydrophilicity Reinforced Adhesion of Anodic Alumina Oxide Template Films to Conducting Substrates for Facile Fabrication of Highly Ordered Nanorod Arrays.

Science.gov (United States)

Wang, Chuanju; Wang, Guiqiang; Yang, Rui; Sun, Xiangyu; Ma, Hui; Sun, Shuqing

2017-01-17

Arrays of ordered nanorods are of special interest in many fields. However, it remains challenging to obtain such arrays on conducting substrates in a facile manner. In this article, we report the fabrication of highly ordered and vertically standing nanorod arrays of both metals and semiconductors on Au films and indium tin oxide glass substrates without an additional layering. In this approach, following the simple hydrophilic treatment of an anodic aluminum oxide (AAO) membrane and conducting substrates, the AAO membrane was transferred onto the modified substrates with excellent adhesion. Subsequently, nanorod arrays of various materials were electrodeposited on the conducting substrates directly. This method avoids any expensive and tedious lithographic and ion milling process, which provides a simple yet robust route to the fabrication of arrays of 1D materials with high aspect ratio on conducting substrates, which shall pave the way for many practical applications in a range of fields.

A high precision time-to-digital converter based on multi-phase clock implemented within Field-Programmable-Gate-Array

International Nuclear Information System (INIS)

Chen Kai; Liu Shubin; An Qi

2010-01-01

In this paper, the design of a coarse-fine interpolation Time-to-Digital Converter (TDC) is implemented in an ALTERA's Cyclone FPGA. The carry-select chain performs as the tapped delay line. The Logic Array Block (LAB) having a propagation delay of 165 ps in the chain is synthesized as delay cell. Coarse counters triggered by the global clock count the more significant bits of the time data. This clock is also fed through the delay line, and LABs create the copies. The replicas are latched by the tested event signal, and the less significant bits are encoded from the latched binary bits. Single-shot resolution of the TDC can be 60 ps. The worst Differential Nonlinearity (DNL) is about 0.2 Least Significant Bit (LSB, 165 ps in this TDC module), and the Integral Nonlinearity (INL) is 0.6 LSB. In comparison with other architectures using the synchronous global clock to sample the taps, this architecture consumed less electric power and logic cells, and is more stable. (authors)

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.

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. PMID:22238659

[High-level expression of heterologous protein based on increased copy number in Saccharomyces cerevisiae].

Science.gov (United States)

Zhang, Xinjie; He, Peng; Tao, Yong; Yang, Yi

2013-11-04

High-level expression system of heterologous protein mediated by internal ribosome entry site (IRES) in Saccharomyces cerevisiae was constructed, which could be used for other applications of S. cerevisiae in metabolic engineering. We constructed co-expression cassette (promoter-mCherry-TIF4631 IRES-URA3) containing promoters Pilv5, Padh2 and Ptdh3 and recombined the co-expression cassette into the genome of W303-1B-A. The URA3+ transformants were selected. By comparing the difference in the mean florescence value of mCherry in transformants, the effect of three promoters was detected in the co-expression cassette. The copy numbers of the interested genes in the genome were determined by Real-Time PCR. We analyzed genetic stability by continuous subculturing transformants in the absence of selection pressure. To verify the application of co-expression cassette, the ORF of mCherry was replaced by beta-galactosidase (LACZ) and xylose reductase (XYL1). The enzyme activities and production of beta-galactosidase and xylose reductase were detected. mCherry has been expressed in the highest-level in transformants with co-expression cassette containing Pilv5 promoter. The highest copy number of DNA fragment integrating in the genome was 47 in transformants containing Pilv5. The engineering strains showed good genetic stability. Xylose reductase was successfully expressed in the co-expression cassette containing Pilv5 promoter and TIF4631 IRES. The highest enzyme activity was 0. 209 U/mg crude protein in the transformants WIX-10. Beta-galactosidase was also expressed successfully. The transformants that had the highest enzyme activity was WIL-1 and the enzyme activity was 12.58 U/mg crude protein. The system mediated by Pilv5 promoter and TIF4631 IRES could express heterologous protein efficiently in S. cerevisiae. This study offered a new strategy for expression of heterologous protein in S. cerevisiae and provided sufficient experimental evidence for metabolic engineering

rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus

Science.gov (United States)

Jansen, M. D.; Bosch, T.; Jansen, W. T. M.; Schouls, L.; Jonker, M. J.; Boel, C. H. E.

2016-01-01

The distinct epidemiology of original hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) and early community-associated MRSA (CA-MRSA) is largely unexplained. S. aureus carries either five or six rRNA operon copies. Evidence is provided for a scenario in which MRSA has adapted to the hospital environment by rRNA operon loss (six to five copies) due to antibiotic pressure. Early CA-MRSA, in contrast, results from wild-type methicillin-susceptible S. aureus (MSSA) that acquired mecA without loss of an rRNA operon. Of the HA-MRSA isolates (n = 77), 67.5% had five rRNA operon copies, compared to 23.2% of the CA-MRSA isolates (n = 69) and 7.7% of MSSA isolates (n = 195) (P operon copies. For all subsets, a correlation between resistance profile and rRNA copy number was found. Furthermore, we showed that in vitro antibiotic pressure may result in rRNA operon copy loss. We also showed that without antibiotic pressure, S. aureus isolates containing six rRNA copies are more fit than isolates with five copies. We conclude that HA-MRSA and cystic fibrosis isolates most likely have adapted to an environment with high antibiotic pressure by the loss of an rRNA operon copy. This loss has facilitated resistance development, which promoted survival in these niches. However, strain fitness decreased, which explains their lack of success in the community. In contrast, CA-MRSA isolates retained six rRNA operon copies, rendering them fitter and thereby able to survive and spread in the community. PMID:27671073

BI-ground microstrip array coil vs. conventional microstrip array coil for mouse imaging at 7 tesla

Science.gov (United States)

Hernández, Ricardo; Terrones, M. A. López; Jakob, P. M.

2012-10-01

At high field strengths, the need for more efficient high frequency coils has grown. Since the radiation losses and the interaction between coil and sample increase proportionally to field strength, the quality factor (Q) and the sensitivity of the coil decrease as consequence of these negative effects. Since Zhang et al proposed in 2001 a new surface coil based on the microstrip transmission line for high frequency, different Tx-Rx phased arrays based on this concept have been already introduced in animal and whole body systems at high field strengths, each of them with different modifications in order to get better field homogeneity, SNR or isolation between coil elements in the array. All these arrays for animals systems have been built for rat imaging. One of these modifications is called BI-Ground Microstrip Array Coil (BIGMAC). The implementation of a smaller two-channel BIGMAC design for mouse imaging is studied and its performance compared to a two-channel conventional Microstrip array at 7 Tesla, the higher isolation by using BIGMAC elements in comparison with conventional Microstrip elements is shown in this work.

Determination of beta-defensin genomic copy number in different populations

DEFF Research Database (Denmark)

Fode, Peder; Jespersgaard, Cathrine; Hardwick, Robert J

2011-01-01

There have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and ß-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with...

Supervised classification of combined copy number and gene expression data

Directory of Open Access Journals (Sweden)

Riccadonna S.

2007-12-01

Full Text Available In this paper we apply a predictive profiling method to genome copy number aberrations (CNA in combination with gene expression and clinical data to identify molecular patterns of cancer pathophysiology. Predictive models and optimal feature lists for the platforms are developed by a complete validation SVM-based machine learning system. Ranked list of genome CNA sites (assessed by comparative genomic hybridization arrays – aCGH and of differentially expressed genes (assessed by microarray profiling with Affy HG-U133A chips are computed and combined on a breast cancer dataset for the discrimination of Luminal/ ER+ (Lum/ER+ and Basal-like/ER- classes. Different encodings are developed and applied to the CNA data, and predictive variable selection is discussed. We analyze the combination of profiling information between the platforms, also considering the pathophysiological data. A specific subset of patients is identified that has a different response to classification by chromosomal gains and losses and by differentially expressed genes, corroborating the idea that genomic CNA can represent an independent source for tumor classification.

Dependently typed array programs don’t go wrong

NARCIS (Netherlands)

Trojahner, K.; Grelck, C.

2009-01-01

The array programming paradigm adopts multidimensional arrays as the fundamental data structures of computation. Array operations process entire arrays instead of just single elements. This makes array programs highly expressive and introduces data parallelism in a natural way. Array programming

Dependently typed array programs don't go wrong

NARCIS (Netherlands)

Trojahner, K.; Grelck, C.

2008-01-01

The array programming paradigm adopts multidimensional arrays as the fundamental data structures of computation. Array operations process entire arrays instead of just single elements. This makes array programs highly expressive and introduces data parallelism in a natural way. Array programming

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.

Carbon nanotube array actuators

International Nuclear Information System (INIS)

Geier, S; Mahrholz, T; Wierach, P; Sinapius, M

2013-01-01

Experimental investigations of highly vertically aligned carbon nanotubes (CNTs), also known as CNT-arrays, are the main focus of this paper. The free strain as result of an active material behavior is analyzed via a novel experimental setup. Previous test experiences of papers made of randomly oriented CNTs, also called Bucky-papers, reveal comparably low free strain. The anisotropy of aligned CNTs promises better performance. Via synthesis techniques like chemical vapor deposition (CVD) or plasma enhanced CVD (PECVD), highly aligned arrays of multi-walled carbon nanotubes (MWCNTs) are synthesized. Two different types of CNT-arrays are analyzed, morphologically first, and optically tested for their active characteristics afterwards. One type of the analyzed arrays features tube lengths of 750–2000 μm with a large variety of diameters between 20 and 50 nm and a wave-like CNT-shape. The second type features a maximum, almost uniform, length of 12 μm and a constant diameter of 50 nm. Different CNT-lengths and array types are tested due to their active behavior. As result of the presented tests, it is reported that the quality of orientation is the most decisive property for excellent active behavior. Due to their alignment, CNT-arrays feature the opportunity to clarify the actuation mechanism of architectures made of CNTs. (paper)

High frequency P(VDF-TrFE) copolymer broadband annular array ultrasound transducers using high density flexible circuit interconnect

Science.gov (United States)

Gottlieb, Emanuel J.; Cannata, Jonathan M.; Hu, Chang Hong; Shung, K. K.

2005-04-01

A kerfless eight element high frequency ultrasound annular array transducer using 9 μm P(VDF-TrFE) bonded to a high density flexible interconnect was fabricated. The flexible circuit composed of Kapton polyimide film with gold electrode pattern of equal area annuli apertures on the top side of a 50 μm thick Kapton polyimide film. Each element had several 30 μm diameter electroplated vias that connected to electrode traces on the bottom side of the Kapton polyimide film. There was a 30 μm spacing between elements. The total aperture of the array was 3.12 mm. The transducer's performance has been modeled by implementing the Redwood version of the Mason model into PSpice and using the Krimholtz, Leedom and Matthaei (KLM) model utilized in the commercial software PiezoCAD. The transducer"s performance was evaluated by measuring the electrical impedance with a HP 4194 impedance analyzer, pulse echo response using a Panametrics 5900 pulser/receiver and crosstalk measurement for each element in the array. The measured electrical impedance for each element was 540 Ω and -84° phase. In order to improve device sensitivity an inductor was attached in series with each element to reduce the insertion loss to 33 dB. The measured average center frequency and bandwidth of each element was 55 MHz and 50% respectively. The measured crosstalk at the center frequency was -45 dB in water.

Array scanner as microdensitometer surrogate: a deal with the devil or . . . a great deal?

Science.gov (United States)

Williams, Donald R.

2005-01-01

Inexpensive and easy-to-use linear and area-array scanners have frequently substituted as densitometers for low-frequency (i.e., large-area) hard copy image metrology. A number of workers and standards committees1 have in fact advocated such use. Increasingly, scanners are also being tasked for high spatial frequency, image microstructure metrology (which is usually reserved for high-performance microdensitometers that use microscope optics), photomultiplier tubes (PMT), and log amps. It is hard to resist their adoption for such use, given the convenience level. The high speed, large scan areas, auto-focus, discomfiting low cost, and low operator skill requirements of commercial off-the-shelf (COTS) scanners makes one question if their use for such purpose is somehow too good to be true. To confidently judge their limitations requires a comprehensive signal and noise spatial frequency performance evaluation with respect to available driver options. This paper will outline and demonstrate evaluation techniques that use existing ISO metrology standards for modulation transfer function (MTF), noise, and dynamic range with a comparison to the performance of a Photometric Data Systems (PDS) microdensitometer.

Array scanner as microdensitometer surrogate: a deal with the devil or… a great deal?

Science.gov (United States)

Williams, Donald R.

2004-10-01

Inexpensive and easy-to-use linear and area-array scanners have frequently substituted as densitometers for low-frequency (i.e., large-area) hard copy image metrology. A number of workers and standards committees1 have in fact advocated such use. Increasingly, scanners are also being tasked for high spatial frequency, image microstructure metrology (which is usually reserved for high-performance microdensitometers that use microscope optics), photomultiplier tubes (PMT), and log amps. It is hard to resist their adoption for such use, given the convenience level. The high speed, large scan areas, auto-focus, discomfiting low cost, and low operator skill requirements of commercial off-the-shelf (COTS) scanners makes one question if their use for such purpose is somehow too good to be true. To confidently judge their limitations requires a comprehensive signal and noise spatial frequency performance evaluation with respect to available driver options. This paper will outline and demonstrate evaluation techniques that use existing ISO metrology standards for modulation transfer function (MTF), noise, and dynamic range with a comparison to the performance of a Photometric Data Systems (PDS) microdensitometer.

Study on the near-field non-linearity (SMILE) of high power diode laser arrays

Science.gov (United States)

Zhang, Hongyou; Jia, Yangtao; Li, Changxuan; Zah, Chung-en; Liu, Xingsheng

2018-02-01

High power laser diodes have been found a wide range of industrial, space, medical applications, characterized by high conversion efficiency, small size, light weight and a long lifetime. However, due to thermal induced stress, each emitter in a semiconductor laser bar or array is displaced along p-n junction, resulting of each emitter is not in a line, called Near-field Non-linearity. Near-field Non-linearity along laser bar (also known as "SMILE") determines the outcome of optical coupling and beam shaping [1]. The SMILE of a laser array is the main obstacle to obtain good optical coupling efficiency and beam shaping from a laser array. Larger SMILE value causes a larger divergence angle and a wider line after collimation and focusing, respectively. In this letter, we simulate two different package structures based on MCC (Micro Channel Cooler) with Indium and AuSn solders, including the distribution of normal stress and the SMILE value. According to the theoretical results, we found the distribution of normal stress on laser bar shows the largest in the middle and drops rapidly near both ends. At last, we did another experiment to prove that the SMILE value of a laser bar was mainly affected by the die bonding process, rather than the operating condition.

The ASTRI mini-array within the future Cherenkov Telescope Array

Directory of Open Access Journals (Sweden)

Vercellone Stefano

2016-01-01

Full Text Available The Cherenkov Telescope Array (CTA is a large collaborative effort aimed at the design and operation of an observatory dedicated to very high-energy gamma-ray astrophysics in the energy range from a few tens of GeV to above 100 TeV, which will yield about an order of magnitude improvement in sensitivity with respect to the current major arrays (H.E.S.S., MAGIC, and VERITAS. Within this framework, the Italian National Institute for Astrophysics is leading the ASTRI project, whose main goals are the design and installation on Mt. Etna (Sicily of an end-to-end dual-mirror prototype of the CTA small size telescope (SST and the installation at the CTA Southern site of a dual-mirror SST mini-array composed of nine units with a relative distance of about 300 m. The innovative dual-mirror Schwarzschild-Couder optical solution adopted for the ASTRI Project allows us to substantially reduce the telescope plate-scale and, therefore, to adopt silicon photo-multipliers as light detectors. The ASTRI mini-array is a wider international effort. The mini-array, sensitive in the energy range 1–100 TeV and beyond with an angular resolution of a few arcmin and an energy resolution of about 10–15%, is well suited to study relatively bright sources (a few × 10−12 erg cm−2 s−1 at 10 TeV at very high energy. Prominent sources such as extreme blazars, nearby well-known BL Lac objects, Galactic pulsar wind nebulae, supernovae remnants, micro-quasars, and the Galactic Center can be observed in a previously unexplored energy range. The ASTRI mini-array will extend the current IACTs sensitivity well above a few tens of TeV and, at the same time, will allow us to compare our results on a few selected targets with those of current (HAWC and future high-altitude extensive air-shower detectors.

Functional impact of global rare copy number variation in autism spectrum disorders.

Science.gov (United States)

Pinto, Dalila; Pagnamenta, Alistair T; Klei, Lambertus; Anney, Richard; Merico, Daniele; Regan, Regina; Conroy, Judith; Magalhaes, Tiago R; Correia, Catarina; Abrahams, Brett S; Almeida, Joana; Bacchelli, Elena; Bader, Gary D; Bailey, Anthony J; Baird, Gillian; Battaglia, Agatino; Berney, Tom; Bolshakova, Nadia; Bölte, Sven; Bolton, Patrick F; Bourgeron, Thomas; Brennan, Sean; Brian, Jessica; Bryson, Susan E; Carson, Andrew R; Casallo, Guillermo; Casey, Jillian; Chung, Brian H Y; Cochrane, Lynne; Corsello, Christina; Crawford, Emily L; Crossett, Andrew; Cytrynbaum, Cheryl; Dawson, Geraldine; de Jonge, Maretha; Delorme, Richard; Drmic, Irene; Duketis, Eftichia; Duque, Frederico; Estes, Annette; Farrar, Penny; Fernandez, Bridget A; Folstein, Susan E; Fombonne, Eric; Freitag, Christine M; Gilbert, John; Gillberg, Christopher; Glessner, Joseph T; Goldberg, Jeremy; Green, Andrew; Green, Jonathan; Guter, Stephen J; Hakonarson, Hakon; Heron, Elizabeth A; Hill, Matthew; Holt, Richard; Howe, Jennifer L; Hughes, Gillian; Hus, Vanessa; Igliozzi, Roberta; Kim, Cecilia; Klauck, Sabine M; Kolevzon, Alexander; Korvatska, Olena; Kustanovich, Vlad; Lajonchere, Clara M; Lamb, Janine A; Laskawiec, Magdalena; Leboyer, Marion; Le Couteur, Ann; Leventhal, Bennett L; Lionel, Anath C; Liu, Xiao-Qing; Lord, Catherine; Lotspeich, Linda; Lund, Sabata C; Maestrini, Elena; Mahoney, William; Mantoulan, Carine; Marshall, Christian R; McConachie, Helen; McDougle, Christopher J; McGrath, Jane; McMahon, William M; Merikangas, Alison; Migita, Ohsuke; Minshew, Nancy J; Mirza, Ghazala K; Munson, Jeff; Nelson, Stanley F; Noakes, Carolyn; Noor, Abdul; Nygren, Gudrun; Oliveira, Guiomar; Papanikolaou, Katerina; Parr, Jeremy R; Parrini, Barbara; Paton, Tara; Pickles, Andrew; Pilorge, Marion; Piven, Joseph; Ponting, Chris P; Posey, David J; Poustka, Annemarie; Poustka, Fritz; Prasad, Aparna; Ragoussis, Jiannis; Renshaw, Katy; Rickaby, Jessica; Roberts, Wendy; Roeder, Kathryn; Roge, Bernadette; Rutter, Michael L; Bierut, Laura J; Rice, John P; Salt, Jeff; Sansom, Katherine; Sato, Daisuke; Segurado, Ricardo; Sequeira, Ana F; Senman, Lili; Shah, Naisha; Sheffield, Val C; Soorya, Latha; Sousa, Inês; Stein, Olaf; Sykes, Nuala; Stoppioni, Vera; Strawbridge, Christina; Tancredi, Raffaella; Tansey, Katherine; Thiruvahindrapduram, Bhooma; Thompson, Ann P; Thomson, Susanne; Tryfon, Ana; Tsiantis, John; Van Engeland, Herman; Vincent, John B; Volkmar, Fred; Wallace, Simon; Wang, Kai; Wang, Zhouzhi; Wassink, Thomas H; Webber, Caleb; Weksberg, Rosanna; Wing, Kirsty; Wittemeyer, Kerstin; Wood, Shawn; Wu, Jing; Yaspan, Brian L; Zurawiecki, Danielle; Zwaigenbaum, Lonnie; Buxbaum, Joseph D; Cantor, Rita M; Cook, Edwin H; Coon, Hilary; Cuccaro, Michael L; Devlin, Bernie; Ennis, Sean; Gallagher, Louise; Geschwind, Daniel H; Gill, Michael; Haines, Jonathan L; Hallmayer, Joachim; Miller, Judith; Monaco, Anthony P; Nurnberger, John I; Paterson, Andrew D; Pericak-Vance, Margaret A; Schellenberg, Gerard D; Szatmari, Peter; Vicente, Astrid M; Vieland, Veronica J; Wijsman, Ellen M; Scherer, Stephen W; Sutcliffe, James S; Betancur, Catalina

2010-07-15

The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.

A High Power InGaN-Based Blue-Violet Laser Diode Array with a Broad-Area Stripe

International Nuclear Information System (INIS)

Chen Ping; Zhao De-Gang; Feng Mei-Xin; Jiang De-Sheng; Liu Zong-Shun; Yang Hui; Zhang Li-Qun; Li De-Yao; Liu Jian-Ping; Wang Hui; Zhu Jian-Jun; Zhang Shu-Ming; Zhang Bao-Shun

2013-01-01

An array of high power InGaN/GaN multi-quantum-well laser diodes with a broad waveguide is fabricated. The laser diode structure is grown on a GaN substrate by metal-organic chemical vapor deposition. The laser diode array consists of five emitter stripes which share common electrodes on one laser chip. The electrical and optical characteristics of the laser diode array are investigated under the pulse current injection with 10kHz frequency and 100 ns pulse width. The laser diode array emits at the wavelength of 409 nm, which is located in the blue-violet region, and the threshold current is 2.9 A. The maximum output light peak power is measured to be 7.5 W at the wavelength of 411.8 nm under the current of 25 A

A genomic copy number signature predicts radiation exposure in post-Chernobyl breast cancer.

Science.gov (United States)

Wilke, Christina M; Braselmann, Herbert; Hess, Julia; Klymenko, Sergiy V; Chumak, Vadim V; Zakhartseva, Liubov M; Bakhanova, Elena V; Walch, Axel K; Selmansberger, Martin; Samaga, Daniel; Weber, Peter; Schneider, Ludmila; Fend, Falko; Bösmüller, Hans C; Zitzelsberger, Horst; Unger, Kristian

2018-04-16

Breast cancer is the second leading cause of cancer death among women worldwide and besides life style, age and genetic risk factors, exposure to ionizing radiation is known to increase the risk for breast cancer. Further, DNA copy number alterations (CNAs), which can result from radiation-induced double-strand breaks, are frequently occurring in breast cancer cells. We set out to identify a signature of CNAs discriminating breast cancers from radiation-exposed and non-exposed female patients. We analyzed resected breast cancer tissues from 68 exposed female Chernobyl clean-up workers and evacuees and 68 matched non-exposed control patients for CNAs by array comparative genomic hybridization analysis (aCGH). Using a stepwise forward-backward selection approach a non-complex CNA signature, that is, less than ten features, was identified in the training data set, which could be subsequently validated in the validation data set (p value < 0.05). The signature consisted of nine copy number regions located on chromosomal bands 7q11.22-11.23, 7q21.3, 16q24.3, 17q21.31, 20p11.23-11.21, 1p21.1, 2q35, 2q35, 6p22.2. The signature was independent of any clinical characteristics of the patients. In all, we identified a CNA signature that has the potential to allow identification of radiation-associated breast cancer at the individual level. © 2018 UICC.