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Sample records for microarray-based allele-specific hybridization

  1. Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.

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    Lena Poulsen

    Full Text Available BACKGROUND: The development of microarray-based genetic tests for diseases that are caused by known mutations is becoming increasingly important. The key obstacle to developing functional genotyping assays is that such mutations need to be genotyped regardless of their location in genomic regions. These regions include large variations in G+C content, and structural features like hairpins. METHODS/FINDINGS: We describe a rational, stable method for screening and combining assay conditions for the genetic analysis of 42 Phenylketonuria-associated mutations in the phenylalanine hydroxylase gene. The mutations are located in regions with large variations in G+C content (20-75%. Custom-made microarrays with different lengths of complementary probe sequences and spacers were hybridized with pooled PCR products of 12 exons from each of 38 individual patient DNA samples. The arrays were washed with eight buffers with different stringencies in a custom-made microfluidic system. The data were used to assess which parameters play significant roles in assay development. CONCLUSIONS: Several assay development methods found suitable probes and assay conditions for a functional test for all investigated mutation sites. Probe length, probe spacer length, and assay stringency sufficed as variable parameters in the search for a functional multiplex assay. We discuss the optimal assay development methods for several different scenarios.

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

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

    2011-01-01

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

  3. Allele-specific physical interactions regulate the heterotic traits in hybrids of Arabidopsis thaliana ecotypes

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    Babita Singh

    2017-10-01

    Full Text Available Heterosis is an important phenomenon for the breeding in agricultural crops as it influences yield related traits such as biomass yield, seed number and weight, adaptive and reproductive traits. However, the level of heterosis greatly varies for different traits and different genotypes. The present study focuses on identification of physical interactions between alleles and their role in transcriptional regulation in heterotic plants. Here, we used two Arabidopsis ecotypes; Col-0 and C24 as parent for crosses. We performed crossing between these ecotypes and screened the F1 hybrids on the basis of different SSR markers. Further, we used Hi-C to capture intra- and inter-chromosomal physical interactions between alleles on genome-wide level. Then, we identified allele-specific chromatin interactions and constructed genome-wide allele-specific contact maps at different resolutions for the entire chromosome. We also performed RNA-seq of hybrids and their parents. RNA-seq analysis identified several differentially expressed genes and non-additively expressed genes in hybrids with respect to their parents. Further, to understand the biological significance of these chromatin interactions, we annotated these interactions and correlated with the transcriptome data. Thus, our study provides alleles-specific chromatin interactions in genome-wide fashion which play a crucial role in regulation of different genes that may be important for heterosis.

  4. Hybrid sterility and evolution in Hawaiian Drosophila: differential gene and allele-specific expression analysis of backcross males.

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    Brill, E; Kang, L; Michalak, K; Michalak, P; Price, D K

    2016-08-01

    The Hawaiian Drosophila are an iconic example of sequential colonization, adaptive radiation and speciation on islands. Genetic and phenotypic analysis of closely related species pairs that exhibit incomplete reproductive isolation can provide insights into the mechanisms of speciation. Drosophila silvestris from Hawai'i Island and Drosophila planitibia from Maui are two closely related allopatric Hawaiian picture-winged Drosophila that produce sterile F1 males but fertile F1 females, a pattern consistent with Haldane's rule. Backcrossing F1 hybrid females between these two species to parental species gives rise to recombinant males with three distinct sperm phenotypes despite a similar genomic background: motile sperm, no sperm (sterile), and immotile sperm. We found that these three reproductive morphologies of backcross hybrid males produce divergent gene expression profiles in testes, as measured with RNA sequencing. There were a total of 71 genes significantly differentially expressed between backcross males with no sperm compared with those backcross males with motile sperm and immotile sperm, but no significant differential gene expression between backcross males with motile sperm and backcross males with immotile sperm. All of these genes were underexpressed in males with no sperm, including a number of genes with previously known activities in adult testis. An allele-specific expression analysis showed overwhelmingly more cis-divergent than trans-divergent genes, with no significant difference in the ratio of cis- and trans-divergent genes among the sperm phenotypes. Overall, the results indicate that the regulation of gene expression involved in sperm production likely diverged relatively rapidly between these two closely related species.

  5. Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa.

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    Fangjun Zhu

    Full Text Available The all-female Amazon molly (Poecilia formosa is the result of a hybridization of the Atlantic molly (P. mexicana and the sailfin molly (P. latipinna approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor.

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

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    Jing Liu

    2011-01-01

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

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

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

    2008-01-15

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

  8. Allele specific hybridization using oligonucleotide probes of very high specific activity: Discrimination of the human β/sup A/ and β/sup S/-globin genes

    International Nuclear Information System (INIS)

    Studencki, A.B.; Wallace, R.B.

    1984-01-01

    The repair activity of E. coli DNA polymerase I (Klenow fragment) was used to prepare nonadecanucleotide hybridization probes which were complementary either to the normal human β-globin (β/sup A/) or to the sickle cell human β-globin (β/sup S/) gene. Template directed polymerization of highly radiolabeled α-/sup 32/P-deoxyribonucleoside triphosphates (3200, 5000 and/or 7800 Ci/mmol) onto nonamer and decamer primers produced probes with specific activities ranging from 1.0 - 2.0 x 10/sup 10/ dpm/μg. The extremely high specific activities of these probes made it possible to detect the β/sup A/ and β/sup S/ single copy gene sequences in as little as 1 μg of total human genomic DNA as well as to discriminate between the homozygous and heterozygous states. This means that it was possible to detect 0.5 - 1.0 x 10/sup -18/ moles of a given single copy sequence

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

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

    2012-03-01

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

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

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    Yamamoto, F; Yamamoto, M

    2004-07-01

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

  11. ALEA: a toolbox for allele-specific epigenomics analysis.

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    Younesy, Hamid; Möller, Torsten; Heravi-Moussavi, Alireza; Cheng, Jeffrey B; Costello, Joseph F; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven J M

    2014-04-15

    The assessment of expression and epigenomic status using sequencing based methods provides an unprecedented opportunity to identify and correlate allelic differences with epigenomic status. We present ALEA, a computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. ALEA provides a customizable pipeline of command line tools for allele-specific analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. The pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data. The package, test data and usage instructions are available online at http://www.bcgsc.ca/platform/bioinfo/software/alea CONTACT: : mkarimi1@interchange.ubc.ca or sjones@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Allele specific expression and methylation in the bumblebee, Bombus terrestris

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    Zoë Lonsdale

    2017-09-01

    Full Text Available The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the as yet unquantified role of genetic cis effects in insect allele specific methylation and expression.

  13. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

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    Carol A Soderlund

    Full Text Available Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor, where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense, and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available

  14. A small asparagine-rich protein required for S-allele-specific pollen rejection in Nicotiana.

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    McClure, B; Mou, B; Canevascini, S; Bernatzky, R

    1999-11-09

    Although S-locus RNases (S-RNases) determine the specificity of pollen rejection in self-incompatible (SI) solanaceous plants, they alone are not sufficient to cause S-allele-specific pollen rejection. To identify non-S-RNase sequences that are required for pollen rejection, a Nicotiana alata cDNA library was screened by differential hybridization. One clone, designated HT, hybridized strongly to RNA from N. alata styles but not to RNA from Nicotiana plumbaginifolia, a species known to lack one or more factors necessary for S-allele-specific pollen rejection. Sequence analysis revealed a 101-residue ORF including a putative secretion signal and an asparagine-rich domain near the C terminus. RNA blot analysis showed that the HT-transcript accumulates in the stigma and style before anthesis. The timing of HT-expression lags slightly behind S(C10)-RNase in SI N. alata S(C10)S(C10) and is well correlated with the onset of S-allele-specific pollen rejection in the style. An antisense-HT construct was prepared to test for a role in pollen rejection. Transformed (N. plumbaginifolia x SI N. alata S(C10)S(C10)) hybrids with reduced levels of HT-protein continued to express S(C10)-RNase but failed to reject S(C10)-pollen. Control hybrids expressing both S(C10)-RNase and HT-protein showed a normal S-allele-specific pollen rejection response. We conclude that HT-protein is directly implicated in pollen rejection.

  15. Allele-specific deletions in mouse tumors identify Fbxw7 as germline modifier of tumor susceptibility.

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    Jesus Perez-Losada

    Full Text Available Genome-wide association studies (GWAS have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5-10%. There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p = 0.001, but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility.

  16. Allele-Specific DNA Methylation Detection by Pyrosequencing®

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    Kristensen, Lasse Sommer; Johansen, Jens Vilstrup; Grønbæk, Kirsten

    2015-01-01

    DNA methylation is an epigenetic modification that plays important roles in healthy as well as diseased cells, by influencing the transcription of genes. In spite the fact that human somatic cells are diploid, most of the currently available methods for the study of DNA methylation do not provide......-effective protocol for allele-specific DNA methylation detection based on Pyrosequencing(®) of methylation-specific PCR (MSP) products including a single nucleotide polymorphism (SNP) within the amplicon....

  17. 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/.

  18. Allele-specific MMP-3 transcription under in vivo conditions

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    Chaoyong, Zhu [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Odeberg, Jacob [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm (Sweden); Hamsten, Anders [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Eriksson, Per [Atherosclerosis Research Unit, King Gustav V Research Institute, Department of Medicine, Karolinska Institute, Stockholm (Sweden)

    2006-09-29

    A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1{beta}, the haplotype containing the 5A-allele was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

  19. QuASAR: quantitative allele-specific analysis of reads.

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    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. DNA microarray-based PCR ribotyping of Clostridium difficile.

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    Schneeberg, Alexander; Ehricht, Ralf; Slickers, Peter; Baier, Vico; Neubauer, Heinrich; Zimmermann, Stefan; Rabold, Denise; Lübke-Becker, Antina; Seyboldt, Christian

    2015-02-01

    This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of Clostridium difficile strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized C. difficile isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray. C. difficile strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50 C. difficile field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis.

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    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-07-01

    Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5'- and 3'-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients.Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3'-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5'-UTR polymorphisms).For neither the 3'- nor the 5'-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance.The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold, in our population

  2. Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris

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    Harindra E. Amarasinghe

    2015-07-01

    Full Text Available Methylation has previously been associated with allele specific expression in ants. Recently, we found methylation is important in worker reproduction in the bumblebee Bombus terrestris. Here we searched for allele specific expression in twelve genes associated with worker reproduction in bees. We found allele specific expression in Ecdysone 20 monooxygenase and IMP-L2-like. Although we were unable to confirm a genetic or epigenetic cause for this allele specific expression, the expression patterns of the two genes match those predicted for imprinted genes.

  3. An allele-specific polymerase chain reaction assay for the ...

    Indian Academy of Sciences (India)

    Unknown

    designated as species A, B (Green and Miles 1980), C. (Subbarao et al 1983), ... 3 | September 2004. O P Singh et al. 276 able to distinguish species A from species B/C when sin- gle mosquito-extract was diluted to 1/200. However such hybridization assay .... in Rameshwaram Island and Sri Lanka only) are not pre- sent.

  4. Allele-specific marker generation and linkage mapping on the Xiphophorus sex chromosomes.

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    Woolcock, B; Kazianis, S; Lucito, R; Walter, R B; Kallman, K D; Morizot, D C; Vielkind, J R

    2006-01-01

    There is great interest in the sex chromosomes of Xiphophorus fishes because both WY/YY and XX/XY sex-determining mechanisms function in these species, with at least one taxon possessing all three types of sex chromosomes, and because in certain interspecific hybrids melanoma arises as a consequence of inheritance of the sex-linked macromelanophore determining locus (MDL). Representational difference analysis (RDA) has been used to clone two sequences from the sex-determining region of X. maculatus, including a cholinergic receptor, nicotinic, delta polypeptide (CHRND) orthologue. Allele-specific assays for these sequences, as well as for the sex-linked XMRK1 and XMRK2 genes, were developed to distinguish W, X, and Y chromosomes derived from a X. maculatus (XX/XY) strain and a X. helleri (WY/YY) strain. Linkage mapping localized these markers to linkage group (LG) 24. No recombinants were observed between XMRK2 and MDL, confirming a role for XMRK2 in macromelanophore development. Although the master sex-determining (SD) locus certainly resides on Xiphophorus LG 24, autosomal loci are probably involved in sex determination as well, as indicated by the abnormal sex ratios in the backcross hybrids that contrast theoretical predictions based on LG 24 genotyping. Marker development and allelic discrimination on the Xiphophorus sex chromosomes should prove highly useful for studies that utilize this genus as an animal model.

  5. Allele-Specific Alternative mRNA processing (ASARP) | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    A software pipeline for prediction of allele-specific alternative RNA processing events using single RNA-seq data. The current version focuses on prediction of alternative splicing and alternative polyadenylation modulated by genetic variants.

  6. Identification of listeria species isolated in Tunisia by Microarray based assay : results of a preliminary study

    International Nuclear Information System (INIS)

    Hmaied, Fatma; Helel, Salma; Barkallah, Insaf; Leberre, V.; Francois, J.M.; Kechrid, A.

    2008-01-01

    Microarray-based assay is a new molecular approach for genetic screening and identification of microorganisms. We have developed a rapid microarray-based assay for the reliable detection and discrimination of Listeria spp. in food and clinical isolates from Tunisia. The method used in the present study is based on the PCR amplification of a virulence factor gene (iap gene). the PCR mixture contained cyanine Cy5labeled dCTP. Therefore, The PCR products were fluorescently labeled. The presence of multiple species-specific sequences within the iap gene enabled us to design different oligoprobes per species. The species-specific sequences of the iap gene used in this study were obtained from genBank and then aligned for phylogenetic analysis in order to identify and retrieve the sequences of homologues of the amplified iap gene analysed. 20 probes were used for detection and identification of 22 food isolates and clinical isolates of Listeria spp (L. monocytogenes, L. ivanovi), L. welshimeri, L. seeligeri, and L. grayi). Each bacterial gene was identified by hybridization to oligoprobes specific for each Listeria species and immobilized on a glass surface. The microarray analysis showed that 5 clinical isolates and 2 food isolates were identified listeria monocytogenes. Concerning the remaining 15 food isolates; 13 were identified listeria innocua and 2 isolates could not be identified by microarray based assay. Further phylogenetic and molecular analysis are required to design more species-specific probes for the identification of Listeria spp. Microarray-based assay is a simple and rapid method used for Listeria species discrimination

  7. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

    Directory of Open Access Journals (Sweden)

    Ni Yunyun

    2012-09-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs have been associated with many aspects of human development and disease, and many non-coding SNPs associated with disease risk are presumed to affect gene regulation. We have previously shown that SNPs within transcription factor binding sites can affect transcription factor binding in an allele-specific and heritable manner. However, such analysis has relied on prior whole-genome genotypes provided by large external projects such as HapMap and the 1000 Genomes Project. This requirement limits the study of allele-specific effects of SNPs in primary patient samples from diseases of interest, where complete genotypes are not readily available. Results In this study, we show that we are able to identify SNPs de novo and accurately from ChIP-seq data generated in the ENCODE Project. Our de novo identified SNPs from ChIP-seq data are highly concordant with published genotypes. Independent experimental verification of more than 100 sites estimates our false discovery rate at less than 5%. Analysis of transcription factor binding at de novo identified SNPs revealed widespread heritable allele-specific binding, confirming previous observations. SNPs identified from ChIP-seq datasets were significantly enriched for disease-associated variants, and we identified dozens of allele-specific binding events in non-coding regions that could distinguish between disease and normal haplotypes. Conclusions Our approach combines SNP discovery, genotyping and allele-specific analysis, but is selectively focused on functional regulatory elements occupied by transcription factors or epigenetic marks, and will therefore be valuable for identifying the functional regulatory consequences of non-coding SNPs in primary disease samples.

  8. QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.

    Science.gov (United States)

    Kalita, Cynthia A; Moyerbrailean, Gregory A; Brown, Christopher; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2018-03-01

    The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRAs), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets. We have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data, we found 602 SNPs with significant (false discovery rate 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high-throughput reporter assays. http://github.com/piquelab/QuASAR/tree/master/mpra. fluca@wayne.edu or rpique@wayne.edu. Supplementary data are available online at Bioinformatics. © The Author (2017). Published by

  9. Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection.

    Science.gov (United States)

    Hommatsu, Manami; Okahashi, Hisamitsu; Ohta, Keisuke; Tamai, Yusuke; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

    2013-01-01

    A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.

  10. Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations.

    Science.gov (United States)

    Jeselsohn, Rinath; Bergholz, Johann S; Pun, Matthew; Cornwell, MacIntosh; Liu, Weihan; Nardone, Agostina; Xiao, Tengfei; Li, Wei; Qiu, Xintao; Buchwalter, Gilles; Feiglin, Ariel; Abell-Hart, Kayley; Fei, Teng; Rao, Prakash; Long, Henry; Kwiatkowski, Nicholas; Zhang, Tinghu; Gray, Nathanael; Melchers, Diane; Houtman, Rene; Liu, X Shirley; Cohen, Ofir; Wagle, Nikhil; Winer, Eric P; Zhao, Jean; Brown, Myles

    2018-02-12

    Estrogen receptor α (ER) ligand-binding domain (LBD) mutations are found in a substantial number of endocrine treatment-resistant metastatic ER-positive (ER + ) breast cancers. We investigated the chromatin recruitment, transcriptional network, and genetic vulnerabilities in breast cancer models harboring the clinically relevant ER mutations. These mutants exhibit both ligand-independent functions that mimic estradiol-bound wild-type ER as well as allele-specific neomorphic properties that promote a pro-metastatic phenotype. Analysis of the genome-wide ER binding sites identified mutant ER unique recruitment mediating the allele-specific transcriptional program. Genetic screens identified genes that are essential for the ligand-independent growth driven by the mutants. These studies provide insights into the mechanism of endocrine therapy resistance engendered by ER mutations and potential therapeutic targets. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data

    OpenAIRE

    Hu, Bo; Ji, Yuan; Xu, Yaomin; Ting, Angela H

    2013-01-01

    Allele-specific methylation (ASM) has long been studied but mainly documented in the context of genomic imprinting and X chromosome inactivation. Taking advantage of the next-generation sequencing technology, we conduct a high-throughput sequencing experiment with four prostate cell lines to survey the whole genome and identify single nucleotide polymorphisms (SNPs) with ASM. A Bayesian approach is proposed to model the counts of short reads for each SNP conditional on its genotypes of multip...

  12. A Fisheye Viewer for microarray-based gene expression data.

    Science.gov (United States)

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

    2006-10-13

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

  13. A fisheye viewer for microarray-based gene expression data

    Directory of Open Access Journals (Sweden)

    Munson Ethan V

    2006-10-01

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

  14. Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation.

    Science.gov (United States)

    Paliwal, Anupam; Temkin, Alexis M; Kerkel, Kristi; Yale, Alexander; Yotova, Iveta; Drost, Natalia; Lax, Simon; Nhan-Chang, Chia-Ling; Powell, Charles; Borczuk, Alain; Aviv, Abraham; Wapner, Ronald; Chen, Xiaowei; Nagy, Peter L; Schork, Nicholas; Do, Catherine; Torkamani, Ali; Tycko, Benjamin

    2013-08-01

    Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.

  15. Genome-wide survey of allele-specific splicing in humans

    Directory of Open Access Journals (Sweden)

    Scheffler Konrad

    2008-06-01

    Full Text Available Abstract Background Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or quantitatively have been reported and allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. However, because the effect of a mutation on the efficiency of mRNA splicing is often difficult to predict, many mutations that cause disease through an effect on splicing are likely to remain undiscovered. Results We have combined a genome-wide scan for sequence polymorphisms likely to affect mRNA splicing with analysis of publicly available Expressed Sequence Tag (EST and exon array data. The genome-wide scan uses published tools and identified 30,977 SNPs located within donor and acceptor splice sites, branch points and exonic splicing enhancer elements. For 1,185 candidate splicing polymorphisms the difference in splicing between alternative alleles was corroborated by publicly available exon array data from 166 lymphoblastoid cell lines. We developed a novel probabilistic method to infer allele-specific splicing from EST data. The method uses SNPs and alternative mRNA isoforms mapped to EST sequences and models both regulated alternative splicing as well as allele-specific splicing. We have also estimated heritability of splicing and report that a greater proportion of genes show evidence of splicing heritability than show heritability of overall gene expression level. Our results provide an extensive resource that can be used to assess the possible effect on splicing of human polymorphisms in putative splice-regulatory sites. Conclusion We report a set of genes showing evidence of allele-specific splicing from an integrated analysis of genomic polymorphisms, EST data and exon array

  16. Rapid ABO genotyping by high-speed droplet allele-specific PCR using crude samples.

    Science.gov (United States)

    Taira, Chiaki; Matsuda, Kazuyuki; Takeichi, Naoya; Furukawa, Satomi; Sugano, Mitsutoshi; Uehara, Takeshi; Okumura, Nobuo; Honda, Takayuki

    2018-01-01

    ABO genotyping has common tools for personal identification of forensic and transplantation field. We developed a new method based on a droplet allele-specific PCR (droplet-AS-PCR) that enabled rapid PCR amplification. We attempted rapid ABO genotyping using crude DNA isolated from dried blood and buccal cells. We designed allele-specific primers for three SNPs (at nucleotides 261, 526, and 803) in exons 6 and 7 of the ABO gene. We pretreated dried blood and buccal cells with proteinase K, and obtained crude DNAs without DNA purification. Droplet-AS-PCR allowed specific amplification of the SNPs at the three loci using crude DNA, with results similar to those for DNA extracted from fresh peripheral blood. The sensitivity of the methods was 5%-10%. The genotyping of extracted DNA and crude DNA were completed within 8 and 9 minutes, respectively. The genotypes determined by the droplet-AS-PCR method were always consistent with those obtained by direct sequencing. The droplet-AS-PCR method enabled rapid and specific amplification of three SNPs of the ABO gene from crude DNA treated with proteinase K. ABO genotyping by the droplet-AS-PCR has the potential to be applied to various fields including a forensic medicine and transplantation medical care. © 2017 Wiley Periodicals, Inc.

  17. Allele-specific cytokine responses at the HLA-C locus, implications for psoriasis

    Science.gov (United States)

    Hundhausen, Christian; Bertoni, Anna; Mak, Rose K; Botti, Elisabetta; Di Meglio, Paola; Clop, Alex; Laggner, Ute; Chimenti, Sergio; Hayday, Adrian C; Barker, Jonathan N; Trembath, Richard C; Capon, Francesca; Nestle, Frank O

    2011-01-01

    Psoriasis is an inflammatory skin disorder that is inherited as a complex trait. Genetic studies have repeatedly highlighted HLA-C as the major determinant for psoriasis susceptibility, with the Cw*0602 allele conferring significant disease risk in a wide-range of populations. Despite the potential importance of HLA-C variation in psoriasis, either via an effect on peptide presentation or immuno-inhibitory activity, allele-specific expression patterns have not been investigated. Here, we used reporter assays to characterize two regulatory variants, which virtually abolished the response to TNF-α (rs2524094) and IFN-γ (rs10657191) in HLA-Cw*0602 and a cluster of related alleles. We validated these findings through the analysis of HLA-Cw*0602 expression in primary keratinocytes treated with TNF-α and IFN-γ. Finally, we showed that HLA-Cw*0602 transcripts are not increased in psoriatic skin lesions, despite highly elevated TNF-α levels. Thus, our findings demonstrate the presence of allele-specific differences in HLA-C expression and indicate that HLA-Cw*0602 is unresponsive to up-regulation by key pro-inflammatory cytokines in psoriasis. These data pave the way for functional studies into the pathogenic role of the major psoriasis susceptibility allele. PMID:22113476

  18. Allele-specific cytokine responses at the HLA-C locus: implications for psoriasis.

    Science.gov (United States)

    Hundhausen, Christian; Bertoni, Anna; Mak, Rose K; Botti, Elisabetta; Di Meglio, Paola; Clop, Alex; Laggner, Ute; Chimenti, Sergio; Hayday, Adrian C; Barker, Jonathan N; Trembath, Richard C; Capon, Francesca; Nestle, Frank O

    2012-03-01

    Psoriasis is an inflammatory skin disorder that is inherited as a complex trait. Genetic studies have repeatedly highlighted HLA-C as the major determinant for psoriasis susceptibility, with the Cw*0602 allele conferring significant disease risk in a wide range of populations. Despite the potential importance of HLA-C variation in psoriasis, either via an effect on peptide presentation or immuno-inhibitory activity, allele-specific expression patterns have not been investigated. Here, we used reporter assays to characterize two regulatory variants, which virtually abolished the response to tumor necrosis factor (TNF)-α (rs2524094) and IFN-γ (rs10657191) in HLA-Cw*0602 and a cluster of related alleles. We validated these findings through the analysis of HLA-Cw*0602 expression in primary keratinocytes treated with TNF-α and IFN-γ. Finally, we showed that HLA-Cw*0602 transcripts are not increased in psoriatic skin lesions, despite highly elevated TNF-α levels. Thus, our findings demonstrate the presence of allele-specific differences in HLA-C expression and indicate that HLA-Cw*0602 is unresponsive to upregulation by key proinflammatory cytokines in psoriasis. These data pave the way for functional studies into the pathogenic role of the major psoriasis susceptibility allele.

  19. Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation.

    Directory of Open Access Journals (Sweden)

    Anupam Paliwal

    2013-08-01

    Full Text Available Allele-specific DNA methylation (ASM is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons, one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs, each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS peaks near CTCF binding sites with ASM.

  20. A DNA Microarray-Based Assay to Detect Dual Infection with Two Dengue Virus Serotypes

    Directory of Open Access Journals (Sweden)

    Alvaro Díaz-Badillo

    2014-04-01

    Full Text Available Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.

  1. Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment.

    Science.gov (United States)

    Waterfall, Christy M; Eisenthal, Robert; Cobb, Benjamin D

    2002-12-20

    A novel method of estimating the kinetic parameters of Taq DNA polymerase during rapid cycle PCR is presented. A model was constructed using a simplified sigmoid function to represent substrate accumulation during PCR in combination with the general equation describing high substrate inhibition for Michaelis-Menten enzymes. The PCR progress curve was viewed as a series of independent reactions where initial rates were accurately measured for each cycle. Kinetic parameters were obtained for allele-specific PCR (AS-PCR) amplification to examine the effect of mismatches on amplification. A high degree of correlation was obtained providing evidence of substrate inhibition as a major cause of the plateau phase that occurs in the later cycles of PCR.

  2. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data.

    Science.gov (United States)

    Hu, Bo; Ji, Yuan; Xu, Yaomin; Ting, Angela H

    2013-05-01

    Allele-specific methylation (ASM) has long been studied but mainly documented in the context of genomic imprinting and X chromosome inactivation. Taking advantage of the next-generation sequencing technology, we conduct a high-throughput sequencing experiment with four prostate cell lines to survey the whole genome and identify single nucleotide polymorphisms (SNPs) with ASM. A Bayesian approach is proposed to model the counts of short reads for each SNP conditional on its genotypes of multiple subjects, leading to a posterior probability of ASM. We flag SNPs with high posterior probabilities of ASM by accounting for multiple comparisons based on posterior false discovery rates. Applying the Bayesian approach to the in-house prostate cell line data, we identify 269 SNPs as candidates of ASM. A simulation study is carried out to demonstrate the quantitative performance of the proposed approach.

  3. Detection of MPL mutations by a novel allele-specific PCR-based strategy.

    Science.gov (United States)

    Furtado, Larissa V; Weigelin, Helmut C; Elenitoba-Johnson, Kojo S J; Betz, Bryan L

    2013-11-01

    MPL mutation testing is recommended in patients with suspected primary myelofibrosis or essential thrombocythemia who lack the JAK2 V617F mutation. MPL mutations can occur at allelic levels below 15%, which may escape detection by commonly used mutation screening methods such as Sanger sequencing. We developed a novel multiplexed allele-specific PCR assay capable of detecting most recurrent MPL exon 10 mutations associated with primary myelofibrosis and essential thrombocythemia (W515L, W515K, W515A, and S505N) down to a sensitivity of 2.5% mutant allele. Test results were reviewed from 15 reference cases and 1380 consecutive specimens referred to our laboratory for testing. Assay performance was compared to Sanger sequencing across a series of 58 specimens with MPL mutations. Positive cases consisted of 45 with W515L, 6 with S505N, 5 with W515K, 1 with W515A, and 1 with both W515L and S505N. Seven cases had mutations below 5% that were undetected by Sanger sequencing. Ten additional cases had mutation levels between 5% and 15% that were not consistently detected by sequencing. All results were easily interpreted in the allele-specific test. This assay offers a sensitive and reliable solution for MPL mutation testing. Sanger sequencing appears insufficiently sensitive for robust MPL mutation detection. Our data also suggest the relative frequency of S505N mutations may be underestimated, highlighting the necessity for inclusion of this mutation in MPL test platforms. Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  4. Allele specific LAMP- gold nanoparticle for characterization of single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Fábio Ferreira Carlos

    2017-12-01

    Full Text Available Due to their relevance as disease biomarkers and for diagnostics, screening of single nucleotide polymorphism (SNPs requires simple and straightforward strategies capable to provide results in medium throughput settings. Suitable approaches relying on isothermal amplification techniques have been evolving to substitute the cumbersome and highly specialized PCR amplification detection schemes. Nonetheless, identification of an individual’s genotype still requires sophisticated equipment and laborious methods.Here, we present a low-cost and reliable approach based on the allele specific loop-mediated isothermal amplification (AS-LAMP coupled to ssDNA functionalized gold nanoparticle (Au-nanoprobe colorimetric sequence discrimination. The Au-nanoprobe integration allows for the colorimetric detection of AS-LAMP amplification product that can be easily interpreted in less than 15 min. We targeted a clinical relevant SNP responsible for lactose intolerance (-13910C/T dbSNP rs#: 4988235 to demonstrate its proof of concept and full potential of this novel approach. Keywords: SNP, Isothermal amplification, Gold nanoparticles, Gold nanoprobes, Lactose intolerance

  5. [Molecular authentication of Jinyinhua formula granule by using allele-specific PCR].

    Science.gov (United States)

    Jiang, Chao; Tu, Li-Chan; Yuan, Yuan; Huang, Lu-Qi; Gao, Wei; Jin, Yan

    2017-07-01

    Traditional authentication method is hard to identify herb's authenticity of traditional Chinese medicine(TCM) formula granules because they have lost all their morphological characteristics. In this study, a new allele-specific PCR method was established for identifying the authentication of Jinyinhua formula granule (made from Lonicerae Japonicae Flos) based on an SNP site in trnL-trnF fragment. Genomic DNA was successfully extracted from Lonicerae Japonicae Flos and its formula granules by using an improved spin column method and then PCR was performed with the designed primer. Approximately 110 bp specific bands was obtained only in the authentic Lonicerae Japonicae Flos and its formula granules, while no bands were found in fake mixed products. In addition, the PCR product sequence was proved from Lonicerae Japonicae Flos trnL-trnF sequence by using BLAST method. Therefore, DNA molecular authentication method could make up the limitations of character identification method and microscopic identification, and quickly identify herb's authenticity of TCM formula granules, with enormous potential for market supervision and quality control. Copyright© by the Chinese Pharmaceutical Association.

  6. Microarray-based ultra-high resolution discovery of genomic deletion mutations

    Science.gov (United States)

    2014-01-01

    Background Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. Results Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. Conclusions Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence. PMID:24655320

  7. Allele-specific gene expression in a wild nonhuman primate population

    Science.gov (United States)

    Tung, J.; Akinyi, M. Y.; Mutura, S.; Altmann, J.; Wray, G. A.; Alberts, S. C.

    2015-01-01

    Natural populations hold enormous potential for evolutionary genetic studies, especially when phenotypic, genetic and environmental data are all available on the same individuals. However, untangling the genotype-phenotype relationship in natural populations remains a major challenge. Here, we describe results of an investigation of one class of phenotype, allele-specific gene expression (ASGE), in the well-studied natural population of baboons of the Amboseli basin, Kenya. ASGE measurements identify cases in which one allele of a gene is overexpressed relative to the alternative allele of the same gene, within individuals, thus providing a control for background genetic and environmental effects. Here, we characterize the incidence of ASGE in the Amboseli baboon population, focusing on the genetic and environmental contributions to ASGE in a set of eleven genes involved in immunity and defence. Within this set, we identify evidence for common ASGE in four genes. We also present examples of two relationships between cis-regulatory genetic variants and the ASGE phenotype. Finally, we identify one case in which this relationship is influenced by a novel gene-environment interaction. Specifically, the dominance rank of an individual’s mother during its early life (an aspect of that individual’s social environment) influences the expression of the gene CCL5 via an interaction with cis-regulatory genetic variation. These results illustrate how environmental and ecological data can be integrated into evolutionary genetic studies of functional variation in natural populations. They also highlight the potential importance of early life environmental variation in shaping the genetic architecture of complex traits in wild mammals. PMID:21226779

  8. An informational view of accession rarity and allele specificity in germplasm banks for management and conservation.

    Science.gov (United States)

    Reyes-Valdés, M Humberto; Burgueño, Juan; Singh, Sukhwinder; Martínez, Octavio; Sansaloni, Carolina Paola

    2018-01-01

    Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and allele frequencies for molecular marker loci, which can be decomposed in allele specificities, as well as in rarity and divergence of accessions. In this way, formulas are provided to calculate the specificity of the different marker alleles with reference to their distribution across accessions, accession rarity, defined as the weighted average of the specificity of its alleles, and divergence, defined by the Kullback-Leibler formula. Albeit being different measures, it is demonstrated that average rarity and divergence are equal for any collection. These parameters can contribute to the knowledge of the structure of a germplasm collection and to make decisions about the preservation of rare variants. The concepts herein developed served as the basis for a strategy for core subset selection called HCore, implemented in a publicly available R script. As a proof of concept, the mathematical view and tools developed in this research were applied to a large collection of Mexican wheat accessions, widely characterized by SNP markers. The most specific alleles were found to be private of a single accession, and the distribution of this parameter had its highest frequencies at low levels of specificity. Accession rarity and divergence had largely symmetrical distributions, and had a positive, albeit non-strictly linear relationship. Comparison of the HCore approach for core subset selection, with three state-of-the-art methods, showed it to be superior for average divergence and rarity, mean genetic distance and diversity. The proposed approach can be used for knowledge extraction and decision making in germplasm collections of

  9. Microarray-based screening of heat shock protein inhibitors.

    Science.gov (United States)

    Schax, Emilia; Walter, Johanna-Gabriela; Märzhäuser, Helene; Stahl, Frank; Scheper, Thomas; Agard, David A; Eichner, Simone; Kirschning, Andreas; Zeilinger, Carsten

    2014-06-20

    Based on the importance of heat shock proteins (HSPs) in diseases such as cancer, Alzheimer's disease or malaria, inhibitors of these chaperons are needed. Today's state-of-the-art techniques to identify HSP inhibitors are performed in microplate format, requiring large amounts of proteins and potential inhibitors. In contrast, we have developed a miniaturized protein microarray-based assay to identify novel inhibitors, allowing analysis with 300 pmol of protein. The assay is based on competitive binding of fluorescence-labeled ATP and potential inhibitors to the ATP-binding site of HSP. Therefore, the developed microarray enables the parallel analysis of different ATP-binding proteins on a single microarray. We have demonstrated the possibility of multiplexing by immobilizing full-length human HSP90α and HtpG of Helicobacter pylori on microarrays. Fluorescence-labeled ATP was competed by novel geldanamycin/reblastatin derivatives with IC50 values in the range of 0.5 nM to 4 μM and Z(*)-factors between 0.60 and 0.96. Our results demonstrate the potential of a target-oriented multiplexed protein microarray to identify novel inhibitors for different members of the HSP90 family. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease.

    Science.gov (United States)

    Chiba, Hirofumi; Kakuta, Yoichi; Kinouchi, Yoshitaka; Kawai, Yosuke; Watanabe, Kazuhiro; Nagao, Munenori; Naito, Takeo; Onodera, Motoyuki; Moroi, Rintaro; Kuroha, Masatake; Kanazawa, Yoshitake; Kimura, Tomoya; Shiga, Hisashi; Endo, Katsuya; Negoro, Kenichi; Nagasaki, Masao; Unno, Michiaki; Shimosegawa, Tooru

    2018-01-01

    Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). We confirmed the existence of cis-regulated ASM around

  11. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease

    Science.gov (United States)

    Chiba, Hirofumi; Kakuta, Yoichi; Kinouchi, Yoshitaka; Kawai, Yosuke; Watanabe, Kazuhiro; Nagao, Munenori; Naito, Takeo; Onodera, Motoyuki; Moroi, Rintaro; Kuroha, Masatake; Kanazawa, Yoshitake; Kimura, Tomoya; Shiga, Hisashi; Endo, Katsuya; Negoro, Kenichi; Nagasaki, Masao; Unno, Michiaki; Shimosegawa, Tooru

    2018-01-01

    Background Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. Methods CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score (ΔRAS¯) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing ΔRAS¯ >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. Results We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of ΔRAS¯ (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 (ΔRAS¯ = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). Conclusions We confirmed the existence of cis-regulated ASM around IBD

  12. Allele-specific expression in the germline of patients with familial pancreatic cancer: An unbiased approach to cancer gene discovery

    OpenAIRE

    Tan, Aik Choon; Fan, Jian-Bing; Karikari, Collins; Bibikova, Marina; Garcia, Eliza Wickham; Zhou, Lixin; Barker, David; Serre, David; Feldmann, Georg; Hruban, Ralph H.; Klein, Alison P.; Goggins, Michael; Couch, Fergus J.; Hudson, Thomas J.; Winslow, Raimond L.

    2007-01-01

    Physiologic allele-specific expression (ASE) in germline tissues occurs during random X-chromosome inactivation1 and in genomic imprinting,2 wherein the two alleles of a gene in a heterozygous individual are not expressed equally. Recent studies have confirmed the existence of ASE in apparently non-imprinted autosomal genes;3–14 however, the extent of ASE in the human genome is unknown. We explored ASE in lymphoblastoid cell lines of 145 individuals using an oligonucleotide array based assay....

  13. Identification and Genetic Diversity of Etambutol Resistant Strains of Mycobacterium Tuberculosis by Allelic-Specific PCR and Spologiotyping

    Directory of Open Access Journals (Sweden)

    Zahra Derakhshani Nezhad

    2012-09-01

    Full Text Available Background & Objectives: Ethambutol is one of the four main drugs in treatment of tuberculosis. The most common mutation associated with this drug resistance usually occurs in codon 306 of embB. The aim of this study was to detect ethambutol resistance using Allele-Specific PCR and Spoligotyping in various subtypes of Mycobacterium tuberculosis.   Methods : 140 sputum specimens were collected from suspected TB patients. They were digested and decontaminated using Pettrof method before culturing them on LJ medium. Drug susceptibility testing was performed on 106 culture positive specimens using proportional method. DNA was extracted from the isolated organisms and subsequently subjected to Allele-Specific PCR to detect any mutationin embB306. Spoligotyping was then used to determine the subtypes.   Results: Out of 106 cultures positive samples, 36 samples (33.9% showed resistance to ethambutol using proportional method. Allele-Specific PCR assay identified 93 as sensitive and 13 (27.6% as resistant strains. The results of PCR were in agreement with result of proportional method. The PCR method revealed that 61.5% of mutation occurred in the first and 38.5% in third nucleotides. Spoligotyping differentiated Mycobacterium tuberculosis strains into Beijing (10 9.4%, Bovis (2 1.8%, CAS (24 22.6%, EAI (1 0.9%, Haarlem (27 25.4%, LAM (5 4.7%, Manu (5 4.7%, T (27 25.4% and U( 2 1,8% families. The high frequency of mutation in embB gene was belonged to Haarlem, CAS and T subfamilies.   Conclusion: Based on results current study, mutations in the genes other than embB might have occurred in the resistant strains that gave negative result in Allele-Specific PCR assay. Therefore other mechanisms of resistance to this antibiotic should be investigated.

  14. Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays.

    Directory of Open Access Journals (Sweden)

    Andrew J P Smith

    Full Text Available Following the widespread use of genome-wide association studies (GWAS, focus is turning towards identification of causal variants rather than simply genetic markers of diseases and traits. As a step towards a high-throughput method to identify genome-wide, non-coding, functional regulatory variants, we describe the technique of allele-specific FAIRE, utilising large-scale genotyping technology (FAIRE-gen to determine allelic effects on chromatin accessibility and regulatory potential. FAIRE-gen was explored using lymphoblastoid cells and the 50,000 SNP Illumina CVD BeadChip. The technique identified an allele-specific regulatory polymorphism within NR1H3 (coding for LXR-α, rs7120118, coinciding with a previously GWAS-identified SNP for HDL-C levels. This finding was confirmed using FAIRE-gen with the 200,000 SNP Illumina Metabochip and verified with the established method of TaqMan allelic discrimination. Examination of this SNP in two prospective Caucasian cohorts comprising 15,000 individuals confirmed the association with HDL-C levels (combined beta = 0.016; p = 0.0006, and analysis of gene expression identified an allelic association with LXR-α expression in heart tissue. Using increasingly comprehensive genotyping chips and distinct tissues for examination, FAIRE-gen has the potential to aid the identification of many causal SNPs associated with disease from GWAS.

  15. Aberrant allele-specific replication, independent of parental origin, in blood cells of cancer patients

    International Nuclear Information System (INIS)

    Dotan, Zohar A; Dotan, Aviva; Ramon, Jacob; Avivi, Lydia

    2008-01-01

    Allelic counterparts of biallelically expressed genes display an epigenetic symmetry normally manifested by synchronous replication, different from genes subjected to monoallelic expression, which normally are characterized by an asynchronous mode of replication (well exemplified by the SNRPN imprinted locus). Malignancy was documented to be associated with gross modifications in the inherent replication-timing coordination between allelic counterparts of imprinted genes as well as of biallelically expressed loci. The cancer-related allelic replication timing aberrations are non-disease specific and appear in peripheral blood cells of cancer patients, including those with solid tumors. As such they offer potential blood markers for non-invasive cancer test. The present study was aimed to gain some insight into the mechanism leading to the replication timing alterations of genes in blood lymphocytes of cancer patients. Peripheral blood samples derived from patients with prostate cancer were chosen to represent the cancerous status, and samples taken from patients with no cancer but with benign prostate hyperplasia were used to portray the normal status. Fluorescence In Situ Hybridization (FISH) replication assay, applied to phytohemagglutinin (PHA)-stimulated blood lymphocytes, was used to evaluate the temporal order (either synchronous or asynchronous) of genes in the patients' cells. We demonstrated that: (i) the aberrant epigenetic profile, as delineated by the cancer status, is a reversible modification, evidenced by our ability to restore the normal patterns of replication in three unrelated loci (CEN15, SNRPN and RB1) by introducing an archetypical demethylating agent, 5-azacytidine; (ii) following the rehabilitating effect of demethylation, an imprinted gene (SNRPN) retains its original parental imprint; and (iii) the choice of an allele between early or late replication in the aberrant asynchronous replication, delineated by the cancer status, is not

  16. Microarray-based analysis of plasma cirDNA epigenetic modification profiling in xenografted mice exposed to intermittent hypoxia

    Directory of Open Access Journals (Sweden)

    Rene Cortese

    2015-09-01

    Full Text Available Intermittent hypoxia (IH during sleep is one of the major abnormalities occurring in patients suffering from obstructive sleep apnea (OSA, a highly prevalent disorder affecting 6–15% of the general population, particularly among obese people. IH has been proposed as a major determinant of oncogenetically-related processes such as tumor growth, invasion and metastasis. During the growth and expansion of tumors, fragmented DNA is released into the bloodstream and enters the circulation. Circulating tumor DNA (cirDNA conserves the genetic and epigenetic profiles from the tumor of origin and can be isolated from the plasma fraction. Here we report a microarray-based epigenetic profiling of cirDNA isolated from blood samples of mice engrafted with TC1 epithelial lung cancer cells and controls, which were exposed to IH during sleep (XenoIH group, n = 3 or control conditions, (i.e., room air (RA; XenoRA group, n = 3 conditions. To prepare the targets for microarray hybridization, we applied a previously developed method that enriches the modified fraction of the cirDNA without amplification of genomic DNA. Regions of differential cirDNA modification between the two groups were identified by hybridizing the enriched fractions for each sample to Affymetrix GeneChip Human Promoter Arrays 1.0R. Microarray raw and processed data were deposited in NCBI's Gene Expression Omnibus (GEO database (accession number: GSE61070.

  17. High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

    Directory of Open Access Journals (Sweden)

    Clark Taane G

    2010-04-01

    Full Text Available Abstract Background Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. Results Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%. Conclusions Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes

  18. Development of allele-specific multiplex PCR to determine the length of poly-T in intron 8 of CFTR

    Directory of Open Access Journals (Sweden)

    Neng Chen

    2014-07-01

    Full Text Available Cystic fibrosis transmembrane conductance regulator (CFTR gene mutation analysis has been implemented for Cystic Fibrosis (CF carrier screening, and molecular diagnosis of CF and congenital bilateral absence of the vas deferens (CBAVD. Although poly-T allele analysis in intron 8 of CFTR is required when a patient is positive for R117H, it is not recommended for routine carrier screening. Therefore, commercial kits for CFTR mutation analysis were designed either to mask the poly-T allele results, unless a patient is R117H positive, or to have the poly-T analysis as a standalone reflex test using the same commercial platform. There are other standalone assays developed to detect poly-T alleles, such as heteroduplex analysis, High Resolution Melting (HRM curve analysis, allele-specific PCR (AS-PCR and Sanger sequencing. In this report, we developed a simple and easy-to-implement multiplex AS-PCR assay using unlabeled standard length primers, which can be used as a reflex or standalone test for CFTR poly-T track analysis. Out of 115 human gDNA samples tested, results from our new AS-PCR matched to the previous known poly-T results or results from Sanger sequencing.

  19. Allele-specific Gene Silencing of Mutant mRNA Restores Cellular Function in Ullrich Congenital Muscular Dystrophy Fibroblasts

    Directory of Open Access Journals (Sweden)

    Satoru Noguchi

    2014-01-01

    Full Text Available Ullrich congenital muscular dystrophy (UCMD is an inherited muscle disorder characterized clinically by muscle weakness, distal joint hyperlaxity, and proximal joint contractures. Sporadic and recessive mutations in the three collagen VI genes, COL6A1, COL6A2, and COL6A3, are reported to be causative. In the sporadic forms, a heterozygous point mutation causing glycine substitution in the triple helical domain has been identified in higher rate. In this study, we examined the efficacy of siRNAs, which target point mutation site, on specific knockdown toward transcripts from mutant allele and evaluated consequent cellular phenotype of UCMD fibroblasts. We evaluated the effect of siRNAs targeted to silence-specific COL6A1 alleles in UCMD fibroblasts, where simultaneous expression of both wild-type and mutant collagen VI resulted in defective collagen localization. Addition of mutant-specific siRNAs allowed normal extracellular localization of collagen VI surrounding fibroblasts, suggesting selective inhibition of mutant collagen VI. Targeting the single-nucleotide COL6A1 c.850G>A (p.G284R mutation responsible a sporadic autosomal dominant form of UCMD can potently and selectively block expression of mutant collagen VI. These results suggest that allele-specific knockdown of the mutant mRNA can potentially be considered as a therapeutic procedure in UCMD due to COL6A1 point mutations.

  20. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

    Directory of Open Access Journals (Sweden)

    Josh Lewis Stern

    2017-12-01

    Full Text Available A mutation in the promoter of the Telomerase Reverse Transcriptase (TERT gene is the most frequent noncoding mutation in cancer. The mutation drives unusual monoallelic expression of TERT, allowing immortalization. Here, we find that DNA methylation of the TERT CpG island (CGI is also allele-specific in multiple cancers. The expressed allele is hypomethylated, which is opposite to cancers without TERT promoter mutations. The continued presence of Polycomb repressive complex 2 (PRC2 on the inactive allele suggests that histone marks of repressed chromatin may be causally linked to high DNA methylation. Consistent with this hypothesis, TERT promoter DNA containing 5-methyl-CpG has much increased affinity for PRC2 in vitro. Thus, CpG methylation and histone marks appear to collaborate to maintain the two TERT alleles in different epigenetic states in TERT promoter mutant cancers. Finally, in several cancers, DNA methylation levels at the TERT CGI correlate with altered patient survival.

  1. Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes.

    Science.gov (United States)

    Stern, Josh Lewis; Paucek, Richard D; Huang, Franklin W; Ghandi, Mahmoud; Nwumeh, Ronald; Costello, James C; Cech, Thomas R

    2017-12-26

    A mutation in the promoter of the Telomerase Reverse Transcriptase (TERT) gene is the most frequent noncoding mutation in cancer. The mutation drives unusual monoallelic expression of TERT, allowing immortalization. Here, we find that DNA methylation of the TERT CpG island (CGI) is also allele-specific in multiple cancers. The expressed allele is hypomethylated, which is opposite to cancers without TERT promoter mutations. The continued presence of Polycomb repressive complex 2 (PRC2) on the inactive allele suggests that histone marks of repressed chromatin may be causally linked to high DNA methylation. Consistent with this hypothesis, TERT promoter DNA containing 5-methyl-CpG has much increased affinity for PRC2 in vitro. Thus, CpG methylation and histone marks appear to collaborate to maintain the two TERT alleles in different epigenetic states in TERT promoter mutant cancers. Finally, in several cancers, DNA methylation levels at the TERT CGI correlate with altered patient survival. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  2. Allelic inhibition of displacement activity: a simplified one tube allele-specific PCR for evaluation of ITPA polymorphisms.

    Science.gov (United States)

    Galmozzi, E; Facchetti, F; Degasperi, E; Aghemo, A; Lampertico, P

    2013-02-01

    Recently, genome-wide association studies (GWAS) in patients with chronic hepatitis C virus (HCV) infection have identified two functional single nucleotide polymorphisms (SNPs) in the inosine triphosphatase (ITPA) gene, that are associated strongly and independently with hemolytic anemia in patients exposed to pegylated-interferon (Peg-IFN) plus ribavirin (RBV) combined therapy. Here has been developed a simplified allele discrimination polymerase chain reaction (PCR) assay named allelic inhibition of displacement activity (AIDA) for evaluation of ITPA polymorphisms. AIDA system relies on three unlabeled primers only, two outer common primers and one inner primer with allele-specific 3' terminus mismatch. DNA samples from 192 patients with chronic HCV infection were used to validate the AIDA system and results were compared with the gold standard TaqMan(®) SNP genotyping assay. Concordant data were obtained for all samples, granting for high specificity of the method. In conclusion, AIDA is a practical one-tube method to reproducibly and to assess accurately rs7270101 and rs1127354 ITPA SNPs. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

    Science.gov (United States)

    Waszak, Sebastian M; Kilpinen, Helena; Gschwind, Andreas R; Orioli, Andrea; Raghav, Sunil K; Witwicki, Robert M; Migliavacca, Eugenia; Yurovsky, Alisa; Lappalainen, Tuuli; Hernandez, Nouria; Reymond, Alexandre; Dermitzakis, Emmanouil T; Deplancke, Bart

    2014-01-15

    High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent-daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. The R package abs filter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter

  5. Robust embryo identification using first polar body single nucleotide polymorphism microarray-based DNA fingerprinting.

    Science.gov (United States)

    Treff, Nathan R; Su, Jing; Kasabwala, Natasha; Tao, Xin; Miller, Kathleen A; Scott, Richard T

    2010-05-01

    This study sought to validate a novel, minimally invasive system for embryo tracking by single nucleotide polymorphism microarray-based DNA fingerprinting of the first polar body. First polar body-based assignments of which embryos implanted and were delivered after multiple ET were 100% consistent with previously validated embryo DNA fingerprinting-based assignments. Copyright 2010 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  6. Infrequent detection of germline allele-specific expression of TGFBR1 in lymphoblasts and tissues of colon cancer patients.

    LENUS (Irish Health Repository)

    Guda, Kishore

    2009-06-15

    Recently, germline allele-specific expression (ASE) of the gene encoding for transforming growth factor-beta type I receptor (TGFBR1) has been proposed to be a major risk factor for cancer predisposition in the colon. Germline ASE results in a lowered expression of one of the TGFBR1 alleles (>1.5-fold), and was shown to occur in approximately 20% of informative familial and sporadic colorectal cancer (CRC) cases. In the present study, using the highly quantitative pyrosequencing technique, we estimated the frequency of ASE in TGFBR1 in a cohort of affected individuals from familial clusters of advanced colon neoplasias (cancers and adenomas with high-grade dysplasia), and also from a cohort of individuals with sporadic CRCs. Cases were considered positive for the presence of ASE if demonstrating an allelic expression ratio <0.67 or >1.5. Using RNA derived from lymphoblastoid cell lines, we find that of 46 informative Caucasian advanced colon neoplasia cases with a family history, only 2 individuals display a modest ASE, with allelic ratios of 1.65 and 1.73, respectively. Given that ASE of TGFBR1, if present, would likely be more pronounced in the colon compared with other tissues, we additionally determined the allele ratios of TGFBR1 in the RNA derived from normal-appearing colonic mucosa of sporadic CRC cases. We, however, found no evidence of ASE in any of 44 informative sporadic cases analyzed. Taken together, we find that germline ASE of TGFBR1, as assayed in lymphoblastoid and colon epithelial cells of colon cancer patients, is a relatively rare event.

  7. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

    Science.gov (United States)

    Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

    2018-03-01

    Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

  8. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

    Directory of Open Access Journals (Sweden)

    Soroush Samadian

    2018-03-01

    Full Text Available Somatic copy number variations (CNVs play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format, lists of non-overlapping genome coordinates for introduction of gains and losses (bed file, and an optional file defining known haplotypes (vcf format. To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total. To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01% while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

  9. Development of Allele-Specific Primer PCR for a Swine TLR2 SNP and Comparison of the Frequency among Several Pig Breeds of Japan and the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Muneta, Y.; Minagawa, Y.; Kusumoto, M.; Shinkai, H.; Uenishi, H.; Šplíchal, Igor

    2012-01-01

    Roč. 74, č. 5 (2012), s. 553-559 ISSN 0916-7250 R&D Projects: GA ČR GA524/09/0365 Institutional support: RVO:61388971 Keywords : allele-specific PCR * Mycoplasma hyopneumoniae * single nucleotide polymorphism Subject RIV: EC - Immunology Impact factor: 0.876, year: 2012

  10. Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation

    DEFF Research Database (Denmark)

    Milani, Lili; Lundmark, Anders; Nordlund, Jessica

    2008-01-01

    To identify genes that are regulated by cis-acting functional elements in acute lymphoblastic leukemia (ALL) we determined the allele-specific expression (ASE) levels of 2, 529 genes by genotyping a genome-wide panel of single nucleotide polymorphisms in RNA and DNA from bone marrow and blood...

  11. Impact of pre-existing MSP142-allele specific immunity on potency of an erythrocytic Plasmodium falciparum vaccine

    Directory of Open Access Journals (Sweden)

    Bergmann-Leitner Elke S

    2012-09-01

    Full Text Available Abstract Background MSP1 is the major surface protein on merozoites and a prime candidate for a blood stage malaria vaccine. Preclinical and seroepidemiological studies have implicated antibodies to MSP1 in protection against blood stage parasitaemia and/or reduced parasite densities, respectively. Malaria endemic areas have multiple strains of Plasmodium falciparum circulating at any given time, giving rise to complex immune responses, an issue which is generally not addressed in clinical trials conducted in non-endemic areas. A lack of understanding of the effect of pre-existing immunity to heterologous parasite strains may significantly contribute to vaccine failure in the field. The purpose of this study was to model the effect of pre-existing immunity to MSP142 on the immunogenicity of blood-stage malaria vaccines based on alternative MSP1 alleles. Methods Inbred and outbred mice were immunized with various recombinant P. falciparum MSP142 proteins that represent the two major alleles of MSP142, MAD20 (3D7 and Wellcome (K1, FVO. Humoral immune responses were analysed by ELISA and LuminexTM, and functional activity of induced MSP142-specific antibodies was assessed by growth inhibition assays. T-cell responses were characterized using ex vivo ELISpot assays. Results Analysis of the immune responses induced by various immunization regimens demonstrated a strong allele-specific response at the T cell level in both inbred and outbred mice. The success of heterologous regimens depended on the degree of homology of the N-terminal p33 portion of the MSP142, likely due to the fact that most T cell epitopes reside in this part of the molecule. Analysis of humoral immune responses revealed a marked cross-reactivity between the alleles. Functional analyses showed that some of the heterologous regimens induced antibodies with improved growth inhibitory activities. Conclusion The development of a more broadly efficacious MSP1 based vaccine may be

  12. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

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    Assawamakin Anunchai

    2007-08-01

    Full Text Available Abstract Background Allele-specific (AS Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. Results This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG draw that allow users to select SNPs and graphically visualize designed primers and their conditions. Conclusion WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number

  13. Typing for HLA-DPB1*03 and HLA-DPB1*06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of "new" DPB1*06 variants

    DEFF Research Database (Denmark)

    Fugger, L; Morling, N; Ryder, L P

    1989-01-01

    DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for the HLA-DPB locus. Typing for the individual DPB alleles was exclusively dependent on the hybridizations of the probe...

  14. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

    Science.gov (United States)

    Zhang, Wenqian; Yu, Ying; Hertwig, Falk; Thierry-Mieg, Jean; Zhang, Wenwei; Thierry-Mieg, Danielle; Wang, Jian; Furlanello, Cesare; Devanarayan, Viswanath; Cheng, Jie; Deng, Youping; Hero, Barbara; Hong, Huixiao; Jia, Meiwen; Li, Li; Lin, Simon M; Nikolsky, Yuri; Oberthuer, André; Qing, Tao; Su, Zhenqiang; Volland, Ruth; Wang, Charles; Wang, May D; Ai, Junmei; Albanese, Davide; Asgharzadeh, Shahab; Avigad, Smadar; Bao, Wenjun; Bessarabova, Marina; Brilliant, Murray H; Brors, Benedikt; Chierici, Marco; Chu, Tzu-Ming; Zhang, Jibin; Grundy, Richard G; He, Min Max; Hebbring, Scott; Kaufman, Howard L; Lababidi, Samir; Lancashire, Lee J; Li, Yan; Lu, Xin X; Luo, Heng; Ma, Xiwen; Ning, Baitang; Noguera, Rosa; Peifer, Martin; Phan, John H; Roels, Frederik; Rosswog, Carolina; Shao, Susan; Shen, Jie; Theissen, Jessica; Tonini, Gian Paolo; Vandesompele, Jo; Wu, Po-Yen; Xiao, Wenzhong; Xu, Joshua; Xu, Weihong; Xuan, Jiekun; Yang, Yong; Ye, Zhan; Dong, Zirui; Zhang, Ke K; Yin, Ye; Zhao, Chen; Zheng, Yuanting; Wolfinger, Russell D; Shi, Tieliu; Malkas, Linda H; Berthold, Frank; Wang, Jun; Tong, Weida; Shi, Leming; Peng, Zhiyu; Fischer, Matthias

    2015-06-25

    Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

  15. Multiplex Detection and Genotyping of Point Mutations Involved in Charcot-Marie-Tooth Disease Using a Hairpin Microarray-Based Assay

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    Yasser Baaj

    2009-01-01

    Full Text Available We previously developed a highly specific method for detecting SNPs with a microarray-based system using stem-loop probes. In this paper we demonstrate that coupling a multiplexing procedure with our microarray method is possible for the simultaneous detection and genotyping of four point mutations, in three different genes, involved in Charcot-Marie-Tooth disease. DNA from healthy individuals and patients was amplified, labeled with Cy3 by multiplex PCR; and hybridized to microarrays. Spot signal intensities were 18 to 74 times greater for perfect matches than for mismatched target sequences differing by a single nucleotide (discrimination ratio for “homozygous” DNA from healthy individuals. “Heterozygous” mutant DNA samples gave signal intensity ratios close to 1 at the positions of the mutations as expected. Genotyping by this method was therefore reliable. This system now combines the principle of highly specific genotyping based on stem-loop structure probes with the advantages of multiplex analysis.

  16. A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

    LENUS (Irish Health Repository)

    Prendergast, James G D

    2012-05-19

    AbstractBackgroundChromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controlling several disease loci. Human genetic variation, DNA methylation, and disease have been intensely studied, uncovering many sites of allele-specific DNA methylation (ASM). However, little is known about the genome-wide occurrence of sites of allele-specific histone modification (ASHM) and their relationship to human disease. The aim of this study was to investigate the extent and characteristics of sites of ASHM in human embryonic stem cells (hESCs).ResultsUsing a statistically rigorous protocol, we investigated the genomic distribution of ASHM in hESCs, and their relationship to sites of allele-specific expression (ASE) and DNA methylation. We found that, although they were rare, sites of ASHM were substantially enriched at loci displaying ASE. Many were also found at known imprinted regions, hence sites of ASHM are likely to be better markers of imprinted regions than sites of ASM. We also found that sites of ASHM and ASE in hESCs colocalize at risk loci for developmental syndromes mediated by deletions, providing insights into the etiology of these disorders.ConclusionThese results demonstrate the potential importance of ASHM patterns in the interpretation of disease loci, and the protocol described provides a basis for similar studies of ASHM in other cell types to further our understanding of human disease susceptibility.

  17. Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection.

    Science.gov (United States)

    Zhang, Qi; Zeng, Xin; Younkin, Sam; Kawli, Trupti; Snyder, Michael P; Keleş, Sündüz

    2016-02-24

    Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies.

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

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    MacInnes Janet I

    2009-02-01

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

  19. Enhanced specificity of TPMT*2 genotyping using unidirectional wild-type and mutant allele-specific scorpion primers in a single tube.

    Directory of Open Access Journals (Sweden)

    Dong Chen

    Full Text Available Genotyping of thiopurine S-methyltransferase (TPMT is recommended for predicting the adverse drug response of thiopurines. In the current study, a novel version of allele-specific PCR (AS-PCR, termed competitive real-time fluorescent AS-PCR (CRAS-PCR was developed to analyze the TPMT*2 genotype in ethnic Chinese. This technique simultaneously uses wild-type and mutant allele-specific scorpion primers in a single reaction. To determine the optimal conditions for both traditional AS-PCR and CRAS-PCR, we used the Taguchi method, an engineering optimization process that balances the concentrations of all components using an orthogonal array rather than a factorial array. Instead of running up to 264 experiments with the conventional factorial method, the Taguchi method achieved the same optimization using only 16 experiments. The optimized CRAS-PCR system completely avoided non-specific amplification occurring in traditional AS-PCR and could be performed at much more relaxed reaction conditions at 1% sensitivity, similar to traditional AS-PCR. TPMT*2 genotyping of 240 clinical samples was consistent with published data. In conclusion, CRAS-PCR is a novel and robust genotyping method, and the Taguchi method is an effective tool for the optimization of molecular analysis techniques.

  20. siRNA-mediated Allele-specific Silencing of a COL6A3 Mutation in a Cellular Model of Dominant Ullrich Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Véronique Bolduc

    2014-01-01

    Full Text Available Congenital muscular dystrophy type Ullrich (UCMD is a severe disorder of early childhood onset for which currently there is no effective treatment. UCMD commonly is caused by dominant-negative mutations in the genes coding for collagen type VI, a major microfibrillar component of the extracellular matrix surrounding the muscle fibers. To explore RNA interference (RNAi as a potential therapy for UCMD, we designed a series of small interfering RNA (siRNA oligos that specifically target the most common mutations resulting in skipping of exon 16 in the COL6A3 gene and tested them in UCMD-derived dermal fibroblasts. Transcript analysis by semiquantitative and quantitative reverse transcriptase PCR showed that two of these siRNAs were the most allele-specific, i.e., they efficiently knocked down the expression from the mutant allele, without affecting the normal allele. In HEK293T cells, these siRNAs selectively suppressed protein expression from a reporter construct carrying the mutation, with no or minimal suppression of the wild-type (WT construct, suggesting that collagen VI protein levels are as also reduced in an allele-specific manner. Furthermore, we found that treating UCMD fibroblasts with these siRNAs considerably improved the quantity and quality of the collagen VI matrix, as assessed by confocal microscopy. Our current study establishes RNAi as a promising molecular approach for treating dominant COL6-related dystrophies.

  1. Microarray-based mutation detection and phenotypic characterization in Korean patients with retinitis pigmentosa

    Science.gov (United States)

    Kim, Cinoo; Kim, Kwang Joong; Bok, Jeong; Lee, Eun-Ju; Kim, Dong-Joon; Oh, Ji Hee; Park, Sung Pyo; Shin, Joo Young; Lee, Jong-Young

    2012-01-01

    Purpose To evaluate microarray-based genotyping technology for the detection of mutations responsible for retinitis pigmentosa (RP) and to perform phenotypic characterization of patients with pathogenic mutations. Methods DNA from 336 patients with RP and 360 controls was analyzed using the GoldenGate assay with microbeads containing 95 previously reported disease-associated mutations from 28 RP genes. Mutations identified by microarray-based genotyping were confirmed by direct sequencing. Segregation analysis and phenotypic characterization were performed in patients with mutations. The disease severity was assessed by visual acuity, electroretinography, optical coherence tomography, and kinetic perimetry. Results Ten RP-related mutations of five RP genes (PRP3 pre-mRNA processing factor 3 homolog [PRPF3], rhodopsin [RHO], phosphodiesterase 6B [PDE6B], peripherin 2 [PRPH2], and retinitis pigmentosa 1 [RP1]) were identified in 26 of the 336 patients (7.7%) and in six of the 360 controls (1.7%). The p.H557Y mutation in PDE6B, which was homozygous in four patients and heterozygous in nine patients, was the most frequent mutation (2.5%). Mutation segregation was assessed in four families. Among the patients with missense mutations, the most severe phenotype occurred in patients with p.D984G in RP1; less severe phenotypes occurred in patients with p.R135W in RHO; a relatively moderate phenotype occurred in patients with p.T494M in PRPF3, p.H557Y in PDE6B, or p.W316G in PRPH2; and a mild phenotype was seen in a patient with p.D190N in RHO. Conclusions The results reveal that the GoldenGate assay may not be an efficient method for molecular diagnosis in RP patients with rare mutations, although it has proven to be reliable and efficient for high-throughput genotyping of single-nucleotide polymorphisms. The clinical features varied according to the mutations. Continuous effort to identify novel RP genes and mutations in a population is needed to improve the efficiency and

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-03-17

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

  3. Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection

    International Nuclear Information System (INIS)

    Zapparoli, Giada V; Jorissen, Robert N; Hewitt, Chelsee A; McBean, Michelle; Westerman, David A; Dobrovic, Alexander

    2013-01-01

    The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10 -4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a

  4. Detection of EGFR mutations in plasma and biopsies from non-small cell lung cancer patients by allele-specific PCR assays

    DEFF Research Database (Denmark)

    Weber, Britta; Meldgaard, Peter; Hager, Henrik

    2014-01-01

    samples with allele-specific PCR assays. METHODS: Pairs of the diagnostic biopsy and plasma obtained just prior to start of erlotinib treatment were collected from 199 patients with adenocarcinoma of non-small-cell lung cancer. DNA from both sample types was isolated and examined for the presence...... of mutations in exons 18-21 of the EGFR gene, employing the cobas(®) EGFR Tissue Test and cobas(®) EGFR Blood Test (in development, Roche Molecular Systems, Inc., CA, USA). RESULTS: Test results were obtained in all 199 (100%) plasma samples and 196/199 (98%) of the biopsies. EGFR-activating mutations were...... identified in 24/199 (12%) plasma samples and 28/196 (14%) biopsy samples, and 17/196 (9%) matched pairs contained the same mutation. Six EGFR mutations were present only in plasma samples but not in the biopsy samples. The overall concordance of the EGFR gene mutations detected in plasma and biopsy tissue...

  5. In Silico Analysis of Microarray-Based Gene Expression Profiles Predicts Tumor Cell Response to Withanolides

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    Thomas Efferth

    2012-05-01

    Full Text Available Withania somnifera (L. Dunal (Indian ginseng, winter cherry, Solanaceae is widely used in traditional medicine. Roots are either chewed or used to prepare beverages (aqueous decocts. The major secondary metabolites of Withania somnifera are the withanolides, which are C-28-steroidal lactone triterpenoids. Withania somnifera extracts exert chemopreventive and anticancer activities in vitro and in vivo. The aims of the present in silico study were, firstly, to investigate whether tumor cells develop cross-resistance between standard anticancer drugs and withanolides and, secondly, to elucidate the molecular determinants of sensitivity and resistance of tumor cells towards withanolides. Using IC50 concentrations of eight different withanolides (withaferin A, withaferin A diacetate, 3-azerininylwithaferin A, withafastuosin D diacetate, 4-B-hydroxy-withanolide E, isowithanololide E, withafastuosin E, and withaperuvin and 19 established anticancer drugs, we analyzed the cross-resistance profile of 60 tumor cell lines. The cell lines revealed cross-resistance between the eight withanolides. Consistent cross-resistance between withanolides and nitrosoureas (carmustin, lomustin, and semimustin was also observed. Then, we performed transcriptomic microarray-based COMPARE and hierarchical cluster analyses of mRNA expression to identify mRNA expression profiles predicting sensitivity or resistance towards withanolides. Genes from diverse functional groups were significantly associated with response of tumor cells to withaferin A diacetate, e.g. genes functioning in DNA damage and repair, stress response, cell growth regulation, extracellular matrix components, cell adhesion and cell migration, constituents of the ribosome, cytoskeletal organization and regulation, signal transduction, transcription factors, and others.

  6. Microarray-based DNA methylation study of Ewing's sarcoma of the bone.

    Science.gov (United States)

    Park, Hye-Rim; Jung, Woon-Won; Kim, Hyun-Sook; Park, Yong-Koo

    2014-10-01

    Alterations in DNA methylation patterns are a hallmark of malignancy. However, the majority of epigenetic studies of Ewing's sarcoma have focused on the analysis of only a few candidate genes. Comprehensive studies are thus lacking and are required. The aim of the present study was to identify novel methylation markers in Ewing's sarcoma using microarray analysis. The current study reports the microarray-based DNA methylation study of 1,505 CpG sites of 807 cancer-related genes from 69 Ewing's sarcoma samples. The Illumina GoldenGate Methylation Cancer Panel I microarray was used, and with the appropriate controls (n=14), a total of 92 hypermethylated genes were identified in the Ewing's sarcoma samples. The majority of the hypermethylated genes were associated with cell adhesion, cell regulation, development and signal transduction. The overall methylation mean values were compared between patients who survived and those that did not. The overall methylation mean was significantly higher in the patients who did not survive (0.25±0.03) than in those who did (0.22±0.05) (P=0.0322). However, the overall methylation mean was not found to significantly correlate with age, gender or tumor location. GDF10 , OSM , APC and HOXA11 were the most significant differentially-methylated genes, however, their methylation levels were not found to significantly correlate with the survival rate. The DNA methylation profile of Ewing's sarcoma was characterized and 92 genes that were significantly hypermethylated were detected. A trend towards a more aggressive behavior was identified in the methylated group. The results of this study indicated that methylation may be significant in the development of Ewing's sarcoma.

  7. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

    Directory of Open Access Journals (Sweden)

    Hsu Hui-Chi

    2011-04-01

    Full Text Available Abstract Background Optimizing treatment through microarray-based molecular subtyping is a promising method to address the problem of heterogeneity in breast cancer; however, current application is restricted to prediction of distant recurrence risk. This study investigated whether breast cancer molecular subtyping according to its global intrinsic biology could be used for treatment customization. Methods Gene expression profiling was conducted on fresh frozen breast cancer tissue collected from 327 patients in conjunction with thoroughly documented clinical data. A method of molecular subtyping based on 783 probe-sets was established and validated. Statistical analysis was performed to correlate molecular subtypes with survival outcome and adjuvant chemotherapy regimens. Heterogeneity of molecular subtypes within groups sharing the same distant recurrence risk predicted by genes of the Oncotype and MammaPrint predictors was studied. Results We identified six molecular subtypes of breast cancer demonstrating distinctive molecular and clinical characteristics. These six subtypes showed similarities and significant differences from the Perou-Sørlie intrinsic types. Subtype I breast cancer was in concordance with chemosensitive basal-like intrinsic type. Adjuvant chemotherapy of lower intensity with CMF yielded survival outcome similar to those of CAF in this subtype. Subtype IV breast cancer was positive for ER with a full-range expression of HER2, responding poorly to CMF; however, this subtype showed excellent survival when treated with CAF. Reduced expression of a gene associated with methotrexate sensitivity in subtype IV was the likely reason for poor response to methotrexate. All subtype V breast cancer was positive for ER and had excellent long-term survival with hormonal therapy alone following surgery and/or radiation therapy. Adjuvant chemotherapy did not provide any survival benefit in early stages of subtype V patients. Subtype V was

  8. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization

    International Nuclear Information System (INIS)

    Kao, Kuo-Jang; Chang, Kai-Ming; Hsu, Hui-Chi; Huang, Andrew T

    2011-01-01

    Optimizing treatment through microarray-based molecular subtyping is a promising method to address the problem of heterogeneity in breast cancer; however, current application is restricted to prediction of distant recurrence risk. This study investigated whether breast cancer molecular subtyping according to its global intrinsic biology could be used for treatment customization. Gene expression profiling was conducted on fresh frozen breast cancer tissue collected from 327 patients in conjunction with thoroughly documented clinical data. A method of molecular subtyping based on 783 probe-sets was established and validated. Statistical analysis was performed to correlate molecular subtypes with survival outcome and adjuvant chemotherapy regimens. Heterogeneity of molecular subtypes within groups sharing the same distant recurrence risk predicted by genes of the Oncotype and MammaPrint predictors was studied. We identified six molecular subtypes of breast cancer demonstrating distinctive molecular and clinical characteristics. These six subtypes showed similarities and significant differences from the Perou-Sørlie intrinsic types. Subtype I breast cancer was in concordance with chemosensitive basal-like intrinsic type. Adjuvant chemotherapy of lower intensity with CMF yielded survival outcome similar to those of CAF in this subtype. Subtype IV breast cancer was positive for ER with a full-range expression of HER2, responding poorly to CMF; however, this subtype showed excellent survival when treated with CAF. Reduced expression of a gene associated with methotrexate sensitivity in subtype IV was the likely reason for poor response to methotrexate. All subtype V breast cancer was positive for ER and had excellent long-term survival with hormonal therapy alone following surgery and/or radiation therapy. Adjuvant chemotherapy did not provide any survival benefit in early stages of subtype V patients. Subtype V was consistent with a unique subset of luminal A intrinsic

  9. Enhancement of allele discrimination by introduction of nucleotide mismatches into siRNA in allele-specific gene silencing by RNAi.

    Directory of Open Access Journals (Sweden)

    Yusuke Ohnishi

    Full Text Available Allele-specific gene silencing by RNA interference (RNAi is therapeutically useful for specifically inhibiting the expression of disease-associated alleles without suppressing the expression of corresponding wild-type alleles. To realize such allele-specific RNAi (ASP-RNAi, the design and assessment of small interfering RNA (siRNA duplexes conferring ASP-RNAi is vital; however, it is also difficult. In a previous study, we developed an assay system to assess ASP-RNAi with mutant and wild-type reporter alleles encoding the Photinus and Renilla luciferase genes. In line with experiments using the system, we realized that it is necessary and important to enhance allele discrimination between mutant and corresponding wild-type alleles. Here, we describe the improvement of ASP-RNAi against mutant alleles carrying single nucleotide variations by introducing base substitutions into siRNA sequences, where original variations are present in the central position. Artificially mismatched siRNAs or short-hairpin RNAs (shRNAs against mutant alleles of the human Prion Protein (PRNP gene, which appear to be associated with susceptibility to prion diseases, were examined using this assessment system. The data indicates that introduction of a one-base mismatch into the siRNAs and shRNAs was able to enhance discrimination between the mutant and wild-type alleles. Interestingly, the introduced mismatches that conferred marked improvement in ASP-RNAi, appeared to be largely present in the guide siRNA elements, corresponding to the 'seed region' of microRNAs. Due to the essential role of the 'seed region' of microRNAs in their association with target RNAs, it is conceivable that disruption of the base-pairing interactions in the corresponding seed region, as well as the central position (involved in cleavage of target RNAs, of guide siRNA elements could influence allele discrimination. In addition, we also suggest that nucleotide mismatches at the 3'-ends of sense

  10. A and MdMYB1 allele-specific markers controlling apple (Malus x domestica Borkh.) skin color and suitability for marker-assisted selection.

    Science.gov (United States)

    Zhang, X J; Wang, L X; Chen, X X; Liu, Y L; Meng, R; Wang, Y J; Zhao, Z Y

    2014-10-31

    Pre-selection for fruit skin color at the seedling stage would be highly advantageous, with marker-assisted selection offering a potential method for apple pre-selection. A and MdMYB1 alleles are allele-specific DNA markers that are potentially associated with apple skin color, and co-segregate with the Rf and Rni loci, respectively. Here, we assessed the potential application of these 2 alleles for marker-assisted breeding across 30 diverse cultivars and 2 apple seedling progenies. The red skin color phenotype was usually associated with the MdMYB1-1 allele and A(1) allele, respectively, while the 2 molecular markers provided approximately 91% predictability in the 'Fuji' x 'Cripps Pink' and 'Fuji' x 'Gala' progenies. The results obtained from the 30 cultivars and 2 progenies were consistent for the 2 molecular markers. Hence, the results supported that Rf and Rni could be located in a gene cluster, or even correspond to alleles of the same gene. Our results are consistent with the hypothesis that red/yellow dimorphism is controlled by a monogenic system, with the presence of the red anthocyanin pigmentation being dominant. In addition, our results supported that the practical utilization of the 2 function markers to efficiently and accurately select red-skinned apple cultivars in apple scion breeding programs.

  11. Multiple Avirulence Loci and Allele-Specific Effector Recognition Control the Pm3 Race-Specific Resistance of Wheat to Powdery Mildew[OPEN

    Science.gov (United States)

    Roffler, Stefan; Stirnweis, Daniel; Treier, Georges; Herren, Gerhard; Korol, Abraham B.; Wicker, Thomas

    2015-01-01

    In cereals, several mildew resistance genes occur as large allelic series; for example, in wheat (Triticum aestivum and Triticum turgidum), 17 functional Pm3 alleles confer agronomically important race-specific resistance to powdery mildew (Blumeria graminis). The molecular basis of race specificity has been characterized in wheat, but little is known about the corresponding avirulence genes in powdery mildew. Here, we dissected the genetics of avirulence for six Pm3 alleles and found that three major Avr loci affect avirulence, with a common locus_1 involved in all AvrPm3-Pm3 interactions. We cloned the effector gene AvrPm3a2/f2 from locus_2, which is recognized by the Pm3a and Pm3f alleles. Induction of a Pm3 allele-dependent hypersensitive response in transient assays in Nicotiana benthamiana and in wheat demonstrated specificity. Gene expression analysis of Bcg1 (encoded by locus_1) and AvrPm3 a2/f2 revealed significant differences between isolates, indicating that in addition to protein polymorphisms, expression levels play a role in avirulence. We propose a model for race specificity involving three components: an allele-specific avirulence effector, a resistance gene allele, and a pathogen-encoded suppressor of avirulence. Thus, whereas a genetically simple allelic series controls specificity in the plant host, recognition on the pathogen side is more complex, allowing flexible evolutionary responses and adaptation to resistance genes. PMID:26452600

  12. Evaluation of efficiency of nested multiplex allele-specific PCR assay for detection of multidrug resistant tuberculosis directly from sputum samples.

    Science.gov (United States)

    Mistri, S K; Sultana, M; Kamal, S M M; Alam, M M; Irin, F; Nessa, J; Ahsan, C R; Yasmin, M

    2016-05-01

    For an effective control of tuberculosis, rapid detection of multidrug resistant tuberculosis (MDR-TB) is necessary. Therefore, we developed a modified nested multiplex allele-specific polymerase chain reaction (MAS-PCR) method that enables rapid MDR-TB detection directly from sputum samples. The efficacy of this method was evaluated using 79 sputum samples collected from suspected tuberculosis patients. The performance of nested MAS-PCR method was compared with other MDR-TB detection methods like drug susceptibility testing (DST) and DNA sequencing. As rifampicin (RIF) resistance conforms to MDR-TB in greater than 90% cases, only the presence of RIF-associated mutations in rpoB gene was determined by DNA sequencing and nested MAS-PCR to detect MDR-TB. The concordance between nested MAS-PCR and DNA sequencing results was found to be 96·3%. When compared with DST, the sensitivity and specificity of nested MAS-PCR for RIF-resistance detection were determined to be 92·9 and 100% respectively. For developing- and high-TB burden countries, molecular-based tests have been recommended by the World Health Organization for rapid detection of MDR-TB. The results of this study indicate that, nested MAS-PCR assay might be a practical and relatively cost effective molecular method for rapid detection of MDR-TB from suspected sputum samples in developing countries with resource poor settings. © 2016 The Society for Applied Microbiology.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  14. SU94. Allele-Specific and Trauma-Related Epigenetic Changes in the FKBP5 Gene: Differences Between Psychotic Patients and Healthy Controls

    Science.gov (United States)

    Mihaljevic, Marina; Franic, Dusica; Soldatovic, Ivan; Andric, Sanja; Mirjanic, Tijana; Novakovic, Ivana; Adzic, Miroslav; Maric, Nadja

    2017-01-01

    Abstract Background: Hypothalamic-pituitary-adrenal (HPA) axis dysregulation is a proposed etiological mechanism of psychosis. Recent studies highlighted impact of the FKBP5 gene and its functional variant rs1360780, which risk (T) allele affects the activity of HPA axis following stress exposure, on psychotic patients exposed to early trauma (1). Additionally, risk allele and trauma dependent FKBP5 demethylation in intron 7 was observed in traumatized individuals (2). Thus, the purpose of this pilot study was to investigate influence of the risk allele and trauma on FKBP5 DNA methylation levels at intron 7 in psychotic patients and to compare it with healthy individuals. Methods: The sample consisted of 24 psychosis spectrum patients and 24 controls matched by age and gender. All participants were genotyped for rs1360780 and divided into 2 groups depending on the presence of the risk allele (risk and nonrisk group). DNA methylation levels at 3 CpG sites (CpG1, CpG2, and CpG3) in intron 7 were analyzed by Sanger sequencing. Early-life adversities were measured by Childhood Trauma Questionnaire. Pearson correlation and t test were performed as appropriate. Results: Analyses revealed decreased FKBP5 methylation at targeted CpG sites and averaged methylation level (AML) at intron 7 in patients compared to controls (P = .026, P = .017, P = .027, and P = .003, respectively). Decreased AML and methylation at CpG3 were observed comparing risk and nonrisk patients’ groups (P = .018 and P = .016, respectively). Additionally, decreased methylation was found in risk patients’ group compared to risk controls’ group. No differences were found comparing nonrisk groups. Furthermore, strong negative associations between trauma and methylation at CpG3 and AML were observed only in risk controls’ group (r = −0.707, P = .007; r = −0.741, P = .004, respectively). Conclusion: Our preliminary results revealed allele-specific epigenetic changes of the FKBP

  15. SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data.

    Science.gov (United States)

    Zhang, Zhongyang; Hao, Ke

    2015-11-01

    Cancer genomes exhibit profound somatic copy number alterations (SCNAs). Studying tumor SCNAs using massively parallel sequencing provides unprecedented resolution and meanwhile gives rise to new challenges in data analysis, complicated by tumor aneuploidy and heterogeneity as well as normal cell contamination. While the majority of read depth based methods utilize total sequencing depth alone for SCNA inference, the allele specific signals are undervalued. We proposed a joint segmentation and inference approach using both signals to meet some of the challenges. Our method consists of four major steps: 1) extracting read depth supporting reference and alternative alleles at each SNP/Indel locus and comparing the total read depth and alternative allele proportion between tumor and matched normal sample; 2) performing joint segmentation on the two signal dimensions; 3) correcting the copy number baseline from which the SCNA state is determined; 4) calling SCNA state for each segment based on both signal dimensions. The method is applicable to whole exome/genome sequencing (WES/WGS) as well as SNP array data in a tumor-control study. We applied the method to a dataset containing no SCNAs to test the specificity, created by pairing sequencing replicates of a single HapMap sample as normal/tumor pairs, as well as a large-scale WGS dataset consisting of 88 liver tumors along with adjacent normal tissues. Compared with representative methods, our method demonstrated improved accuracy, scalability to large cancer studies, capability in handling both sequencing and SNP array data, and the potential to improve the estimation of tumor ploidy and purity.

  16. Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek’s disease virus infection via analysis of allele-specific expression

    Directory of Open Access Journals (Sweden)

    Sean eMaceachern

    2012-01-01

    Full Text Available Marek’s disease (MD is a commercially important neoplastic disease of chickens caused by Marek’s disease virus (MDV, an oncogenic alphaherpesvirus. Selecting for increased genetic resistance to MD is a control strategy that can augment vaccinal control measures. To identify high-confidence candidate MD resistance genes, we conducted a genome-wide screen for allele-specific expression (ASE amongst F1 progeny of two inbred chicken lines that differ in MD resistance. High throughput sequencing was used to profile transcriptomes from pools of uninfected and infected individuals at 4 days post-infection to identify any genes showing ASE in response to MDV infection. RNA sequencing identified 22,655 single nucleotide polymorphisms (SNPs of which 5,360 in 3,773 genes exhibited significant allelic imbalance. Illumina GoldenGate assays were subsequently used to quantify regulatory variation controlled at the gene (cis and elsewhere in the genome (trans by examining differences in expression between F1 individuals and artificial F1 RNA pools over 6 time periods in 1,536 of the most significant SNPs identified by RNA sequencing. Allelic imbalance as a result of cis-regulatory changes was confirmed in 861 of the 1,233 GoldenGate assays successfully examined. Furthermore we have identified 7 genes that display trans-regulation only in infected animals and approximately 500 SNP that show a complex interaction between cis- and trans-regulatory changes. Our results indicate ASE analyses are a powerful approach to identify regulatory variation responsible for differences in transcript abundance in genes underlying complex traits. And the genes with SNPs exhibiting ASE provide a strong foundation to further investigate the causative polymorphisms and genetic mechanisms for MD resistance. Finally, the methods used here for identifying specific genes and SNPs may have practical implications for applying marker-assisted selection to complex traits that are

  17. Minority drug-resistant HIV-1 variants in treatment naïve East-African and Caucasian patients detected by allele-specific real-time PCR.

    Directory of Open Access Journals (Sweden)

    Halime Ekici

    Full Text Available To assess the presence of two major non-nucleoside reverse transcriptase inhibitors (NNRTI drug resistance mutations (DRMs, Y181C and K103N, in minor viral quasispecies of treatment naïve HIV-1 infected East-African and Swedish patients by allele-specific polymerase chain reaction (AS-PCR.Treatment naïve adults (n=191 with three epidemiological backgrounds were included: 92 Ethiopians living in Ethiopia; 55 East-Africans who had migrated to Sweden; and 44 Caucasians living in Sweden. The pol gene was analysed by standard population sequencing and by AS-PCR for the detection of Y181C and K103N.The Y181C was detected in the minority quasispecies of six Ethiopians (6.5%, in two Caucasians (4.5%, and in one East-African (1.8%. The K103N was detected in one East- African (1.8%, by both methods. The proportion of mutants ranged from 0.25% to 17.5%. Additional DRMs were found in all three treatment naïve patient groups by population sequencing.Major NNRTI mutations can be found by AS-PCR in minor quasispecies of treatment naïve HIV-1 infected Ethiopians living in Ethiopia, in East-African and Caucasian patients living in Sweden in whom population sequencing reveal wild-type virus only. Surveys with standard sequencing are likely to underestimate transmitted drug resistance and the presence of resistant minor quasispecies in treatment naïve patients should be topic for future large scale studies.

  18. Mutant Allele-Specific Uncoupling of PENETRATION3 Functions Reveals Engagement of the ATP-Binding Cassette Transporter in Distinct Tryptophan Metabolic Pathways1[OPEN

    Science.gov (United States)

    Lu, Xunli; Dittgen, Jan; Piślewska-Bednarek, Mariola; Molina, Antonio; Schneider, Bernd; Doubský, Jan; Schneeberger, Korbinian; Schulze-Lefert, Paul

    2015-01-01

    Arabidopsis (Arabidopsis thaliana) PENETRATION (PEN) genes quantitatively contribute to the execution of different forms of plant immunity upon challenge with diverse leaf pathogens. PEN3 encodes a plasma membrane-resident pleiotropic drug resistance-type ATP-binding cassette transporter and is thought to act in a pathogen-inducible and PEN2 myrosinase-dependent metabolic pathway in extracellular defense. This metabolic pathway directs the intracellular biosynthesis and activation of tryptophan-derived indole glucosinolates for subsequent PEN3-mediated efflux across the plasma membrane at pathogen contact sites. However, PEN3 also functions in abiotic stress responses to cadmium and indole-3-butyric acid (IBA)-mediated auxin homeostasis in roots, raising the possibility that PEN3 exports multiple functionally unrelated substrates. Here, we describe the isolation of a pen3 allele, designated pen3-5, that encodes a dysfunctional protein that accumulates in planta like wild-type PEN3. The specific mutation in pen3-5 uncouples PEN3 functions in IBA-stimulated root growth modulation, callose deposition induced with a conserved peptide epitope of bacterial flagellin (flg22), and pathogen-inducible salicylic acid accumulation from PEN3 activity in extracellular defense, indicating the engagement of multiple PEN3 substrates in different PEN3-dependent biological processes. We identified 4-O-β-d-glucosyl-indol-3-yl formamide (4OGlcI3F) as a pathogen-inducible, tryptophan-derived compound that overaccumulates in pen3 leaf tissue and has biosynthesis that is dependent on an intact PEN2 metabolic pathway. We propose that a precursor of 4OGlcI3F is the PEN3 substrate in extracellular pathogen defense. These precursors, the shared indole core present in IBA and 4OGlcI3F, and allele-specific uncoupling of a subset of PEN3 functions suggest that PEN3 transports distinct indole-type metabolites in distinct biological processes. PMID:26023163

  19. Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis

    OpenAIRE

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

    2004-01-01

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

  20. Allele-specific primer polymerase chain reaction for a single nucleotide polymorphism (C1205T) of swine Toll-like receptor 5 and comparison of the allelic frequency among several pig breeds in Japan and the Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Muneta, Y.; Minagawa, Y.; Kusumoto, M.; Shinkai, H.; Uenishi, H.; Šplíchal, Igor

    2012-01-01

    Roč. 56, č. 6 (2012), s. 385-391 ISSN 0385-5600 R&D Projects: GA ČR GA524/09/0365 Institutional support: RVO:61388971 Keywords : allele-specific PCR * Salmonella enterica serovar Choleraesuis * single nucleotide polymorphism Subject RIV: EC - Immunology Impact factor: 1.545, year: 2012

  1. Efficacy of a novel PCR- and microarray-based method in diagnosis of a prosthetic joint infection

    Science.gov (United States)

    2014-01-01

    Background and purpose Polymerase chain reaction (PCR) methods enable detection and species identification of many pathogens. We assessed the efficacy of a new PCR and microarray-based platform for detection of bacteria in prosthetic joint infections (PJIs). Methods This prospective study involved 61 suspected PJIs in hip and knee prostheses and 20 negative controls. 142 samples were analyzed by Prove-it Bone and Joint assay. The laboratory staff conducting the Prove-it analysis were not aware of the results of microbiological culture and clinical findings. The results of the analysis were compared with diagnosis of PJIs defined according to the Musculoskeletal Infection Society (MSIS) criteria and with the results of microbiological culture. Results 38 of 61 suspected PJIs met the definition of PJI according to the MSIS criteria. Of the 38 patients, the PCR detected bacteria in 31 whereas bacterial culture was positive in 28 patients. 15 of the PJI patients were undergoing antimicrobial treatment as the samples for analysis were obtained. When antimicrobial treatment had lasted 4 days or more, PCR detected bacteria in 6 of the 9 patients, but positive cultures were noted in only 2 of the 9 patients. All PCR results for the controls were negative. Of the 61 suspected PJIs, there were false-positive PCR results in 6 cases. Interpretation The Prove-it assay was helpful in PJI diagnostics during ongoing antimicrobial treatment. Without preceding treatment with antimicrobials, PCR and microarray-based assay did not appear to give any additional information over culture. PMID:24564748

  2. Rapid extraction of genomic DNA from saliva for HLA typing on microarray based on magnetic nanobeads

    Energy Technology Data Exchange (ETDEWEB)

    Xie Xin; Zhang Xu E-mail: shinezhang@hotmail.com; Yu Bingbin; Gao Huafang; Zhang Huan; Fei Weiyang

    2004-09-01

    A series of simplified protocols are developed for extracting genomic DNA from saliva by using the magnetic nanobeads as absorbents. In these protocols, both the enrichment of the target cells and the adsorption of DNA can be achieved simultaneously by our functionally modified magnetic beads in one step, and the DNA-nanobeads complex can be used as PCR templates. HLA typing based on an oligonucleotide array was conducted by hybridization with the PCR products. The result shows that the protocols are robust and sensitive.

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

    Science.gov (United States)

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

    2004-11-01

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

  4. Inter- and intra-individual variation in allele-specific DNA methylation and gene expression in children conceived using assisted reproductive technology.

    Directory of Open Access Journals (Sweden)

    Nahid Turan

    2010-07-01

    Full Text Available Epidemiological studies have reported a higher incidence of rare disorders involving imprinted genes among children conceived using assisted reproductive technology (ART, suggesting that ART procedures may be disruptive to imprinted gene methylation patterns. We examined intra- and inter-individual variation in DNA methylation at the differentially methylated regions (DMRs of the IGF2/H19 and IGF2R loci in a population of children conceived in vitro or in vivo. We found substantial variation in allele-specific methylation at both loci in both groups. Aberrant methylation of the maternal IGF2/H19 DMR was more common in the in vitro group, and the overall variance was also significantly greater in the in vitro group. We estimated the number of trophoblast stem cells in each group based on approximation of the variance of the binomial distribution of IGF2/H19 methylation ratios, as well as the distribution of X chromosome inactivation scores in placenta. Both of these independent measures indicated that placentas of the in vitro group were derived from fewer stem cells than the in vivo conceived group. Both IGF2 and H19 mRNAs were significantly lower in placenta from the in vitro group. Although average birth weight was lower in the in vitro group, we found no correlation between birth weight and IGF2 or IGF2R transcript levels or the ratio of IGF2/IGF2R transcript levels. Our results show that in vitro conception is associated with aberrant methylation patterns at the IGF2/H19 locus. However, very little of the inter- or intra-individual variation in H19 or IGF2 mRNA levels can be explained by differences in maternal DMR DNA methylation, in contrast to the expectations of current transcriptional imprinting models. Extraembryonic tissues of embryos cultured in vitro appear to be derived from fewer trophoblast stem cells. It is possible that this developmental difference has an effect on placental and fetal growth.

  5. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

    Science.gov (United States)

    Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

    2016-08-18

    Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

  6. Establishment of real time allele specific locked nucleic acid quantitative PCR for detection of HBV YIDD (ATT mutation and evaluation of its application.

    Directory of Open Access Journals (Sweden)

    Yongbin Zeng

    Full Text Available BACKGROUND: Long-term use of nucleos(tide analogues can increase risk of HBV drug-resistance mutations. The rtM204I (ATT coding for isoleucine is one of the most important resistance mutation sites. Establishing a simple, rapid, reliable and highly sensitive assay to detect the resistant mutants as early as possible is of great clinical significance. METHODS: Recombinant plasmids for HBV YMDD (tyrosine-methionine-aspartate-aspartate and YIDD (tyrosine-isoleucine-aspartate-aspartate were constructed by TA cloning. Real time allele specific locked nucleic acid quantitative PCR (RT-AS-LNA-qPCR with SYBR Green I was established by LNA-modified primers and evaluated with standard recombinant plasmids, clinical templates (the clinical wild type and mutant HBV DNA mixture and 102 serum samples from nucleos(tide analogues-experienced patients. The serum samples from a chronic hepatitis B (CHB patient firstly received LMV mono therapy and then switched to LMV + ADV combined therapy were also dynamically analyzed for 10 times. RESULTS: The linear range of the assay was between 1×10(9 copies/μl and 1 × 10(2 copies/μl. The low detection limit was 1 × 10(1 copies/μl. Sensitivity of the assay were 10(-6, 10(-4 and 10(-2 in the wild-type background of 1 × 10(9 copies/μl, 1 × 10(7 copies/μl and 1 × 10(5 copies/μl, respectively. The sensitivity of the assay in detection of clinical samples was 0.03%. The complete coincidence rate between RT-AS-LNA-qPCR and direct sequencing was 91.2% (93/102, partial coincidence rate was 8.8% (9/102, and no complete discordance was observed. The two assays showed a high concordance (Kappa = 0.676, P = 0.000. Minor variants can be detected 18 weeks earlier than the rebound of HBV DNA load and alanine aminotransferase level. CONCLUSIONS: A rapid, cost-effective, high sensitive, specific and reliable method of RT-AS-LNA-qPCR with SYBR Green I for early and absolute quantification of HBV YIDD (ATT coding for isoleucine

  7. Microarray-based analysis of differential gene expression between infective and noninfective larvae of Strongyloides stercoralis.

    Directory of Open Access Journals (Sweden)

    Roshan Ramanathan

    2011-05-01

    Full Text Available Differences between noninfective first-stage (L1 and infective third-stage (L3i larvae of parasitic nematode Strongyloides stercoralis at the molecular level are relatively uncharacterized. DNA microarrays were developed and utilized for this purpose.Oligonucleotide hybridization probes for the array were designed to bind 3,571 putative mRNA transcripts predicted by analysis of 11,335 expressed sequence tags (ESTs obtained as part of the Nematode EST project. RNA obtained from S. stercoralis L3i and L1 was co-hybridized to each array after labeling the individual samples with different fluorescent tags. Bioinformatic predictions of gene function were developed using a novel cDNA Annotation System software. We identified 935 differentially expressed genes (469 L3i-biased; 466 L1-biased having two-fold expression differences or greater and microarray signals with a p value<0.01. Based on a functional analysis, L1 larvae have a larger number of genes putatively involved in transcription (p = 0.004, and L3i larvae have biased expression of putative heat shock proteins (such as hsp-90. Genes with products known to be immunoreactive in S. stercoralis-infected humans (such as SsIR and NIE had L3i biased expression. Abundantly expressed L3i contigs of interest included S. stercoralis orthologs of cytochrome oxidase ucr 2.1 and hsp-90, which may be potential chemotherapeutic targets. The S. stercoralis ortholog of fatty acid and retinol binding protein-1, successfully used in a vaccine against Ancylostoma ceylanicum, was identified among the 25 most highly expressed L3i genes. The sperm-containing glycoprotein domain, utilized in a vaccine against the nematode Cooperia punctata, was exclusively found in L3i biased genes and may be a valuable S. stercoralis target of interest.A new DNA microarray tool for the examination of S. stercoralis biology has been developed and provides new and valuable insights regarding differences between infective and

  8. Prevalence, identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia.

    Science.gov (United States)

    Hmaïed, F; Helel, S; Le Berre, V; François, J-M; Leclercq, A; Lecuit, M; Smaoui, H; Kechrid, A; Boudabous, A; Barkallah, I

    2014-02-01

    We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates. Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for human listeriosis isolated in hospital of Tunis were included. Multiplex PCR serogrouping and pulsed field gel electrophoresis (PFGE) applying the enzyme AscI and ApaI were used for the characterization of isolates of L. monocytogenes. We have developed a rapid microarray-based assay to a reliable discrimination of species within the Listeria genus. The prevalence of Listeria spp. in food samples was estimated at 14% by using classical biochemical identification. Two samples were assigned to L. monocytogenes and 12 to L. innocua. DNA microarray allowed unambiguous identification of Listeria species. Our results obtained by microarray-based assay were in accordance with the biochemical identification. The two food L. monocytogenes isolates were assigned to the PCR serogroup IIa (serovar 1/2a). Whereas human L. monocytogenes isolates were of PCR serogroup IVb, (serovars 4b). These isolates present a high similarity in PFGE. Food L. monocytogenes isolates were classified into two different pulsotypes. These pulsotypes were different from that of the five strains responsible for the human cases. We confirmed the presence of Listeria spp. in variety of food samples in Tunis. Increased food and clinical surveillance must be taken into consideration in Tunisia to identify putative infections sources. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  9. A microarray-based genetic screen for yeast chronological aging factors.

    Directory of Open Access Journals (Sweden)

    Mirela Matecic

    2010-04-01

    Full Text Available Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging. In this study we utilized the budding yeast, Saccharomyces cerevisiae, in a large-scale screen for genes that function in the regulation of chronological lifespan, which is defined by the number of days that non-dividing cells remain viable. A pooled collection of viable haploid gene deletion mutants, each tagged with unique identifying DNA "bar-code" sequences was chronologically aged in liquid culture. Viable mutants in the aging population were selected at several time points and then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags. Multiple short- and long-lived mutants were identified using this approach. Among the confirmed short-lived mutants were those defective for autophagy, indicating a key requirement for the recycling of cellular organelles in longevity. Defects in autophagy also prevented lifespan extension induced by limitation of amino acids in the growth media. Among the confirmed long-lived mutants were those defective in the highly conserved de novo purine biosynthesis pathway (the ADE genes, which ultimately produces IMP and AMP. Blocking this pathway extended lifespan to the same degree as calorie (glucose restriction. A recently discovered cell-extrinsic mechanism of chronological aging involving acetic acid secretion and toxicity was suppressed in a long-lived ade4Delta mutant and exacerbated by a short-lived atg16Delta autophagy mutant. The identification of multiple novel effectors of yeast chronological lifespan will greatly aid in the elucidation of mechanisms that cells and organisms utilize in slowing down the aging process.

  10. Microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis

    CSIR Research Space (South Africa)

    Barros, E

    2009-05-01

    Full Text Available of Eucalyptus grandis planting stock that exhibit preferred wood qualities is thus a priority of the South African forestry industry. The researchers used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression...

  11. Lipoprotein(a) and HIV: Allele-Specific Apolipoprotein(a) Levels Predict Carotid Intima-Media Thickness in HIV-Infected Young Women in the Women's Interagency HIV Study.

    Science.gov (United States)

    Enkhmaa, Byambaa; Anuurad, Erdembileg; Zhang, Wei; Li, Chin-Shang; Kaplan, Robert; Lazar, Jason; Merenstein, Dan; Karim, Roksana; Aouizerat, Brad; Cohen, Mardge; Butler, Kenneth; Pahwa, Savita; Ofotokun, Igho; Adimora, Adaora A; Golub, Elizabeth; Berglund, Lars

    2017-05-01

    In the general population, lipoprotein(a) [Lp(a)] has been established as an independent causal risk factor for cardiovascular disease. Lp(a) levels are to a major extent regulated by a size polymorphism in the apolipoprotein(a) [apo(a)] gene. The roles of Lp(a)/apo(a) in human immunodeficiency virus (HIV)-related elevated cardiovascular disease risk remain unclear. The associations between total plasma Lp(a) level, allele-specific apo(a) level, an Lp(a) level carried by individual apo(a) alleles, and common carotid artery intima-media thickness were assessed in 150 HIV-infected and 100 HIV-uninfected women in the WIHS (Women's Interagency HIV Study). Linear regression analyses with and without adjustments were used. The cohort was young (mean age, ≈31 years), with the majority being Blacks (≈70%). The prevalence of a small size apo(a) (≤22 Kringle repeats) or a high Lp(a) level (≥30 mg/dL) was similar by HIV status. Total plasma Lp(a) level ( P =0.029) and allele-specific apo(a) level carried by the smaller apo(a) sizes ( P =0.022) were significantly associated with carotid artery intima-media thickness in the HIV-infected women only. After accounting for confounders (age, race, smoking, body mass index, blood pressure, hepatitis C virus coinfection, menopause, plasma lipids, treatment status, CD4 + T cell count, and HIV/RNA viral load), the association remained significant for both Lp(a) ( P =0.035) and allele-specific apo(a) level carried by the smaller apo(a) sizes ( P =0.010) in the HIV-infected women. Notably, none of the other lipids/lipoproteins was associated with carotid artery intima-media thickness. Lp(a) and allele-specific apo(a) levels predict carotid artery intima-media thickness in HIV-infected young women. Further research is needed to identify underlying mechanisms of an increased Lp(a) atherogenicity in HIV infection. © 2017 American Heart Association, Inc.

  12. Development of a microarray-based assay for efficient testing of new HSP70/DnaK inhibitors.

    Science.gov (United States)

    Mohammadi-Ostad-Kalayeh, Sona; Hrupins, Vjaceslavs; Helmsen, Sabine; Ahlbrecht, Christin; Stahl, Frank; Scheper, Thomas; Preller, Matthias; Surup, Frank; Stadler, Marc; Kirschning, Andreas; Zeilinger, Carsten

    2017-12-15

    A facile method for testing ATP binding in a highly miniaturized microarray environment using human HSP70 and DnaK from Mycobacterium tuberculosis as biological targets is reported. Supported by molecular modelling studies we demonstrate that the position of the fluorescence label on ATP has a strong influence on the binding to human HSP70. Importantly, the label has to be positioned on the adenine ring and not to the terminal phosphate group. Unlabelled ATP displaced bound Cy5-ATP from HSP70 in the micromolar range. The affinity of a well-known HSP70 inhibitor VER155008 for the ATP binding site in HSP70 was determined, with a EC 50 in the micromolar range, whereas reblastin, a HSP90-inhibitor, did not compete for ATP in the presence of HSP70. The applicability of the method was demonstrated by screening a small compound library of natural products. This unraveled that terphenyls rickenyl A and D, recently isolated from cultures of the fungus Hypoxylon rickii, are inhibitors of HSP70. They compete with ATP for the chaperone in the range of 29 µM (Rickenyl D) and 49 µM (Rickenyl A). Furthermore, the microarray-based test system enabled protein-protein interaction analysis using full-length HSP70 and HSP90 proteins. The labelled full-length human HSP90 binds with a half-maximal affinity of 5.5 µg/ml (∼40 µM) to HSP70. The data also demonstrate that the microarray test has potency for many applications from inhibitor screening to target-oriented interaction studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Development of an allele-specific PCR assay for simultaneous sero-typing of avian pathogenic Escherichia coli predominant O1, O2, O18 and O78 strains.

    Science.gov (United States)

    Wang, Shaohui; Meng, Qingmei; Dai, Jianjun; Han, Xiangan; Han, Yue; Ding, Chan; Liu, Haiwen; Yu, Shengqing

    2014-01-01

    Systemic infections by avian pathogenic Escherichia coli (APEC) are economically devastating to poultry industries worldwide. E. coli strains belonging to serotypes O1, O2, O18 and O78 are preferentially associated with avian colibacillosis. The rfb gene cluster controlling O antigen synthesis is usually various among different E. coli serotypes. In present study, the rfb gene clusters of E. coli serotypes O1, O2, O18 and O78 were characterized and compared. Based on the serotype-specific genes in rfb gene cluster, an allele-specific polymerase chain reaction (PCR) assay was developed. This PCR assay was highly specific and reliable for sero-typing of APEC O1, O2, O18 and O78 strains. The sensitivity of the assay was determined as 10 pg DNA or 10 colony forming units (CFUs) bacteria for serotypes O2 and O18 strains, and 500 pg DNA or 1,000 CFUs bacteria for serotypes O1 and O78 strains. Using this PCR system, APEC isolates and the infected tissue samples were categorized successfully. Furthermore, it was able to differentiate the serotypes for the samples with multi-agglutination in the traditional serum agglutination assay. Therefore, the allele-specific PCR is more simple, rapid and accurate assay for APEC diagnosis, epidemiologic study and vaccine development.

  14. Development of an allele-specific PCR assay for simultaneous sero-typing of avian pathogenic Escherichia coli predominant O1, O2, O18 and O78 strains.

    Directory of Open Access Journals (Sweden)

    Shaohui Wang

    Full Text Available Systemic infections by avian pathogenic Escherichia coli (APEC are economically devastating to poultry industries worldwide. E. coli strains belonging to serotypes O1, O2, O18 and O78 are preferentially associated with avian colibacillosis. The rfb gene cluster controlling O antigen synthesis is usually various among different E. coli serotypes. In present study, the rfb gene clusters of E. coli serotypes O1, O2, O18 and O78 were characterized and compared. Based on the serotype-specific genes in rfb gene cluster, an allele-specific polymerase chain reaction (PCR assay was developed. This PCR assay was highly specific and reliable for sero-typing of APEC O1, O2, O18 and O78 strains. The sensitivity of the assay was determined as 10 pg DNA or 10 colony forming units (CFUs bacteria for serotypes O2 and O18 strains, and 500 pg DNA or 1,000 CFUs bacteria for serotypes O1 and O78 strains. Using this PCR system, APEC isolates and the infected tissue samples were categorized successfully. Furthermore, it was able to differentiate the serotypes for the samples with multi-agglutination in the traditional serum agglutination assay. Therefore, the allele-specific PCR is more simple, rapid and accurate assay for APEC diagnosis, epidemiologic study and vaccine development.

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

    Science.gov (United States)

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

    2016-05-01

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

  16. Rapid identification of carbapenemase genes in gram-negative bacteria with an oligonucleotide microarray-based assay.

    Directory of Open Access Journals (Sweden)

    Sascha D Braun

    Full Text Available Rapid molecular identification of carbapenemase genes in Gram-negative bacteria is crucial for infection control and prevention, surveillance and for epidemiological purposes. Furthermore, it may have a significant impact upon determining the appropriate initial treatment and greatly benefit for critically ill patients. A novel oligonucleotide microarray-based assay was developed to simultaneously detect genes encoding clinically important carbapenemases as well as selected extended (ESBL and narrow spectrum (NSBL beta-lactamases directly from clonal culture material within few hours. Additionally, a panel of species specific markers was included to identify Escherichia coli, Pseudomonas aeruginosa, Citrobacter freundii/braakii, Klebsiella pneumoniae and Acinetobacter baumannii. The assay was tested using a panel of 117 isolates collected from urinary, blood and stool samples. For these isolates, phenotypic identifications and susceptibility tests were available. An independent detection of carbapenemase, ESBL and NSBL genes was carried out by various external reference laboratories using PCR methods. In direct comparison, the microarray correctly identified 98.2% of the covered carbapenemase genes. This included blaVIM (13 out of 13, blaGIM (2/2, blaKPC (27/27, blaNDM (5/5, blaIMP-2/4/7/8/13/14/15/16/31 (10/10, blaOXA-23 (12/13, blaOXA-40-group (7/7, blaOXA-48-group (32/33, blaOXA-51 (1/1 and blaOXA-58 (1/1. Furthermore, the test correctly identified additional beta-lactamases [blaOXA-1 (16/16, blaOXA-2 (4/4, blaOXA-9 (33/33, OXA-10 (3/3, blaOXA-51 (25/25, blaOXA-58 (2/2, CTX-M1/M15 (17/17 and blaVIM (1/1]. In direct comparison to phenotypical identification obtained by VITEK or MALDI-TOF systems, 114 of 117 (97.4% isolates, including Acinetobacter baumannii (28/28, Enterobacter spec. (5/5, Escherichia coli (4/4, Klebsiella pneumoniae (62/63, Klebsiella oxytoca (0/2, Pseudomonas aeruginosa (12/12, Citrobacter freundii (1/1 and Citrobacter

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

    Science.gov (United States)

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

    2009-06-01

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

  18. DNA microarray-based solid-phase RT-PCR for rapid detection and identification of influenza virus type A and subtypes H5 and H7

    DEFF Research Database (Denmark)

    Yi, Sun; Dhumpa, Raghuram; Bang, Dang Duong

    2011-01-01

    of RNA extract in the liquid phase with sequence-specific nested PCR on the solid phase. A simple ultraviolet cross-linking method was used to immobilize the DNA probes over an unmodified glass surface, which makes solid-phase PCR a convenient possibility for AIV screening. The testing of 33 avian fecal....... In this article, a DNA microarray-based solid-phase polymerase chain reaction (PCR) approach has been developed for rapid detection of influenza virus type A and for simultaneous identification of pathogenic virus subtypes H5 and H7. This solid-phase RT-PCR method combined reverse-transcription amplification...

  19. The − 5 A/G single-nucleotide polymorphism in the core promoter region of MT2A and its effect on allele-specific gene expression and Cd, Zn and Cu levels in laryngeal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Starska, Katarzyna, E-mail: katarzyna.starska@umed.lodz.pl [I Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Kopcinskiego 22, 90-153 Łódź (Poland); Krześlak, Anna; Forma, Ewa [Department of Cytobiochemistry, University of Łódź, Pomorska 142/143, 90-236 Łódź (Poland); Olszewski, Jurek [II Department of Otolaryngology and Laryngological Oncology, Medical University of Łódź, Żeromskiego 113, 90-549 Łódź (Poland); Morawiec-Sztandera, Alina [Department of Head and Neck Surgery, Medical University of Łódź, Paderewskiego 4, 93-509 Łódź (Poland); Aleksandrowicz, Paweł [Department of Otolaryngology and Laryngological Oncology, Medical University of Lublin, Jaczewskiego 8, 20-954 Lublin (Poland); Lewy-Trenda, Iwona [Department of Pathology, Medical University of Łódź, Pomorska 251, 92-213 Łódź (Poland); and others

    2014-10-15

    Metallothioneins (MTs) are low molecular weight, cysteine-rich heavy metal-binding proteins which participate in the mechanisms of Zn homeostasis, and protect against toxic metals. MTs contain metal-thiolate cluster groups and suppress metal toxicity by binding to them. The aim of this study was to determine the − 5 A/G (rs28366003) single-nucleotide polymorphism (SNP) in the core promoter region of the MT2A gene and to investigate its effect on allele-specific gene expression and Cd, Zn and Cu content in squamous cell laryngeal cancer (SCC) and non-cancerous laryngeal mucosa (NCM) as a control. The MT2A promoter region − 5 A/G SNP was determined by restriction fragment length polymorphism using 323 SCC and 116 NCM. MT2A gene analysis was performed by quantitative real-time PCR. The frequency of A allele carriage was 94.2% and 91.8% in SCC and NCM, respectively, while G allele carriage was detected in 5.8% and 8.2% of SCC and NCM samples, respectively. As a result, a significant association was identified between the − 5 A/G SNP in the MT2A gene with mRNA expression in both groups. Metal levels were analyzed by flame atomic absorption spectrometry. The significant differences were identified between A/A and both the A/G and G/G genotypes, with regard to the concentration of the contaminating metal. The Spearman rank correlation results showed that the MT2A expression and Cd, Zn, Cu levels were negatively correlated. Results obtained in this study suggest that − 5 A/G SNP in MT2A gene may have an effect on allele-specific gene expression and accumulation of metal levels in laryngeal cancer. - Highlights: • MT2A gene expression and metal content in laryngeal cancer tissues • Association between SNP (rs28366003) and expression of MT2A • Significant associations between the SNP and Cd, Zn and Cu levels • Negative correlation between MT2A gene expression and Cd, Zn and Cu levels.

  20. The − 5 A/G single-nucleotide polymorphism in the core promoter region of MT2A and its effect on allele-specific gene expression and Cd, Zn and Cu levels in laryngeal cancer

    International Nuclear Information System (INIS)

    Starska, Katarzyna; Krześlak, Anna; Forma, Ewa; Olszewski, Jurek; Morawiec-Sztandera, Alina; Aleksandrowicz, Paweł; Lewy-Trenda, Iwona

    2014-01-01

    Metallothioneins (MTs) are low molecular weight, cysteine-rich heavy metal-binding proteins which participate in the mechanisms of Zn homeostasis, and protect against toxic metals. MTs contain metal-thiolate cluster groups and suppress metal toxicity by binding to them. The aim of this study was to determine the − 5 A/G (rs28366003) single-nucleotide polymorphism (SNP) in the core promoter region of the MT2A gene and to investigate its effect on allele-specific gene expression and Cd, Zn and Cu content in squamous cell laryngeal cancer (SCC) and non-cancerous laryngeal mucosa (NCM) as a control. The MT2A promoter region − 5 A/G SNP was determined by restriction fragment length polymorphism using 323 SCC and 116 NCM. MT2A gene analysis was performed by quantitative real-time PCR. The frequency of A allele carriage was 94.2% and 91.8% in SCC and NCM, respectively, while G allele carriage was detected in 5.8% and 8.2% of SCC and NCM samples, respectively. As a result, a significant association was identified between the − 5 A/G SNP in the MT2A gene with mRNA expression in both groups. Metal levels were analyzed by flame atomic absorption spectrometry. The significant differences were identified between A/A and both the A/G and G/G genotypes, with regard to the concentration of the contaminating metal. The Spearman rank correlation results showed that the MT2A expression and Cd, Zn, Cu levels were negatively correlated. Results obtained in this study suggest that − 5 A/G SNP in MT2A gene may have an effect on allele-specific gene expression and accumulation of metal levels in laryngeal cancer. - Highlights: • MT2A gene expression and metal content in laryngeal cancer tissues • Association between SNP (rs28366003) and expression of MT2A • Significant associations between the SNP and Cd, Zn and Cu levels • Negative correlation between MT2A gene expression and Cd, Zn and Cu levels

  1. Comparison of allele-specific PCR, created restriction-site PCR, and PCR with primer-introduced restriction analysis methods used for screening complex vertebral malformation carriers in Holstein cattle

    Science.gov (United States)

    Altınel, Ahmet

    2017-01-01

    Complex vertebral malformation (CVM) is an inherited, autosomal recessive disorder of Holstein cattle. The aim of this study was to compare sensitivity, specificity, positive and negative predictive values, accuracy, and rapidity of allele-specific polymerase chain reaction (AS-PCR), created restriction-site PCR (CRS-PCR), and PCR with primer-introduced restriction analysis (PCR-PIRA), three methods used in identification of CVM carriers in a Holstein cattle population. In order to screen for the G>T mutation in the solute carrier family 35 member A3 (SLC35A3) gene, DNA sequencing as the gold standard method was used. The prevalence of carriers and the mutant allele frequency were 3.2% and 0.016, respectively, among Holstein cattle in the Thrace region of Turkey. Among the three methods, the fastest but least accurate was AS-PCR. Although the rapidity of CRS-PCR and PCR-PIRA were nearly equal, the accuracy of PCR-PIRA was higher than that of CRS-PCR. Therefore, among the three methods, PCR-PIRA appears to be the most efficacious for screening of mutant alleles when identifying CVM carriers in a Holstein cattle population. PMID:28927256

  2. Development of an allele-specific, loop-mediated, isothermal amplification method (AS-LAMP to detect the L1014F kdr-w mutation in Anopheles gambiae s. l.

    Directory of Open Access Journals (Sweden)

    Badolo Athanase

    2012-07-01

    Full Text Available Abstract Background Malaria control relies heavily on treated bed nets and indoor residual spraying with pyrethroid insecticides. Unfortunately, the resistance to pyrethroid insecticides, mainly due to the kdr mutation, is spreading in the main malaria vector Anopheles gambiae s.l., decreasing the insecticides’ efficacy. To manage the insecticide resistance rapidly and flexibly, simple and effective tools for the early detection of resistant mosquitoes are needed. This study aimed to develop an allele-specific, loop-mediated, isothermal amplification (AS-LAMP method to detect the West African-type kdr mutation (kdr-w; L1014F in field-collected mosquitoes. Methods DNA fragments of the wild-type and the mutated kdr gene were used to select the primers and develop the method. The primers were designed with the mutation at the 5’ end of the backward inner primer (BIP. The AS-LAMP method was compared to the AS-PCR method using the genomic DNA of 120 field-collected mosquitoes. Results The AS-LAMP method could discriminate between the wild-type homozygote, the heterozygote, and the kdr-w homozygote within 75 min. The AS-LAMP method has the advantage of being faster and at least as sensitive and specific as the AS-PCR method. Conclusions The AS-LAMP method can be used to detect the kdr mutation for quick decision-making, even in less well-equipped laboratories.

  3. Microarray-based analysis of IncA/C plasmid-associated genes from multidrug-resistant Salmonella enterica.

    Science.gov (United States)

    Lindsey, Rebecca L; Frye, Jonathan G; Fedorka-Cray, Paula J; Meinersmann, Richard J

    2011-10-01

    In the family Enterobacteriaceae, plasmids have been classified according to 27 incompatibility (Inc) or replicon types that are based on the inability of different plasmids with the same replication mechanism to coexist in the same cell. Certain replicon types such as IncA/C are associated with multidrug resistance (MDR). We developed a microarray that contains 286 unique 70-mer oligonucleotide probes based on sequences from five IncA/C plasmids: pYR1 (Yersinia ruckeri), pPIP1202 (Yersinia pestis), pP99-018 (Photobacterium damselae), pSN254 (Salmonella enterica serovar Newport), and pP91278 (Photobacterium damselae). DNA from 59 Salmonella enterica isolates was hybridized to the microarray and analyzed for the presence or absence of genes. These isolates represented 17 serovars from 14 different animal hosts and from different geographical regions in the United States. Qualitative cluster analysis was performed using CLUSTER 3.0 to group microarray hybridization results. We found that IncA/C plasmids occurred in two lineages distinguished by a major insertion-deletion (indel) region that contains genes encoding mostly hypothetical proteins. The most variable genes were represented by transposon-associated genes as well as four antimicrobial resistance genes (aphA, merP, merA, and aadA). Sixteen mercury resistance genes were identified and highly conserved, suggesting that mercury ion-related exposure is a stronger pressure than anticipated. We used these data to construct a core IncA/C genome and an accessory genome. The results of our studies suggest that the transfer of antimicrobial resistance determinants by transfer of IncA/C plasmids is somewhat less common than exchange within the plasmids orchestrated by transposable elements, such as transposons, integrating and conjugative elements (ICEs), and insertion sequence common regions (ISCRs), and thus pose less opportunity for exchange of antimicrobial resistance.

  4. SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea

    Directory of Open Access Journals (Sweden)

    Oelofse Dean

    2010-04-01

    Full Text Available Abstract Background Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L. Walp. We aimed to use this method to enrich for genes expressed during drought stress in a drought tolerant cowpea line. However, current methods were inefficient in screening libraries and management of the sequence data, and thus there was a need to develop software tools to facilitate the process. Results Forward and reverse cDNA libraries enriched for cowpea drought response genes were screened on microarrays, and the R software package SSHscreen 2.0.1 was developed (i to normalize the data effectively using spike-in control spot normalization, and (ii to select clones for sequencing based on the calculation of enrichment ratios with associated statistics. Enrichment ratio 3 values for each clone showed that 62% of the forward library and 34% of the reverse library clones were significantly differentially expressed by drought stress (adjusted p value 88% of the clones in both libraries were derived from rare transcripts in the original tester samples, thus supporting the notion that suppression subtractive hybridization enriches for rare transcripts. A set of 118 clones were chosen for sequencing, and drought-induced cowpea genes were identified, the most interesting encoding a late embryogenesis abundant Lea5 protein, a glutathione S-transferase, a thaumatin, a universal stress protein, and a wound induced protein. A lipid transfer protein and several components of photosynthesis were down-regulated by the drought stress. Reverse transcriptase quantitative PCR confirmed the enrichment ratio values for the selected cowpea genes. SSHdb, a web-accessible database, was developed to manage the clone sequences and combine the SSHscreen data with sequence annotations derived from BLAST and Blast2GO. The self-BLAST function within SSHdb grouped

  5. Validation of a Multiplex Allele-Specific Polymerase Chain Reaction Assay for Detection of KRAS Gene Mutations in Formalin-Fixed, Paraffin-Embedded Tissues from Colorectal Cancer Patients.

    Directory of Open Access Journals (Sweden)

    Sirirat Seekhuntod

    Full Text Available Patients with KRAS mutations do not respond to epidermal growth factor receptor (EGFR inhibitors and fail to benefit from adjuvant chemotherapy. Mutation analysis of KRAS is needed before starting treatment with monoclonal anti-EGFR antibodies in patients with metastatic colorectal cancer (mCRC. The objective of this study is to develop a multiplex allele-specific PCR (MAS-PCR assay to detect KRAS mutations.We developed a single-tube MAS-PCR assay for the detection of seven KRAS mutations (G12D, G12A, G12R, G12C, G12S, G12V, and G13D. We performed MAS-PCR assay analysis for KRAS on DNA isolated from 270 formalin-fixed paraffin-embedded (FFPE colorectal cancer tissues. Sequences of all 270 samples were determined by pyrosequencing. Seven known point-mutation DNA samples diluted with wild-type DNA were assayed to determine the limitation of detection and reproducibility of the MAS-PCR assay.Overall, the results of MAS-PCR assay were in good concordance with pyrosequencing, and only seven discordant samples were found. The MAS-PCR assay reproducibly detected 1 to 2% mutant alleles. The most common mutations were G13D in codon 13 (49.17%, G12D (25.83% and G12V (12.50% in codon 12.The MAS-PCR assay provides a rapid, cost-effective, and reliable diagnostic tool for accurate detection of KRAS mutations in routine FFPE colorectal cancer tissues.

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

    Directory of Open Access Journals (Sweden)

    Pesta David

    2003-06-01

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

  7. Experience With Rapid Microarray-Based Diagnostic Technology and Antimicrobial Stewardship for Patients With Gram-Positive Bacteremia.

    Science.gov (United States)

    Neuner, Elizabeth A; Pallotta, Andrea M; Lam, Simon W; Stowe, David; Gordon, Steven M; Procop, Gary W; Richter, Sandra S

    2016-11-01

    OBJECTIVE To describe the impact of rapid diagnostic microarray technology and antimicrobial stewardship for patients with Gram-positive blood cultures. DESIGN Retrospective pre-intervention/post-intervention study. SETTING A 1,200-bed academic medical center. PATIENTS Inpatients with blood cultures positive for Staphylococcus aureus, Enterococcus faecalis, E. faecium, Streptococcus pneumoniae, S. pyogenes, S. agalactiae, S. anginosus, Streptococcus spp., and Listeria monocytogenes during the 6 months before and after implementation of Verigene Gram-positive blood culture microarray (BC-GP) with an antimicrobial stewardship intervention. METHODS Before the intervention, no rapid diagnostic technology was used or antimicrobial stewardship intervention was undertaken, except for the use of peptide nucleic acid fluorescent in situ hybridization and MRSA agar to identify staphylococcal isolates. After the intervention, all Gram-positive blood cultures underwent BC-GP microarray and the antimicrobial stewardship intervention consisting of real-time notification and pharmacist review. RESULTS In total, 513 patients with bacteremia were included in this study: 280 patients with S. aureus, 150 patients with enterococci, 82 patients with stretococci, and 1 patient with L. monocytogenes. The number of antimicrobial switches was similar in the pre-BC-GP (52%; 155 of 300) and post-BC-GP (50%; 107 of 213) periods. The time to antimicrobial switch was significantly shorter in the post-BC-GP group than in the pre-BC-GP group: 48±41 hours versus 75±46 hours, respectively (P<.001). The most common antimicrobial switch was de-escalation and time to de-escalation, was significantly shorter in the post-BC-GP group than in the pre-BC-GP group: 53±41 hours versus 82±48 hours, respectively (P<.001). There was no difference in mortality or hospital length of stay as a result of the intervention. CONCLUSIONS The combination of a rapid microarray diagnostic test with an antimicrobial

  8. Detection of the V1016G mutation in the voltage-gated sodium channel gene of Aedes aegypti (Diptera: Culicidae) by allele-specific PCR assay, and its distribution and effect on deltamethrin resistance in Thailand.

    Science.gov (United States)

    Stenhouse, Steven A; Plernsub, Suriya; Yanola, Jintana; Lumjuan, Nongkran; Dantrakool, Anchalee; Choochote, Wej; Somboon, Pradya

    2013-08-30

    Resistance to pyrethroid insecticides is widespread among populations of Aedes aegypti, the main vector for the dengue virus. Several different point mutations within the voltage-gated sodium channel (VGSC) gene contribute to such resistance. A mutation at position 1016 in domain II, segment 6 of the VGSC gene in Ae. aegypti leads to a valine to glycine substitution (V1016G) that confers resistance to deltamethrin. This study developed and utilized an allele-specific PCR (AS-PCR) assay that could be used to detect the V1016G mutation. The assay was validated against a number of sequenced DNA samples of known genotype and was determined to be in complete agreement. Larvae and pupae were collected from various localities throughout Thailand. Samples were reared to adulthood and their resistance status against deltamethrin was determined by standard WHO susceptibility bioassays. Deltamethrin-resistant and susceptible insects were then genotyped for the V1016G mutation. Additionally, some samples were genotyped for a second mutation at position 1534 in domain III (F1534C) which is also known to confer pyrethroid resistance. The bioassay results revealed an overall mortality of 77.6%. Homozygous 1016G individuals survived at higher rates than either heterozygous or wild-type (1016 V) mosquitoes. The 1016G mutation was significantly and positively associated with deltamethrin resistance and was widely distributed throughout Thailand. Interestingly, wild-type 1016 V mosquitoes tested were homozygous for the 1534C mutation, and all heterozygous mosquitoes were also heterozygous for 1534C. Mutant homozygous (G/G) mosquitoes expressed the wild-type (F/F) at position 1534. However, the presence of the 1534C mutation was not associated with deltamethrin resistance. Our bioassay results indicate that all populations sampled display some degree of resistance to deltamethrin. Homozygous 1016G mosquitoes were far likelier to survive such exposure. However, resistance in some

  9. Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission.

    Directory of Open Access Journals (Sweden)

    Andrea Hauser

    Full Text Available Pregnant HIV-infected women were screened for the development of HIV-1 drug resistance after implementation of a triple-antiretroviral transmission prophylaxis as recommended by the WHO in 2006. The study offered the opportunity to compare amplicon-based 454 ultra-deep sequencing (UDS and allele-specific real-time PCR (ASPCR for the detection of drug-resistant minor variants in the HIV-1 reverse transcriptase (RT.Plasma samples from 34 Tanzanian women were previously analysed by ASPCR for key resistance mutations in the viral RT selected by AZT, 3TC, and NVP (K70R, K103N, Y181C, M184V, T215Y/F. In this study, the RT region of the same samples was investigated by amplicon-based UDS for resistance mutations using the 454 GS FLX System.Drug-resistant HIV-variants were identified in 69% (20/29 of women by UDS and in 45% (13/29 by ASPCR. The absolute number of resistance mutations identified by UDS was twice that identified by ASPCR (45 vs 24. By UDS 14 of 24 ASPCR-detected resistance mutations were identified at the same position. The overall concordance between UDS and ASPCR was 61.0% (25/41. The proportions of variants quantified by UDS were approximately 2-3 times lower than by ASPCR. Amplicon generation from samples with viral loads below 20,000 copies/ml failed more frequently by UDS compared to ASPCR (limit of detection = 650 copies/ml, resulting in missing or insufficient sequence coverage.Both methods can provide useful information about drug-resistant minor HIV-1 variants. ASPCR has a higher sensitivity than UDS, but is restricted to single resistance mutations. In contrast, UDS is limited by its requirement for high viral loads to achieve sufficient sequence coverage, but the sequence information reveals the complete resistance patterns within the genomic region analysed. Improvements to the UDS limit of detection are in progress, and UDS could then facilitate monitoring of drug-resistant minor variants in the HIV-1 quasispecies.

  10. From High-Throughput Microarray-Based Screening to Clinical Application: The Development of a Second Generation Multigene Test for Breast Cancer Prognosis

    Directory of Open Access Journals (Sweden)

    Carsten Denkert

    2013-08-01

    Full Text Available Several multigene tests have been developed for breast cancer patients to predict the individual risk of recurrence. Most of the first generation tests rely on proliferation-associated genes and are commonly carried out in central reference laboratories. Here, we describe the development of a second generation multigene assay, the EndoPredict test, a prognostic multigene expression test for estrogen receptor (ER positive, human epidermal growth factor receptor (HER2 negative (ER+/HER2− breast cancer patients. The EndoPredict gene signature was initially established in a large high-throughput microarray-based screening study. The key steps for biomarker identification are discussed in detail, in comparison to the establishment of other multigene signatures. After biomarker selection, genes and algorithms were transferred to a diagnostic platform (reverse transcription quantitative PCR (RT-qPCR to allow for assaying formalin-fixed, paraffin-embedded (FFPE samples. A comprehensive analytical validation was performed and a prospective proficiency testing study with seven pathological laboratories finally proved that EndoPredict can be reliably used in the decentralized setting. Three independent large clinical validation studies (n = 2,257 demonstrated that EndoPredict offers independent prognostic information beyond current clinicopathological parameters and clinical guidelines. The review article summarizes several important steps that should be considered for the development process of a second generation multigene test and offers a means for transferring a microarray signature from the research laboratory to clinical practice.

  11. DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence.

    Science.gov (United States)

    Koide, Tie; Zaini, Paulo A; Moreira, Leandro M; Vêncio, Ricardo Z N; Matsukuma, Adriana Y; Durham, Alan M; Teixeira, Diva C; El-Dorry, Hamza; Monteiro, Patrícia B; da Silva, Ana Claudia R; Verjovski-Almeida, Sergio; da Silva, Aline M; Gomes, Suely L

    2004-08-01

    Xylella fastidiosa is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of Xylella pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that X. fastidiosa strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease.

  12. Microarray-based identification and RT-PCR test screening for epithelial-specific mRNAs in peripheral blood of patients with colon cancer

    Directory of Open Access Journals (Sweden)

    Coppola Domenico

    2006-10-01

    Full Text Available Abstract Background The efficacy of screening for colorectal cancer using a simple blood-based assay for the detection of tumor cells disseminated in the circulation at an early stage of the disease is gaining positive feedback from several lines of research. This method seems able to reduce colorectal cancer mortality and may replace colonoscopy as the most effective means of detecting colonic lesions. Methods In this work, we present a new microarray-based high-throughput screening method to identifying candidate marker mRNAs for the early detection of epithelial cells diluted in peripheral blood cells. This method includes 1. direct comparison of different samples of colonic mucosa and of blood cells to identify consistent epithelial-specific mRNAs from among 20,000 cDNA assayed by microarray slides; 2. identification of candidate marker mRNAs by data analysis, which allowed selection of only 10 putative differentially expressed genes; 3. Selection of some of the most suitable mRNAs (TMEM69, RANBP3 and PRSS22 that were assayed in blood samples from normal subjects and patients with colon cancer as possible markers for the presence of epithelial cells in the blood, using reverse transcription – polymerase chain reaction (RT-PCR. Results Our present results seem to provide an indication, for the first time obtained by genome-scale screening, that a suitable and consistent colon epithelium mRNA marker may be difficult to identify. Conclusion The design of new approaches to identify such markers is warranted.

  13. The acylphosphatase (Acyp) alleles associate with male hybrid sterility in Drosophila.

    Science.gov (United States)

    Michalak, Pawel; Ma, Daina

    2008-06-15

    Hybrid defects are believed to result from genetic incompatibilities between genes that have evolved in separate parental lineages. These genetic dysfunctions on the hybrid genomic background, also known as Dobzhansky-Muller incompatibilities, can be an incipient signature of speciation, and as such - a subject of active research. Here we present evidence that Acyp locus (CG16870) that encodes acylphosphatase, a small enzyme that catalyzes the hydrolysis of acylphosphates and participates in ion transport across biological membranes, is involved in genetic incompatibilities leading to male sterility in hybrids between Drosophila simulans and D. mauritiana. There is a strong association between Acyp alleles (genotype) and the sterility/fertility pattern (phenotype), as well as between the phenotype, the genotype and its transcriptional activity. Allele-specific expression in hybrids heterozygous for Acyp suggests a cis-type regulation of this gene, where an allele from one of the parental species (D. simulans) is consistently overexpressed.

  14. An allele-specific polymerase chain reaction assay for the ...

    Indian Academy of Sciences (India)

    Unknown

    designated as species A, B (Green and Miles 1980), C. (Subbarao et al 1983), ... onstrated in laboratory feeding experiments on three members of An. .... in Rameshwaram Island and Sri Lanka only) are not pre- sent. For example, in most of ...

  15. An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies.

    Science.gov (United States)

    Martín, Verónica; Perales, Celia; Fernández-Algar, María; Dos Santos, Helena G; Garrido, Patricia; Pernas, María; Parro, Víctor; Moreno, Miguel; García-Pérez, Javier; Alcamí, José; Torán, José Luis; Abia, David; Domingo, Esteban; Briones, Carlos

    2016-01-01

    The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5-10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.

  16. DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces.

    Directory of Open Access Journals (Sweden)

    Pragathi B Shridhar

    Full Text Available Escherichia coli O104:H4, a hybrid pathotype reported in a large 2011 foodborne outbreak in Germany, has not been detected in cattle feces. However, cattle harbor and shed in the feces other O104 serotypes, particularly O104:H7, which has been associated with sporadic cases of diarrhea in humans. The objective of our study was to assess the virulence potential of Shiga toxin-producing E. coli (STEC O104:H7 isolated from feces of feedlot cattle using DNA microarray. Six strains of STEC O104:H7 isolated from cattle feces were analyzed using FDA-E. coli Identification (ECID DNA microarray to determine their virulence profiles and compare them to the human strains (clinical of O104:H7, STEC O104:H4 (German outbreak strain, and O104:H21 (milk-associated Montana outbreak strain. Scatter plots were generated from the array data to visualize the gene-level differences between bovine and human O104 strains, and Pearson correlation coefficients (r were determined. Splits tree was generated to analyze relatedness between the strains. All O104:H7 strains, both bovine and human, similar to O104:H4 and O104:H21 outbreak strains were negative for intimin (eae. The bovine strains were positive for Shiga toxin 1 subtype c (stx1c, enterohemolysin (ehxA, tellurite resistance gene (terD, IrgA homolog protein (iha, type 1 fimbriae (fimH, and negative for genes that code for effector proteins of type III secretory system. The six cattle O104 strains were closely related (r = 0.86-0.98 to each other, except for a few differences in phage related and non-annotated genes. One of the human clinical O104:H7 strains (2011C-3665 was more closely related to the bovine O104:H7 strains (r = 0.81-0.85 than the other four human clinical O104:H7 strains (r = 0.75-0.79. Montana outbreak strain (O104:H21 was more closely related to four of the human clinical O104:H7 strains than the bovine O104:H7 strains. None of the bovine E. coli O104 strains carried genes characteristic of E

  17. A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus

    Science.gov (United States)

    2011-01-01

    Background Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers. Results SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome. Conclusions The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping

  18. Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus

    Directory of Open Access Journals (Sweden)

    Futahashi Ryo

    2012-05-01

    Full Text Available Abstract Background Body coloration is an ecologically important trait that is often involved in prey-predator interactions through mimicry and crypsis. Although this subject has attracted the interest of biologists and the general public, our scientific knowledge on the subject remains fragmentary. In the caterpillar of the swallowtail butterfly Papilio xuthus, spectacular changes in the color pattern are observed; the insect mimics bird droppings (mimetic pattern as a young larva, and switches to a green camouflage coloration (cryptic pattern in the final instar. Despite the wide variety and significance of larval color patterns, few studies have been conducted at a molecular level compared with the number of studies on adult butterfly wing patterns. Results To obtain a catalog of genes involved in larval mimetic and cryptic pattern formation, we constructed expressed sequence tag (EST libraries of larval epidermis for P. xuthus, and P. polytes that contained 20,736 and 5,376 clones, respectively, representing one of the largest collections available in butterflies. A comparison with silkworm epidermal EST information revealed the high expression of putative blue and yellow pigment-binding proteins in Papilio species. We also designed a microarray from the EST dataset information, analyzed more than five stages each for six markings, and confirmed spatial expression patterns by whole-mount in situ hybridization. Hence, we succeeded in elucidating many novel marking-specific genes for mimetic and cryptic pattern formation, including pigment-binding protein genes, the melanin-associated gene yellow-h3, the ecdysteroid synthesis enzyme gene 3-dehydroecdysone 3b-reductase, and Papilio-specific genes. We also found many cuticular protein genes with marking specificity that may be associated with the unique surface nanostructure of the markings. Furthermore, we identified two transcription factors, spalt and ecdysteroid signal-related E75, as genes

  19. The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays.

    Science.gov (United States)

    Dubrovin, E V; Presnova, G V; Rubtsova, M Yu; Egorov, A M; Grigorenko, V G; Yaminsky, I V

    2015-01-01

    Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

  20. Hybrid reactors

    International Nuclear Information System (INIS)

    Moir, R.W.

    1980-01-01

    The rationale for hybrid fusion-fission reactors is the production of fissile fuel for fission reactors. A new class of reactor, the fission-suppressed hybrid promises unusually good safety features as well as the ability to support 25 light-water reactors of the same nuclear power rating, or even more high-conversion-ratio reactors such as the heavy-water type. One 4000-MW nuclear hybrid can produce 7200 kg of 233 U per year. To obtain good economics, injector efficiency times plasma gain (eta/sub i/Q) should be greater than 2, the wall load should be greater than 1 MW.m -2 , and the hybrid should cost less than 6 times the cost of a light-water reactor. Introduction rates for the fission-suppressed hybrid are usually rapid

  1. Amplificação gênica alelo-específica na caracterização das hemoglobinas S, C e D e as interações entre elas e talassemias beta Allele-specific genic amplification in the characterization of hemoglobins S, C, D and interactions among them and with beta thalassemia

    Directory of Open Access Journals (Sweden)

    Luciane Cristina Bertholo

    2006-08-01

    possible interactions, based on the allele-specific genic amplification (PCR-AE with the use in parallel two primers that differ at their 3’ extremities and are complementary to the normal or mutated sequences. RESULTS AND DISCUSSION: The results make evident the validation of this methodology in the characterization of these mutations, once this procedure is easy to execute,to reproduce, as well as it is possible to be applied to a significative number of samples.

  2. Hybrid composites

    CSIR Research Space (South Africa)

    Jacob John, Maya

    2009-04-01

    Full Text Available mixed short sisal/glass hybrid fibre reinforced low density polyethylene composites was investigated by Kalaprasad et al [25].Chemical surface modifications such as alkali, acetic anhydride, stearic acid, permanganate, maleic anhydride, silane...

  3. Hybrid intermediaries

    OpenAIRE

    Cetorelli, Nicola

    2014-01-01

    I introduce the concept of hybrid intermediaries: financial conglomerates that control a multiplicity of entity types active in the "assembly line" process of modern financial intermediation, a system that has become known as shadow banking. The complex bank holding companies of today are the best example of hybrid intermediaries, but I argue that financial firms from the "nonbank" space can just as easily evolve into conglomerates with similar organizational structure, thus acquiring the cap...

  4. Prediction of the optimum hybridization conditions of dot-blot-SNP analysis using estimated melting temperature of oligonucleotide probes.

    Science.gov (United States)

    Shiokai, Sachiko; Kitashiba, Hiroyasu; Nishio, Takeshi

    2010-08-01

    Although the dot-blot-SNP technique is a simple cost-saving technique suitable for genotyping of many plant individuals, optimization of hybridization and washing conditions for each SNP marker requires much time and labor. For prediction of the optimum hybridization conditions for each probe, we compared T (m) values estimated from nucleotide sequences using the DINAMelt web server, measured T (m) values, and hybridization conditions yielding allele-specific signals. The estimated T (m) values were comparable to the measured T (m) values with small differences of less than 3 degrees C for most of the probes. There were differences of approximately 14 degrees C between the specific signal detection conditions and estimated T (m) values. Change of one level of SSC concentrations of 0.1, 0.2, 0.5, and 1.0x SSC corresponded to a difference of approximately 5 degrees C in optimum signal detection temperature. Increasing the sensitivity of signal detection by shortening the exposure time to X-ray film changed the optimum hybridization condition for specific signal detection. Addition of competitive oligonucleotides to the hybridization mixture increased the suitable hybridization conditions by 1.8. Based on these results, optimum hybridization conditions for newly produced dot-blot-SNP markers will become predictable.

  5. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes.

    Science.gov (United States)

    Long, Yunming; Zhao, Lifeng; Niu, Baixiao; Su, Jing; Wu, Hao; Chen, Yuanling; Zhang, Qunyu; Guo, Jingxin; Zhuang, Chuxiong; Mei, Mantong; Xia, Jixing; Wang, Lan; Wu, Haibin; Liu, Yao-Guang

    2008-12-02

    Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM(+)SaF(+), whereas all japonica cultivars have SaM(-)SaF(-) that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM(-). This allele-specific gamete elimination results from a selective interaction of SaF(+) with SaM(-), a truncated protein, but not with SaM(+) because of the presence of an inhibitory domain, although SaM(+) is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding.

  6. Hybrid stars

    Indian Academy of Sciences (India)

    Hybrid stars. AsHOK GOYAL. Department of Physics and Astrophysics, University of Delhi, Delhi 110 007, India. Abstract. Recently there have been important developments in the determination of neutron ... number and the electric charge. ... available to the system to rearrange concentration of charges for a given fraction of.

  7. Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

    Science.gov (United States)

    Paschold, Anja; Jia, Yi; Marcon, Caroline; Lund, Steve; Larson, Nick B.; Yeh, Cheng-Ting; Ossowski, Stephan; Lanz, Christa; Nettleton, Dan; Schnable, Patrick S.; Hochholdinger, Frank

    2012-01-01

    Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all high-confidence maize genes were expressed in at least one genotype. Nearly 70% of all expressed genes were differentially expressed between the two parents and 42%–55% of expressed genes were differentially expressed between one of the parents and one of the hybrids. In both hybrids, ∼10% of expressed genes exhibited nonadditive gene expression. Consistent with the dominance model (i.e., complementation) for heterosis, 1124 genes that were expressed in the hybrids were expressed in only one of the two parents. For 65 genes, it could be shown that this was a consequence of complementation of genomic presence/absence variation. For dozens of other genes, alleles from the inactive inbred were activated in the hybrid, presumably via interactions with regulatory factors from the active inbred. As a consequence of these types of complementation, both hybrids expressed more genes than did either parental inbred. Finally, in hybrids, ∼14% of expressed genes exhibited allele-specific expression (ASE) levels that differed significantly from the parental-inbred expression ratios, providing further evidence for interactions of regulatory factors from one parental genome with target genes from the other parental genome. PMID:23086286

  8. Hybrid Qualifications

    DEFF Research Database (Denmark)

    Against the background of increasing qualification needs there is a growing awareness of the challenge to widen participation in processes of skill formation and competence development. At the same time, the issue of permeability between vocational education and training (VET) and general education...... has turned out as a major focus of European education and training policies and certainly is a crucial principle underlying the European Qualifications Framework (EQF). In this context, «hybrid qualifications» (HQ) may be seen as an interesting approach to tackle these challenges as they serve «two...

  9. Hybrid Gear

    Science.gov (United States)

    Handschuh, Robert F. (Inventor); Roberts, Gary D. (Inventor)

    2016-01-01

    A hybrid gear consisting of metallic outer rim with gear teeth and metallic hub in combination with a composite lay up between the shaft interface (hub) and gear tooth rim is described. The composite lay-up lightens the gear member while having similar torque carrying capability and it attenuates the impact loading driven noise/vibration that is typical in gear systems. The gear has the same operational capability with respect to shaft speed, torque, and temperature as an all-metallic gear as used in aerospace gear design.

  10. Intuitionistic hybrid logic

    DEFF Research Database (Denmark)

    Braüner, Torben

    2011-01-01

    Intuitionistic hybrid logic is hybrid modal logic over an intuitionistic logic basis instead of a classical logical basis. In this short paper we introduce intuitionistic hybrid logic and we give a survey of work in the area.......Intuitionistic hybrid logic is hybrid modal logic over an intuitionistic logic basis instead of a classical logical basis. In this short paper we introduce intuitionistic hybrid logic and we give a survey of work in the area....

  11. Hybridized Tetraquarks

    CERN Document Server

    Esposito, A.; Polosa, A.D.

    2016-01-01

    We propose a new interpretation of the neutral and charged X, Z exotic hadron resonances. Hybridized-tetraquarks are neither purely compact tetraquark states nor bound or loosely bound molecules. The latter would require a negative or zero binding energy whose counterpart in h-tetraquarks is a positive quantity. The formation mechanism of this new class of hadrons is inspired by that of Feshbach metastable states in atomic physics. The recent claim of an exotic resonance in the Bs pi+- channel by the D0 collaboration and the negative result presented subsequently by the LHCb collaboration are understood in this scheme, together with a considerable portion of available data on X, Z particles. Considerations on a state with the same quantum numbers as the X(5568) are also made.

  12. Continuity controlled Hybrid Automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation

  13. Continuity Controlled Hybrid Automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2004-01-01

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation of

  14. Continuity controlled hybrid automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2004-01-01

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation of

  15. Continuity controlled hybrid automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2006-01-01

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation of

  16. Corporate Hybrid Bonds

    OpenAIRE

    Ahlberg, Johan; Jansson, Anton

    2016-01-01

    Hybrid securities do not constitute a new phenomenon in the Swedish capital markets. Most commonly, hybrids issued by Swedish real estate companies in recent years are preference shares. Corporate hybrid bonds on the other hand may be considered as somewhat of a new-born child in the family of hybrid instruments. These do, as all other hybrid securities, share some equity-like and some debt-like characteristics. Nevertheless, since 2013 the interest for the instrument has grown rapidly and ha...

  17. Hybrid XRF

    International Nuclear Information System (INIS)

    Heckel, J.

    2002-01-01

    Full text: In the last 10 years significant innovations of EDXRF, e.g. total reflection XRF or polarized beam XRF, were utilized in different industrial applications. The decrease of background within the spectra was the goal of these developments. Excellent detection limits and sensitivities demonstrate the success of these new techniques. Nevertheless, further improvements are possible by using Si drift detectors. These detectors allow the processing of input count rates up to 10 6 cps in comparison to 10 5 of Si(Li) detectors. New excitation optics are necessary to produce such count rates. One possibility is the use of doubly curved crystals between tube and sample. These crystals enable the reflection of the primary beam within the given solid angle (0.4π) of an end window tube to the sample. Using such brightness optics excellent sensitivities mainly for light elements are achievable. The combination of a BRAGG crystal as a wavelength dispersive component and a solid state detector as an energy dispersive component creates a new technique: hybrid XRF. Copyright (2002) Australian X-ray Analytical Association Inc. Copyright (2002) Australian X-ray Analytical Association Inc

  18. Hybrid mimics and hybrid vigor in Arabidopsis

    Science.gov (United States)

    Wang, Li; Greaves, Ian K.; Groszmann, Michael; Wu, Li Min; Dennis, Elizabeth S.; Peacock, W. James

    2015-01-01

    F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture. PMID:26283378

  19. Hybrid Management in Hospitals

    DEFF Research Database (Denmark)

    Byrkjeflot, Haldor; Jespersen, Peter Kragh

    2010-01-01

    Artiklen indeholder et litteraturbaseret studium af ledelsesformer i sygehuse, hvor sundhedsfaglig ledelse og generel ledelse mikses til hybride ledelsesformer......Artiklen indeholder et litteraturbaseret studium af ledelsesformer i sygehuse, hvor sundhedsfaglig ledelse og generel ledelse mikses til hybride ledelsesformer...

  20. Hydraulic Hybrid Vehicles

    Science.gov (United States)

    EPA and the United Parcel Service (UPS) have developed a hydraulic hybrid delivery vehicle to explore and demonstrate the environmental benefits of the hydraulic hybrid for urban pick-up and delivery fleets.

  1. Mesoscale hybrid calibration artifact

    Science.gov (United States)

    Tran, Hy D.; Claudet, Andre A.; Oliver, Andrew D.

    2010-09-07

    A mesoscale calibration artifact, also called a hybrid artifact, suitable for hybrid dimensional measurement and the method for make the artifact. The hybrid artifact has structural characteristics that make it suitable for dimensional measurement in both vision-based systems and touch-probe-based systems. The hybrid artifact employs the intersection of bulk-micromachined planes to fabricate edges that are sharp to the nanometer level and intersecting planes with crystal-lattice-defined angles.

  2. Hybrid quantum information processing

    Energy Technology Data Exchange (ETDEWEB)

    Furusawa, Akira [Department of Applied Physics, School of Engineering, The University of Tokyo (Japan)

    2014-12-04

    I will briefly explain the definition and advantage of hybrid quantum information processing, which is hybridization of qubit and continuous-variable technologies. The final goal would be realization of universal gate sets both for qubit and continuous-variable quantum information processing with the hybrid technologies. For that purpose, qubit teleportation with a continuousvariable teleporter is one of the most important ingredients.

  3. A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus.

    Directory of Open Access Journals (Sweden)

    Bethany A Stahl

    Full Text Available Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual, and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.

  4. A four-element based transposon system for allele specific tagging ...

    Indian Academy of Sciences (India)

    The four-element based construct would include both Ds and dSpm along with relevant marker genes and .... subsequent generations after transposition has taken place so as to ..... Cardon G H, Frey M, Seadler H and Gierl A 1993 Definition.

  5. DQB1*06:02 allele-specific expression varies by allelic dosage, not narcolepsy status

    DEFF Research Database (Denmark)

    Weiner Lachmi, Karin; Lin, Ling; Kornum, Birgitte Rahbek

    2012-01-01

    The association of narcolepsy-cataplexy, a sleep disorder caused by the loss of hypocretin/orexin neurons in the hypothalamus, with DQA1*01:02-DQB1*06:02 is one of the tightest known single-allele human leukocyte antigen (HLA) associations. In this study, we explored genome-wide expression...

  6. Differential ACE expression among tissues in allele-specific Wistar rat lines

    NARCIS (Netherlands)

    Kamilic, Jelena; Lely, A. Titia; van Goor, Harry; Buikema, Hendrik; Tent, Hilde; Navis, Gerjan J.; Korstanje, Ron

    In humans, the insertion/deletion polymorphism in the angiotensin converting enzyme (ACE) gene accounts for half of the variance in plasma ACE activity. The deletion allele is associated with high plasma ACE activity, cardiovascular disease, and renal disease. In rat, a similar association is found

  7. Mutations in the p53 homolog p63: allele-specific developmental syndromes in humans.

    NARCIS (Netherlands)

    Bokhoven, J.H.L.M. van; McKeon, F.

    2002-01-01

    p63 is the most recently discovered but most ancient member of the p53 family. In marked contrast to p53, p63 is highly expressed in embryonic ectoderm and in the basal, regenerative layers of many epithelial tissues in the adult. The p63-knockout mouse dies at birth and lacks limbs, epidermis,

  8. Allele-specific characterization of alanine: glyoxylate aminotransferase variants associated with primary hyperoxaluria.

    Directory of Open Access Journals (Sweden)

    Melissa D Lage

    Full Text Available Primary Hyperoxaluria Type 1 (PH1 is a rare autosomal recessive kidney stone disease caused by deficiency of the peroxisomal enzyme alanine: glyoxylate aminotransferase (AGT, which is involved in glyoxylate detoxification. Over 75 different missense mutations in AGT have been found associated with PH1. While some of the mutations have been found to affect enzyme activity, stability, and/or localization, approximately half of these mutations are completely uncharacterized. In this study, we sought to systematically characterize AGT missense mutations associated with PH1. To facilitate analysis, we used two high-throughput yeast-based assays: one that assesses AGT specific activity, and one that assesses protein stability. Approximately 30% of PH1-associated missense mutations are found in conjunction with a minor allele polymorphic variant, which can interact to elicit complex effects on protein stability and trafficking. To better understand this allele interaction, we functionally characterized each of 34 mutants on both the major (wild-type and minor allele backgrounds, identifying mutations that synergize with the minor allele. We classify these mutants into four distinct categories depending on activity/stability results in the different alleles. Twelve mutants were found to display reduced activity in combination with the minor allele, compared with the major allele background. When mapped on the AGT dimer structure, these mutants reveal localized regions of the protein that appear particularly sensitive to interactions with the minor allele variant. While the majority of the deleterious effects on activity in the minor allele can be attributed to synergistic interaction affecting protein stability, we identify one mutation, E274D, that appears to specifically affect activity when in combination with the minor allele.

  9. Genetic analysis of gamma-ray mutagenesis in yeast. II. Allele-specific control of mutagenesis

    International Nuclear Information System (INIS)

    McKee, R.H.; Lawrence, C.W.

    1979-01-01

    We find that partially different sets of gene functions are required for the production of different kinds of mutations induced by 60 Co γ rays in Saccharomyces cerevisiae. This observation is very similar to others made previously with respect to uv mutagenesis and confirms the conclusion that such distinctive patterns of genetic control reflect properties of the test alleles and their genetic locations, rather than the kinds of lesions required to revert them. The data also support the model of mutagenic repair outlined in the first paper of this series in which partially different sets of gene functions are required for the production of different kinds of mutations, the formation of mutations at different genetic sites and the induction of mutations by different mutagens

  10. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

    DEFF Research Database (Denmark)

    Favero, Francesco; Joshi, Tejal; Marquard, Andrea Marion

    2015-01-01

    : Comparison between Sequenza/exome and SNP/ASCAT revealed strong correlation in cellularity (Pearson’s r = 0.90) and ploidy estimates (r = 0.42, or r = 0.94 after manual inspecting alternative solutions). This performance was noticeably superior to previously published algorithms. In addition, in artificial...

  11. Rapid identification of capybara (Hydrochaeris hydrochaeris through allele-specific PCR

    Directory of Open Access Journals (Sweden)

    Flávio Henrique-Silva

    2005-07-01

    Full Text Available The capybara is the largest rodent in the world and is widely distributed throughout Central and South America.  It is an animal of economic interest due to the pleasant flavor of its meat and higher protein content in comparison  to beef and pork meat.  The hide, hair and fat also have economic advantages. Thus,  as an animal with such high economic potential, it is the target of hunters, even though  hunting capybara is prohibited by law in Brazil.   Due to their  similarities,  capybara meat  is easily confused with  pork  meat.   This  occurs  upon  the apprehension of the  meat  from hunters, as well as in some restaurants that serve capybara meat that was slaughtered clandestinely. In both cases, when the meat is confiscated, those responsible for the crimes claim it is pork meat,  hindering  the enforcement of the law. A practical  course was ministered  to undergraduate biology students enrolled in the elective course Introduction to Genetic  Engineering  at Federal  University  of Sao Carlos (UFSCar, Sao Paulo  State, Brazil.  The  objective  of the  course was to establish  and  apply  a Polymerase  Chain  Reaction  (PCR assay to identify capybara meat and discriminate it in relation  to other types of meat,  including pork. Primers  were designed based  on 12S rRNA,  transthyretin and  growth  hormone  receptor  genes.  The primers generated  capybara specific fragments  of approximately 220, 290 and 330 bp for transthyretin,12S rRNA  and  growth  hormone  receptor,  respectively.   The  duplexes  developed  in the  present work can be used effectively to discriminate capybara meat  from other  animals,  contributing to combating predatory capybara hunting. The results were extensively discussed and the students have contributed to written a paper  to be submitted to a publication.

  12. Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides

    Directory of Open Access Journals (Sweden)

    Matos Isa

    2011-12-01

    Full Text Available Abstract Background Squalius alburnoides is an Iberian cyprinid fish resulting from an interspecific hybridisation between Squalius pyrenaicus females (P genome and males of an unknown Anaecypris hispanica-like species (A genome. S. alburnoides is an allopolyploid hybridogenetic complex, which makes it a likely candidate for ploidy mosaicism occurrence, and is also an interesting model to address questions about gene expression regulation and genomic interactions. Indeed, it was previously suggested that in S. alburnoides triploids (PAA composition silencing of one of the three alleles (mainly of the P allele occurs. However, not a whole haplome is inactivated but a more or less random inactivation of alleles varying between individuals and even between organs of the same fish was seen. In this work we intended to correlate expression differences between individuals and/or between organs to the occurrence of mosaicism, evaluating if mosaics could explain previous observations and its impact on the assessment of gene expression patterns. Results To achieve our goal, we developed flow cytometry and cell sorting protocols for this system generating more homogenous cellular and transcriptional samples. With this set-up we detected 10% ploidy mosaicism within the S. alburnoides complex, and determined the allelic expression profiles of ubiquitously expressed genes (rpl8; gapdh and β-actin in cells from liver and kidney of mosaic and non-mosaic individuals coming from different rivers over a wide geographic range. Conclusions Ploidy mosaicism occurs sporadically within the S. alburnoides complex, but in a frequency significantly higher than reported for other organisms. Moreover, we could exclude the influence of this phenomenon on the detection of variable allelic expression profiles of ubiquitously expressed genes (rpl8; gapdh and β-actin in cells from liver and kidney of triploid individuals. Finally, we determined that the expression patterns previously detected only in a narrow geographic range is not a local restricted phenomenon but is pervasive in rivers where S. pyrenaicus is sympatric with S. alburnoides. We discuss mechanisms that could lead to the formation of mosaic S. alburnoides and hypothesise about a relaxation of the mechanisms that impose a tight control over mitosis and ploidy control in mixoploids.

  13. Marine Fish Hybridization

    KAUST Repository

    He, Song

    2017-04-01

    Natural hybridization is reproduction (without artificial influence) between two or more species/populations which are distinguishable from each other by heritable characters. Natural hybridizations among marine fishes were highly underappreciated due to limited research effort; it seems that this phenomenon occurs more often than is commonly recognized. As hybridization plays an important role in biodiversity processes in the marine environment, detecting hybridization events and investigating hybridization is important to understand and protect biodiversity. The first chapter sets the framework for this disseration study. The Cohesion Species Concept was selected as the working definition of a species for this study as it can handle marine fish hybridization events. The concept does not require restrictive species boundaries. A general history and background of natural hybridization in marine fishes is reviewed during in chapter as well. Four marine fish hybridization cases were examed and documented in Chapters 2 to 5. In each case study, at least one diagnostic nuclear marker, screened from among ~14 candidate markers, was found to discriminate the putative hybridizing parent species. To further investigate genetic evidence to support the hybrid status for each hybrid offspring in each case, haploweb analysis on diagnostic markers (nuclear and/or mitochondrial) and the DAPC/PCA analysis on microsatellite data were used. By combining the genetic evidences, morphological traits, and ecological observations together, the potential reasons that triggered each hybridization events and the potential genetic/ecology effects could be discussed. In the last chapter, sequences from 82 pairs of hybridizing parents species (for which COI barcoding sequences were available either on GenBank or in our lab) were collected. By comparing the COI fragment p-distance between each hybridizing parent species, some general questions about marine fish hybridization were discussed: Is

  14. Microarray-based large scale detection of single feature ...

    Indian Academy of Sciences (India)

    Sphingolipid metabolism. Glycerolipid metabolism. Arginine and proline metabolism. Brassinosteroid biosynthesis. Protein processing in endoplasmic re culum. Cyanoamino acid metabolism. Circadian rhythm - plant. Fructose and mannose metabolism. Pyruvate metabolism. Photosynthesis beta-Alanine metabolism.

  15. Microarray-based large scale detection of single feature ...

    Indian Academy of Sciences (India)

    2015-12-08

    Dec 8, 2015 ... mental stages was used to identify single feature polymorphisms (SFPs). ... on a high-density oligonucleotide expression array in which. ∗ ..... The sign (+/−) with SFPs indicates direction of polymorphism. In the. (−) sign (i.e. ...

  16. Microarray based comparative genome-wide expression profiling of ...

    African Journals Online (AJOL)

    pg

    2014-03-05

    Mar 5, 2014 ... 45/F. ALL. 18/M. Fever, anaemia, enlarge lymph glands in children. Child having >50-60% blast cells in. TLC, TLC >20,000/cm mm. Vincristine (1.5 mg/m2), doxorubicin (25 mg/m2), prednisone. (40 mg/m2),. L-asparaginase (10,000 units iv/ alternate day), methotrexate. (12 mg/m2intrathecal). ALL. 6/M. ALL.

  17. Microarray-Based Identification of Transcription Factor Target Genes

    NARCIS (Netherlands)

    Gorte, M.; Horstman, A.; Page, R.B.; Heidstra, R.; Stromberg, A.; Boutilier, K.A.

    2011-01-01

    Microarray analysis is widely used to identify transcriptional changes associated with genetic perturbation or signaling events. Here we describe its application in the identification of plant transcription factor target genes with emphasis on the design of suitable DNA constructs for controlling TF

  18. Microarray-based cancer prediction using soft computing approach.

    Science.gov (United States)

    Wang, Xiaosheng; Gotoh, Osamu

    2009-05-26

    One of the difficulties in using gene expression profiles to predict cancer is how to effectively select a few informative genes to construct accurate prediction models from thousands or ten thousands of genes. We screen highly discriminative genes and gene pairs to create simple prediction models involved in single genes or gene pairs on the basis of soft computing approach and rough set theory. Accurate cancerous prediction is obtained when we apply the simple prediction models for four cancerous gene expression datasets: CNS tumor, colon tumor, lung cancer and DLBCL. Some genes closely correlated with the pathogenesis of specific or general cancers are identified. In contrast with other models, our models are simple, effective and robust. Meanwhile, our models are interpretable for they are based on decision rules. Our results demonstrate that very simple models may perform well on cancerous molecular prediction and important gene markers of cancer can be detected if the gene selection approach is chosen reasonably.

  19. Microarray-based RNA profiling of breast cancer

    DEFF Research Database (Denmark)

    Larsen, Martin J; Thomassen, Mads; Tan, Qihua

    2014-01-01

    analyzed the same 234 breast cancers on two different microarray platforms. One dataset contained known batch-effects associated with the fabrication procedure used. The aim was to assess the significance of correcting for systematic batch-effects when integrating data from different platforms. We here...

  20. Henkin and Hybrid Logic

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Huertas, Antonia; Manzano, Maria

    2014-01-01

    Leon Henkin was not a modal logician, but there is a branch of modal logic that has been deeply influenced by his work. That branch is hybrid logic, a family of logics that extend orthodox modal logic with special proposition symbols (called nominals) that name worlds. This paper explains why...... Henkin’s techniques are so important in hybrid logic. We do so by proving a completeness result for a hybrid type theory called HTT, probably the strongest hybrid logic that has yet been explored. Our completeness result builds on earlier work with a system called BHTT, or basic hybrid type theory...... is due to the first-order perspective, which lies at the heart of Henin’s best known work and hybrid logic....

  1. Hybrid Action Systems

    DEFF Research Database (Denmark)

    Ronkko, Mauno; Ravn, Anders P.

    1997-01-01

    a differential action, which allows differential equations as primitive actions. The extension allows us to model hybrid systems with both continuous and discrete behaviour. The main result of this paper is an extension of such a hybrid action system with parallel composition. The extension does not change...... the original meaning of the parallel composition, and therefore also the ordinary action systems can be composed in parallel with the hybrid action systems....

  2. Nanoscale Organic Hybrid Electrolytes

    KAUST Repository

    Nugent, Jennifer L.

    2010-08-20

    Nanoscale organic hybrid electrolytes are composed of organic-inorganic hybrid nanostructures, each with a metal oxide or metallic nanoparticle core densely grafted with an ion-conducting polyethylene glycol corona - doped with lithium salt. These materials form novel solvent-free hybrid electrolytes that are particle-rich, soft glasses at room temperature; yet manifest high ionic conductivity and good electrochemical stability above 5V. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Nanoscale Organic Hybrid Electrolytes

    KAUST Repository

    Nugent, Jennifer L.; Moganty, Surya S.; Archer, Lynden A.

    2010-01-01

    Nanoscale organic hybrid electrolytes are composed of organic-inorganic hybrid nanostructures, each with a metal oxide or metallic nanoparticle core densely grafted with an ion-conducting polyethylene glycol corona - doped with lithium salt. These materials form novel solvent-free hybrid electrolytes that are particle-rich, soft glasses at room temperature; yet manifest high ionic conductivity and good electrochemical stability above 5V. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. HYBRID VEHICLE CONTROL SYSTEM

    Directory of Open Access Journals (Sweden)

    V. Dvadnenko

    2016-06-01

    Full Text Available The hybrid vehicle control system includes a start–stop system for an internal combustion engine. The system works in a hybrid mode and normal vehicle operation. To simplify the start–stop system, there were user new possibilities of a hybrid car, which appeared after the conversion. Results of the circuit design of the proposed system of basic blocks are analyzed.

  5. Hybrid radiator cooling system

    Science.gov (United States)

    France, David M.; Smith, David S.; Yu, Wenhua; Routbort, Jules L.

    2016-03-15

    A method and hybrid radiator-cooling apparatus for implementing enhanced radiator-cooling are provided. The hybrid radiator-cooling apparatus includes an air-side finned surface for air cooling; an elongated vertically extending surface extending outwardly from the air-side finned surface on a downstream air-side of the hybrid radiator; and a water supply for selectively providing evaporative cooling with water flow by gravity on the elongated vertically extending surface.

  6. Toronto hybrid taxi pilot

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, M. [CrossChasm Technologies, Cambridge, ON (Canada); Marans, B. [Toronto Atmospheric Fund, ON (Canada)

    2009-10-15

    This paper provided details of a hybrid taxi pilot program conducted to compare the on-road performance of Toyota Camry hybrid vehicles against conventional vehicles over a 1-year period in order to determine the business case and air emission reductions associated with the use of hybrid taxi cabs. Over 750,000 km worth of fuel consumption was captured from 10 Toyota Camry hybrids, a Toyota Prius, and 5 non-hybrid Camry vehicles over an 18-month period. The average real world fuel consumption for the taxis demonstrated that the Toyota Prius has the lowest cost of ownership, while the non-hybrid Camry has the highest cost of ownership. Carbon dioxide (CO{sub 2}) reductions associated with the 10 Camry hybrid taxis were calculated at 236 tonnes over a 7-year taxi service life. Results suggested that the conversion of Toronto's 5680 taxis would yield annual CO{sub 2} emission reductions of over 19,000 tonnes. All hybrid purchasers identified themselves as highly likely to purchase a hybrid again. 5 tabs., 9 figs.

  7. Managing hybrid marketing systems.

    Science.gov (United States)

    Moriarty, R T; Moran, U

    1990-01-01

    As competition increases and costs become critical, companies that once went to market only one way are adding new channels and using new methods - creating hybrid marketing systems. These hybrid marketing systems hold the promise of greater coverage and reduced costs. But they are also hard to manage; they inevitably raise questions of conflict and control: conflict because marketing units compete for customers; control because new indirect channels are less subject to management authority. Hard as they are to manage, however, hybrid marketing systems promise to become the dominant design, replacing the "purebred" channel strategy in all kinds of businesses. The trick to managing the hybrid is to analyze tasks and channels within and across a marketing system. A map - the hybrid grid - can help managers make sense of their hybrid system. What the chart reveals is that channels are not the basic building blocks of a marketing system; marketing tasks are. The hybrid grid forces managers to consider various combinations of channels and tasks that will optimize both cost and coverage. Managing conflict is also an important element of a successful hybrid system. Managers should first acknowledge the inevitability of conflict. Then they should move to bound it by creating guidelines that spell out which customers to serve through which methods. Finally, a marketing and sales productivity (MSP) system, consisting of a central marketing database, can act as the central nervous system of a hybrid marketing system, helping managers create customized channels and service for specific customer segments.

  8. Toronto hybrid taxi pilot

    International Nuclear Information System (INIS)

    Stevens, M.; Marans, B.

    2009-10-01

    This paper provided details of a hybrid taxi pilot program conducted to compare the on-road performance of Toyota Camry hybrid vehicles against conventional vehicles over a 1-year period in order to determine the business case and air emission reductions associated with the use of hybrid taxi cabs. Over 750,000 km worth of fuel consumption was captured from 10 Toyota Camry hybrids, a Toyota Prius, and 5 non-hybrid Camry vehicles over an 18-month period. The average real world fuel consumption for the taxis demonstrated that the Toyota Prius has the lowest cost of ownership, while the non-hybrid Camry has the highest cost of ownership. Carbon dioxide (CO 2 ) reductions associated with the 10 Camry hybrid taxis were calculated at 236 tonnes over a 7-year taxi service life. Results suggested that the conversion of Toronto's 5680 taxis would yield annual CO 2 emission reductions of over 19,000 tonnes. All hybrid purchasers identified themselves as highly likely to purchase a hybrid again. 5 tabs., 9 figs.

  9. Hybrid FOSS Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Armstrong researchers are continuing their efforts to further develop FOSS technologies. A hybrid FOSS technique (HyFOSS) employs conventional continuous grating...

  10. From hybrid swarms to swarms of hybrids

    Science.gov (United States)

    Stohlgren, Thomas J.; Szalanski, Allen L; Gaskin, John F.; Young, Nicholas E.; West, Amanda; Jarnevich, Catherine S.; Tripodi, Amber

    2014-01-01

    Science has shown that the introgression or hybridization of modern humans (Homo sapiens) with Neanderthals up to 40,000 YBP may have led to the swarm of modern humans on earth. However, there is little doubt that modern trade and transportation in support of the humans has continued to introduce additional species, genotypes, and hybrids to every country on the globe. We assessed the utility of species distributions modeling of genotypes to assess the risk of current and future invaders. We evaluated 93 locations of the genus Tamarix for which genetic data were available. Maxent models of habitat suitability showed that the hybrid, T. ramosissima x T. chinensis, was slightly greater than the parent taxa (AUCs > 0.83). General linear models of Africanized honey bees, a hybrid cross of Tanzanian Apis mellifera scutellata and a variety of European honey bee including A. m. ligustica, showed that the Africanized bees (AUC = 0.81) may be displacing European honey bees (AUC > 0.76) over large areas of the southwestern U.S. More important, Maxent modeling of sub-populations (A1 and A26 mitotypes based on mDNA) could be accurately modeled (AUC > 0.9), and they responded differently to environmental drivers. This suggests that rapid evolutionary change may be underway in the Africanized bees, allowing the bees to spread into new areas and extending their total range. Protecting native species and ecosystems may benefit from risk maps of harmful invasive species, hybrids, and genotypes.

  11. Hybridization in geese

    NARCIS (Netherlands)

    Ottenburghs, Jente; Hooft, van Pim; Wieren, van Sipke E.; Ydenberg, Ronald C.; Prins, Herbert H.T.

    2016-01-01

    The high incidence of hybridization in waterfowl (ducks, geese and swans) makes this bird group an excellent study system to answer questions related to the evolution and maintenance of species boundaries. However, knowledge on waterfowl hybridization is biased towards ducks, with a large

  12. Mirror hybrid reactor studies

    International Nuclear Information System (INIS)

    Bender, D.J.

    1978-01-01

    The hybrid reactor studies are reviewed. The optimization of the point design and work on a reference design are described. The status of the nuclear analysis of fast spectrum blankets, systems studies for fissile fuel producing hybrid reactor, and the mechanical design of the machine are reviewed

  13. Hybrid Universities in Malaysia

    Science.gov (United States)

    Lee, Molly; Wan, Chang Da; Sirat, Morshidi

    2017-01-01

    Are Asian universities different from those in Western countries? Premised on the hypothesis that Asian universities are different because of hybridization between Western academic models and local traditional cultures, this paper investigates the hybrid characteristics in Malaysian universities resulting from interaction between contemporary…

  14. Cardiac hybrid imaging

    Energy Technology Data Exchange (ETDEWEB)

    Gaemperli, Oliver [University Hospital Zurich, Cardiac Imaging, Zurich (Switzerland); University Hospital Zurich, Nuclear Cardiology, Cardiovascular Center, Zurich (Switzerland); Kaufmann, Philipp A. [University Hospital Zurich, Cardiac Imaging, Zurich (Switzerland); Alkadhi, Hatem [University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland)

    2014-05-15

    Hybrid cardiac single photon emission computed tomography (SPECT)/CT imaging allows combined assessment of anatomical and functional aspects of cardiac disease. In coronary artery disease (CAD), hybrid SPECT/CT imaging allows detection of coronary artery stenosis and myocardial perfusion abnormalities. The clinical value of hybrid imaging has been documented in several subsets of patients. In selected groups of patients, hybrid imaging improves the diagnostic accuracy to detect CAD compared to the single imaging techniques. Additionally, this approach facilitates functional interrogation of coronary stenoses and guidance with regard to revascularization procedures. Moreover, the anatomical information obtained from CT coronary angiography or coronary artery calcium scores (CACS) adds prognostic information over perfusion data from SPECT. The use of cardiac hybrid imaging has been favoured by the dissemination of dedicated hybrid systems and the release of dedicated image fusion software, which allow simple patient throughput for hybrid SPECT/CT studies. Further technological improvements such as more efficient detector technology to allow for low-radiation protocols, ultra-fast image acquisition and improved low-noise image reconstruction algorithms will be instrumental to further promote hybrid SPECT/CT in research and clinical practice. (orig.)

  15. Hybrid job shop scheduling

    NARCIS (Netherlands)

    Schutten, Johannes M.J.

    1995-01-01

    We consider the problem of scheduling jobs in a hybrid job shop. We use the term 'hybrid' to indicate that we consider a lot of extensions of the classic job shop, such as transportation times, multiple resources, and setup times. The Shifting Bottleneck procedure can be generalized to deal with

  16. Hybrid Shipboard Microgrids

    DEFF Research Database (Denmark)

    Othman @ Marzuki, Muzaidi Bin; Anvari-Moghaddam, Amjad; Guerrero, Josep M.

    2017-01-01

    Strict regulation on emissions of air pollutants imposed by the maritime authorities has led to the introduction of hybrid microgrids to the shipboard power systems (SPSs) which acts toward energy efficient ships with less pollution. A hybrid energy system can include different means of generation...

  17. Hybrid intelligent engineering systems

    CERN Document Server

    Jain, L C; Adelaide, Australia University of

    1997-01-01

    This book on hybrid intelligent engineering systems is unique, in the sense that it presents the integration of expert systems, neural networks, fuzzy systems, genetic algorithms, and chaos engineering. It shows that these new techniques enhance the capabilities of one another. A number of hybrid systems for solving engineering problems are presented.

  18. Editorial: Hybrid Systems

    DEFF Research Database (Denmark)

    Olderog, Ernst-Rüdiger; Ravn, Anders Peter

    2007-01-01

    An introduction to three papers in a special issue on Hybrid Systems. These paper were first presented at an IFIP WG 2.2 meeting in Skagen 2005.......An introduction to three papers in a special issue on Hybrid Systems. These paper were first presented at an IFIP WG 2.2 meeting in Skagen 2005....

  19. Course on hybrid calculation

    International Nuclear Information System (INIS)

    Weill, J.; Tellier; Bonnemay; Craigne; Chareton; Di Falco

    1969-02-01

    After a definition of hybrid calculation (combination of analogue and digital calculation) with a distinction between series and parallel hybrid computing, and a description of a hybrid computer structure and of task sharing between computers, this course proposes a description of hybrid hardware used in Saclay and Cadarache computing centres, and of operations performed by these systems. The next part addresses issues related to programming languages and software. The fourth part describes how a problem is organised for its processing on these computers. Methods of hybrid analysis are then addressed: resolution of optimisation problems, of partial differential equations, and of integral equations by means of different methods (gradient, maximum principle, characteristics, functional approximation, time slicing, Monte Carlo, Neumann iteration, Fischer iteration)

  20. Hybrid functional pseudopotentials

    Science.gov (United States)

    Yang, Jing; Tan, Liang Z.; Rappe, Andrew M.

    2018-02-01

    The consistency between the exchange-correlation functional used in pseudopotential construction and in the actual density functional theory calculation is essential for the accurate prediction of fundamental properties of materials. However, routine hybrid density functional calculations at present still rely on generalized gradient approximation pseudopotentials due to the lack of hybrid functional pseudopotentials. Here, we present a scheme for generating hybrid functional pseudopotentials, and we analyze the importance of pseudopotential density functional consistency for hybrid functionals. For the PBE0 hybrid functional, we benchmark our pseudopotentials for structural parameters and fundamental electronic gaps of the Gaussian-2 (G2) molecular dataset and some simple solids. Our results show that using our PBE0 pseudopotentials in PBE0 calculations improves agreement with respect to all-electron calculations.

  1. Comparative Genomic Hybridization Analysis of Yersinia enterocolitica and Yersinia pseudotuberculosis Identifies Genetic Traits to Elucidate Their Different Ecologies

    Directory of Open Access Journals (Sweden)

    Kaisa Jaakkola

    2015-01-01

    Full Text Available Enteropathogenic Yersinia enterocolitica and Yersinia pseudotuberculosis are both etiological agents for intestinal infection known as yersiniosis, but their epidemiology and ecology bear many differences. Swine are the only known reservoir for Y. enterocolitica 4/O:3 strains, which are the most common cause of human disease, while Y. pseudotuberculosis has been isolated from a variety of sources, including vegetables and wild animals. Infections caused by Y. enterocolitica mainly originate from swine, but fresh produce has been the source for widespread Y. pseudotuberculosis outbreaks within recent decades. A comparative genomic hybridization analysis with a DNA microarray based on three Yersinia enterocolitica and four Yersinia pseudotuberculosis genomes was conducted to shed light on the genomic differences between enteropathogenic Yersinia. The hybridization results identified Y. pseudotuberculosis strains to carry operons linked with the uptake and utilization of substances not found in living animal tissues but present in soil, plants, and rotting flesh. Y. pseudotuberculosis also harbors a selection of type VI secretion systems targeting other bacteria and eukaryotic cells. These genetic traits are not found in Y. enterocolitica, and it appears that while Y. pseudotuberculosis has many tools beneficial for survival in varied environments, the Y. enterocolitica genome is more streamlined and adapted to their preferred animal reservoir.

  2. Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing® technology

    Directory of Open Access Journals (Sweden)

    Gallagher Margaret L

    2009-08-01

    Full Text Available Abstract Background Identification of CYP2A6 alleles associated with reduced enzyme activity is important in the study of inter-individual differences in drug metabolism. CYP2A6*12 is a hybrid allele that results from unequal crossover between CYP2A6 and CYP2A7 genes. The 5' regulatory region and exons 1–2 are derived from CYP2A7, and exons 3–9 are derived from CYP2A6. Conventional methods for detection of CYP2A6*12 consist of two-step PCR protocols that are laborious and unsuitable for high-throughput genotyping. We developed a rapid and accurate method to detect the CYP2A6*12 allele by Pyrosequencing technology. Methods A single set of PCR primers was designed to specifically amplify both the CYP2A6*1 wild-type allele and the CYP2A6*12 hybrid allele. An internal Pyrosequencing primer was used to generate allele-specific sequence information, which detected homozygous wild-type, heterozygous hybrid, and homozygous hybrid alleles. We first validated the assay on 104 DNA samples that were also genotyped by conventional two-step PCR and by cycle sequencing. CYP2A6*12 allele frequencies were then determined using the Pyrosequencing assay on 181 multi-ethnic DNA samples from subjects of African American, European Caucasian, Pacific Rim, and Hispanic descent. Finally, we streamlined the Pyrosequencing assay by integrating liquid handling robotics into the workflow. Results Pyrosequencing results demonstrated 100% concordance with conventional two-step PCR and cycle sequencing methods. Allele frequency data showed slightly higher prevalence of the CYP2A6*12 allele in European Caucasians and Hispanics. Conclusion This Pyrosequencing assay proved to be a simple, rapid, and accurate alternative to conventional methods, which can be easily adapted to the needs of higher-throughput studies.

  3. Hybrid electric vehicles TOPTEC

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-06-21

    This one-day TOPTEC session began with an overview of hybrid electric vehicle technology. Updates were given on alternative types of energy storage, APU control for low emissions, simulation programs, and industry and government activities. The keynote speech was about battery technology, a key element to the success of hybrids. The TOPEC concluded with a panel discussion on the mission of hybrid electric vehicles, with a perspective from industry and government experts from United States and Canada on their view of the role of this technology.

  4. Hybrid systems with constraints

    CERN Document Server

    Daafouz, Jamal; Sigalotti, Mario

    2013-01-01

    Control theory is the main subject of this title, in particular analysis and control design for hybrid dynamic systems.The notion of hybrid systems offers a strong theoretical and unified framework to cope with the modeling, analysis and control design of systems where both continuous and discrete dynamics interact. The theory of hybrid systems has been the subject of intensive research over the last decade and a large number of diverse and challenging problems have been investigated. Nevertheless, many important mathematical problems remain open.This book is dedicated mainly to

  5. Towers of hybrid mesons

    International Nuclear Information System (INIS)

    Semay, Claude; Buisseret, Fabien; Silvestre-Brac, Bernard

    2009-01-01

    A hybrid meson is a quark-antiquark pair in which, contrary to ordinary mesons, the gluon field is in an excited state. In the framework of constituent models, the interaction potential is assumed to be the energy of an excited string. An approximate, but accurate, analytical solution of the Schroedinger equation with such a potential is presented. When applied to hybrid charmonia and bottomonia, towers of states are predicted in which the masses are a linear function of a harmonic oscillator band number for the quark-antiquark pair. Such a formula could be a reliable guide for the experimental detection of heavy hybrid mesons.

  6. Hybrid Bloch brane

    Energy Technology Data Exchange (ETDEWEB)

    Bazeia, D.; Lima, Elisama E.M.; Losano, L. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, PB (Brazil)

    2017-02-15

    This work reports on models described by two real scalar fields coupled with gravity in the five-dimensional spacetime, with a warped geometry involving one infinite extra dimension. Through a mechanism that smoothly changes a thick brane into a hybrid brane, one investigates the appearance of hybrid branes hosting internal structure, characterized by the splitting on the energy density and the volcano potential, induced by the parameter which controls interactions between the two scalar fields. In particular, we investigate distinct symmetric and asymmetric hybrid brane scenarios. (orig.)

  7. Formula hybrid SAE.

    Science.gov (United States)

    2013-09-01

    User-friendly tools are needed for undergraduates to learn about component sizing, powertrain integration, and control : strategies for student competitions involving hybrid vehicles. A TK Solver tool was developed at the University of Idaho for : th...

  8. Hybrid adsorptive membrane reactor

    Science.gov (United States)

    Tsotsis, Theodore T [Huntington Beach, CA; Sahimi, Muhammad [Altadena, CA; Fayyaz-Najafi, Babak [Richmond, CA; Harale, Aadesh [Los Angeles, CA; Park, Byoung-Gi [Yeosu, KR; Liu, Paul K. T. [Lafayette Hill, PA

    2011-03-01

    A hybrid adsorbent-membrane reactor in which the chemical reaction, membrane separation, and product adsorption are coupled. Also disclosed are a dual-reactor apparatus and a process using the reactor or the apparatus.

  9. Hybrid plasmachemical reactor

    Energy Technology Data Exchange (ETDEWEB)

    Lelevkin, V. M., E-mail: lelevkin44@mail.ru; Smirnova, Yu. G.; Tokarev, A. V. [Kyrgyz-Russian Slavic University (Kyrgyzstan)

    2015-04-15

    A hybrid plasmachemical reactor on the basis of a dielectric barrier discharge in a transformer is developed. The characteristics of the reactor as functions of the dielectric barrier discharge parameters are determined.

  10. Marine Fish Hybridization

    KAUST Repository

    He, Song

    2017-01-01

    for each hybrid offspring in each case, haploweb analysis on diagnostic markers (nuclear and/or mitochondrial) and the DAPC/PCA analysis on microsatellite data were used. By combining the genetic evidences, morphological traits, and ecological observations

  11. Hybrid vertical cavity laser

    DEFF Research Database (Denmark)

    Chung, Il-Sug; Mørk, Jesper

    2010-01-01

    A new hybrid vertical cavity laser structure for silicon photonics is suggested and numerically investigated. It incorporates a silicon subwavelength grating as a mirror and a lateral output coupler to a silicon ridge waveguide.......A new hybrid vertical cavity laser structure for silicon photonics is suggested and numerically investigated. It incorporates a silicon subwavelength grating as a mirror and a lateral output coupler to a silicon ridge waveguide....

  12. Human hybrid hybridoma

    Energy Technology Data Exchange (ETDEWEB)

    Tiebout, R.F.; van Boxtel-Oosterhof, F.; Stricker, E.A.M.; Zeijlemaker, W.P.

    1987-11-15

    Hybrid hybridomas are obtained by fusion of two cells, each producing its own antibody. Several authors have reported the construction of murine hybrid hybridomas with the aim to obtain bispecific monoclonal antibodies. The authors have investigated, in a model system, the feasibility of constructing a human hybrid hybridoma. They fused two monoclonal cell lines: an ouabain-sensitive and azaserine/hypoxanthine-resistant Epstein-Barr virus-transformed human cell line that produces an IgG1kappa antibody directed against tetanus toxiod and an azaserine/hypoxanthine-sensitive and ouabain-resistant human-mouse xenohybrid cell line that produces a human IgG1lambda antibody directed against hepatitis-B surface antigen. Hybrid hybridoma cells were selected in culture medium containing azaserine/hypoxanthine and ouabain. The hybrid nature of the secreted antibodies was analyzed by means of two antigen-specific immunoassay. The results show that it is possible, with the combined use of transformation and xenohybridization techniques, to construct human hybrid hybridomas that produce bispecific antibodies. Bispecific antibodies activity was measured by means of two radioimmunoassays.

  13. Systems for hybrid cars

    Science.gov (United States)

    Bitsche, Otmar; Gutmann, Guenter

    Not only sharp competition but also legislation are pushing development of hybrid drive trains. Based on conventional internal combustion engine (ICE) vehicles, these drive trains offer a wide range of benefits from reduced fuel consumption and emission to multifaceted performance improvements. Hybrid electric drive trains may also facilitate the introduction of fuel cells (FC). The battery is the key component for all hybrid drive trains, as it dominates cost and performance issues. The selection of the right battery technology for the specific automotive application is an important task with an impact on costs of development and use. Safety, power, and high cycle life are a must for all hybrid applications. The greatest pressure to reduce cost is in soft hybrids, where lead-acid embedded in a considerate management presents the cheapest solution, with a considerable improvement in performance needed. From mild to full hybridization, an improvement in specific power makes higher costs more acceptable, provided that the battery's service life is equivalent to the vehicle's lifetime. Today, this is proven for the nickel-metal hydride system. Lithium ion batteries, which make use of a multiple safety concept, and with some development anticipated, provide even better prospects in terms of performance and costs. Also, their scalability permits their application in battery electric vehicles—the basis for better performance and enhanced user acceptance. Development targets for the batteries are discussed with a focus on system aspects such as electrical and thermal management and safety.

  14. Generation and characterization of tribenuron-methyl herbicide-resistant rapeseed (Brasscia napus) for hybrid seed production using chemically induced male sterility.

    Science.gov (United States)

    Li, Haitao; Li, Juanjuan; Zhao, Bo; Wang, Jing; Yi, Licong; Liu, Chao; Wu, Jiangsheng; King, Graham J; Liu, Kede

    2015-01-01

    Identification and molecular analysis of four tribenuron-methyl resistant mutants in Brassica napus , which would be very useful in hybrid production using a Chemically induced male sterility system. Chemically induced male sterility (CIMS) systems dependent on chemical hybridization agents (CHAs) like tribenuron-methyl (TBM) represent an important approach for practical utilization of heterosis in rapeseed. However, when spraying the female parents with TBM to induce male sterility the male parents must be protected with a shield to avoid injury to the stamens, which would otherwise complicate the seed production protocol and increase the cost of hybrid seed production. Here we report the first proposed application of a herbicide-resistant cultivar in hybrid production, using a CIMS system based on identifying four TBM-resistant mutants in Brassica napus. Genetic analysis indicated that the TBM resistance was controlled by a single dominant nuclear gene. An in vitro enzyme activity assay for acetohydroxyacid synthase (AHAS) suggested that the herbicide resistance is caused by a gain-of-function mutation in a copy of AHAS genes. Comparative sequencing of the mutants and wild type BnaA.AHAS.a coding sequences identified a C-to-T transition at either position 535 or 536 from the translation start site, which resulted in a substitution of proline with serine or leucine at position 197 according to the Arabidopsis thaliana protein sequence. An allele-specific dCAPS marker developed from the C536T variation co-segregated with the herbicide resistance. Transgenic A. thaliana plants expressing BnaA.ahas3.a conferred herbicide resistance, which confirmed that the P197 substitution in BnaA.AHAS.a was responsible for the herbicide resistance. Moreover, the TBM-resistant lines maintain normal male fertility under TBM treatment and can be of practical value in hybrid seed production using CIMS.

  15. Hybrid Propulsion Demonstration Program 250K Hybrid Motor

    Science.gov (United States)

    Story, George; Zoladz, Tom; Arves, Joe; Kearney, Darren; Abel, Terry; Park, O.

    2003-01-01

    The Hybrid Propulsion Demonstration Program (HPDP) program was formed to mature hybrid propulsion technology to a readiness level sufficient to enable commercialization for various space launch applications. The goal of the HPDP was to develop and test a 250,000 pound vacuum thrust hybrid booster in order to demonstrate hybrid propulsion technology and enable manufacturing of large hybrid boosters for current and future space launch vehicles. The HPDP has successfully conducted four tests of the 250,000 pound thrust hybrid rocket motor at NASA's Stennis Space Center. This paper documents the test series.

  16. Fusion-fission hybrid reactors

    International Nuclear Information System (INIS)

    Greenspan, E.

    1984-01-01

    This chapter discusses the range of characteristics attainable from hybrid reactor blankets; blanket design considerations; hybrid reactor designs; alternative fuel hybrid reactors; multi-purpose hybrid reactors; and hybrid reactors and the energy economy. Hybrid reactors are driven by a fusion neutron source and include fertile and/or fissile material. The fusion component provides a copious source of fusion neutrons which interact with a subcritical fission component located adjacent to the plasma or pellet chamber. Fissile fuel and/or energy are the main products of hybrid reactors. Topics include high F/M blankets, the fissile (and tritium) breeding ratio, effects of composition on blanket properties, geometrical considerations, power density and first wall loading, variations of blanket properties with irradiation, thermal-hydraulic and mechanical design considerations, safety considerations, tokamak hybrid reactors, tandem-mirror hybrid reactors, inertial confinement hybrid reactors, fusion neutron sources, fissile-fuel and energy production ability, simultaneous production of combustible and fissile fuels, fusion reactors for waste transmutation and fissile breeding, nuclear pumped laser hybrid reactors, Hybrid Fuel Factories (HFFs), and scenarios for hybrid contribution. The appendix offers hybrid reactor fundamentals. Numerous references are provided

  17. Research on Hybrid Vehicle Drivetrain

    Science.gov (United States)

    Xie, Zhongzhi

    Hybrid cars as a solution to energy saving, emission reduction measures, have received widespread attention. Motor drive system as an important part of the hybrid vehicles as an important object of study. Based on the hybrid electric vehicle powertrain control system for permanent magnet synchronous motor as the object of study. Can be applied to hybrid car compares the characteristics of traction motors, chose permanent magnet synchronous Motors as drive motors for hybrid vehicles. Building applications in hybrid cars in MATLAB/Simulink simulation model of permanent-magnet synchronous motor speed control system and analysis of simulation results.

  18. New hybrid systems

    International Nuclear Information System (INIS)

    Bernardin, B.

    2001-01-01

    New hybrid systems are made up of a subcritical core, a spallation target and a proton accelerator. The neutrons that are produced in the target by the flux of protons are necessary to maintain the chain reaction of fission. Some parameters that are important for a classical nuclear reactor like doppler coefficient or delayed neutron fraction do not matter in a hybrid system. In a PWR-type reactor or in a fast reactor the concentration of actinides has a bad impact on these 2 parameters, so it is justified to study hybrid systems as actinide transmuters. The hybrid system, because of its external source of neutrons can put aside an important reactivity margin. This reactivity margin can be used to design safer nuclear reactors (particularly in some situations of reactivity accidents) or to irradiate fuel elements containing high concentrations of minor actinides that could not be allowed in a classical reactor. This article reviews various ways of integrating hybrid systems in a population of already existing nuclear reactors in order to manage quantities of plutonium, of minor actinides or of long-life fission products. (A.C.)

  19. The Hybrid Museum: Hybrid Economies of Meaning

    DEFF Research Database (Denmark)

    Vestergaard, Vitus

    2013-01-01

    Social media has created new ways of communicating and has brought about a new distinctive ethos. New literacies are not simply about new technology but also about this new ethos. Many museums are embracing this ethos by what is often called participatory practices. From a sociocultural perspective...... this article shows that there are two different museum mindsets where the second mindset leans towards participatory practices. It is shown how a museum can support a hybrid economy of meaning that builds on both a user generated economy of meaning and an institutional economy of meaning and adds value to both...

  20. Hybrid system concepts

    International Nuclear Information System (INIS)

    Landeyro, P.A.

    1995-01-01

    Hybrid systems studied for fissile material production, were reconsidered for minor actinide and long-lived fission product destruction as alternative to the traditional final disposal of nuclear waste. Now there are attempts to extend the use of the concepts developed for minor actinide incineration to plutonium burning. The most promising hybrid system concept considers fuel and target both as liquids. From the results obtained, the possibility to adopt composite targets seems the most promising solution, but still there remains the problem of Pu production, not acceptable in a burning system. This kind of targets can be mainly used for fissile material production, while for accelerator driven burners it is most convenient to use a liquid lead target. The most suitable solvent is heavy water for minor actinide annihilation in the blanket of a hybrid system. Due to the criticality conditions and the necessity of electric energy production, the blanket using plutonium dissolved in molten salts is the most convenient one. (author)

  1. Hybrid strategies in nanolithography

    Energy Technology Data Exchange (ETDEWEB)

    Saavedra, Hector M; Mullen, Thomas J; Zhang Pengpeng; Dewey, Daniel C; Claridge, Shelley A; Weiss, Paul S [Department of Chemistry, The Pennsylvania State University, University Park, PA 16802 (United States)], E-mail: psw@cnsi.ucla.edu

    2010-03-15

    Hybrid nanoscale patterning strategies combine the registration and addressability of conventional lithographic techniques with the chemical and physical functionality enabled by intermolecular, electrostatic and/or biological interactions. This review aims to highlight and to provide a comprehensive description of recent developments in hybrid nanoscale patterning strategies that enhance existing lithographic techniques or can be used to fabricate functional chemical patterns that interact with their environment. These functional structures create new capabilities, such as the fabrication of physicochemical surfaces that can recognize and capture analytes from complex liquid or gaseous mixtures. The nanolithographic techniques we describe can be classified into three general areas: traditional lithography, soft lithography and scanning-probe lithography. The strengths and limitations of each hybrid patterning technique will be discussed, along with the current and potential applications of the resulting patterned, functional surfaces.

  2. The tokamak hybrid reactor

    International Nuclear Information System (INIS)

    Kelly, J.L.; Rose, R.P.

    1981-01-01

    At a time when the potential benefits of various energy options are being seriously evaluated in many countries through-out the world, it is both timely and important to evaluate the practical application of fusion reactors for their economical production of nuclear fissile fuels from fertile fuels. The fusion hybrid reactor represents a concept that could assure the availability of adequate fuel supplies for a proven nuclear technology and have the potential of being an electrical energy source as opposed to an energy consumer as are the present fuel enrichment processes. Westinghouse Fusion Power Systems Department, under Contract No. EG-77-C-02-4544 with the Department of Energy, Office of Fusion Energy, has developed a preliminary conceptual design for an early twenty-first century fusion hybrid reactor called the commercial Tokamak Hybrid Reactor (CTHR). This design was developed as a first generation commercial plant producing fissile fuel to support a significant number of client Light Water Reactor (LWR) Plants. To the depth this study has been performed, no insurmountable technical problems have been identified. The study has provided a basis for reasonable cost estimates of the hybrid plants as well as the hybrid/LWR system busbar electricity costs. This energy system can be optimized to have a net cost of busbar electricity that is equivalent to the conventional LWR plant, yet is not dependent on uranium ore prices or standard enrichment costs, since the fusion hybrid can be fueled by numerous fertile fuel resources. A nearer-term concept is also defined using a beam driven fusion driver in lieu of the longer term ignited operating mode. (orig.)

  3. Hybride textuelle Strukturen und hybride textuelle Einheiten. Ein ...

    African Journals Online (AJOL)

    carrying set of all hybrid hierarchical structures are element-heterogeneous whilst the structure- carrying set of all ... grams of hierarchical hybrid article structures, the nodes for those text segments that establish the hybrid status of .... der; d ∈ ArtA ⊣ G|WAr (= Artikelangabe, anhand derer das Genus (= G) und zugleich die ...

  4. Hydraulic Hybrid Vehicle Publications | Transportation Research | NREL

    Science.gov (United States)

    Hydraulic Hybrid Vehicle Publications Hydraulic Hybrid Vehicle Publications The following technical papers and fact sheets provide information about NREL's hydraulic hybrid fleet vehicle evaluations . Refuse Trucks Project Startup: Evaluating the Performance of Hydraulic Hybrid Refuse Vehicles. Bob

  5. Doubts about hybrids

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

    The natural draught wet cooling tower with a height of 160 m is considerably taller than the 80 m high hybrid cooling tower, but the latter has a considerably larger diameter. Spray losses for both types are about 4.5 kg/sec for a thermal output of 2500 MW. Apart from the pump load, the natural cooling tower requires no power. Apart from higher pump loads, the hybrid cooling tower requires power for the fans. The energy demand for this purpose is 1.5 to 3% of the nett powerstation output. For the Isar 2 nuclear powerstation this would mean a reduction in puput of about 35 MW. (orig.) [de

  6. Analog and hybrid computing

    CERN Document Server

    Hyndman, D E

    2013-01-01

    Analog and Hybrid Computing focuses on the operations of analog and hybrid computers. The book first outlines the history of computing devices that influenced the creation of analog and digital computers. The types of problems to be solved on computers, computing systems, and digital computers are discussed. The text looks at the theory and operation of electronic analog computers, including linear and non-linear computing units and use of analog computers as operational amplifiers. The monograph examines the preparation of problems to be deciphered on computers. Flow diagrams, methods of ampl

  7. Toyota hybrid synergy drive

    Energy Technology Data Exchange (ETDEWEB)

    Gautschi, H.

    2008-07-01

    This presentation made at the Swiss 2008 research conference on traffic by Hannes Gautschi, director of service and training at the Toyota company in Switzerland, takes a look at Toyota's hybrid drive vehicles. The construction of the vehicles and their combined combustion engines and electric generators and drives is presented and the combined operation of these components is described. Braking and energy recovery are discussed. Figures on the performance, fuel consumption and CO{sub 2} output of the hybrid vehicles are compared with those of conventional vehicles.

  8. Mirror fusion--fission hybrids

    International Nuclear Information System (INIS)

    Lee, J.D.

    1978-01-01

    The fusion-fission concept and the mirror fusion-fission hybrid program are outlined. Magnetic mirror fusion drivers and blankets for hybrid reactors are discussed. Results of system analyses are presented and a reference design is described

  9. Security in hybrid cloud computing

    OpenAIRE

    Koudelka, Ondřej

    2016-01-01

    This bachelor thesis deals with the area of hybrid cloud computing, specifically with its security. The major aim of the thesis is to analyze and compare the chosen hybrid cloud providers. For the minor aim this thesis compares the security challenges of hybrid cloud as opponent to other deployment models. In order to accomplish said aims, this thesis defines the terms cloud computing and hybrid cloud computing in its theoretical part. Furthermore the security challenges for cloud computing a...

  10. Hybrid Ventilation Air Flow Process

    DEFF Research Database (Denmark)

    Heiselberg, Per Kvols

    The scope of this annex is therefore to obtain better knowledge of the use of hybrid ventilation technologies. The annex focus on development of control strategies for hybrid ventilation, on development of methods to predict hybrid ventilation performance in office buildings and on implementation...

  11. Teelt van hybride wintertarwerassen

    NARCIS (Netherlands)

    Timmer, R.D.; Paauw, J.G.M.

    2003-01-01

    Om de mogelijkheden van de teelt van hybride wintertarwerassen onder Nederlandse omstandigheden in beeld te brengen zijn er van 2000-2002 proeven uitgevoerd op het PPO-proefbedrijf te Lelystad. In deze proeven zijn een 4-tal hybriderassen (Hybnos, Hyno-braba, Hyno-esta, Mercury) vergeleken met een

  12. Hybrid FSAE Vehicle Realization

    Science.gov (United States)

    2010-12-01

    The goal of this multi-year project is to create a fully functional University of Idaho entry in the hybrid FSAE competition. Vehicle integration is underway as part of a variety of 2010-11 senior design projects. This leverages a variety of analytic...

  13. Electric and hybrid vehicles

    Science.gov (United States)

    1979-01-01

    Report characterizes state-of-the-art electric and hybrid (combined electric and heat engine) vehicles. Performance data for representative number of these vehicles were obtained from track and dynamometer tests. User experience information was obtained from fleet operators and individual owners of electric vehicles. Data on performance and physical characteristics of large number of vehicles were obtained from manufacturers and available literature.

  14. Nuclear hybrid energy infrastructure

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Vivek; Tawfik, Magdy S.

    2015-02-01

    The nuclear hybrid energy concept is becoming a reality for the US energy infrastructure where combinations of the various potential energy sources (nuclear, wind, solar, biomass, and so on) are integrated in a hybrid energy system. This paper focuses on challenges facing a hybrid system with a Small Modular Reactor at its core. The core of the paper will discuss efforts required to develop supervisory control center that collects data, supports decision-making, and serves as an information hub for supervisory control center. Such a center will also be a model for integrating future technologies and controls. In addition, advanced operations research, thermal cycle analysis, energy conversion analysis, control engineering, and human factors engineering will be part of the supervisory control center. Nuclear hybrid energy infrastructure would allow operators to optimize the cost of energy production by providing appropriate means of integrating different energy sources. The data needs to be stored, processed, analyzed, trended, and projected at right time to right operator to integrate different energy sources.

  15. Hybridization of biomedical circuitry

    Science.gov (United States)

    Rinard, G. A.

    1978-01-01

    The design and fabrication of low power hybrid circuits to perform vital signs monitoring are reported. The circuits consist of: (1) clock; (2) ECG amplifier and cardiotachometer signal conditioner; (3) impedance pneumobraph and respiration rate processor; (4) hear/breath rate processor; (5) temperature monitor; and (6) LCD display.

  16. Glueballs, Hybrids and Exotics

    Science.gov (United States)

    Reyes, M. A.; Moreno, G.

    2006-09-01

    We comment on the physics analysis carried out by the Experimental High Energy Physics (EHEP) group of the Instituto de Fisica of the University of Guanajuato (IFUG), Mexico. In particular, this group has been involved in analysis carried out to search for glueball, hybrid and exotic candidates.

  17. Hybrid wars’ information component

    Directory of Open Access Journals (Sweden)

    T. A. Nevskaya

    2015-01-01

    Full Text Available The war of the new generation - hybrid war, the information component which is directed not so much on the direct destruction of the enemy, how to achieve the goals without warfare. Fighting in the information field is no less important than immediate military action.

  18. Glueballs, Hybrids and Exotics

    International Nuclear Information System (INIS)

    Reyes, M. A.; Moreno, G.

    2006-01-01

    We comment on the physics analysis carried out by the Experimental High Energy Physics (EHEP) group of the Instituto de Fisica of the University of Guanajuato (IFUG), Mexico. In particular, this group has been involved in analysis carried out to search for glueball, hybrid and exotic candidates

  19. Hybrid quantum computation

    International Nuclear Information System (INIS)

    Sehrawat, Arun; Englert, Berthold-Georg; Zemann, Daniel

    2011-01-01

    We present a hybrid model of the unitary-evolution-based quantum computation model and the measurement-based quantum computation model. In the hybrid model, part of a quantum circuit is simulated by unitary evolution and the rest by measurements on star graph states, thereby combining the advantages of the two standard quantum computation models. In the hybrid model, a complicated unitary gate under simulation is decomposed in terms of a sequence of single-qubit operations, the controlled-z gates, and multiqubit rotations around the z axis. Every single-qubit and the controlled-z gate are realized by a respective unitary evolution, and every multiqubit rotation is executed by a single measurement on a required star graph state. The classical information processing in our model requires only an information flow vector and propagation matrices. We provide the implementation of multicontrol gates in the hybrid model. They are very useful for implementing Grover's search algorithm, which is studied as an illustrative example.

  20. Hybrid keyword search auctions

    KAUST Repository

    Goel, Ashish; Munagala, Kamesh

    2009-01-01

    Search auctions have become a dominant source of revenue generation on the Internet. Such auctions have typically used per-click bidding and pricing. We propose the use of hybrid auctions where an advertiser can make a per-impression as well as a per-click bid, and the auctioneer then chooses one of the two as the pricing mechanism. We assume that the advertiser and the auctioneer both have separate beliefs (called priors) on the click-probability of an advertisement. We first prove that the hybrid auction is truthful, assuming that the advertisers are risk-neutral. We then show that this auction is superior to the existing per-click auction in multiple ways: 1. We show that risk-seeking advertisers will choose only a per-impression bid whereas risk-averse advertisers will choose only a per-click bid, and argue that both kind of advertisers arise naturally. Hence, the ability to bid in a hybrid fashion is important to account for the risk characteristics of the advertisers. 2. For obscure keywords, the auctioneer is unlikely to have a very sharp prior on the click-probabilities. In such situations, we show that having the extra information from the advertisers in the form of a per-impression bid can result in significantly higher revenue. 3. An advertiser who believes that its click-probability is much higher than the auctioneer's estimate can use per-impression bids to correct the auctioneer's prior without incurring any extra cost. 4. The hybrid auction can allow the advertiser and auctioneer to implement complex dynamic programming strategies to deal with the uncertainty in the click-probability using the same basic auction. The per-click and per-impression bidding schemes can only be used to implement two extreme cases of these strategies. As Internet commerce matures, we need more sophisticated pricing models to exploit all the information held by each of the participants. We believe that hybrid auctions could be an important step in this direction. The hybrid

  1. Hybrid keyword search auctions

    KAUST Repository

    Goel, Ashish

    2009-01-01

    Search auctions have become a dominant source of revenue generation on the Internet. Such auctions have typically used per-click bidding and pricing. We propose the use of hybrid auctions where an advertiser can make a per-impression as well as a per-click bid, and the auctioneer then chooses one of the two as the pricing mechanism. We assume that the advertiser and the auctioneer both have separate beliefs (called priors) on the click-probability of an advertisement. We first prove that the hybrid auction is truthful, assuming that the advertisers are risk-neutral. We then show that this auction is superior to the existing per-click auction in multiple ways: 1. We show that risk-seeking advertisers will choose only a per-impression bid whereas risk-averse advertisers will choose only a per-click bid, and argue that both kind of advertisers arise naturally. Hence, the ability to bid in a hybrid fashion is important to account for the risk characteristics of the advertisers. 2. For obscure keywords, the auctioneer is unlikely to have a very sharp prior on the click-probabilities. In such situations, we show that having the extra information from the advertisers in the form of a per-impression bid can result in significantly higher revenue. 3. An advertiser who believes that its click-probability is much higher than the auctioneer\\'s estimate can use per-impression bids to correct the auctioneer\\'s prior without incurring any extra cost. 4. The hybrid auction can allow the advertiser and auctioneer to implement complex dynamic programming strategies to deal with the uncertainty in the click-probability using the same basic auction. The per-click and per-impression bidding schemes can only be used to implement two extreme cases of these strategies. As Internet commerce matures, we need more sophisticated pricing models to exploit all the information held by each of the participants. We believe that hybrid auctions could be an important step in this direction. The

  2. Epitaxial growth of hybrid nanostructures

    Science.gov (United States)

    Tan, Chaoliang; Chen, Junze; Wu, Xue-Jun; Zhang, Hua

    2018-02-01

    Hybrid nanostructures are a class of materials that are typically composed of two or more different components, in which each component has at least one dimension on the nanoscale. The rational design and controlled synthesis of hybrid nanostructures are of great importance in enabling the fine tuning of their properties and functions. Epitaxial growth is a promising approach to the controlled synthesis of hybrid nanostructures with desired structures, crystal phases, exposed facets and/or interfaces. This Review provides a critical summary of the state of the art in the field of epitaxial growth of hybrid nanostructures. We discuss the historical development, architectures and compositions, epitaxy methods, characterization techniques and advantages of epitaxial hybrid nanostructures. Finally, we provide insight into future research directions in this area, which include the epitaxial growth of hybrid nanostructures from a wider range of materials, the study of the underlying mechanism and determining the role of epitaxial growth in influencing the properties and application performance of hybrid nanostructures.

  3. Mirror hybrid reactor optimization studies

    International Nuclear Information System (INIS)

    Bender, D.J.

    1976-01-01

    A system model of the mirror hybrid reactor has been developed. The major components of the model include (1) the reactor description, (2) a capital cost analysis, (3) various fuel management schemes, and (4) an economic analysis that includes the hybrid plus its associated fission burner reactors. The results presented describe the optimization of the mirror hybrid reactor, the objective being to minimize the cost of electricity from the hybrid fission-burner reactor complex. We have examined hybrid reactors with two types of blankets, one containing natural uranium, the other thorium. The major difference between the two optimized reactors is that the uranium hybrid is a significant net electrical power producer, whereas the thorium hybrid just about breaks even on electrical power. Our projected costs for fissile fuel production are approximately 50 $/g for 239 Pu and approximately 125 $/g for 233 U

  4. Energy Efficiency Comparison between Hydraulic Hybrid and Hybrid Electric Vehicles

    Directory of Open Access Journals (Sweden)

    Jia-Shiun Chen

    2015-05-01

    Full Text Available Conventional vehicles tend to consume considerable amounts of fuel, which generates exhaust gases and environmental pollution during intermittent driving cycles. Therefore, prospective vehicle designs favor improved exhaust emissions and energy consumption without compromising vehicle performance. Although pure electric vehicles feature high performance and low pollution characteristics, their limitations are their short driving range and high battery costs. Hybrid electric vehicles (HEVs are comparatively environmentally friendly and energy efficient, but cost substantially more compared with conventional vehicles. Hydraulic hybrid vehicles (HHVs are mainly operated using engines, or using alternate combinations of engine and hydraulic power sources while vehicles accelerate. When the hydraulic system accumulator is depleted, the conventional engine reengages; concurrently, brake-regenerated power is recycled and reused by employing hydraulic motor–pump modules in circulation patterns to conserve fuel and recycle brake energy. This study adopted MATLAB Simulink to construct complete HHV and HEV models for backward simulations. New European Driving Cycles were used to determine the changes in fuel economy. The output of power components and the state-of-charge of energy could be retrieved. Varying power component models, energy storage component models, and series or parallel configurations were combined into seven different vehicle configurations: the conventional manual transmission vehicle, series hybrid electric vehicle, series hydraulic hybrid vehicle, parallel hybrid electric vehicle, parallel hydraulic hybrid vehicle, purely electric vehicle, and hydraulic-electric hybrid vehicle. The simulation results show that fuel consumption was 21.80% lower in the series hydraulic hybrid vehicle compared to the series hybrid electric vehicle; additionally, fuel consumption was 3.80% lower in the parallel hybrid electric vehicle compared to the

  5. Sneutrino Hybrid Inflation

    International Nuclear Information System (INIS)

    Antusch, Stefan

    2006-01-01

    We review the scenario of sneutrino hybrid inflation, where one of the singlet sneutrinos, the superpartners of the right-handed neutrinos, plays the role of the inflaton. In a minimal model of sneutrino hybrid inflation, the spectral index is given by ns ≅ 1 + 2γ. With γ = 0.025 ± 0.01 constrained by WMAP, a running spectral index vertical bar dns/dlnk vertical bar << vertical barγvertical bar and a tensor-to-scalar ratio r << γ2 are predicted. Small neutrino masses arise from the seesaw mechanism, with heavy masses for the singlet (s)neutrinos generated by the vacuum expectation value of the waterfall field after inflation. The baryon asymmetry of the universe can be explained by non-thermal leptogenesis via sneutrino inflaton decay, with low reheat temperature TRH ≅ 106 GeV

  6. Hybrid-secure MPC 

    DEFF Research Database (Denmark)

    Lucas, Christoph; Raub, Dominik; Maurer, Ueli

    2010-01-01

    of the adversary, without being aware of the actual adversarial setting. Thus, hybrid-secure MPC protocols allow for graceful degradation of security. We present a hybrid-secure MPC protocol that provides an optimal trade-off between IT robustness and computational privacy: For any robustness parameter ρ ... obtain one MPC protocol that is simultaneously IT secure with robustness for up to t ≤ ρ actively corrupted parties, IT secure with fairness (no robustness) for up to t ... in the universal composability (UC) framework (based on a network of secure channels, a broadcast channel, and a common reference string). It achieves the bound on the trade-off between robustness and privacy shown by Ishai et al. [CRYPTO'06] and Katz [STOC'07], the bound on fairness shown by Cleve [STOC'86...

  7. Hybrid superconducting magnetic suspensions

    International Nuclear Information System (INIS)

    Tixador, P.; Hiebel, P.; Brunet, Y.; Chaud, X.; Gautier-Picard, P.

    1996-01-01

    Superconductors, especially high T c ones, are the most attractive materials to design stable and fully passive magnetic suspensions which have to control five degrees of freedom. The hybrid superconducting magnetic suspensions present high performances and a simple cooling mode. They consist of a permanent magnet bearing, stabilized by a suitable magnet-superconductor structure. Several designs are given and compared in terms of forces and stiffnesses. The design of the magnet bearing plays an important part. The superconducting magnetic bearing participates less in levitation but must provide a high stabilizing stiffness. This is achieved by the magnet configuration, a good material in term of critical current density and field cooling. A hybrid superconducting suspension for a flywheel is presented. This system consists of a magnet thrust bearing stabilized by superconductors interacting with an alternating polarity magnet structure. First tests and results are reported. Superconducting materials are magnetically melt-textured YBaCuO

  8. The Power of Hybridization

    CERN Multimedia

    CERN. Geneva

    2011-01-01

    Programming languages always seem to do some things well but not others: Python punts when it comes to user interfaces, Java’s artificial complexity prevents rapid development and produces tangles, and it will be awhile before we see benefits from C++ concurrency work. The cognitive load of languages and their blind spots increases the cost of experimentation, impeding your ability to fail fast and iterate. If you use a single language to solve your problem, you are binding yourself to the worldview limitations and the mistakes made by the creator of that language. Consider increasing your wiggle room by crossing language boundaries, complementing a language that is powerful in one area with a different language powerful in another. Language hybridization can speed development to quickly discover your real problems, giving you more time to fix them. After making a case for hybridizing your thinking in general, I will present a number of simple examples; first showing the benefits of using other languages...

  9. Tokamak hybrid study

    International Nuclear Information System (INIS)

    Tenney, F.H.

    1976-09-01

    A report on one year of study of a tokamak hybrid reactor is presented. The plasma is maintained by both D and T beams. To obtain long burn times a poloidal field divertor is required. Both the single null and the double null style of divertor are considered. The blanket consists of a neutron multiplier region containing natural uranium followed by burner regions of molten salt (flibe) loaded with PuF 3 to enhance the energy multiplication. Economic analysis has been applied only recently to a variety of reactor sizes and plasma conditions. Early indications suggest that the most attractive hybrids will have large plasmas of major radius in excess of 8 meters

  10. Tokamak hybrid study

    International Nuclear Information System (INIS)

    Tenney, F.H.

    1976-01-01

    A report on one year of study of a tokamak hybrid reactor is given. The plasma is maintained by both D and T beams. To obtain long burn times a poloidal field divertor is required. Both the single null and the double null style of divertor are considered. The blanket consists of a neutron multiplier region containing natural uranium followed by burner regions of molten salt (flibe) loaded with PuF 3 to enhance the energy multiplication. Economic analysis has been applied only recently to a variety of reactor sizes and plasma conditions. Early indications suggest that the most attractive hybrids will have large plasmas of major radius in excess of 8 meters

  11. Hybrid undulator numerical optimization

    Energy Technology Data Exchange (ETDEWEB)

    Hairetdinov, A.H. [Kurchatov Institute, Moscow (Russian Federation); Zukov, A.A. [Solid State Physics Institute, Chernogolovka (Russian Federation)

    1995-12-31

    3D properties of the hybrid undulator scheme arc studied numerically using PANDIRA code. It is shown that there exist two well defined sets of undulator parameters which provide either maximum on-axis field amplitude or minimal higher harmonics amplitude of the basic undulator field. Thus the alternative between higher field amplitude or pure sinusoidal field exists. The behavior of the undulator field amplitude and harmonics structure for a large set of (undulator gap)/(undulator wavelength) values is demonstrated.

  12. Hybrid electroluminescent devices

    Science.gov (United States)

    Shiang, Joseph John; Duggal, Anil Raj; Michael, Joseph Darryl

    2010-08-03

    A hybrid electroluminescent (EL) device comprises at least one inorganic diode element and at least one organic EL element that are electrically connected in series. The absolute value of the breakdown voltage of the inorganic diode element is greater than the absolute value of the maximum reverse bias voltage across the series. The inorganic diode element can be a power diode, a Schottky barrier diode, or a light-emitting diode.

  13. Mirror hybrid reactors

    International Nuclear Information System (INIS)

    Moir, R.W.

    1978-01-01

    The fusion-fission hybrid is a combination of the fusion and fission processes, having features which are complementary. Fission energy is running out of readily available fuel, and fusion has extra neutrons which can be used to breed that fission fuel. Fusion would have to take on an extra burden of radioactivity, but this early application would give fusion, which does not work well enough now to make power, practical experience which may accelerate development of pure fusion

  14. The challenge of hybridization

    CERN Document Server

    Caccia, Massimo

    2000-01-01

    Hybridization of pixel detector systems has to satisfy tight requirements: high yield, long term reliability, mechanical stability, thermal compliance and robustness have to go together with low passive mass added to the system, radiation hardness, flexibility in the technology end eventually low cost. The current technologies for the interconnection of the front-end chips and the sensor are reviewed and compared, together with the solutions for the interface to the far-end electronics.

  15. Asymmetric Hybrid Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Chumanov, George [Clemson Univ., SC (United States)

    2015-11-05

    Hybrid Nanoparticles (AHNs) are rationally-designed multifunctional nanostructures and novel building blocks for the next generation of advanced materials and devices. Nanoscale materials attract considerable interest because of their unusual properties and potential for practical applications. Most of the activity in this field is focused on the synthesis of homogeneous nanoparticles from metals, metal oxides, semiconductors, and polymers. It is well recognized that properties of nanoparticles can be further enhanced if they are made as hybrid structures. This program is concerned with the synthesis, characterization, and application of such hybrid structures termed AHNs. AHNs are composed of a homogeneous core and several caps of different materials deposited on its surface (Fig. 1). Combined properties of the core and the caps as well as new properties that arise from core-cap and cap-cap interactions render AHNs multifunctional. In addition, specific chemical reactivity of the caps enables directional self-assembly of AHNs into complex architectures that are not possible with only spherical nanoparticles.

  16. Hybrid2 - The hybrid power system simulation model

    Energy Technology Data Exchange (ETDEWEB)

    Baring-Gould, E.I.; Green, H.J.; Dijk, V.A.P. van [National Renewable Energy Lab., Golden, CO (United States); Manwell, J.F. [Univ. of Massachusetts, Amherst, MA (United States)

    1996-12-31

    There is a large-scale need and desire for energy in remote communities, especially in the developing world; however the lack of a user friendly, flexible performance prediction model for hybrid power systems incorporating renewables hindered the analysis of hybrids as options to conventional solutions. A user friendly model was needed with the versatility to simulate the many system locations, widely varying hardware configurations, and differing control options for potential hybrid power systems. To meet these ends, researchers from the National Renewable Energy Laboratory (NREL) and the University of Massachusetts (UMass) developed the Hybrid2 software. This paper provides an overview of the capabilities, features, and functionality of the Hybrid2 code, discusses its validation and future plans. Model availability and technical support provided to Hybrid2 users are also discussed. 12 refs., 3 figs., 4 tabs.

  17. First-Order Hybrid Logic

    DEFF Research Database (Denmark)

    Braüner, Torben

    2011-01-01

    Hybrid logic is an extension of modal logic which allows us to refer explicitly to points of the model in the syntax of formulas. It is easy to justify interest in hybrid logic on applied grounds, with the usefulness of the additional expressive power. For example, when reasoning about time one...... often wants to build up a series of assertions about what happens at a particular instant, and standard modal formalisms do not allow this. What is less obvious is that the route hybrid logic takes to overcome this problem often actually improves the behaviour of the underlying modal formalism....... For example, it becomes far simpler to formulate proof-systems for hybrid logic, and completeness results can be proved of a generality that is simply not available in modal logic. That is, hybridization is a systematic way of remedying a number of known deficiencies of modal logic. First-order hybrid logic...

  18. Hybrid solar lighting distribution systems and components

    Science.gov (United States)

    Muhs, Jeffrey D [Lenoir City, TN; Earl, Dennis D [Knoxville, TN; Beshears, David L [Knoxville, TN; Maxey, Lonnie C [Powell, TN; Jordan, John K [Oak Ridge, TN; Lind, Randall F [Lenoir City, TN

    2011-07-05

    A hybrid solar lighting distribution system and components having at least one hybrid solar concentrator, at least one fiber receiver, at least one hybrid luminaire, and a light distribution system operably connected to each hybrid solar concentrator and each hybrid luminaire. A controller operates all components.

  19. Completeness in Hybrid Type Theory

    DEFF Research Database (Denmark)

    Areces, Carlos; Blackburn, Patrick Rowan; Huertas, Antonia

    2014-01-01

    We show that basic hybridization (adding nominals and @ operators) makes it possible to give straightforward Henkin-style completeness proofs even when the modal logic being hybridized is higher-order. The key ideas are to add nominals as expressions of type t, and to extend to arbitrary types th......-style intensional models; we build, as simply as we can, hybrid logicover Henkin’s logic...

  20. Glueballs, hybrids, multiquarks

    Energy Technology Data Exchange (ETDEWEB)

    Klempt, Eberhard [Helmholtz-Institut fuer Strahlen-und Kernphysik der Rheinischen Friedrich-Wilhelms Universitaet, Nussallee 14-16, D-53115 Bonn (Germany)], E-mail: klempt@hiskp.uni-bonn.de; Zaitsev, Alexander [Institute for High-Energy Physics, Moscow Region, RU-142284 Protvino (Russian Federation)

    2007-12-15

    Glueballs, hybrids and multiquark states are predicted as bound states in models guided by quantum chromo dynamics (QCD), by QCD sum rules or QCD on a lattice. Estimates for the (scalar) glueball ground state are in the mass range from 1000 to 1800 MeV, followed by a tensor and a pseudoscalar glueball at higher mass. Experiments have reported evidence for an abundance of meson resonances with 0{sup -+},0{sup ++} and 2{sup ++} quantum numbers. In particular, the sector of scalar mesons is full of surprises starting from the elusive {sigma} and {kappa} mesons. The a{sub 0}(980) and f{sub 0}(980), discussed extensively in the literature, are reviewed with emphasis on their Janus-like appearance as KK-bar molecules, tetraquark states or qq-bar mesons. Most exciting is the possibility that the three mesons f{sub 0}(1370), f{sub 0}(1500), and f{sub 0}(1710) might reflect the appearance of a scalar glueball in the world of quarkonia. However, the existence of f{sub 0}(1370) is not beyond doubt and there is evidence that both f{sub 0}(1500) and f{sub 0}(1710) are flavour octet states, possibly in a tetraquark composition. We suggest a scheme in which the scalar glueball is dissolved into the wide background into which all scalar flavour-singlet mesons collapse. There is an abundance of meson resonances with the quantum numbers of the {eta}. Three states are reported below 1.5GeV/c{sup 2} whereas quark models expect only one, perhaps two. One of these states, {iota}(1440), was the prime glueball candidate for a long time. We show that {iota}(1440) is the first radial excitation of the {eta} meson. Hybrids may have exotic quantum numbers which are not accessible by qq-bar mesons. There are several claims for J{sup PC}=1{sup -+} exotics, some of them with properties as predicted from the flux tube model interpreting the quark-antiquark binding by a gluon string. The evidence for these states depends partly on the assumption that meson-meson interactions are dominated by s

  1. Allele-specific transactivation of matrix metalloproteinase 7 by FOXA2 and correlation with plasma levels in idiopathic pulmonary fibrosis.

    Science.gov (United States)

    Richards, Thomas J; Park, Chunghyun; Chen, Yiliang; Gibson, Kevin F; Peter Di, Y; Pardo, Annie; Watkins, Simon C; Choi, Augustine M K; Selman, Moises; Pilewski, Joseph; Kaminski, Naftali; Zhang, Yingze

    2012-04-15

    Idiopathic pulmonary fibrosis (IPF) is a complex disease with poorly understood etiology. Previously, we reported upregulation of matrix metalloproteinase 7 (MMP7) in both lung and peripheral blood of IPF patients. Here we report evidence for genetic correlation of plasma levels and promoter polymorphisms (rs11568818 and rs11568819) of MMP7 in a well-characterized IPF cohort. Both the AA genotype of rs11568818 and the CT genotype of rs11568819 were found to be significantly associated with higher MMP7 plasma levels. These associations were observed only in IPF patients and not in healthy controls. The G-to-A transition of rs11568818 resulted in a novel binding site for the forkhead box A2 (FOXA2) transcription factor, a key regulator of embryonic lung development and proper function of the mature lung. In vitro, this transition led to increased sensitivity of the MMP7 promoter to FOXA2. In IPF lungs, FOXA2 was localized in the nucleus of epithelial cells that expressed MMP7 in the cytoplasm. These results suggest that increased sensitivity of the polymorphic MMP7 promoter to FOXA2 provides one of the genetic bases for the upregulation of MMP7 in IPF.

  2. Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays

    DEFF Research Database (Denmark)

    Smith, Frank Andrew; Howard, Philip; Shah, Sonia

    2012-01-01

    Following the widespread use of genome-wide association studies (GWAS), focus is turning towards identification of causal variants rather than simply genetic markers of diseases and traits. As a step towards a high-throughput method to identify genome-wide, non-coding, functional regulatory...... discrimination. Examination of this SNP in two prospective Caucasian cohorts comprising 15,000 individuals confirmed the association with HDL-C levels (combined beta = 0.016; p = 0.0006), and analysis of gene expression identified an allelic association with LXR-α expression in heart tissue. Using increasingly...

  3. Poultry Allele-Specific Expression (ASE) of CD4+ T Cells in Response to Marek’s Disease Virus Infection

    Science.gov (United States)

    Marek’s disease (MD) is a T cell lymphoma disease of poultry induced by Marek’s disease virus (MDV), a highly oncogenic alphaherpesvirus. To identify high-confidence candidate genes of MD genetic resistance, transcriptomic data in CD4+ T cells were obtained from MDV infected and non-infected groups ...

  4. The Pleiotropic Phenotype of Apc Mutations in the Mouse: Allele Specificity and Effects of the Genetic Background

    Science.gov (United States)

    Halberg, Richard B.; Chen, Xiaodi; Amos-Landgraf, James M.; White, Alanna; Rasmussen, Kristin; Clipson, Linda; Pasch, Cheri; Sullivan, Ruth; Pitot, Henry C.; Dove, William F.

    2008-01-01

    Familial adenomatous polyposis (FAP) is a human cancer syndrome characterized by the development of hundreds to thousands of colonic polyps and extracolonic lesions including desmoid fibromas, osteomas, epidermoid cysts, and congenital hypertrophy of the pigmented retinal epithelium. Afflicted individuals are heterozygous for mutations in the APC gene. Detailed investigations of mice heterozygous for mutations in the ortholog Apc have shown that other genetic factors strongly influence the phenotype. Here we report qualitative and quantitative modifications of the phenotype of Apc mutants as a function of three genetic variables: Apc allele, p53 allele, and genetic background. We have found major differences between the Apc alleles Min and 1638N in multiplicity and regionality of intestinal tumors, as well as in incidence of extracolonic lesions. By contrast, Min mice homozygous for either of two different knockout alleles of p53 show similar phenotypic effects. These studies illustrate the classic principle that functional genetics is enriched by assessing penetrance and expressivity with allelic series. The mouse permits study of an allelic gene series on multiple genetic backgrounds, thereby leading to a better understanding of gene action in a range of biological processes. PMID:18723878

  5. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

    OpenAIRE

    Bruce, Jeff; Pugh, Trevor; Samadian, Soroush

    2017-01-01

    Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To ad...

  6. Concurrence of High Fat Diet and APOE Gene Induces Allele Specific Metabolic and Mental Stress Changes in an AD Model

    Directory of Open Access Journals (Sweden)

    Yifat Segev

    2016-09-01

    Full Text Available Aging is the main risk factor for neurodegenerative diseases, including Alzheimer’s disease (AD. However, evidence indicates that the pathological process begins long before actual cognitive or pathological symptoms are apparent. The long asymptomatic phase and complex integration between genetic, environmental, and metabolic factors make it one of the most challenging diseases to understand and cure. In the present study, we asked whether an environmental factor such as high-fat diet would synergize with a genetic factor to affect the metabolic and cognitive state in the ApoE4 mouse model of AD. Our data suggest that a high-fat diet induces diabetes mellitus-like metabolism in ApoE4 mice, as well as changes in BACE1 protein levels between the two ApoE strains. Furthermore, high-fat diet induces anxiety in this AD mouse model. Our results suggest that young ApoE4 carriers are prone to psychological stress and metabolic abnormalities related to AD, which can easily be triggered via high-fat nutrition.

  7. Concurrence of High Fat Diet and APOE Gene Induces Allele Specific Metabolic and Mental Stress Changes in an AD Model

    OpenAIRE

    Yifat Segev; Adva Livne; Meshi Mints; Kobi Rosenblum; Kobi Rosenblum

    2016-01-01

    Aging is the main risk factor for neurodegenerative diseases, including Alzheimer’s disease (AD). However, evidence indicates that the pathological process begins long before actual cognitive or pathological symptoms are apparent. The long asymptomatic phase and complex integration between genetic, environmental, and metabolic factors make it one of the most challenging diseases to understand and cure. In the present study, we asked whether an environmental factor such as high-fat diet would ...

  8. Hybrid spectral CT reconstruction.

    Directory of Open Access Journals (Sweden)

    Darin P Clark

    Full Text Available Current photon counting x-ray detector (PCD technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID. In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM. Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with

  9. Hybrid spectral CT reconstruction

    Science.gov (United States)

    Clark, Darin P.

    2017-01-01

    Current photon counting x-ray detector (PCD) technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID). In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM). Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with a spectral

  10. Hybrid Maritime Warfare

    DEFF Research Database (Denmark)

    Schaub Jr, Gary John; Murphy, Martin; Hoffman, Frank

    2017-01-01

    Russia’s use of hybrid warfare techniques has raised concerns about the security of the Baltic States. Gary Schaub, Jr, Martin Murphy and Frank G Hoffman recommend a series of measures to augment NATO’s Readiness Action Plan in the Baltic region, including increasing the breadth and depth of naval...... exercises, and improving maritime domain awareness through cooperative programmes. They also suggest unilateral and cooperative measures to develop a sound strategic communications strategy to counter Moscow’s information operations, reduce dependence on Russian energy supplies and build the resilience...

  11. Indexical Hybrid Tense Logic

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Jørgensen, Klaus Frovin

    2012-01-01

    In this paper we explore the logic of now, yesterday, today and tomorrow by combining the semantic approach to indexicality pioneered by Hans Kamp [9] and refined by David Kaplan [10] with hybrid tense logic. We first introduce a special now nominal (our @now corresponds to Kamp’s original now...... operator N) and prove completeness results for both logical and contextual validity. We then add propositional constants to handle yesterday, today and tomorrow; our system correctly treats sentences like “Niels will die yesterday” as contextually unsatisfiable. Building on our completeness results for now......, we prove completeness for the richer language, again for both logical and contextual validity....

  12. Hybrid Dark Matter

    OpenAIRE

    Chao, Wei

    2018-01-01

    Dark matter can be produced in the early universe via the freeze-in or freeze-out mechanisms. Both scenarios were investigated in references, but the production of dark matters via the combination of these two mechanisms are not addressed. In this paper we propose a hybrid dark matter model where dark matters have two components with one component produced thermally and the other one produced non-thermally. We present for the first time the analytical calculation for the relic abundance of th...

  13. Reflections on Intellectual Hybridity

    Directory of Open Access Journals (Sweden)

    Kimala Price

    2012-05-01

    Full Text Available Drawing from the growing literature on interdisciplinarity and my own experiences as an intellectual hybrid, I discuss the personal and institutional challenges inherent in crossing disciplinary boundaries in the academy. I argue that boundary crossing is a natural occurrence and that the issue of (interdisciplinarity is a matter of degree and of determining who gets to define the boundaries. Defining boundaries is not merely an intellectual enterprise, but also a political act that delineates what is, or is not, legitimate scholarship. This issue is especially salient to women's and gender studies during times of economic distress and educational budget cuts.

  14. The Hybrid Advantage: Graduate Student Perspectives of Hybrid Education Courses

    Science.gov (United States)

    Hall, Sarah; Villareal, Donna

    2015-01-01

    Hybrid courses combine online and face-to-face learning environments. To organize and teach hybrid courses, instructors must understand the uses of multiple online learning tools and face-toface classroom activities to promote and monitor the progress of students. The purpose of this phenomenological study was to explore the perspectives of…

  15. Hybrid vehicle potential assessment. Volume 7: Hybrid vehicle review

    Science.gov (United States)

    Leschly, K. O.

    1979-01-01

    Review of hybrid vehicles built during the past ten years or planned to be built in the near future is presented. An attempt is made to classify and analyze these vehicles to get an overall picture of their key characteristics. The review includes onroad hybrid passenger cars, trucks, vans, and buses.

  16. Nonminimally coupled hybrid inflation

    International Nuclear Information System (INIS)

    Koh, Seoktae; Minamitsuji, Masato

    2011-01-01

    We discuss the hybrid inflation model where the inflaton field is nonminimally coupled to gravity. In the Jordan frame, the potential contains φ 4 term as well as terms in the original hybrid inflation model. In our model, inflation can be classified into the type (I) and the type (II). In the type (I), inflation is terminated by the tachyonic instability of the waterfall field, while in the type (II) by the violation of slow-roll conditions. In our model, the reheating takes place only at the true minimum and even in the case (II) finally the tachyonic instability occurs after the termination of inflation. For a negative nonminimal coupling, inflation takes place in the vacuum-dominated region, in the large field region, or near the local minimum/maximum. Inflation in the vacuum-dominated region becomes either the type (I) or (II), resulting in a blue or red spectrum of the curvature perturbations, respectively. Inflation around the local maximum can be either the type (I) or the type (II), which results in the red spectrum of the curvature perturbations, while around the local minimum it must be the type (I), which results in the blue spectrum. In the large field region, to terminate inflation, potential in the Einstein frame must be positively tilted, always resulting in the red spectrum. We then numerically solve the equations of motion to investigate the whole dynamics of inflaton and confirm that the spectrum of curvature perturbations changes from red to blue ones as scales become smaller.

  17. Hybrid Turbine Electric Vehicle

    Science.gov (United States)

    Viterna, Larry A.

    1997-01-01

    Hybrid electric power trains may revolutionize today's ground passenger vehicles by significantly improving fuel economy and decreasing emissions. The NASA Lewis Research Center is working with industry, universities, and Government to develop and demonstrate a hybrid electric vehicle. Our partners include Bowling Green State University, the Cleveland Regional Transit Authority, Lincoln Electric Motor Division, the State of Ohio's Department of Development, and Teledyne Ryan Aeronautical. The vehicle will be a heavy class urban transit bus offering double the fuel economy of today's buses and emissions that are reduced to 1/10th of the Environmental Protection Agency's standards. At the heart of the vehicle's drive train is a natural-gas-fueled engine. Initially, a small automotive engine will be tested as a baseline. This will be followed by the introduction of an advanced gas turbine developed from an aircraft jet engine. The engine turns a high-speed generator, producing electricity. Power from both the generator and an onboard energy storage system is then provided to a variable-speed electric motor attached to the rear drive axle. An intelligent power-control system determines the most efficient operation of the engine and energy storage system.

  18. Hybrid spread spectrum radio system

    Science.gov (United States)

    Smith, Stephen F [London, TN; Dress, William B [Camas, WA

    2010-02-09

    Systems and methods are described for hybrid spread spectrum radio systems. A method, includes receiving a hybrid spread spectrum signal including: fast frequency hopping demodulating and direct sequence demodulating a direct sequence spread spectrum signal, wherein multiple frequency hops occur within a single data-bit time and each bit is represented by chip transmissions at multiple frequencies.

  19. The governance of hybrid organisations

    DEFF Research Database (Denmark)

    Spear, Roger; Cornforth, Chris

    2010-01-01

    The focus of this chapter is on the governance of third sector organizations (TSOs) and the challenges that are raised by hybridity. In particular it will focus on the question how does hybridity affect governance structures and processes and the challenges that governing bodies face?...

  20. Electric/Hybrid Vehicle Simulation

    Science.gov (United States)

    Slusser, R. A.; Chapman, C. P.; Brennand, J. P.

    1985-01-01

    ELVEC computer program provides vehicle designer with simulation tool for detailed studies of electric and hybrid vehicle performance and cost. ELVEC simulates performance of user-specified electric or hybrid vehicle under user specified driving schedule profile or operating schedule. ELVEC performs vehicle design and life cycle cost analysis.

  1. Electric-hybrid-vehicle simulation

    Science.gov (United States)

    Pasma, D. C.

    The simulation of electric hybrid vehicles is to be performed using experimental data to model propulsion system components. The performance of an existing ac propulsion system will be used as the baseline for comparative purposes. Hybrid components to be evaluated include electrically and mechanically driven flywheels, and an elastomeric regenerative braking system.

  2. Design Principles for Hybrid Ventilation

    DEFF Research Database (Denmark)

    Heiselberg, Per

    For many years mechanical and natural ventilation systems have developed separately. Naturally, the next step in this development is the development of ventilation concepts that utilize and combine the best features from each system to create a new type of ventilation system -Hybrid Ventilation. ....... The hybrid ventilation concepts, design challenges and - principles are discussed and illustrated by four building examples....

  3. Conceptual innovations in hybrid reactors

    International Nuclear Information System (INIS)

    Greenspan, E.; Miley, G.H.

    1980-01-01

    A number of innovations in the conception of fusion-fission hybrid reactors, including the blanket, the fusion driver, the coupling of the fusion and the fission components as well as the application of hybrid reactors are described, and their feasibility assessed

  4. Hybrid laser-arc welding

    DEFF Research Database (Denmark)

    Hybrid laser-arc welding (HLAW) is a combination of laser welding with arc welding that overcomes many of the shortfalls of both processes. This important book gives a comprehensive account of hybrid laser-arc welding technology and applications. The first part of the book reviews...... the characteristics of the process, including the properties of joints produced by hybrid laser-arc welding and ways of assessing weld quality. Part II discusses applications of the process to such metals as magnesium alloys, aluminium and steel as well as the use of hybrid laser-arc welding in such sectors as ship...... building and the automotive industry. With its distinguished editor and international team of contributors, Hybrid laser-arc welding, will be a valuable source of reference for all those using this important welding technology. Professor Flemming Ove Olsen works in the Department of Manufacturing...

  5. Laser driven fusion fission hybrids

    International Nuclear Information System (INIS)

    Hansen, L.F.; Maniscalco, J.A.

    1977-11-01

    The role of the fusion-fission hybrid reactor (FFHR) as a fissile fuel and/or power producer is discussed. As long range options to supply the world energy needs, hybrid-fueled thermal-burner reactors are compared to liquid metal fast breeder reactors (LMFBR). A discussion of different fuel cycles (thorium, depleted uranium, and spent fuel) is presented in order to compare the energy multiplication, the production of fissile fuel, the laser efficiency and pellet gain requirements of the hybrid reactor. Lawrence Livermore Laboratory (LLL) has collaborated with Bechtel Corporation and with Westinghouse in two engineering design studies of laser fusion driven hybrid power plants. The hybrid designs which have resulted from these two studies are briefly described and analyzed by considering operational parameters, such as energy multiplication, power density, burn-up and plutonium production as a function time

  6. Hybrid Natural Inflation

    Science.gov (United States)

    Ross, Graham G.; Germán, Gabriel; Vázquez, J. Alberto

    2016-05-01

    We construct two simple effective field theory versions of Hybrid Natural Inflation (HNI) that illustrate the range of its phenomenological implications. The resulting inflationary sector potential, V = Δ4(1 + acos( ϕ/f)), arises naturally, with the inflaton field a pseudo-Nambu-Goldstone boson. The end of inflation is triggered by a waterfall field and the conditions for this to happen are determined. Also of interest is the fact that the slow-roll parameter ɛ (and hence the tensor r) is a non-monotonic function of the field with a maximum where observables take universal values that determines the maximum possible tensor to scalar ratio r. In one of the models the inflationary scale can be as low as the electroweak scale. We explore in detail the associated HNI phenomenology, taking account of the constraints from Black Hole production, and perform a detailed fit to the Planck 2015 temperature and polarisation data.

  7. Hybrid Natural Inflation

    International Nuclear Information System (INIS)

    Ross, Graham G.; Germán, Gabriel; Vázquez, J. Alberto

    2016-01-01

    We construct two simple effective field theory versions of Hybrid Natural Inflation (HNI) that illustrate the range of its phenomenological implications. The resulting inflationary sector potential, V=Δ"4(1+acos (ϕ/f)), arises naturally, with the inflaton field a pseudo-Nambu-Goldstone boson. The end of inflation is triggered by a waterfall field and the conditions for this to happen are determined. Also of interest is the fact that the slow-roll parameter ϵ (and hence the tensor r) is a non-monotonic function of the field with a maximum where observables take universal values that determines the maximum possible tensor to scalar ratio r. In one of the models the inflationary scale can be as low as the electroweak scale. We explore in detail the associated HNI phenomenology, taking account of the constraints from Black Hole production, and perform a detailed fit to the Planck 2015 temperature and polarisation data.

  8. Hybrid powertrain system

    Science.gov (United States)

    Grillo, Ricardo C.; O'Neil, Walter K.; Preston, David M.

    2005-09-20

    A hybrid powertrain system is provided that includes a first prime mover having a rotational output, a second prime mover having a rotational output, and a transmission having a main shaft supporting at least two main shaft gears thereon. The transmission includes a first independent countershaft drivingly connected to the first prime mover and including at least one ratio gear supported thereon that meshes with a respective main shaft gear. A second independent countershaft is drivingly connected to the second prime mover and includes at least one ratio gear supported thereon that meshes with a respective main shaft gear. The ratio gears on the first and second countershafts cooperate with the main shaft gears to provide at least one gear ratio between the first and second countershafts and the main shaft. A shift control mechanism selectively engages and disengages the first and second countershafts for rotation with the main shaft.

  9. Hybrid vehicle control

    Science.gov (United States)

    Shallvari, Iva; Velnati, Sashidhar; DeGroot, Kenneth P.

    2015-07-28

    A method and apparatus for heating a catalytic converter's catalyst to an efficient operating temperature in a hybrid electric vehicle when the vehicle is in a charge limited mode such as e.g., the charge depleting mode or when the vehicle's high voltage battery is otherwise charge limited. The method and apparatus determine whether a high voltage battery of the vehicle is incapable of accepting a first amount of charge associated with a first procedure to warm-up the catalyst. If it is determined that the high voltage battery is incapable of accepting the first amount of charge, a second procedure with an acceptable amount of charge is performed to warm-up the catalyst.

  10. Hyper- and hybrid nonlocality

    Science.gov (United States)

    Li, Yanna; Gessner, Manuel; Li, Weidong; Smerzi, Augusto

    2018-02-01

    The controlled generation and identification of quantum correlations, usually encoded in either qubits or continuous degrees of freedom, builds the foundation of quantum information science. Recently, more sophisticated approaches, involving a combination of two distinct degrees of freedom, have been proposed to improve on the traditional strategies. Hyperentanglement describes simultaneous entanglement in more than one distinct degree of freedom, whereas hybrid entanglement refers to entanglement shared between a discrete and a continuous degree of freedom. In this work we propose a scheme that allows us to combine the two approaches, and to extend them to the strongest form of quantum correlations. Specifically, we show how two identical, initially separated particles can be manipulated to produce Bell nonlocality among their spins, among their momenta, as well as across their spins and momenta. We discuss possible experimental realizations with atomic and photonic systems.

  11. Hybrid Electric Transit Bus

    Science.gov (United States)

    Viterna, Larry A.

    1997-01-01

    A government, industry, and university cooperative is developing an advanced hybrid electric city transit bus. Goals of this effort include doubling the fuel economy compared to current buses and reducing emissions to one-tenth of current EPA standards. Unique aspects of the vehicle's power system include the use of ultra-capacitors as an energy storage system, and a planned natural gas fueled turbogenerator developed from a small jet engine. Power from both the generator and energy storage system is provided to a variable speed electric motor attached to the rear axle. At over 15000 kg gross weight, this is the largest vehicle of its kind ever built using ultra-capacitor energy storage. This paper describes the overall power system architecture, the evolution of the control strategy, and its performance over industry standard drive cycles.

  12. Hybrid Magnetic Shielding

    Science.gov (United States)

    Royal, Kevin; Crawford, Christopher; Mullins, Andrew; Porter, Greg; Blanton, Hunter; Johnstone, Connor; Kistler, Ben; Olivera, Daniela

    2017-09-01

    The search for the electric dipole moment of the neutron requires the ambient magnetic field to be on the pT scale which is accomplished with large magnetic shielding rooms. These rooms are fitted with large mu-metal sheets to allow for passive cancellation of background magnetic fields. Active shielding technology cannot uniformly cancel background magnetic fields. These issues can be remedied by combining the methods into a hybrid system. The design used is composed of panels that have an active layer of cancellation between two sheets of mu-metal. The panels form a cube and draw in magnetic fields perpendicular to the surface which can then be reduced using active shielding. This work is supported by the Department of Energy under Contract DE-SC0008107.

  13. A Hybrid Imagination

    DEFF Research Database (Denmark)

    Jamison, Andrew; Christensen, Steen Hyldgaard; Botin, Lars

    “hubris” that is so much taken for granted in contemporary science and engineering discourses and practices with a sense of cooperation and social responsibility. The book portrays the history of science and technology as an underlying tension between hubris – literally the ambition to “play god...... an alternative approach, devoting special attention to the role played by social and cultural movements in the making of science and technology. They show how social and cultural movements, from the Renaissance of the late 15th century to the environmental and global justice movements of our time, have provided......” on the part of many a scientist and engineer and neglect the consequences - and a hybrid imagination, connecting scientific “facts” and technological “artifacts” with cultural understanding. The book concludes with chapters on the recent transformations in the modes of scientific and technological production...

  14. Hybrid Action Systems

    DEFF Research Database (Denmark)

    Rönnkö, M.; Ravn, Anders Peter; Sere, K.

    2003-01-01

    In this paper we investigate the use of action systems with differential actions in the specifcation of hybrid systems. As the main contribution we generalize the definition of a differential action, allowing the use of arbitrary relations over model variables and their time......-derivatives in modelling continuous-time dynamics. The generalized differential action has an intuitively appealing predicate transformer semantics, which we show to be both conjunctive and monotonic. In addition, we show that differential actions blend smoothly with conventional actions in action systems, even under...... parallel composition. Moreover, as the strength of the action system formalism is the support for stepwise development by refinement, we investigate refinement involving a differential action. We show that, due to the predicate transformer semantics, standard action refinement techniques apply also...

  15. Nanoporous hybrid electrolytes

    KAUST Repository

    Schaefer, Jennifer L.

    2011-01-01

    Oligomer-suspended SiO2-polyethylene glycol nanoparticles are studied as porous media electrolytes. At SiO2 volume fractions, , bracketing a critical value y ≈ 0.29, the suspensions jam and their mechanical modulus increase by more than seven orders. For >y, the mean pore diameter is close to the anion size, yet the ionic conductivity remains surprisingly high and can be understood, at all , using a simple effective medium model proposed by Maxwell. SiO 2-polyethylene glycol hybrid electrolytes are also reported to manifest attractive electrochemical stability windows (0.3-6.3 V) and to reach a steady-state interfacial impedance when in contact with metallic lithium. © 2010 The Royal Society of Chemistry.

  16. Hybrid Filter Membrane

    Science.gov (United States)

    Laicer, Castro; Rasimick, Brian; Green, Zachary

    2012-01-01

    Cabin environmental control is an important issue for a successful Moon mission. Due to the unique environment of the Moon, lunar dust control is one of the main problems that significantly diminishes the air quality inside spacecraft cabins. Therefore, this innovation was motivated by NASA s need to minimize the negative health impact that air-suspended lunar dust particles have on astronauts in spacecraft cabins. It is based on fabrication of a hybrid filter comprising nanofiber nonwoven layers coated on porous polymer membranes with uniform cylindrical pores. This design results in a high-efficiency gas particulate filter with low pressure drop and the ability to be easily regenerated to restore filtration performance. A hybrid filter was developed consisting of a porous membrane with uniform, micron-sized, cylindrical pore channels coated with a thin nanofiber layer. Compared to conventional filter media such as a high-efficiency particulate air (HEPA) filter, this filter is designed to provide high particle efficiency, low pressure drop, and the ability to be regenerated. These membranes have well-defined micron-sized pores and can be used independently as air filters with discreet particle size cut-off, or coated with nanofiber layers for filtration of ultrafine nanoscale particles. The filter consists of a thin design intended to facilitate filter regeneration by localized air pulsing. The two main features of this invention are the concept of combining a micro-engineered straight-pore membrane with nanofibers. The micro-engineered straight pore membrane can be prepared with extremely high precision. Because the resulting membrane pores are straight and not tortuous like those found in conventional filters, the pressure drop across the filter is significantly reduced. The nanofiber layer is applied as a very thin coating to enhance filtration efficiency for fine nanoscale particles. Additionally, the thin nanofiber coating is designed to promote capture of

  17. Hybrid computing - Generalities and bibliography

    International Nuclear Information System (INIS)

    Neel, Daniele

    1970-01-01

    This note presents the content of a research thesis. It describes the evolution of hybrid computing systems, discusses the benefits and shortcomings of analogue or hybrid systems, discusses the building up of an hybrid system (requires properties), comments different possible uses, addresses the issues of language and programming, discusses analysis methods and scopes of application. An appendix proposes a bibliography on these issues and notably the different scopes of application (simulation, fluid dynamics, biology, chemistry, electronics, energy, errors, space, programming languages, hardware, mechanics, and optimisation of equations or processes, physics) [fr

  18. Research of a hybrid undulator

    International Nuclear Information System (INIS)

    Ma Youwu; Wu Bing; Liu Bo

    1995-12-01

    A 1.5 m tapered hybrid undulator has been designed and built for mid-infrared free electron laser experiments at CIAE. The undulator utilizes the REC-steel hybrid configuration. The magnetic gap and magnetic field taper can be continuously adjusted. The rms error of the peak field is less than 0.53%. The electron trajectory deviation is around 0.03 mm. The design of undulator, sorting of magnets in hybrid undulator using simulated annealing technique, the motion of electron beam in the ideal and measured magnetic field, magnetic field measurement technique and magnetic field adjustment are described. (6 refs., 10 figs., 1 tab)

  19. Interspecific Hybridization within Ornamental Plants

    DEFF Research Database (Denmark)

    Kuligowska, Katarzyna

    commercially important genera of ornamental plants: Kalanchoë and Hibiscus. The nature of hybridization barriers hampering hybrid production was investigated during pre- and post-fertilization stages. For each genus the interspecific crosses of Kalanchoë species and Hibiscus species, abnormal germination...... and growth of pollen tubes, as well as lower frequencies of pollen tubes were observed in specific cross-combinations. Post-fertilization barriers related to endosperm development and hybrid incompatibility were also observed in Kalanchoë and Hibiscus genus, respectively. Qualitative and quantitative...

  20. Triplex in-situ hybridization

    Science.gov (United States)

    Fresco, Jacques R.; Johnson, Marion D.

    2002-01-01

    Disclosed are methods for detecting in situ the presence of a target sequence in a substantially double-stranded nucleic acid segment, which comprises: a) contacting in situ under conditions suitable for hybridization a substantially double-stranded nucleic acid segment with a detectable third strand, said third strand being capable of hybridizing to at least a portion of the target sequence to form a triple-stranded structure, if said target sequence is present; and b) detecting whether hybridization between the third strand and the target sequence has occured.

  1. Evolution of hybrid defect networks

    International Nuclear Information System (INIS)

    Martins, C. J. A. P.

    2009-01-01

    We apply a recently developed analytic model for the evolution of monopole networks to the case of monopoles attached to one string, usually known as hybrid networks. We discuss scaling solutions for both local and global hybrid networks, and also find an interesting application for the case of vortons. Our quantitative results agree with previous estimates in indicating that the hybrid networks will usually annihilate soon after the string-forming phase transition. However, we also show that in some specific circumstances these networks can survive considerably more than a Hubble time.

  2. Program Hybrid/GDH. Revision

    International Nuclear Information System (INIS)

    Blann, M.; Bisplinghoff, J.

    1975-10-01

    This code is the most recent in a series of codes for doing a-priori pre-equilibrium decay calculations. It has been written to permit the user to exercise many options at time of execution. It will, for example, permit calculation with either Hybrid model or the geometry dependent Hybrid model (GDH). Intranuclear transition rates can be calculated using either a nucleon-nucleon scattering approach (improved over earlier results) or based on the imaginary optical potential. Transition rates based on exciton lifetimes can be selected (as suggested in the Hybrid model formulation) or an average lifetime for each n-exciton configuration may be selected

  3. Compositional Modelling of Stochastic Hybrid Systems

    NARCIS (Netherlands)

    Strubbe, S.N.

    2005-01-01

    In this thesis we present a modelling framework for compositional modelling of stochastic hybrid systems. Hybrid systems consist of a combination of continuous and discrete dynamics. The state space of a hybrid system is hybrid in the sense that it consists of a continuous component and a discrete

  4. Alternative Fuels Data Center: Hybrid Electric Vehicles

    Science.gov (United States)

    . A wide variety of hybrid electric vehicle models is currently available. Although HEVs are often -go traffic), further improving fuel economy. Mild hybrid systems cannot power the vehicle using Hybrid Electric Vehicles to someone by E-mail Share Alternative Fuels Data Center: Hybrid Electric

  5. Hybrid Electric Vehicle Testing | Transportation Research | NREL

    Science.gov (United States)

    Hybrid Electric Vehicle Evaluations Hybrid Electric Vehicle Evaluations How Hybrid Electric Vehicles Work Hybrid electric vehicles combine a primary power source, an energy storage system, and an is used to propel the vehicle during normal drive cycles. The batteries supply additional power for

  6. Hybrid Electric Vehicle Publications | Transportation Research | NREL

    Science.gov (United States)

    Hybrid Electric Vehicle Publications Hybrid Electric Vehicle Publications The following technical papers, conference papers, and fact sheets provide information about NREL's hybrid electric fleet vehicle Class 8 Hybrid Electric Delivery Trucks. Mike Lammert. (2011) FedEx Delivery Trucks In-Use and Vehicle

  7. Hybridization and management of oak populations

    Science.gov (United States)

    Oliver Gailing

    2017-01-01

    Hybridization can result in the transfer of adaptations among species and may contribute to speciation processes. On the other hand, hybridization can also result in a loss of species diversity due to asymmetric gene flow between species (genetic swamping) and in low hybrid fitness. An understanding of the outcomes of interspecific hybridization is crucial for the...

  8. HYBRIDIZATION AND CHAMELEONIC JOURNALISM

    Directory of Open Access Journals (Sweden)

    Adriana Schryver Kurtz

    2016-12-01

    Full Text Available O texto aborda a crescente hibridização entre o Jornalismo e demais formatos midiáticos como resultado natural de um processo que já está na própria raiz da comunicação enquanto atividade histórica. A lógica interna e as potencialidades estéticas e discursivas do fenômeno são analisadas a partir das convergências entre jornalismo e cinema. Para tanto, utiliza o falso documentário Zelig (1983, texto fílmico de Woody Allen, híbrido por natureza, postulado como um microcosmo rico em pistas e sugestões para refletir sobre a fusão entre conteúdos informativos e não informativos.   PALAVRAS-CHAVE: Hibridização; Jornalismo; Cinema; Zelig.       ABSTRACT The text discusses the growing hybridization between journalism and other media formats as a natural result of a process that is already in the very root of communication while historical activity. The internal logic and the aesthetic and discursive potential of the phenomenon are analyzed through the convergences between journalism and cinema. Therefore, uses the mockumentary Zelig (1983, filmic text of Woody Allen, hybrid by nature, postulated as a microcosm rich in clues and suggestions to reflect about the merger between informative and uninformative content.      KEYWORDS: Hybridization; Journalism; Cinema; Zelig.     RESUMEN El texto aborda la creciente hibridación entre el periodismo y otros formatos de medios como um resultado natural de un proceso que ya está en la raíz misma de la comunicación mientras actividad histórica. Se analizan la lógica interna y el potencial estético y discursivo del fenómeno a través de las convergencias entre el periodismo y el cine. Para ello, utiliza el falso documental Zelig (1983, texto fílmico de Woody Allen, híbrido en su naturaleza, postulado como un microcosmos rico en pistas y sugerencias para reflexionar sobre la fusión entre contenidos informativos y no informativos.      PALABRAS CLAVE: Hibridaci

  9. Optical Properties of Hybrid Nanomaterials

    Indian Academy of Sciences (India)

    owner

    K. George Thomas. Photosciences & Photonics Group. National Institute for Interdisciplinary. Science and Technology (NIIST), CSIR,. Trivandrum- 695 019, INDIA. (kgt@vsnl.com). Optical Properties of Hybrid. Nanomaterials ...

  10. Hybrid-Vehicle Transmission System

    Science.gov (United States)

    Lupo, G.; Dotti, G.

    1985-01-01

    Continuously-variable transmission system for hybrid vehicles couples internal-combustion engine and electric motor section, either individually or in parallel, to power vehicle wheels during steering and braking.

  11. MTU hybrid powerpack for railcars

    Energy Technology Data Exchange (ETDEWEB)

    Lehmann, Ingo; Schmalzing, Claus-Oliver [MTU Friedrichshafen GmbH (Germany); Werner, Claus [DB RegioNetz Verkehrs GmbH (Germany); Bold, Uwe [DB Systemtechnik Engineering Kassel (Germany)

    2011-11-15

    Up to 25 percent lower fuel consumption and emission-free train movements in station areas are possible with the MTU hybrid drive system. First field tests on tracks of the Deutsche Bahn started in autumn 2011. (orig.)

  12. Design Procedure for Hybrid Ventilation

    DEFF Research Database (Denmark)

    Heiselberg, Per; Tjelflaat, Per Olaf

    Mechanical and natural ventilation systems have developed separately during many years. The natural next step in this development is development of ventilation concepts that utilises and combines the best features from each system into a new type of ventilation system - Hybrid Ventilation....... Buildings with hybrid ventilation often include other sustainable technologies and an energy optimisation requires an integrated approach in the design of the building and its mechanical systems. Therefore, the hybrid ventilation design procedure differs from the design procedure for conventional HVAC....... The first ideas on a design procedure for hybrid ventilation is presented and the different types of design methods, that is needed in different phases of the design process, is discussed....

  13. Epigenomics: dissecting hybridization and polyploidization.

    Science.gov (United States)

    Jackson, Scott A

    2017-06-19

    Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication affect gene expression.

  14. Real and Hybrid Atomic Orbitals.

    Science.gov (United States)

    Cook, D. B.; Fowler, P. W.

    1981-01-01

    Demonstrates that the Schrodinger equation for the hydrogenlike atom separates in both spheroconal and prolate spheroidal coordinates and that these separations provide a sound theoretical basis for the real and hybrid atomic orbitals. (Author/SK)

  15. Optimizing hybrid spreading in metapopulations.

    Science.gov (United States)

    Zhang, Changwang; Zhou, Shi; Miller, Joel C; Cox, Ingemar J; Chain, Benjamin M

    2015-04-29

    Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemics, and examine the optimum balance between spreading mechanisms in terms of achieving the maximum outbreak size. We show the existence of critically hybrid epidemics where neither spreading mechanism alone can cause a noticeable spread but a combination of the two spreading mechanisms would produce an enormous outbreak. Our results provide new strategies for maximising beneficial epidemics and estimating the worst outcome of damaging hybrid epidemics.

  16. Hybrid mask for deep etching

    KAUST Repository

    Ghoneim, Mohamed T.

    2017-01-01

    Deep reactive ion etching is essential for creating high aspect ratio micro-structures for microelectromechanical systems, sensors and actuators, and emerging flexible electronics. A novel hybrid dual soft/hard mask bilayer may be deposited during

  17. Hybrid Fuel Cell Technology Overview

    Energy Technology Data Exchange (ETDEWEB)

    None available

    2001-05-31

    For the purpose of this STI product and unless otherwise stated, hybrid fuel cell systems are power generation systems in which a high temperature fuel cell is combined with another power generating technology. The resulting system exhibits a synergism in which the combination performs with an efficiency far greater than can be provided by either system alone. Hybrid fuel cell designs under development include fuel cell with gas turbine, fuel cell with reciprocating (piston) engine, and designs that combine different fuel cell technologies. Hybrid systems have been extensively analyzed and studied over the past five years by the Department of Energy (DOE), industry, and others. These efforts have revealed that this combination is capable of providing remarkably high efficiencies. This attribute, combined with an inherent low level of pollutant emission, suggests that hybrid systems are likely to serve as the next generation of advanced power generation systems.

  18. Nitrous Paraffin Hybrid, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The Nitrous Oxide Paraffin Hybrid engine (N2OP) is a proposed technology designed to provide small launch vehicles with high specific impulse, indefinitely storable...

  19. Hybrid Materials for Molecular Sieves

    NARCIS (Netherlands)

    ten Elshof, Johan E.; Klein, Lisa; Aparicio, Mario; Jitianu, Andrei

    2016-01-01

    Hybrid microporous organosilica membranes for molecular separations made by acid-catalyzed solgel synthesis from bridged silsesquioxane precursors have demonstrated good performance in terms of flux and selectivity and remarkable hydrothermal stability in various pervaporation and gas separation

  20. Hybrid quantum-classical master equations

    International Nuclear Information System (INIS)

    Diósi, Lajos

    2014-01-01

    We discuss hybrid master equations of composite systems, which are hybrids of classical and quantum subsystems. A fairly general form of hybrid master equations is suggested. Its consistency is derived from the consistency of Lindblad quantum master equations. We emphasize that quantum measurement is a natural example of exact hybrid systems. We derive a heuristic hybrid master equation of time-continuous position measurement (monitoring). (paper)

  1. Hybrid particles and associated methods

    Science.gov (United States)

    Fox, Robert V; Rodriguez, Rene; Pak, Joshua J; Sun, Chivin

    2015-02-10

    Hybrid particles that comprise a coating surrounding a chalcopyrite material, the coating comprising a metal, a semiconductive material, or a polymer; a core comprising a chalcopyrite material and a shell comprising a functionalized chalcopyrite material, the shell enveloping the core; or a reaction product of a chalcopyrite material and at least one of a reagent, heat, and radiation. Methods of forming the hybrid particles are also disclosed.

  2. Hybrid spacecraft attitude control system

    OpenAIRE

    Renuganth Varatharajoo; Ramly Ajir; Tamizi Ahmad

    2016-01-01

    The hybrid subsystem design could be an attractive approach for futurespacecraft to cope with their demands. The idea of combining theconventional Attitude Control System and the Electrical Power System ispresented in this article. The Combined Energy and Attitude ControlSystem (CEACS) consisting of a double counter rotating flywheel assemblyis investigated for small satellites in this article. Another hybrid systemincorporating the conventional Attitude Control System into the ThermalControl...

  3. Optimizing Hybrid Spreading in Metapopulations.

    OpenAIRE

    Zhang, C.; Zhou, S.; Miller, J. C.; Cox, I. J.; Chain, B. M.

    2015-01-01

    Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemic...

  4. Optimizing Hybrid Spreading in Metapopulations

    OpenAIRE

    Zhang, Changwang; Zhou, Shi; Miller, Joel C.; Cox, Ingemar J.; Chain, Benjamin M.

    2014-01-01

    Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemic...

  5. Hybrid spacecraft attitude control system

    Directory of Open Access Journals (Sweden)

    Renuganth Varatharajoo

    2016-02-01

    Full Text Available The hybrid subsystem design could be an attractive approach for futurespacecraft to cope with their demands. The idea of combining theconventional Attitude Control System and the Electrical Power System ispresented in this article. The Combined Energy and Attitude ControlSystem (CEACS consisting of a double counter rotating flywheel assemblyis investigated for small satellites in this article. Another hybrid systemincorporating the conventional Attitude Control System into the ThermalControl System forming the Combined Attitude and Thermal ControlSystem (CATCS consisting of a "fluid wheel" and permanent magnets isalso investigated for small satellites herein. The governing equationsdescribing both these novel hybrid subsystems are presented and theironboard architectures are numerically tested. Both the investigated novelhybrid spacecraft subsystems comply with the reference missionrequirements.The hybrid subsystem design could be an attractive approach for futurespacecraft to cope with their demands. The idea of combining theconventional Attitude Control System and the Electrical Power System ispresented in this article. The Combined Energy and Attitude ControlSystem (CEACS consisting of a double counter rotating flywheel assemblyis investigated for small satellites in this article. Another hybrid systemincorporating the conventional Attitude Control System into the ThermalControl System forming the Combined Attitude and Thermal ControlSystem (CATCS consisting of a "fluid wheel" and permanent magnets isalso investigated for small satellites herein. The governing equationsdescribing both these novel hybrid subsystems are presented and theironboard architectures are numerically tested. Both the investigated novelhybrid spacecraft subsystems comply with the reference missionrequirements.

  6. Optimal control of hybrid vehicles

    CERN Document Server

    Jager, Bram; Kessels, John

    2013-01-01

    Optimal Control of Hybrid Vehicles provides a description of power train control for hybrid vehicles. The background, environmental motivation and control challenges associated with hybrid vehicles are introduced. The text includes mathematical models for all relevant components in the hybrid power train. The power split problem in hybrid power trains is formally described and several numerical solutions detailed, including dynamic programming and a novel solution for state-constrained optimal control problems based on Pontryagin’s maximum principle.   Real-time-implementable strategies that can approximate the optimal solution closely are dealt with in depth. Several approaches are discussed and compared, including a state-of-the-art strategy which is adaptive for vehicle conditions like velocity and mass. Two case studies are included in the book: ·        a control strategy for a micro-hybrid power train; and ·        experimental results obtained with a real-time strategy implemented in...

  7. Hybrid power source

    Science.gov (United States)

    Singh, Harmohan N.

    2012-06-05

    A hybrid power system is comprised of a high energy density element such as a fuel-cell and high power density elements such as a supercapacitor banks. A DC/DC converter electrically connected to the fuel cell and converting the energy level of the energy supplied by the fuel cell. A first switch is electrically connected to the DC/DC converter. First and second supercapacitors are electrically connected to the first switch and a second switch. A controller is connected to the first switch and the second switch, monitoring charge levels of the supercapacitors and controls the switching in response to the charge levels. A load is electrically connected to the second switch. The first switch connects the DC/DC converter to the first supercapacitor when the second switch connects the second supercapacitor to the load. The first switch connects the DC/DC converter to the second supercapacitor when the second switch connects the first supercapacitor to the load.

  8. Protaper--hybrid technique.

    Science.gov (United States)

    Simon, Stephane; Lumley, Philip; Tomson, Phillip; Pertot, Wilhelm-Joseph; Machtou, Pierre

    2008-03-01

    Crown down preparation is the most known and described technique since the introduction of Nickel Titanium (NiTi) rotary instruments in endodontics. This technique gives good results but has limitations, such as not addressing the initial anatomy of oval or dumb-bell shaped canals. The specific design of the Protaper instruments allows use of them with a different technique and, specifically, with a brushing motion in the body of the canal. The recent introduction of hand Protaper files has expanded the range of application of this system, especially in curved canals. The 'hybrid technique', using rotary and hand files, and the advantages of the combination of both instruments, are clearly described in this article. Used with this technique, the Protaper is a very safe system to use, and more controllable, for both inexperienced and experienced practitioners alike, than other systems. To understand the precautions needed with rotary files, and how to use them to preserve the anatomy of the canal and get a tapered shaping, even in severely curved canals.

  9. Comparative genomic hybridization.

    Science.gov (United States)

    Pinkel, Daniel; Albertson, Donna G

    2005-01-01

    Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

  10. Hybrid Arrays for Chemical Sensing

    Science.gov (United States)

    Kramer, Kirsten E.; Rose-Pehrsson, Susan L.; Johnson, Kevin J.; Minor, Christian P.

    In recent years, multisensory approaches to environment monitoring for chemical detection as well as other forms of situational awareness have become increasingly popular. A hybrid sensor is a multimodal system that incorporates several sensing elements and thus produces data that are multivariate in nature and may be significantly increased in complexity compared to data provided by single-sensor systems. Though a hybrid sensor is itself an array, hybrid sensors are often organized into more complex sensing systems through an assortment of network topologies. Part of the reason for the shift to hybrid sensors is due to advancements in sensor technology and computational power available for processing larger amounts of data. There is also ample evidence to support the claim that a multivariate analytical approach is generally superior to univariate measurements because it provides additional redundant and complementary information (Hall, D. L.; Linas, J., Eds., Handbook of Multisensor Data Fusion, CRC, Boca Raton, FL, 2001). However, the benefits of a multisensory approach are not automatically achieved. Interpretation of data from hybrid arrays of sensors requires the analyst to develop an application-specific methodology to optimally fuse the disparate sources of data generated by the hybrid array into useful information characterizing the sample or environment being observed. Consequently, multivariate data analysis techniques such as those employed in the field of chemometrics have become more important in analyzing sensor array data. Depending on the nature of the acquired data, a number of chemometric algorithms may prove useful in the analysis and interpretation of data from hybrid sensor arrays. It is important to note, however, that the challenges posed by the analysis of hybrid sensor array data are not unique to the field of chemical sensing. Applications in electrical and process engineering, remote sensing, medicine, and of course, artificial

  11. Hybrid platform. Economical hybrid drive for commercial vehicles; Hybrid Plattform. Wirtschaftlicher Hybridantrieb fuer Nutzfahrzeuge

    Energy Technology Data Exchange (ETDEWEB)

    Wallner, S.; Lamke, M.; Mohr, M.; Sedlacek, M.; Speck, F.D. [ZF Friedrichshafen AG, Friedrichshafen (Germany)

    2011-07-01

    Up to now, hybrid systems have been adapted to their specific requirements in the various applications for trucks, buses as well as mobile and building machines. From a technical point of view, this does indeed result in optimized hybrid drives for each single vehicle application, but due to small volumes, such single developments are critical from a business point of view. ZF Friedrichshafen AG is providing a solution to the technical and economical requirements of the cost-sensitive CV segment in the form of a modular CV parallel hybrid platform composed of a hybrid module system, an inverter, a battery system, and a hybrid software integrated into the overall vehicle. Thanks to the intelligent combination of assemblies and the use of as many identical parts as possible, platforms are realized which cover power ranges between 60 and 120 kW, voltage ranges between 350 and 650 V, and battery capacities between 2 and 4 kWh. The dimensions of the platform elements are such that integration into the diverse commercial vehicle applications is made easy. The hybrid software required for the vehicle-specific functions is also configurable for the mentioned CV applications. (orig.)

  12. Mechanical and thermal design of hybrid blankets

    International Nuclear Information System (INIS)

    Schultz, K.R.

    1978-01-01

    The thermal and mechanical aspects of hybrid reactor blanket design considerations are discussed. This paper is intended as a companion to that of J. D. Lee of Lawrence Livermore Laboratory on the nuclear aspects of hybrid reactor blanket design. The major design characteristics of hybrid reactor blankets are discussed with emphasis on the areas of difference between hybrid reactors and standard fusion or fission reactors. Specific examples are used to illustrate the design tradeoffs and choices that must be made in hybrid reactor design. These examples are drawn from the work on the Mirror Hybrid Reactor

  13. Hybrid pine for tough sites

    International Nuclear Information System (INIS)

    Davidson, W.H.

    1994-01-01

    A test planting of 30 first- and second-generation pitch x loblolly pine (pinus rigida x P. taeda) hybrids was established on a West Virginia minesoil in 1985. The site was considered orphaned because earlier attempts at revegetation were unsuccessful. The soil was acid (pH 4.6), lacking in nutrients, and compacted. Vegetation present at the time of planting consisted of a sparse cover of tall fescue (Festuca arundinacea) and poverty grass (Danthonia spicata) and a few sourwood (Oxydendrum arboreum) and mountain laurel (Kalmia latifolia) seedlings. In the planting trial, 30 different hybrids were set out in 4 tree linear plots replicated 5 times. The seedlings had been grown in containers for 1 yr before outplanting. Evaluations made after 6 growing seasons showed overall plantation survival was 93%; six hybrids and one open-pollinated cross survived 100%. Individual tree heights ranged from 50 to 425 cm with a plantation average of 235 cm (7.7 ft). Eleven of the hybrids had average heights that exceeded the plantation average. Another test planting of tree and shrub species on this site has very poor survival. Therefore, pitch x loblolly hybrid pine can be recommended for reclaiming this and similar sites

  14. Case for the fusion hybrid

    International Nuclear Information System (INIS)

    Rose, R.P.

    1981-01-01

    The use of nuclear fusion to produce fuel for nuclear fission power stations is discussed in the context of a crucial need for future energy options. The fusion hybrid is first considered as an element in the future of nuclear fission power to provide long term assurance of adequate fuel supplies for both breeder and convertor reactors. Generic differences in neutronic characteristics lead to a fuel production potential of fusion-fission hybrid systems which is significantly greater than that obtainable with fission systems alone. Furthermore, cost benefit studies show a variety of scenarios in which the hybrid offers sufficient potential to justify development costs ranging in the tens of billions of dollars. The hybrid is then considered as an element in the ultimate development of fusion electric power. The hybrid offers a near term application of fusion where experience with the requisite technologies can be derived as a vital step in mapping a credible route to eventual commercial feasibility of pure fusion systems. Finally, the criteria for assessment of future energy options are discussed with prime emphasis on the need for rational comparision of alternatives

  15. Genomic networks of hybrid sterility.

    Directory of Open Access Journals (Sweden)

    Leslie M Turner

    2014-02-01

    Full Text Available Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities". The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL. Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is

  16. Hybrid magnets at Tohoku University

    International Nuclear Information System (INIS)

    Muto, Yoshio; Nakagawa, Yasuaki; Noto, Koshichi; Hoshi, Akira; Miura, Shigeto; Watanabe, Kazuo; Kido, Giyuu

    1984-01-01

    The High Field Laboratory for Superconducting Materials was established in April 1981 at Tohoku University in order to provide research facilities for the development of superconducting materials suitable for superconducting magnets for the plasma confinement in fusion reactors. Main facilities of this laboratory are three hybrid magnets up to 30 Tesla dc magnetic fields with inner bores from 32 to 52mm in diameter. The magnets consist of superconducting outer solenoids and water-cooled inner ones with a maximum steady power dissipation of 8 MW. The design and construction of these three hybrid magnets have finished in last three years, and two of them (HM-3;20T, 32 mm bore and HM-2; 23T, 52 mm bore) have already opened to scientists and engineers in the superconductivity and other fields. The rated field of the third hybrid magnet (HM-1) is 31 (or 29) Tesla in a bore of 32 (or 52) mm in diameter. By this hybrid system we have succeeded to produce 29.3 Tesla on April 21, 1984. Detailed descriptions are presented on the superconducting magnets, power supplies and cooling systems for them, water-cooled magnets, dc-high power source and water-cooled system for them, the monitoring and control system for the hybrid magnets including a super-minicomputer system, a hard-wired interlock system for the safety of human beings and machines, and so on. The fourth hybrid magnet system which aims at 35 Tesla as the next phase is also discussed. (author)

  17. Genomic networks of hybrid sterility.

    Science.gov (United States)

    Turner, Leslie M; White, Michael A; Tautz, Diethard; Payseur, Bret A

    2014-02-01

    Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities"). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad

  18. Review of laser hybrid welding

    DEFF Research Database (Denmark)

    Bagger, Claus

    2004-01-01

    In this artucle an overview og the hybrid welding process is given. After a short historic overview, a review of the fundamental phenomenon taking place when a laser (CO2 or Nd:YAG) interacts in the same molten pool as a more conventional source of energy, e.g. tungsten in-active gas, plasma......, or metal inactive gas/metal active gas.This is followed by reports of how the many process parameters governing the hybrid welding process can be set and how the choice of secondary energy source, shielding gas, etc. can affect the overall welding process....

  19. Reverse hybrid total hip arthroplasty

    DEFF Research Database (Denmark)

    Wangen, Helge; Havelin, Leif I.; Fenstad, Anne M

    2017-01-01

    Background and purpose - The use of a cemented cup together with an uncemented stem in total hip arthroplasty (THA) has become popular in Norway and Sweden during the last decade. The results of this prosthetic concept, reverse hybrid THA, have been sparsely described. The Nordic Arthroplasty....... Patients and methods - From the NARA, we extracted data on reverse hybrid THAs from January 1, 2000 until December 31, 2013. 38,415 such hips were studied and compared with cemented THAs. The Kaplan-Meier method and Cox regression analyses were used to estimate the prosthesis survival and the relative risk...

  20. Hard electroproduction of hybrid mesons

    International Nuclear Information System (INIS)

    Anikin, I.V.; LPT Universite Paris-Sud, Orsay; Szymanowski, L.; Teryaev, O.V.; ); Wallon, S.

    2005-01-01

    We estimate the sizeable cross section for deep exclusive electroproduction of an exotic J PC = 1 -+ hybrid meson in the Bjorken regime. The production amplitude scales like the one for usual meson electroproduction, i.e. as 1/Q 2 . This is due to the non-vanishing leading twist distribution amplitude for the hybrid meson, which may be normalized thanks to its relation to the energy momentum tensor and to the QCD sum rules technique. The hard amplitude is considered up to next-to-leading order in as and we explore the consequences of fixing the renormalization scale ambiguity through the BLM procedure. (author)

  1. Inference in hybrid Bayesian networks

    International Nuclear Information System (INIS)

    Langseth, Helge; Nielsen, Thomas D.; Rumi, Rafael; Salmeron, Antonio

    2009-01-01

    Since the 1980s, Bayesian networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability techniques (like fault trees and reliability block diagrams). However, limitations in the BNs' calculation engine have prevented BNs from becoming equally popular for domains containing mixtures of both discrete and continuous variables (the so-called hybrid domains). In this paper we focus on these difficulties, and summarize some of the last decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability.

  2. Hybrid Magnetics and Power Applications

    DEFF Research Database (Denmark)

    Mo, Wai Keung; Paasch, Kasper

    2017-01-01

    A hybrid magnetic approach, merging two different magnetic core properites such as ferrite and iron powder cores, is an effective solution for power converter applications. It can offer similar magnetic properties to that of magnetic powder cores but showing less copper loss than powder cores....... In order to prevent ferrite core saturation, placing an effective air gap within the ferrite core is a key method to obtain optimum hybrid magnetic performance. Furthermore, a relatively large inductance at low loading current is an excellent way to minimze power loss in order to achieve high efficiency...

  3. Essentialism, hybridism and cultural critique

    DEFF Research Database (Denmark)

    Frello, Birgitta

    2007-01-01

    to social and cultural critique. Through a critical discussion of the concept of hybridity, I argue that rather than expecting to find definite emancipating or suppressing capacities connected to constructions of the ‘hybrid' and the ‘pure', we should focus on how these two poles are invested with meaning...... and related to power. Hence, while insisting on Cultural Studies' commitment to social and cultural critique, I argue that this critique would benefit from an analytical sensitivity towards the uses and abuses of the discursive power to designate meaningful and legitimate subject positions, rather than...

  4. Hybrid Simulation of Composite Structures

    DEFF Research Database (Denmark)

    Høgh, Jacob Herold

    experiment. The technique has primarily been used within earthquake engineering but many other fields of engineering have utilized the method with benefit. However, these previous efforts have focused on structures with a simple boundary between the numerical and physical substructure i.e. few degrees...... the transfer system and the control and monitoring techniques in the shared boundary is therefore a key issue in this type of hybrid simulation. During the research, hybrid simulation platforms have been programmed capable of running on different time scales with advanced control and monitoring techniques...

  5. From hybrid-media system to hybrid-media politicians

    DEFF Research Database (Denmark)

    Blach-Ørsten, Mark; Eberholst, Mads Kæmsgaard; Burkal, Rasmus

    2017-01-01

    ’ media use is changing rapidly; 15%–16% of Danish candidates used Twitter in 2011 but 68% in 2015. In this large-sample content analysis, party leaders have high traditional-news-media and low Twitter presence, and younger candidates visa-versa, but some politicians have high presence in both. Hybrid...

  6. Field errors in hybrid insertion devices

    International Nuclear Information System (INIS)

    Schlueter, R.D.

    1995-02-01

    Hybrid magnet theory as applied to the error analyses used in the design of Advanced Light Source (ALS) insertion devices is reviewed. Sources of field errors in hybrid insertion devices are discussed

  7. Field errors in hybrid insertion devices

    Energy Technology Data Exchange (ETDEWEB)

    Schlueter, R.D. [Lawrence Berkeley Lab., CA (United States)

    1995-02-01

    Hybrid magnet theory as applied to the error analyses used in the design of Advanced Light Source (ALS) insertion devices is reviewed. Sources of field errors in hybrid insertion devices are discussed.

  8. ADVANCED HYBRID PARTICULATE COLLECTOR

    Energy Technology Data Exchange (ETDEWEB)

    Ye Zhuang; Stanley J. Miller; Michelle R. Olderbak; Rich Gebert

    2001-12-01

    A new concept in particulate control, called an advanced hybrid particulate collector (AHPC), is being developed under funding from the U.S. Department of Energy. The AHPC combines the best features of electrostatic precipitators (ESPs) and baghouses in an entirely novel manner. The AHPC concept combines fabric filtration and electrostatic precipitation in the same housing, providing major synergism between the two methods, both in the particulate collection step and in transfer of dust to the hopper. The AHPC provides ultrahigh collection efficiency, overcoming the problem of excessive fine-particle emissions with conventional ESPs, and solves the problem of reentrainment and re-collection of dust in conventional baghouses. Phase I of the development effort consisted of design, construction, and testing of a 5.7-m{sup 3}/min (200-acfm) working AHPC model. Results from both 8-hr parametric tests and 100-hr proof-of-concept tests with two different coals demonstrated excellent operability and greater than 99.99% fine-particle collection efficiency. Since all of the developmental goals of Phase I were met, the approach was scaled up in Phase II to a size of 255 m{sup 3}/min (9000 acfm) (equivalent in size to 2.5 MW) and was installed on a slipstream at the Big Stone Power Plant. For Phase II, the AHPC at Big Stone Power Plant was operated continuously from late July 1999 until mid-December 1999. The Phase II results were highly successful in that ultrahigh particle collection efficiency was achieved, pressure drop was well controlled, and system operability was excellent. For Phase III, the AHPC was modified into a more compact configuration, and components were installed that were closer to what would be used in a full-scale commercial design. The modified AHPC was operated from April to July 2000. While operational results were acceptable during this time, inspection of bags in the summer of 2000 revealed some membrane damage to the fabric that appeared to be

  9. Constructing decidable hybrid systems with velocity bounds

    NARCIS (Netherlands)

    Belta, C.; Habets, L.C.G.J.M.

    2004-01-01

    In this paper, the question of bi-similarity between hybrid systems and their discrete quotients is studied from a new point of view. We consider two classes of hybrid systems: piecewise affine hybrid systems on simplices and piecewise multi-affine systems on multi-dimensional rectangles. Given a

  10. Deriving simulators for hybrid Chi models

    NARCIS (Netherlands)

    Beek, van D.A.; Man, K.L.; Reniers, M.A.; Rooda, J.E.; Schiffelers, R.R.H.

    2006-01-01

    The hybrid Chi language is formalism for modeling, simulation and verification of hybrid systems. The formal semantics of hybrid Chi allows the definition of provably correct implementations for simulation, verification and realtime control. This paper discusses the principles of deriving an

  11. Hybrid Doctoral Program: Innovative Practices and Partnerships

    Science.gov (United States)

    Alvich, Dori; Manning, JoAnn; McCormick, Kathy; Campbell, Robert

    2012-01-01

    This paper reflects on how one mid-Atlantic University innovatively incorporated technology into the development of a hybrid doctoral program in educational leadership. The paper describes a hybrid doctoral degree program using a rigorous design; challenges of reworking a traditional syllabus of record to a hybrid doctoral program; the perceptions…

  12. Internal combustion engines in hybrid vehicles

    NARCIS (Netherlands)

    Mourad, S.; Weijer, C.J.T. van de; Beckman, D.E.

    1998-01-01

    In this paper the use of internal combustion engines in hybrid powertrains is investigated. The substantial difference between the use of internal combustion engines in conventional and in hybrid vehicles mean that engines for hybrid vehicles should be designed specifically for the purpose. At the

  13. Hybrid Logical Analyses of the Ambient Calculus

    DEFF Research Database (Denmark)

    Bolander, Thomas; Hansen, Rene Rydhof

    2010-01-01

    In this paper, hybrid logic is used to formulate three control flow analyses for Mobile Ambients, a process calculus designed for modelling mobility. We show that hybrid logic is very well-suited to express the semantic structure of the ambient calculus and how features of hybrid logic can...

  14. The Hybrid Automobile and the Atkinson Cycle

    Science.gov (United States)

    Feldman, Bernard J.

    2008-01-01

    The hybrid automobile is a strikingly new automobile technology with a number of new technological features that dramatically improve energy efficiency. This paper will briefly describe how hybrid automobiles work; what are these new technological features; why the Toyota Prius hybrid internal combustion engine operates on the Atkinson cycle…

  15. Hybrid synchronization of hyperchaotic Lu system

    Indian Academy of Sciences (India)

    In this paper, we study the hybrid synchronization between two identical hyperchaotic Lu systems. Hybrid synchronization of hyperchaotic Lu system is achieved through synchronization of two pairs of states and anti-synchronization of the other two pairs of states. Active controls are designed to achieve hybrid ...

  16. Formal Description of Hybrid Systems

    DEFF Research Database (Denmark)

    Zhou, Chaochen; Ji, Wang; Ravn, Anders P.

    1996-01-01

    A language to describe hybrid systems, i.e. networks of communicating discrete and continuous processes, is proposed. A semantics of the language is given in Extended Duration Calculus, a real-time interval logic with a proof system that allows reasoning in mathematical analysis about continuous ...

  17. Hybrid mesons with auxiliary fields

    International Nuclear Information System (INIS)

    Buisseret, F.; Mathieu, V.

    2006-01-01

    Hybrid mesons are exotic mesons in which the color field is not in the ground state. Their understanding deserves interest from a theoretical point of view, because it is intimately related to nonperturbative aspects of QCD. Moreover, it seems that some recently detected particles, such as the π 1 (1600) and the Y(4260), are serious hybrid candidates. In this work, we investigate the description of such exotic hadrons by applying the auxiliary fields technique (also known as the einbein field method) to the widely used spinless Salpeter Hamiltonian with appropriate linear confinement. Instead of the usual numerical resolution, this technique allows to find simplified analytical mass spectra and wave functions of the Hamiltonian, which still lead to reliable qualitative predictions. We analyse and compare two different descriptions of hybrid mesons, namely a two-body q system with an excited flux tube, or a three-body qg system. We also compute the masses of the 1 -+ hybrids. Our results are shown to be in satisfactory agreement with lattice QCD and other effective models. (orig.)

  18. The threat of hybrid Phytophthoras

    Science.gov (United States)

    The majority of invasive plant pathogens have resulted from the introduction of exotic organisms. However, another mechanism for invasiveness results from hybridization between species. This phenomenon has been documented in plants and animals, but its role in plant pathology has only recently been ...

  19. Hybrid cycles for micro generation

    International Nuclear Information System (INIS)

    Campanari, S.

    2000-01-01

    This paper deals with the main features of two emerging technologies in the field of small-scale power generation, micro turbines and Solid Oxide Fuel Cells, discussing the extremely high potential of their combination into hybrid cycles and their possible role for distributed cogeneration [it

  20. Inference in hybrid Bayesian networks

    DEFF Research Database (Denmark)

    Lanseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

    2009-01-01

    Since the 1980s, Bayesian Networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability-techniques (like fault trees...... decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability....

  1. Towards Modelling of Hybrid Systems

    DEFF Research Database (Denmark)

    Wisniewski, Rafal

    2006-01-01

    system consists of a number of dynamical systems that are glued together according to information encoded in the discrete part of the system. We develop a definition of a hybrid system as a functor from the category generated by a transition system to the category of directed topological spaces. Its...

  2. Transgressive Hybrids as Hopeful Monsters.

    Science.gov (United States)

    Dittrich-Reed, Dylan R; Fitzpatrick, Benjamin M

    2013-06-01

    The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt's infamous "hopeful monster". Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, "monstrous" phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts "hopeless" monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts "hopeful" monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant "hopeful monsters" will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.

  3. Hybrid winding concept for toroids

    DEFF Research Database (Denmark)

    Schneider, Henrik; Andersen, Thomas; Knott, Arnold

    2013-01-01

    and placement machinery. This opens up the possibility for both an automated manufacturing process and an automated production process of toroidal magnetics such as power inductors, filtering inductors, air core inductors, transformers etc. Both the proposed hybrid and the common wire wound winding...

  4. Hybrid technology for regional railcars

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Christoph [DVV Eurailpress, Hamburg (Germany)

    2012-05-15

    It is possible to reduce the fuel consumed by diesel railcars operating short-distance regional services by making use of newly developed hybrid technology. Voith Turbo is setting out to produce evidence of that through two completely different projects. (orig.)

  5. Sugar pine and its hybrids

    Science.gov (United States)

    W. B. Critchfield; B. B. Kinloch

    1986-01-01

    Unlike most white pines, sugar pine (Pinus lambertiana) is severely restricted in its ability to hybridize with other species. It has not been successfully crossed with any other North American white pine, nor with those Eurasian white pines it most closely resembles. Crosses with the dissimilar P. koraiensis and P....

  6. Organic and hybrid solar cells

    CERN Document Server

    Huang, Hui

    2014-01-01

    This book delivers a comprehensive evaluation of organic and hybrid solar cells and identifies their fundamental principles and numerous applications. Great attention is given to the charge transport mechanism, donor and acceptor materials, interfacial materials, alternative electrodes, device engineering and physics, and device stability. The authors provide an industrial perspective on the future of photovoltaic technologies.

  7. Multifunctional hybrids for electromagnetic absorption

    International Nuclear Information System (INIS)

    Huynen, I.; Quievy, N.; Bailly, C.; Bollen, P.; Detrembleur, C.; Eggermont, S.; Molenberg, I.; Thomassin, J.M.; Urbanczyk, L.

    2011-01-01

    Highlights: → EM absorption requires low dielectric constant and ∼1 S/m electrical conductivity. → New hybrids were processed with CNT-filled polymer foam inserted in Al honeycomb. → The EM absorption in the GHz range is superior to any known material. → A closed form model is used to guide the design of the hybrid. → The architectured material is light with potential for thermal management. - Abstract: Electromagnetic (EM) interferences are ubiquitous in modern technologies and impact on the reliability of electronic devices and on living cells. Shielding by EM absorption, which is preferable over reflection in certain instances, requires combining a low dielectric constant with high electrical conductivity, which are antagonist properties in the world of materials. A novel class of hybrid materials for EM absorption in the gigahertz range has been developed based on a hierarchical architecture involving a metallic honeycomb filled with a carbon nanotube-reinforced polymer foam. The waveguide characteristics of the honeycomb combined with the performance of the foam lead to unexpectedly large EM power absorption over a wide frequency range, superior to any known material. The peak absorption frequency can be tuned by varying the shape of the honeycomb unit cell. A closed form model of the EM reflection and absorption provides a tool for the optimization of the hybrid. This designed material sets the stage for a new class of sandwich panels combining high EM absorption with mass efficiency, stiffness and thermal management.

  8. Information transmission on hybrid networks

    Science.gov (United States)

    Chen, Rongbin; Cui, Wei; Pu, Cunlai; Li, Jie; Ji, Bo; Gakis, Konstantinos; Pardalos, Panos M.

    2018-01-01

    Many real-world communication networks often have hybrid nature with both fixed nodes and moving modes, such as the mobile phone networks mainly composed of fixed base stations and mobile phones. In this paper, we discuss the information transmission process on the hybrid networks with both fixed and mobile nodes. The fixed nodes (base stations) are connected as a spatial lattice on the plane forming the information-carrying backbone, while the mobile nodes (users), which are the sources and destinations of information packets, connect to their current nearest fixed nodes respectively to deliver and receive information packets. We observe the phase transition of traffic load in the hybrid network when the packet generation rate goes from below and then above a critical value, which measures the network capacity of packets delivery. We obtain the optimal speed of moving nodes leading to the maximum network capacity. We further improve the network capacity by rewiring the fixed nodes and by considering the current load of fixed nodes during packets transmission. Our purpose is to optimize the network capacity of hybrid networks from the perspective of network science, and provide some insights for the construction of future communication infrastructures.

  9. Shape Memory Composite Hybrid Hinge

    Science.gov (United States)

    Fang, Houfei; Im, Eastwood; Lin, John; Scarborough, Stephen

    2012-01-01

    There are two conventional types of hinges for in-space deployment applications. The first type is mechanically deploying hinges. A typical mechanically deploying hinge is usually composed of several tens of components. It is complicated, heavy, and bulky. More components imply higher deployment failure probability. Due to the existence of relatively moving components among a mechanically deploying hinge, it unavoidably has microdynamic problems. The second type of conventional hinge relies on strain energy for deployment. A tape-spring hinge is a typical strain energy hinge. A fundamental problem of a strain energy hinge is that its deployment dynamic is uncontrollable. Usually, its deployment is associated with a large impact, which is unacceptable for many space applications. Some damping technologies have been experimented with to reduce the impact, but they increased the risks of an unsuccessful deployment. Coalescing strain energy components with shape memory composite (SMC) components to form a hybrid hinge is the solution. SMCs are well suited for deployable structures. A SMC is created from a high-performance fiber and a shape memory polymer resin. When the resin is heated to above its glass transition temperature, the composite becomes flexible and can be folded or packed. Once cooled to below the glass transition temperature, the composite remains in the packed state. When the structure is ready to be deployed, the SMC component is reheated to above the glass transition temperature, and it returns to its as-fabricated shape. A hybrid hinge is composed of two strain energy flanges (also called tape-springs) and one SMC tube. Two folding lines are placed on the SMC tube to avoid excessive strain on the SMC during folding. Two adapters are used to connect the hybrid hinge to its adjacent structural components. While the SMC tube is heated to above its glass transition temperature, a hybrid hinge can be folded and stays at folded status after the temperature

  10. A hybrid air conditioner driven by a hybrid solar collector

    Science.gov (United States)

    Al-Alili, Ali

    The objective of this thesis is to search for an efficient way of utilizing solar energy in air conditioning applications. The current solar Air Conditioners (A/C)s suffer from low Coefficient of Performance (COP) and performance degradation in hot and humid climates. By investigating the possible ways of utilizing solar energy in air conditioning applications, the bottlenecks in these approaches were identified. That resulted in proposing a novel system whose subsystem synergy led to a COP higher than unity. The proposed system was found to maintain indoor comfort at a higher COP compared to the most common solar A/Cs, especially under very hot and humid climate conditions. The novelty of the proposed A/C is to use a concentrating photovoltaic/thermal collector, which outputs thermal and electrical energy simultaneously, to drive a hybrid A/C. The performance of the hybrid A/C, which consists of a desiccant wheel, an enthalpy wheel, and a vapor compression cycle (VCC), was investigated experimentally. This work also explored the use of a new type of desiccant material, which can be regenerated with a low temperature heat source. The experimental results showed that the hybrid A/C is more effective than the standalone VCC in maintaining the indoor conditions within the comfort zone. Using the experimental data, the COP of the hybrid A/C driven by a hybrid solar collector was found to be at least double that of the current solar A/Cs. The innovative integration of its subsystems allows each subsystem to do what it can do best. That leads to lower energy consumption which helps reduce the peak electrical loads on electric utilities and reduces the consumer operating cost since less energy is purchased during the on peak periods and less solar collector area is needed. In order for the proposed A/C to become a real alternative to conventional systems, its performance and total cost were optimized using the experimentally validated model. The results showed that for an

  11. Overview of hybrid electric vehicle trend

    Science.gov (United States)

    Wang, Haomiao; Yang, Weidong; Chen, Yingshu; Wang, Yun

    2018-04-01

    With the increase of per capita energy consumption, environmental pollution is worsening. Using new alternative sources of energy, reducing the use of conventional fuel-powered engines is imperative. Due to the short period, pure electric vehicles cannot be mass-produced and there are many problems such as imperfect charging facilities. Therefore, the development of hybrid electric vehicles is particularly important in a certain period. In this paper, the classification of hybrid vehicle, research status of hybrid vehicle and future development trends of hybrid vehicles is introduced. It is conducive to the public understanding of hybrid electric vehicles, which has a certain theoretical significance.

  12. Gasoline hybrid pneumatic engine for efficient vehicle powertrain hybridization

    OpenAIRE

    Dimitrova, Zlatina; Maréchal, François

    2015-01-01

    The largest applied convertors in passenger cars are the internal combustion engines – gasoline, diesel, adapted also for operating on alternative fuels and hybrid modes. The number of components that are necessary to realize modern future propulsion system is inexorably increasing. The need for efficiency improvement of the vehicle energy system induces the search for an innovative methodology during the design process. In this article the compressed air is investigated as an innovative solu...

  13. Hybrid methods for cybersecurity analysis :

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Warren Leon,; Dunlavy, Daniel M.

    2014-01-01

    Early 2010 saw a signi cant change in adversarial techniques aimed at network intrusion: a shift from malware delivered via email attachments toward the use of hidden, embedded hyperlinks to initiate sequences of downloads and interactions with web sites and network servers containing malicious software. Enterprise security groups were well poised and experienced in defending the former attacks, but the new types of attacks were larger in number, more challenging to detect, dynamic in nature, and required the development of new technologies and analytic capabilities. The Hybrid LDRD project was aimed at delivering new capabilities in large-scale data modeling and analysis to enterprise security operators and analysts and understanding the challenges of detection and prevention of emerging cybersecurity threats. Leveraging previous LDRD research e orts and capabilities in large-scale relational data analysis, large-scale discrete data analysis and visualization, and streaming data analysis, new modeling and analysis capabilities were quickly brought to bear on the problems in email phishing and spear phishing attacks in the Sandia enterprise security operational groups at the onset of the Hybrid project. As part of this project, a software development and deployment framework was created within the security analyst work ow tool sets to facilitate the delivery and testing of new capabilities as they became available, and machine learning algorithms were developed to address the challenge of dynamic threats. Furthermore, researchers from the Hybrid project were embedded in the security analyst groups for almost a full year, engaged in daily operational activities and routines, creating an atmosphere of trust and collaboration between the researchers and security personnel. The Hybrid project has altered the way that research ideas can be incorporated into the production environments of Sandias enterprise security groups, reducing time to deployment from months and

  14. Genetic basis to hybrid inviability is more complex than hybrid male sterility in Caenorhabditis nematodes.

    Science.gov (United States)

    Bundus, Joanna D; Wang, Donglin; Cutter, Asher D

    2018-04-07

    Hybrid male sterility often evolves before female sterility or inviability of hybrids, implying that the accumulation of divergence between separated lineages should lead hybrid male sterility to have a more polygenic basis. However, experimental evidence is mixed. Here, we use the nematodes Caenorhabditis remanei and C. latens to characterize the underlying genetic basis of asymmetric hybrid male sterility and hybrid inviability. We demonstrate that hybrid male sterility is consistent with a simple genetic basis, involving a single X-autosome incompatibility. We also show that hybrid inviability involves more genomic compartments, involving diverse nuclear-nuclear incompatibilities, a mito-nuclear incompatibility, and maternal effects. These findings demonstrate that male sensitivity to genetic perturbation may be genetically simple compared to hybrid inviability in Caenorhabditis and motivates tests of generality for the genetic architecture of hybrid incompatibility across the breadth of phylogeny.

  15. Stochastic effects in hybrid inflation

    Science.gov (United States)

    Martin, Jérôme; Vennin, Vincent

    2012-02-01

    Hybrid inflation is a two-field model where inflation ends due to an instability. In the neighborhood of the instability point, the potential is very flat and the quantum fluctuations dominate over the classical motion of the inflaton and waterfall fields. In this article, we study this regime in the framework of stochastic inflation. We numerically solve the two coupled Langevin equations controlling the evolution of the fields and compute the probability distributions of the total number of e-folds and of the inflation exit point. Then, we discuss the physical consequences of our results, in particular, the question of how the quantum diffusion can affect the observable predictions of hybrid inflation.

  16. Towards an expansive hybrid psychology

    DEFF Research Database (Denmark)

    Brinkmann, Svend

    2011-01-01

    sources of mediators that are the brain, the body, social practices and technological artefacts. It is argued that the mind is normative in the sense that mental processes do not simply happen, but can be done more or less well, and thus are subject to normative appraisal. The expanded hybrid psychology......This article develops an integrative theory of the mind by examining how the mind, understood as a set of skills and dispositions, depends upon four sources of mediators. Harré’s hybrid psychology is taken as a meta-theoretical starting point, but is expanded significantly by including the four...... is meant to assist in integrating theoretical perspectives and research interests that are often thought of as incompatible, among them neuroscience, phenomenology of the body, social practice theory and technology studies. A main point of the article is that these perspectives each are necessary...

  17. Adaptive hybrid control of manipulators

    Science.gov (United States)

    Seraji, H.

    1987-01-01

    Simple methods for the design of adaptive force and position controllers for robot manipulators within the hybrid control architecuture is presented. The force controller is composed of an adaptive PID feedback controller, an auxiliary signal and a force feedforward term, and it achieves tracking of desired force setpoints in the constraint directions. The position controller consists of adaptive feedback and feedforward controllers and an auxiliary signal, and it accomplishes tracking of desired position trajectories in the free directions. The controllers are capable of compensating for dynamic cross-couplings that exist between the position and force control loops in the hybrid control architecture. The adaptive controllers do not require knowledge of the complex dynamic model or parameter values of the manipulator or the environment. The proposed control schemes are computationally fast and suitable for implementation in on-line control with high sampling rates.

  18. Model Reduction of Hybrid Systems

    DEFF Research Database (Denmark)

    Shaker, Hamid Reza

    gramians. Generalized gramians are the solutions to the observability and controllability Lyapunov inequalities. In the first framework the projection matrices are found based on the common generalized gramians. This framework preserves the stability of the original switched system for all switching...... is guaranteed to be preserved for arbitrary switching signal. To compute the common generalized gramians linear matrix inequalities (LMI’s) need to be solved. These LMI’s are not always feasible. In order to solve the problem of conservatism, the second framework is presented. In this method the projection......High-Technological solutions of today are characterized by complex dynamical models. A lot of these models have inherent hybrid/switching structure. Hybrid/switched systems are powerful models for distributed embedded systems design where discrete controls are applied to continuous processes...

  19. Hybrid inflation exit through tunneling

    International Nuclear Information System (INIS)

    Garbrecht, Bjoern; Konstandin, Thomas

    2007-01-01

    For hybrid inflationary potentials, we derive the tunneling rate from field configurations along the flat direction towards the waterfall regime. This process competes with the classically rolling evolution of the scalar fields and needs to be strongly subdominant for phenomenologically viable models. Tunneling may exclude models with a mass scale below 10 12 GeV, but can be suppressed by small values of the coupling constants. We find that tunneling is negligible for those models, which do not require fine tuning in order to cancel radiative corrections, in particular for GUT-scale SUSY inflation. In contrast, electroweak scale hybrid inflation is not viable, unless the inflaton-waterfall field coupling is smaller than approximately 10 -11

  20. The fusion-fission hybrid

    International Nuclear Information System (INIS)

    Teller, E.

    1985-01-01

    As the history of the development of fusion energy shows, a sustained controlled fusion reaction is much more difficult to produce than rapid uncontrolled release of fusion energy. Currently, the ''magnetic bottle'' technique shows sufficient progress that it might applied for the commercial fuel production of /sup 233/U, suitable for use in fission reactors, by developing a fusion-fission hybrid. Such a device would consist of a fusion chamber core surrounded by a region containing cladded uranium pellets cooled by helium, with lithium salts also present to produce tritium to refuel the fusion process. Successful development of this hybrid might be possible within 10 y, and would provide both experience and funds for further development of controlled fusion energy

  1. Position list word aligned hybrid

    DEFF Research Database (Denmark)

    Deliege, Francois; Pedersen, Torben Bach

    2010-01-01

    Compressed bitmap indexes are increasingly used for efficiently querying very large and complex databases. The Word Aligned Hybrid (WAH) bitmap compression scheme is commonly recognized as the most efficient compression scheme in terms of CPU efficiency. However, WAH compressed bitmaps use a lot...... of storage space. This paper presents the Position List Word Aligned Hybrid (PLWAH) compression scheme that improves significantly over WAH compression by better utilizing the available bits and new CPU instructions. For typical bit distributions, PLWAH compressed bitmaps are often half the size of WAH...... bitmaps and, at the same time, offer an even better CPU efficiency. The results are verified by theoretical estimates and extensive experiments on large amounts of both synthetic and real-world data....

  2. Complex Hybrid Inflation and Baryogenesis

    OpenAIRE

    Delepine, David; Martinez, Carlos; Urena-Lopez, L. Arturo

    2006-01-01

    We propose a hybrid inflation model with a complex waterfall field which contains an interaction term that breaks the U(1) global symmetry associated to the waterfall field charge. We show that the asymmetric evolution of the real and imaginary parts of the complex field during the phase transition at the end of inflation translates into a charge asymmetry. The latter strongly depends on the vev of the waterfall field, which is well constrained by diverse cosmological observations.

  3. Complex Hybrid Inflation and Baryogenesis

    International Nuclear Information System (INIS)

    Delepine, David; Martinez, Carlos; Urena-Lopez, L. Arturo

    2007-01-01

    We propose a hybrid inflation model with a complex waterfall field which contains an interaction term that breaks the U(1) global symmetry associated with the waterfall field charge. We show that the asymmetric evolution of the real and imaginary parts of the complex field during the phase transition at the end of inflation translates into a charge asymmetry. The latter strongly depends on the vacuum expectation value of the waterfall field, which is well constrained by diverse cosmological observations

  4. Complex hybrid inflation and baryogenesis.

    Science.gov (United States)

    Delepine, David; Martínez, Carlos; Ureña-López, L Arturo

    2007-04-20

    We propose a hybrid inflation model with a complex waterfall field which contains an interaction term that breaks the U(1) global symmetry associated with the waterfall field charge. We show that the asymmetric evolution of the real and imaginary parts of the complex field during the phase transition at the end of inflation translates into a charge asymmetry. The latter strongly depends on the vacuum expectation value of the waterfall field, which is well constrained by diverse cosmological observations.

  5. Energy Efficient Hydraulic Hybrid Drives

    OpenAIRE

    Rydberg, Karl-Erik

    2009-01-01

    Energy efficiency of propulsion systems for cars, trucks and construction machineries has become one of the most important topics in today’s mobile system design, mainly because of increased fuel costs and new regulations about engine emissions, which is needed to save the environment. To meet the increased requirements on higher efficiency and better functionality, components and systems have been developed over the years. For the last ten years the development of hybrid systems can be divid...

  6. Photosystem Inspired Peptide Hybrid Catalysts

    Science.gov (United States)

    2017-06-07

    materials defined at the molecular level. We propose a novel way to make hybrid catalyst composed of inorganic nanomaterials and peptides. The...Distribution approved for public release. AF Office Of Scientific Research (AFOSR)/ IOA Arlington, Virginia 22203 Air Force Research Laboratory Air...ORGANIZATION NAME(S) AND ADDRESS(ES) SEOUL NATIONAL UNIVERSITY SNUR&DB FOUNDATION RESEARCH PARK CENTER SEOUL, 151742 KR 8. PERFORMING ORGANIZATION REPORT

  7. Active and Passive Hybrid Sensor

    Science.gov (United States)

    Carswell, James R.

    2010-01-01

    A hybrid ocean wind sensor (HOWS) can map ocean vector wind in low to hurricane-level winds, and non-precipitating and precipitating conditions. It can acquire active and passive measurements through a single aperture at two wavelengths, two polarizations, and multiple incidence angles. Its low profile, compact geometry, and low power consumption permits installation on air craft platforms, including high-altitude unmanned aerial vehicles (UAVs).

  8. Hybrid and hierarchical composite materials

    CERN Document Server

    Kim, Chang-Soo; Sano, Tomoko

    2015-01-01

    This book addresses a broad spectrum of areas in both hybrid materials and hierarchical composites, including recent development of processing technologies, structural designs, modern computer simulation techniques, and the relationships between the processing-structure-property-performance. Each topic is introduced at length with numerous  and detailed examples and over 150 illustrations.   In addition, the authors present a method of categorizing these materials, so that representative examples of all material classes are discussed.

  9. Hybrid Maritime Satellite Communication Antenna

    DEFF Research Database (Denmark)

    Smith, Thomas Gunst

    Hybrid antennas for a maritime satellite communication terminal with simultaneous operation at L- and Ka-band have been investigated. The frequency bands of interest are 1; 525:0 1; 660:5 MHz (RX+TX, RHCP), 19:7 20:2 (RX, LHCP) and 29:5 30:0 GHz (TX, RHCP), which are all part of the Inmarsat BGAN...

  10. Small Hybrid Solar Power System

    OpenAIRE

    Kane, El Hadj Malick; Larrain, Diego; Favrat, Daniel

    2001-01-01

    This paper introduces a novel of mini-hybrid solar power plant integrating a field of solar concentrators, two superposed Organic Rankine Cycles (ORC) and a (bio)Diesel engine. Turbines for the organic Rankine Cycles are hermetic scroll expander-generators. Sun tracking solar collectors are composed of rows of flat mirror bands (CEP) arranged in a plane, which focus the solar energy onto a collector tube similar to those used in SEGS plant in California. The wast...

  11. Small Hybrid Solar Power System

    OpenAIRE

    Kane, El Hadj Malick; Favrat, Daniel; Larrain, Diego; Allani, Yassine

    2003-01-01

    This paper introduces a novel of mini-hybrid solar power plant integrating a field of solar concentrators, two superposed Organic Rankine Cycles (ORC) and a (bio)Diesel engine. Turbines for the organic Rankine Cycles are hermetic scroll expander-generators. Sun tracking solar collectors are composed of rows of flat mirror bands (CEP) arranged in a plane, which focus the solar energy onto a collector tube similar to those used in SEGS plant in California. The waste heat from both...

  12. Hybrid dynamics for currency modeling

    OpenAIRE

    Theodosopoulos, Ted; Trifunovic, Alex

    2006-01-01

    We present a simple hybrid dynamical model as a tool to investigate behavioral strategies based on trend following. The multiplicative symbolic dynamics are generated using a lognormal diffusion model for the at-the-money implied volatility term structure. Thus, are model exploits information from derivative markets to obtain qualititative properties of the return distribution for the underlier. We apply our model to the JPY-USD exchange rate and the corresponding 1mo., 3mo., 6mo. and 1yr. im...

  13. CERN manufactured hybrid photon detectors

    CERN Multimedia

    Maximilien Brice

    2004-01-01

    These hybrid photon detectors (HPDs) produce an electric signal from a single photon. An electron is liberated from a photocathode and accelerated to a silicon pixel array allowing the location of the photon on the cathode to be recorded. The electronics and optics for these devices have been developed in close collaboration with industry. HPDs have potential for further use in astrophysics and medical imaging.

  14. The plus-hybrid effect on the grain yield of two ZP maize hybrids

    Directory of Open Access Journals (Sweden)

    Božinović Sofija

    2010-01-01

    Full Text Available The combined effect of cytoplasmic male sterility and xenia on maize hybrid traits is referred to as the plus-hybrid effect. Two studied ZP hybrids differently responded to this effect for grain yield. All plus-hybrid combinations of the firstly observed hybrid had a higher yield than their fertile counterparts, but not significantly, while only one combination of the second hybrid positively responded, also without statistical significance. It seems that the observed effect mostly depended on the genotype of the female component.

  15. Hybrid rail gun electromagnetic accelerators

    International Nuclear Information System (INIS)

    Chen, K.W.; Hachen, H.; Lee, A.; Legh, G.; Lin, T.; Mattay, S.; Wipf, S.

    1983-01-01

    Theoretical and experimental investigations on hybrid rail accelerators are presented. It is shown that the side surface areas and in some cases sabots of the projectile can be used to provide substantial amount of additional thrust. Moreover, it is shown that in most cases examined, external magnetic fields can be conveniently incorporated in the accelerator designs to supplement the rail-induced fields. Total thrusts in excess of 10 MN for kilogram-sized projectiles can in principle be established with driving currents of the order of 1 MA. No obvious stress limitations are foreseen. The percentages of thrust from external magnetic fields are sufficiently high that the use of which should be encouraged. The increased flexibility in the projectile shapes available permits the use of the proposed hybrid electromagnetic launcher technology in a variety of new areas, such as thrust boosts in conventional chemical rockets and other similar applications. Furthermore, the additional thrust obtained from the use of side surface areas greatly increases the maximum permissable thrust otherwise limited by material strength considerations. Thrust analyses for projectiles in several hybrid rail accelerator designs are discussed. Some laboratory experimental observations are presented

  16. Gravity localization on hybrid branes

    Directory of Open Access Journals (Sweden)

    D.F.S. Veras

    2016-03-01

    Full Text Available This work deals with gravity localization on codimension-1 brane worlds engendered by compacton-like kinks, the so-called hybrid branes. In such scenarios, the thin brane behavior is manifested when the extra dimension is outside the compact domain, where the energy density is non-trivial, instead of asymptotically as in the usual thick brane models. The zero mode is trapped in the brane, as required. The massive modes, although not localized in the brane, have important phenomenological implications such as corrections to the Newton's law. We study such corrections in the usual thick domain wall and in the hybrid brane scenarios. By means of suitable numerical methods, we attain the mass spectrum for the graviton and the corresponding wavefunctions. The spectra possess the usual linearly increasing behavior from the Kaluza–Klein theories. Further, we show that the 4D gravitational force is slightly increased at short distances. The first eigenstate contributes highly for the correction to the Newton's law. The subsequent normalized solutions have diminishing contributions. Moreover, we find out that the phenomenology of the hybrid brane is not different from the usual thick domain wall. The use of numerical techniques for solving the equations of the massive modes is useful for matching possible phenomenological measurements in the gravitational law as a probe to warped extra dimensions.

  17. The conference hybrid control room

    International Nuclear Information System (INIS)

    Gieci, A.; Caucik, J.; Macko, J.

    2008-01-01

    An original concept of a hybrid control room was developed for the Mochovce-3 and Mochovce-4 reactor units which are under construction. The basic idea underlying the concept is that the control room should be a main working place for the operators (reactor operator and turbine operator) and for the shift supervisor, designed as a comprehensive unit desk shaped so that all members of the control room crew are in a face-to-face contact constantly. The main desk consists of three clearly identified areas serving the operators and the unit supervisor as their main working places. A soft control system is installed at the main working places. A separate safety-related working place, designed as a panel with classical instrumentations at the conference hybrid control room, is provided in case of abnormal conditions or emergency situation. Principles of ergonomics and cognitive engineering were taken into account when designing the new conference hybrid control room for the Mochovce-3 and -4 reactor units. The sizes, propositions, shapes and disposition of the equipment at the control room have been created and verified by using virtual reality tools. (orig.)

  18. The future of hybrid vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Vangraefschepe, F.; Menegazzi, P.

    2004-12-15

    This new demand from the U.S. market is being taken very seriously by key players in the field. GM and Daimler Chrysler have announced an alliance for the joint development of a hybrid vehicle scheduled to reach the market by 2007. Development projects of this type will require capital investment of several hundred million dollars over the period. Given that it is now imperative to cut greenhouse gas emissions, the hybrid vehicle offers a credible alternative. It is already on the market, despite the constraints inherent to a configuration combining an electric motor and an internal combustion engine, and despite the added cost. The technical choices are complex and varied, depending on the objectives: potential CO{sub 2} emissions gains range from a few percentage points to over 45%, depending on the engine/motor architecture. The gasoline hybrid vehicle is emerging as an alternative to the diesel engine, especially in Japan and the United States, but its growth will depend on the ability of the motor industry to reduce the added cost.

  19. Hybrid metric-Palatini stars

    Science.gov (United States)

    Danilǎ, Bogdan; Harko, Tiberiu; Lobo, Francisco S. N.; Mak, M. K.

    2017-02-01

    We consider the internal structure and the physical properties of specific classes of neutron, quark and Bose-Einstein condensate stars in the recently proposed hybrid metric-Palatini gravity theory, which is a combination of the metric and Palatini f (R ) formalisms. It turns out that the theory is very successful in accounting for the observed phenomenology, since it unifies local constraints at the Solar System level and the late-time cosmic acceleration, even if the scalar field is very light. In this paper, we derive the equilibrium equations for a spherically symmetric configuration (mass continuity and Tolman-Oppenheimer-Volkoff) in the framework of the scalar-tensor representation of the hybrid metric-Palatini theory, and we investigate their solutions numerically for different equations of state of neutron and quark matter, by adopting for the scalar field potential a Higgs-type form. It turns out that the scalar-tensor definition of the potential can be represented as an Clairaut differential equation, and provides an explicit form for f (R ) given by f (R )˜R +Λeff, where Λeff is an effective cosmological constant. Furthermore, stellar models, described by the stiff fluid, radiation-like, bag model and the Bose-Einstein condensate equations of state are explicitly constructed in both general relativity and hybrid metric-Palatini gravity, thus allowing an in-depth comparison between the predictions of these two gravitational theories. As a general result it turns out that for all the considered equations of state, hybrid gravity stars are more massive than their general relativistic counterparts. Furthermore, two classes of stellar models corresponding to two particular choices of the functional form of the scalar field (constant value, and logarithmic form, respectively) are also investigated. Interestingly enough, in the case of a constant scalar field the equation of state of the matter takes the form of the bag model equation of state describing

  20. Hybrid cryptosystem RSA - CRT optimization and VMPC

    Science.gov (United States)

    Rahmadani, R.; Mawengkang, H.; Sutarman

    2018-03-01

    Hybrid cryptosystem combines symmetric algorithms and asymmetric algorithms. This combination utilizes speeds on encryption/decryption processes of symmetric algorithms and asymmetric algorithms to secure symmetric keys. In this paper we propose hybrid cryptosystem that combine symmetric algorithms VMPC and asymmetric algorithms RSA - CRT optimization. RSA - CRT optimization speeds up the decryption process by obtaining plaintext with dp and p key only, so there is no need to perform CRT processes. The VMPC algorithm is more efficient in software implementation and reduces known weaknesses in RC4 key generation. The results show hybrid cryptosystem RSA - CRT optimization and VMPC is faster than hybrid cryptosystem RSA - VMPC and hybrid cryptosystem RSA - CRT - VMPC. Keyword : Cryptography, RSA, RSA - CRT, VMPC, Hybrid Cryptosystem.

  1. Parametric systems analysis for ICF hybrid reactors

    International Nuclear Information System (INIS)

    Berwald, D.H.; Maniscalco, J.A.; Chapin, D.L.

    1981-01-01

    Parametric design and systems analysis for inertial confinement fusion-fission hybrids are presented. These results were generated as part of the Electric Power Research Institute (EPRI) sponsored Feasibility Assessment of Fusion-Fission Hybrids, using an Inertial Confinement Fusion (ICF) hybrid power plant design code developed in conjunction with the feasibility assessment. The SYMECON systems analysis code, developed by Westinghouse, was used to generate economic results for symbiotic electricity generation systems consisting of the hybrid and its client Light Water Reactors (LWRs). These results explore the entire fusion parameter space for uranium fast fission blanket hybrids, thorium fast fission blanket hybrids, and thorium suppressed fission blanket types are discussed, and system sensitivities to design uncertainties are explored

  2. Hybrid soft computing approaches research and applications

    CERN Document Server

    Dutta, Paramartha; Chakraborty, Susanta

    2016-01-01

    The book provides a platform for dealing with the flaws and failings of the soft computing paradigm through different manifestations. The different chapters highlight the necessity of the hybrid soft computing methodology in general with emphasis on several application perspectives in particular. Typical examples include (a) Study of Economic Load Dispatch by Various Hybrid Optimization Techniques, (b) An Application of Color Magnetic Resonance Brain Image Segmentation by ParaOptiMUSIG activation Function, (c) Hybrid Rough-PSO Approach in Remote Sensing Imagery Analysis,  (d) A Study and Analysis of Hybrid Intelligent Techniques for Breast Cancer Detection using Breast Thermograms, and (e) Hybridization of 2D-3D Images for Human Face Recognition. The elaborate findings of the chapters enhance the exhibition of the hybrid soft computing paradigm in the field of intelligent computing.

  3. Molecular aspects in inflammatory events of temporomandibular joint: Microarray-based identification of mediators

    Directory of Open Access Journals (Sweden)

    Naomi Ogura

    2015-02-01

    Full Text Available Synovial inflammation (synovitis frequently accompanies intracapsular pathologic conditions of the temporomandibular joint (TMJ such as internal derangement (ID and/or osteoarthritis (OA, and is suggested to be associated with symptom severity. To identify the putative factors associated with synovitis, we investigated interleukin (IL-1β- and/or tumor necrosis factor (TNF-α-responsive genes of fibroblast-like synoviocytes (FLS from patients with ID and/or OA of TMJ using microarray analysis. In this review, we first summarize the FLS of TMJ and the signaling pathways of IL-1β and TNF-α. Next, we show the up-regulated genes in FLS after stimulation with IL-1β or TNF-α, and summarize the gene functions based on recent studies. Among the top 10 up-regulated factors, molecules such as IL-6 and cycrooxygense-2 have been well characterized and investigated in the inflammatory responses and tissue destruction associated with joint diseases such as RA and OA, but the roles of some molecules remain unclear. The FLS reaction can lead to the synthesis and release of a wide variety of inflammatory mediators. Some of these mediators are detected in joint tissues and synovial fluids under intracapsular pathologic conditions, and may represent potential targets for therapeutic interventions in ID and/or OA of TMJ.

  4. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Science.gov (United States)

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis

    NARCIS (Netherlands)

    Dols, J.A.M.; Smit, P.W.; Kort, R.; Reid, G.; Schuren, F.H.J.; Tempelman, H.; Bontekoe, T.R.; Korporaal, H.; Boon, M.E.

    2011-01-01

    Objective: The objective was to examine the use of a tailor-made DNA microarray containing probes representing the vaginal microbiota to examine bacterial vaginosis. Study Design: One hundred one women attending a health center for HIV testing in South Africa were enrolled. Stained, liquid-based

  6. Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis

    NARCIS (Netherlands)

    Dols, Joke A M; Smit, Pieter W; Kort, Remco; Reid, Gregor; Schuren, Frank H J; Tempelman, Hugo; Bontekoe, Tj Romke; Korporaal, Hans; Boon, Mathilde E

    OBJECTIVE: The objective was to examine the use of a tailor-made DNA microarray containing probes representing the vaginal microbiota to examine bacterial vaginosis. STUDY DESIGN: One hundred one women attending a health center for HIV testing in South Africa were enrolled. Stained, liquid-based

  7. Microarray-based IgE detection in tears of patients with vernal keratoconjunctivitis.

    Science.gov (United States)

    Leonardi, Andrea; Borghesan, Franco; Faggian, Diego; Plebani, Mario

    2015-11-01

    A specific allergen sensitization can be demonstrated in approximately half of the vernal keratoconjunctivitis (VKC) patients by conventional allergic tests. The measurement of specific IgE in tears using a multiplex allergen microarray may offer advantages to identify local sensitization to a specific allergen. In spring-summer 2011, serum and tears samples were collected from 10 active VKC patients (three females, seven males) and 10 age-matched normal subjects. Skin prick test, symptoms score and full ophthalmological examination were performed. Specific serum and tear IgE were assayed using ImmunoCAP ISAC, a microarray containing 103 components derived from 47 allergens. Normal subjects resulted negative for the presence of specific IgE both in serum and in tears. Of the 10 VKC patients, six resulted positive to specific IgE in serum and/or tears. In three of these six patients, specific IgE was found positive only in tears. Cross-reactivity between specific markers was found in three patients. Grass, tree, mites, animal but also food allergen-specific IgE were found in tears. Conjunctival provocation test performed out of season confirmed the specific local conjunctival reactivity. Multiple specific IgE measurements with single protein allergens using a microarray technique in tear samples are a useful, simple and non-invasive diagnostic tool. ImmunoCAP ISAC detects allergen sensitization at component level and adds important information by defining both cross- and co-sensitization to a large variety of allergen molecules. The presence of specific IgE only in tears of VKC patients reinforces the concept of possible local sensitization. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. The Influence of Single Nucleotide Polymorphism Microarray-Based Molecular Karyotype on Preimplantation Embryonic Development Potential.

    Directory of Open Access Journals (Sweden)

    Gang Li

    Full Text Available In order to investigate the influence of the molecular karyotype based on single nucleotide polymorphism (SNP microarray on embryonic development potential in preimplantation genetic diagnosis (PGD, we retrospectively analyzed the clinical data generated by PGD using embryos retrieved from parents with chromosome rearrangements in our center. In total, 929 embryos from 119 couples had exact diagnosis and development status. The blastocyst formation rate of balanced molecular karyotype embryos was 56.6% (276/488, which was significantly higher than that of genetic imbalanced embryos 24.5% (108/441 (P35 respectively. Blastocyst formation rates of male and female embryos were 44.5% (183/411 and 38.8% (201/518 respectively, with no significant difference between them (P>0.05. The rates of balanced molecular karyotype embryos vary from groups of embryos with different cell numbers at 68 hours after insemination. The blastocyst formation rate of embryos with 6-8 cells (48.1% was significantly higher than that of embryos with 8 cells (42.9% (P8 cells, embryos with 6-8 blastomeres have higher rate of balanced molecular karyotype and blastocyst formation.

  9. Microarray-based classification of diffuse large B-cell lymphoma

    DEFF Research Database (Denmark)

    Poulsen, Christian Bjørn; Borup, Rehannah; Nielsen, Finn Cilius

    2005-01-01

    on the Affymetrix HG-U133A oligonucleotide arrays and improve the classification, we determined the expression profiles of pretreatment, diagnostic samples from 52 primary nodal DLBCL. METHODS AND RESULTS: First, three previously published gene lists were converted to the HG-U133A probe sets and used......OBJECTIVE: Hierarchical clusterings of diffuse large B-cell lymphoma (DLBCL) based on gene expression signatures have previously been used to classify DLBCL into Germinal Center B-cell (GCB) and Activated B-cell (ABC) types. To examine if it was feasible to perform a cross-platform validation...... for hierarchical clustering. In this way, three subtypes, including the GCB type (n = 20), the ABC type (n = 25) and an intermediate group, Type-3 (n = 5), were distinguished. The CD10 and Bcl-6 expression as well as t(14;18) translocation were prevalent, but not exclusive to the GCB type. By contrast, MUM1...

  10. Microarray-Based Gene Expression Profiling to Elucidate Effectiveness of Fermented Codonopsis lanceolata in Mice

    Directory of Open Access Journals (Sweden)

    Woon Yong Choi

    2014-04-01

    Full Text Available In this study, the effect of Codonopsis lanceolata fermented by lactic acid on controlling gene expression levels related to obesity was observed in an oligonucleotide chip microarray. Among 8170 genes, 393 genes were up regulated and 760 genes were down regulated in feeding the fermented C. lanceolata (FCL. Another 374 genes were up regulated and 527 genes down regulated without feeding the sample. The genes were not affected by the FCL sample. It was interesting that among those genes, Chytochrome P450, Dmbt1, LOC76487, and thyroid hormones, etc., were mostly up or down regulated. These genes are more related to lipid synthesis. We could conclude that the FCL possibly controlled the gene expression levels related to lipid synthesis, which resulted in reducing obesity. However, more detailed protein expression experiments should be carried out.

  11. Microarray-Based Gene Expression Analysis for Veterinary Pathologists: A Review.

    Science.gov (United States)

    Raddatz, Barbara B; Spitzbarth, Ingo; Matheis, Katja A; Kalkuhl, Arno; Deschl, Ulrich; Baumgärtner, Wolfgang; Ulrich, Reiner

    2017-09-01

    High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms. The scientific literature concerning high-throughput data-mining techniques usually addresses mathematicians or computer scientists as the target audience. In contrast, the present review provides the reader with a clear and systematic basis from a veterinary pathologist's perspective. Therefore, the aims are (1) to introduce the reader to the necessary methodological background; (2) to introduce the sequential steps commonly performed in a microarray analysis including quality control, annotation, normalization, selection of differentially expressed genes, clustering, gene ontology and pathway analysis, analysis of manually selected genes, and biomarker discovery; and (3) to provide references to publically available and user-friendly software suites. In summary, the data analysis methods presented within this review will enable veterinary pathologists to analyze high-throughput transcriptome data obtained from their own experiments, supplemental data that accompany scientific publications, or public repositories in order to obtain a more in-depth insight into underlying disease mechanisms.

  12. Biosensing enhancement using passive mixing structures for microarray-based sensors

    Czech Academy of Sciences Publication Activity Database

    Lynn, Nicholas Scott; Martínez-López, J.I.; Bocková, Markéta; Adam, Pavel; Coello, V.; Siller, R.H.; Homola, Jiří

    2014-01-01

    Roč. 54, 15 April (2014), s. 506-514 ISSN 0956-5663 R&D Projects: GA ČR GBP205/12/G118 Institutional support: RVO:67985882 Keywords : Microfluidic mixing * Biosensors * Microfluidics Subject RIV: BO - Biophysics Impact factor: 6.409, year: 2014

  13. Missing value imputation in DNA microarrays based on conjugate gradient method.

    Science.gov (United States)

    Dorri, Fatemeh; Azmi, Paeiz; Dorri, Faezeh

    2012-02-01

    Analysis of gene expression profiles needs a complete matrix of gene array values; consequently, imputation methods have been suggested. In this paper, an algorithm that is based on conjugate gradient (CG) method is proposed to estimate missing values. k-nearest neighbors of the missed entry are first selected based on absolute values of their Pearson correlation coefficient. Then a subset of genes among the k-nearest neighbors is labeled as the best similar ones. CG algorithm with this subset as its input is then used to estimate the missing values. Our proposed CG based algorithm (CGimpute) is evaluated on different data sets. The results are compared with sequential local least squares (SLLSimpute), Bayesian principle component analysis (BPCAimpute), local least squares imputation (LLSimpute), iterated local least squares imputation (ILLSimpute) and adaptive k-nearest neighbors imputation (KNNKimpute) methods. The average of normalized root mean squares error (NRMSE) and relative NRMSE in different data sets with various missing rates shows CGimpute outperforms other methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Microarray-based screening of differentially expressed genes in glucocorticoid-induced avascular necrosis

    Science.gov (United States)

    Huang, Gangyong; Wei, Yibing; Zhao, Guanglei; Xia, Jun; Wang, Siqun; Wu, Jianguo; Chen, Feiyan; Chen, Jie; Shi, Jingshen

    2017-01-01

    The underlying mechanisms of glucocorticoid (GC)-induced avascular necrosis of the femoral head (ANFH) have yet to be fully understood, in particular the mechanisms associated with the change of gene expression pattern. The present study aimed to identify key genes with a differential expression pattern in GC-induced ANFH. E-MEXP-2751 microarray data were downloaded from the ArrayExpress database. Differentially expressed genes (DEGs) were identified in 5 femoral head samples of steroid-induced ANFH rats compared with 5 placebo-treated rat samples. Gene Ontology (GO) and pathway enrichment analyses were performed upon these DEGs. A total 93 DEGs (46 upregulated and 47 downregulated genes) were identified in GC-induced ANFH samples. These DEGs were enriched in different GO terms and pathways, including chondrocyte differentiation and detection of chemical stimuli. The enrichment map revealed that skeletal system development was interconnected with several other GO terms by gene overlap. The literature mined network analysis revealed that 5 upregulated genes were associated with femoral necrosis, including parathyroid hormone receptor 1 (PTHR1), vitamin D (1,25-Dihydroxyvitamin D3) receptor (VDR), collagen, type II, α1, proprotein convertase subtilisin/kexin type 6 and zinc finger protein 354C (ZFP354C). In addition, ZFP354C and VDR were identified to transcription factors. Furthermore, PTHR1 was revealed to interact with VDR, and α-2-macroglobulin (A2M) interacted with fibronectin 1 (FN1) in the PPI network. PTHR1 may be involved in GC-induced ANFH via interacting with VDR. A2M may also be involved in the development of GC-induced ANFH through interacting with FN1. An improved understanding of the molecular mechanisms underlying GC-induced ANFH may provide novel targets for diagnostics and therapeutic treatment. PMID:28393228

  15. Improved microarray-based decision support with graph encoded interactome data.

    Directory of Open Access Journals (Sweden)

    Anneleen Daemen

    Full Text Available In the past, microarray studies have been criticized due to noise and the limited overlap between gene signatures. Prior biological knowledge should therefore be incorporated as side information in models based on gene expression data to improve the accuracy of diagnosis and prognosis in cancer. As prior knowledge, we investigated interaction and pathway information from the human interactome on different aspects of biological systems. By exploiting the properties of kernel methods, relations between genes with similar functions but active in alternative pathways could be incorporated in a support vector machine classifier based on spectral graph theory. Using 10 microarray data sets, we first reduced the number of data sources relevant for multiple cancer types and outcomes. Three sources on metabolic pathway information (KEGG, protein-protein interactions (OPHID and miRNA-gene targeting (microRNA.org outperformed the other sources with regard to the considered class of models. Both fixed and adaptive approaches were subsequently considered to combine the three corresponding classifiers. Averaging the predictions of these classifiers performed best and was significantly better than the model based on microarray data only. These results were confirmed on 6 validation microarray sets, with a significantly improved performance in 4 of them. Integrating interactome data thus improves classification of cancer outcome for the investigated microarray technologies and cancer types. Moreover, this strategy can be incorporated in any kernel method or non-linear version of a non-kernel method.

  16. Microarray-based transcriptomic analysis of differences between long-term gregarious and solitarious desert locusts.

    Directory of Open Access Journals (Sweden)

    Liesbeth Badisco

    Full Text Available Desert locusts (Schistocerca gregaria show an extreme form of phenotypic plasticity and can transform between a cryptic solitarious phase and a swarming gregarious phase. The two phases differ extensively in behavior, morphology and physiology but very little is known about the molecular basis of these differences. We used our recently generated Expressed Sequence Tag (EST database derived from S. gregaria central nervous system (CNS to design oligonucleotide microarrays and compare the expression of thousands of genes in the CNS of long-term gregarious and solitarious adult desert locusts. This identified 214 differentially expressed genes, of which 40% have been annotated to date. These include genes encoding proteins that are associated with CNS development and modeling, sensory perception, stress response and resistance, and fundamental cellular processes. Our microarray analysis has identified genes whose altered expression may enable locusts of either phase to deal with the different challenges they face. Genes for heat shock proteins and proteins which confer protection from infection were upregulated in gregarious locusts, which may allow them to respond to acute physiological challenges. By contrast the longer-lived solitarious locusts appear to be more strongly protected from the slowly accumulating effects of ageing by an upregulation of genes related to anti-oxidant systems, detoxification and anabolic renewal. Gregarious locusts also had a greater abundance of transcripts for proteins involved in sensory processing and in nervous system development and plasticity. Gregarious locusts live in a more complex sensory environment than solitarious locusts and may require a greater turnover of proteins involved in sensory transduction, and possibly greater neuronal plasticity.

  17. A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

    Directory of Open Access Journals (Sweden)

    Wang Lily

    2008-07-01

    Full Text Available Abstract Background Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deployment. Use of the most accurate classification algorithms available for microarray gene expression data is a critical ingredient in order to develop the best possible molecular signatures for patient care. As suggested by a large body of literature to date, support vector machines can be considered "best of class" algorithms for classification of such data. Recent work, however, suggests that random forest classifiers may outperform support vector machines in this domain. Results In the present paper we identify methodological biases of prior work comparing random forests and support vector machines and conduct a new rigorous evaluation of the two algorithms that corrects these limitations. Our experiments use 22 diagnostic and prognostic datasets and show that support vector machines outperform random forests, often by a large margin. Our data also underlines the importance of sound research design in benchmarking and comparison of bioinformatics algorithms. Conclusion We found that both on average and in the majority of microarray datasets, random forests are outperformed by support vector machines both in the settings when no gene selection is performed and when several popular gene selection methods are used.

  18. Introgressive hybridization as a promoter of genome reshuffling in natural homoploid fish hybrids (Cyprinidae, Leuciscinae)

    Czech Academy of Sciences Publication Activity Database

    Pereira, C. S.; Aboim, M. A.; Ráb, Petr; Collares-Pereira, M. J.

    2014-01-01

    Roč. 112, č. 3 (2014), s. 343-350 ISSN 0018-067X Institutional support: RVO:67985904 Keywords : comparative genome hybridization * hybrid zones * introgression Subject RIV: EG - Zoology Impact factor: 3.805, year: 2014

  19. Plug-In Hybrid Electric Vehicle Basics | NREL

    Science.gov (United States)

    Plug-In Hybrid Electric Vehicle Basics Plug-In Hybrid Electric Vehicle Basics Imagine being able to one that's in a standard hybrid electric vehicle. The larger battery pack allows plug-in hybrids to between fill-ups) that's very similar to the range of a conventional vehicle. A plug-in hybrid vehicle's

  20. Parallel Hybrid Vehicle Optimal Storage System

    Science.gov (United States)

    Bloomfield, Aaron P.

    2009-01-01

    A paper reports the results of a Hybrid Diesel Vehicle Project focused on a parallel hybrid configuration suitable for diesel-powered, medium-sized, commercial vehicles commonly used for parcel delivery and shuttle buses, as the missions of these types of vehicles require frequent stops. During these stops, electric hybridization can effectively recover the vehicle's kinetic energy during the deceleration, store it onboard, and then use that energy to assist in the subsequent acceleration.

  1. Cosmological dynamics of a hybrid chameleon scenario

    OpenAIRE

    Nozari, Kourosh; Rashidi, N.

    2013-01-01

    We consider a hybrid scalar field which is non-minimally coupled to the matter and models a chameleon cosmology. By introducing an effective potential, we study the dependence of the effective potential's minimum and hybrid chameleon field's masses to the local matter density. In a dynamical system technique, we analyze the phase space of this two-field chameleon model, find its fixed points and study their stability. We show that the hybrid chameleon domination solution is a stable attractor...

  2. Genomic Prediction of Barley Hybrid Performance

    Directory of Open Access Journals (Sweden)

    Norman Philipp

    2016-07-01

    Full Text Available Hybrid breeding in barley ( L. offers great opportunities to accelerate the rate of genetic improvement and to boost yield stability. A crucial requirement consists of the efficient selection of superior hybrid combinations. We used comprehensive phenotypic and genomic data from a commercial breeding program with the goal of examining the potential to predict the hybrid performances. The phenotypic data were comprised of replicated grain yield trials for 385 two-way and 408 three-way hybrids evaluated in up to 47 environments. The parental lines were genotyped using a 3k single nucleotide polymorphism (SNP array based on an Illumina Infinium assay. We implemented ridge regression best linear unbiased prediction modeling for additive and dominance effects and evaluated the prediction ability using five-fold cross validations. The prediction ability of hybrid performances based on general combining ability (GCA effects was moderate, amounting to 0.56 and 0.48 for two- and three-way hybrids, respectively. The potential of GCA-based hybrid prediction requires that both parental components have been evaluated in a hybrid background. This is not necessary for genomic prediction for which we also observed moderate cross-validated prediction abilities of 0.51 and 0.58 for two- and three-way hybrids, respectively. This exemplifies the potential of genomic prediction in hybrid barley. Interestingly, prediction ability using the two-way hybrids as training population and the three-way hybrids as test population or vice versa was low, presumably, because of the different genetic makeup of the parental source populations. Consequently, further research is needed to optimize genomic prediction approaches combining different source populations in barley.

  3. Deep electroproduction of exotic hybrid mesons

    International Nuclear Information System (INIS)

    Anikin, I.V.; Pire, B.; Szymanowski, L.; Teryaev, O.V.; Wallon, S.

    2004-01-01

    We evaluate the leading order amplitude for the deep exclusive electroproduction of an exotic hybrid meson in the Bjorken regime. We show that, contrarily to naive expectation, this amplitude factorizes at the twist 2 level and thus scales like usual meson electroproduction when the virtual photon and the hybrid meson are longitudinally polarized. Exotic hybrid mesons may thus be studied in electroproduction experiments at JLAB, HERA (HERMES) or CERN (Compass)

  4. Frontier battery development for hybrid vehicles

    OpenAIRE

    Lewis, Heather; Park, Haram; Paolini, Maion

    2012-01-01

    Abstract Background Interest in hybrid-electric vehicles (HEVs) has recently spiked, partly due to an increasingly negative view toward the U.S. foreign oil dependency and environmental concerns. Though HEVs are becoming more common, they have a significant price premium over gasoline-powered vehicles. One of the primary drivers of this “hybrid premium” is the cost of the vehicles’ batteries. This paper focuses on these batteries used in hybrid vehicles, examines the types of batteries used f...

  5. Hybrid Reactor designs in the United States

    International Nuclear Information System (INIS)

    Wolkenhauer, W.C.

    1978-01-01

    This paper reviews the current, active, interrelated Hybrid Reactor development programs in the United States, and offers a probable future course of action for the technology. The Department of Energy (DOE) program primarily emphasizes development of Hybrid Reactors that are optimized for proliferation resistance. The Electric Power Research Institute (EPRI) program concentrates on avenues for Hybrid Reactor commercialization. The history of electrical generation technology has been one of steady movement toward higher power densities and higher quality fuels. An apparent advantage of the Hybrid Reactor option is that it follows this trend

  6. Prospects for Hybrid Breeding in Bioenergy Grasses

    DEFF Research Database (Denmark)

    Aguirre, Andrea Arias; Studer, Bruno; Frei, Ursula

    2012-01-01

    , we address crucial topics to implement hybrid breeding, such as the availability and development of heterotic groups, as well as biological mechanisms for hybridization control such as self-incompatibility (SI) and male sterility (MS). Finally, we present potential hybrid breeding schemes based on SI...... of different hybrid breeding schemes to optimally exploit heterosis for biomass yield in perennial ryegrass (Lolium perenne L.) and switchgrass (Panicum virgatum), two perennial model grass species for bioenergy production. Starting with a careful evaluation of current population and synthetic breeding methods...

  7. Current status of hybrid coronary revascularization.

    Science.gov (United States)

    Jaik, Nikhil P; Umakanthan, Ramanan; Leacche, Marzia; Solenkova, Natalia; Balaguer, Jorge M; Hoff, Steven J; Ball, Stephen K; Zhao, David X; Byrne, John G

    2011-10-01

    Hybrid coronary revascularization combines coronary artery bypass surgery with percutaneous coronary intervention techniques to treat coronary artery disease. The potential benefits of such a technique are to offer the patients the best available treatments for coronary artery disease while minimizing the risks of the surgery. Hybrid coronary revascularization has resulted in the establishment of new 'hybrid operating suites', which incorporate and integrate the capabilities of a cardiac surgery operating room with that of an interventional cardiology laboratory. Hybrid coronary revascularization has greatly augmented teamwork and cooperation between both fields and has demonstrated encouraging as well as good initial outcomes.

  8. New hybrid systems: strategy and research programs

    International Nuclear Information System (INIS)

    Thomas, J.B.

    2001-01-01

    This short article gives a status of research and experimental programs concerning new hybrid systems. A hybrid system is made up of a subcritical core, a spallation target and of a particle accelerator that delivers a proton beam. The main asset of hybrid systems is to provide a large reactivity margin that would be very valuable to transmute actinide nuclei efficiently. As a consequence hybrid systems could be considered as actinide burner reactors integrated to a large population of classical nuclear reactors dedicated to electricity production. (A.C.)

  9. Techno-economic comparison of series hybrid, plug-in hybrid, fuel cell and regular cars

    NARCIS (Netherlands)

    van Vliet, O.P.R.|info:eu-repo/dai/nl/288519361; Kruithof, T.; Turkenburg, W.C.|info:eu-repo/dai/nl/073416355; Faaij, A.P.C.|info:eu-repo/dai/nl/10685903X

    2010-01-01

    We examine the competitiveness of series hybrid compared to fuel cell, parallel hybrid, and regular cars. We use public domain data to determine efficiency, fuel consumption, total costs of ownership and greenhouse gas emissions resulting from drivetrain choices. The series hybrid drivetrain can be

  10. Hybrid Qualifications Country report Denmark

    DEFF Research Database (Denmark)

    Jørgensen, Christian Helms

    2010-01-01

    The report explores the institutional and functional relations between the higher education (tertiary sector) and vocational education (higher secondary education) and the labour market. In the report are included descriptions of the history, funding, outcomes, institutional realisation and term ...... and range of hybrid qualifications in the national system. In addition some recommendations for constructive further developments are given.......The report explores the institutional and functional relations between the higher education (tertiary sector) and vocational education (higher secondary education) and the labour market. In the report are included descriptions of the history, funding, outcomes, institutional realisation and term...

  11. Hybrid Model of Content Extraction

    DEFF Research Database (Denmark)

    Qureshi, Pir Abdul Rasool; Memon, Nasrullah

    2012-01-01

    We present a hybrid model for content extraction from HTML documents. The model operates on Document Object Model (DOM) tree of the corresponding HTML document. It evaluates each tree node and associated statistical features like link density and text distribution across the node to predict...... significance of the node towards overall content provided by the document. Once significance of the nodes is determined, the formatting characteristics like fonts, styles and the position of the nodes are evaluated to identify the nodes with similar formatting as compared to the significant nodes. The proposed...

  12. Hybrid Chernoff Tau-Leap

    KAUST Repository

    Moraes, Alvaro

    2016-01-06

    Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

  13. Hybrid Chernoff Tau-Leap

    KAUST Repository

    Moraes, Alvaro

    2015-01-07

    Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

  14. Hybrid Chernoff Tau-Leap

    KAUST Repository

    Moraes, Alvaro

    2014-01-06

    Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

  15. An introduction to hybrid fusion

    International Nuclear Information System (INIS)

    Reynolds, J.A.

    1982-01-01

    This report gives a brief introduction to some hybrid fusion proposals. The idea is to take advantage of the high neutron energy in fusion compared to fission either to breed fuel more efficiently than in a fast reactor, or increase the power output by fission of U 238 or transmute radioactive waste. The penalty is an increased cost and complexity of the blanket and the loss of environmental and safety arguments for fusion systems which rest on their low inventory of radioactive materials. (author)

  16. Hybrid-Source Impedance Networks

    DEFF Research Database (Denmark)

    Li, Ding; Gao, Feng; Loh, Poh Chiang

    2010-01-01

    Hybrid-source impedance networks have attracted attention among researchers because of their flexibility in performing buck-boost energy conversion. To date, three distinct types of impedance networks can be summarized for implementing voltage-type inverters with another three types summarized...... for current-type inverters. These impedance networks can in principle be combined into two generic network entities, before multiple of them can further be connected together by applying any of the two proposed generalized cascading concepts. The resulting two-level and three-level inverters implemented using...

  17. Hydrostatic and hybrid bearing design

    CERN Document Server

    Rowe, W B

    1983-01-01

    Hydrostatic and Hybrid Bearing Design is a 15-chapter book that focuses on the bearing design and testing. This book first describes the application of hydrostatic bearings, as well as the device pressure, flow, force, power, and temperature. Subsequent chapters discuss the load and flow rate of thrust pads; circuit design, flow control, load, and stiffness; and the basis of the design procedures and selection of tolerances. The specific types of bearings, their design, dynamics, and experimental methods and testing are also shown. This book will be very valuable to students of engineering des

  18. IMPULSE CONTROL HYBRID ELECTRICAL SYSTEM

    Directory of Open Access Journals (Sweden)

    A. A. Lobaty

    2016-01-01

    Full Text Available This paper extends the recently introduced approach for modeling and solving the optimal control problem of fixedswitched mode DC-DC power converter. DCDC converters are a class of electric power circuits that used extensively in regulated DC power supplies, DC motor drives of different types, in Photovoltaic Station energy conversion and other applications due to its advantageous features in terms of size, weight and reliable performance. The main problem in controlling this type converters is in their hybrid nature as the switched circuit topology entails different modes of operation, each of it with its own associated linear continuous-time dynamics.This paper analyses the modeling and controller synthesis of the fixed-frequency buck DC-DC converter, in which the transistor switch is operated by a pulse sequence with constant frequency. In this case the regulation of the DC component of the output voltage is via the duty cycle. The optimization of the control system is based on the formation of the control signal at the output.It is proposed to solve the problem of optimal control of a hybrid system based on the formation of the control signal at the output of the controller, which minimizes a given functional integral quality, which is regarded as a linear quadratic Letov-Kalman functional. Search method of optimal control depends on the type of mathematical model of control object. In this case, we consider a linear deterministic model of the control system, which is common for the majority of hybrid electrical systems. For this formulation of the optimal control problem of search is a problem of analytical design of optimal controller, which has the analytical solution.As an example of the hybrid system is considered a step-down switching DC-DC converter, which is widely used in various electrical systems: as an uninterruptible power supply, battery charger for electric vehicles, the inverter in solar photovoltaic power plants.. A

  19. Coordinated hybrid automatic repeat request

    KAUST Repository

    Makki, Behrooz

    2014-11-01

    We develop a coordinated hybrid automatic repeat request (HARQ) approach. With the proposed scheme, if a user message is correctly decoded in the first HARQ rounds, its spectrum is allocated to other users, to improve the network outage probability and the users\\' fairness. The results, which are obtained for single- and multiple-antenna setups, demonstrate the efficiency of the proposed approach in different conditions. For instance, with a maximum of M retransmissions and single transmit/receive antennas, the diversity gain of a user increases from M to (J+1)(M-1)+1 where J is the number of users helping that user.

  20. Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization.

    Science.gov (United States)

    Warren, Kerryn A; Ritzman, Terrence B; Humphreys, Robyn A; Percival, Christopher J; Hallgrímsson, Benedikt; Ackermann, Rebecca Rogers

    2018-03-01

    Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F 1 ) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F 1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F 1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Hybrid system power generation'wind-photovoltaic' connected to the ...

    African Journals Online (AJOL)

    Hybrid system power generation'wind-photovoltaic' connected to the ... from Hybrid System, power delivered to or from grid and phase voltage of the inverter leg. ... Renewable Energy, Electrical Network 220 kV, Hybrid System, Solar, MPPT.

  2. Quantum technologies with hybrid systems

    Science.gov (United States)

    Kurizki, Gershon; Bertet, Patrice; Kubo, Yuimaru; Mølmer, Klaus; Petrosyan, David; Rabl, Peter; Schmiedmayer, Jörg

    2015-03-01

    An extensively pursued current direction of research in physics aims at the development of practical technologies that exploit the effects of quantum mechanics. As part of this ongoing effort, devices for quantum information processing, secure communication, and high-precision sensing are being implemented with diverse systems, ranging from photons, atoms, and spins to mesoscopic superconducting and nanomechanical structures. Their physical properties make some of these systems better suited than others for specific tasks; thus, photons are well suited for transmitting quantum information, weakly interacting spins can serve as long-lived quantum memories, and superconducting elements can rapidly process information encoded in their quantum states. A central goal of the envisaged quantum technologies is to develop devices that can simultaneously perform several of these tasks, namely, reliably store, process, and transmit quantum information. Hybrid quantum systems composed of different physical components with complementary functionalities may provide precisely such multitasking capabilities. This article reviews some of the driving theoretical ideas and first experimental realizations of hybrid quantum systems and the opportunities and challenges they present and offers a glance at the near- and long-term perspectives of this fascinating and rapidly expanding field.

  3. Hybrid Thermochemical/Biological Processing

    Science.gov (United States)

    Brown, Robert C.

    The conventional view of biorefineries is that lignocellulosic plant material will be fractionated into cellulose, hemicellulose, lignin, and terpenes before these components are biochemically converted into market products. Occasionally, these plants include a thermochemical step at the end of the process to convert recalcitrant plant components or mixed waste streams into heat to meet thermal energy demands elsewhere in the facility. However, another possibility for converting high-fiber plant materials is to start by thermochemically processing it into a uniform intermediate product that can be biologically converted into a bio-based product. This alternative route to bio-based products is known as hybrid thermochemical/biological processing. There are two distinct approaches to hybrid processing: (a) gasification followed by fermentation of the resulting gaseous mixture of carbon monoxide (CO), hydrogen (H2), and carbon dioxide (CO2) and (b) fast pyrolysis followed by hydrolysis and/or fermentation of the anhydrosugars found in the resulting bio-oil. This article explores this "cart before the horse" approach to biorefineries.

  4. Evaporator modeling - A hybrid approach

    International Nuclear Information System (INIS)

    Ding Xudong; Cai Wenjian; Jia Lei; Wen Changyun

    2009-01-01

    In this paper, a hybrid modeling approach is proposed to model two-phase flow evaporators. The main procedures for hybrid modeling includes: (1) Based on the energy and material balance, and thermodynamic principles to formulate the process fundamental governing equations; (2) Select input/output (I/O) variables responsible to the system performance which can be measured and controlled; (3) Represent those variables existing in the original equations but are not measurable as simple functions of selected I/Os or constants; (4) Obtaining a single equation which can correlate system inputs and outputs; and (5) Identify unknown parameters by linear or nonlinear least-squares methods. The method takes advantages of both physical and empirical modeling approaches and can accurately predict performance in wide operating range and in real-time, which can significantly reduce the computational burden and increase the prediction accuracy. The model is verified with the experimental data taken from a testing system. The testing results show that the proposed model can predict accurately the performance of the real-time operating evaporator with the maximum error of ±8%. The developed models will have wide applications in operational optimization, performance assessment, fault detection and diagnosis

  5. Hybrid context aware recommender systems

    Science.gov (United States)

    Jain, Rajshree; Tyagi, Jaya; Singh, Sandeep Kumar; Alam, Taj

    2017-10-01

    Recommender systems and context awareness is currently a vital field of research. Most hybrid recommendation systems implement content based and collaborative filtering techniques whereas this work combines context and collaborative filtering. The paper presents a hybrid context aware recommender system for books and movies that gives recommendations based on the user context as well as user or item similarity. It also addresses the issue of dimensionality reduction using weighted pre filtering based on dynamically entered user context and preference of context. This unique step helps to reduce the size of dataset for collaborative filtering. Bias subtracted collaborative filtering is used so as to consider the relative rating of a particular user and not the absolute values. Cosine similarity is used as a metric to determine the similarity between users or items. The unknown ratings are calculated and evaluated using MSE (Mean Squared Error) in test and train datasets. The overall process of recommendation has helped to personalize recommendations and give more accurate results with reduced complexity in collaborative filtering.

  6. Quantum technologies with hybrid systems

    Science.gov (United States)

    Kurizki, Gershon; Bertet, Patrice; Kubo, Yuimaru; Mølmer, Klaus; Petrosyan, David; Rabl, Peter; Schmiedmayer, Jörg

    2015-01-01

    An extensively pursued current direction of research in physics aims at the development of practical technologies that exploit the effects of quantum mechanics. As part of this ongoing effort, devices for quantum information processing, secure communication, and high-precision sensing are being implemented with diverse systems, ranging from photons, atoms, and spins to mesoscopic superconducting and nanomechanical structures. Their physical properties make some of these systems better suited than others for specific tasks; thus, photons are well suited for transmitting quantum information, weakly interacting spins can serve as long-lived quantum memories, and superconducting elements can rapidly process information encoded in their quantum states. A central goal of the envisaged quantum technologies is to develop devices that can simultaneously perform several of these tasks, namely, reliably store, process, and transmit quantum information. Hybrid quantum systems composed of different physical components with complementary functionalities may provide precisely such multitasking capabilities. This article reviews some of the driving theoretical ideas and first experimental realizations of hybrid quantum systems and the opportunities and challenges they present and offers a glance at the near- and long-term perspectives of this fascinating and rapidly expanding field. PMID:25737558

  7. Quantum technologies with hybrid systems.

    Science.gov (United States)

    Kurizki, Gershon; Bertet, Patrice; Kubo, Yuimaru; Mølmer, Klaus; Petrosyan, David; Rabl, Peter; Schmiedmayer, Jörg

    2015-03-31

    An extensively pursued current direction of research in physics aims at the development of practical technologies that exploit the effects of quantum mechanics. As part of this ongoing effort, devices for quantum information processing, secure communication, and high-precision sensing are being implemented with diverse systems, ranging from photons, atoms, and spins to mesoscopic superconducting and nanomechanical structures. Their physical properties make some of these systems better suited than others for specific tasks; thus, photons are well suited for transmitting quantum information, weakly interacting spins can serve as long-lived quantum memories, and superconducting elements can rapidly process information encoded in their quantum states. A central goal of the envisaged quantum technologies is to develop devices that can simultaneously perform several of these tasks, namely, reliably store, process, and transmit quantum information. Hybrid quantum systems composed of different physical components with complementary functionalities may provide precisely such multitasking capabilities. This article reviews some of the driving theoretical ideas and first experimental realizations of hybrid quantum systems and the opportunities and challenges they present and offers a glance at the near- and long-term perspectives of this fascinating and rapidly expanding field.

  8. Hybrid photonic-crystal fiber

    Science.gov (United States)

    Markos, Christos; Travers, John C.; Abdolvand, Amir; Eggleton, Benjamin J.; Bang, Ole

    2017-10-01

    This article offers an extensive survey of results obtained using hybrid photonic-crystal fibers (PCFs) which constitute one of the most active research fields in contemporary fiber optics. The ability to integrate novel and functional materials in solid- and hollow-core PCFs through various postprocessing methods has enabled new directions toward understanding fundamental linear and nonlinear phenomena as well as novel application aspects, within the fields of optoelectronics, material and laser science, remote sensing, and spectroscopy. Here the recent progress in the field of hybrid PCFs is reviewed from scientific and technological perspectives, focusing on how different fluids, solids, and gases can significantly extend the functionality of PCFs. The first part of this review discusses the efforts to develop tunable linear and nonlinear fiber-optic devices using PCFs infiltrated with various liquids, glasses, semiconductors, and metals. The second part concentrates on recent and state-of-the-art advances in the field of gas-filled hollow-core PCFs. Extreme ultrafast gas-based nonlinear optics toward light generation in the extreme wavelength regions of vacuum ultraviolet, pulse propagation, and compression dynamics in both atomic and molecular gases, and novel soliton-plasma interactions are reviewed. A discussion of future prospects and directions is also included.

  9. Formal Engineering Hybrid Systems: Semantic Underpinnings

    NARCIS (Netherlands)

    Bujorianu, M.C.; Bujorianu, L.M.

    2008-01-01

    In this work we investigate some issues in applying formal methods to hybrid system development and develop a categorical framework. We study the themes of stochastic reasoning, heterogeneous formal specification and retrenchment. Hybrid systems raise a rich pallets of aspects that need to be

  10. A Hybrid Approach to Teaching Managerial Economics

    Science.gov (United States)

    Metzgar, Matthew

    2014-01-01

    Many institutions in higher education are experimenting with hybrid teaching approaches to undergraduate courses. Online resources may provide a number of advantages to students as compared to in-class approaches. Research regarding the effectiveness of hybrid approaches is mixed and still accumulating. This paper discusses the use of a hybrid…

  11. Functional Abstraction of Stochastic Hybrid Systems

    NARCIS (Netherlands)

    Bujorianu, L.M.; Blom, Henk A.P.; Hermanns, H.

    2006-01-01

    The verification problem for stochastic hybrid systems is quite difficult. One method to verify these systems is stochastic reachability analysis. Concepts of abstractions for stochastic hybrid systems are needed to ease the stochastic reachability analysis. In this paper, we set up different ways

  12. Design Principles for Natural and Hybrid Ventilation

    OpenAIRE

    Heiselberg, Per

    2000-01-01

    For many years mechanical and natural ventilation systems have developed separately. Naturally, the next step in this development is the development of ventilation concepts that utilize and combine the best features from each system to create a new type of ventilation system- Hybrid Ventilation. The hybrid ventilation concepts, design challenges and principles are discussed and illustrated by four building examples.

  13. Hybrid reactors: Nuclear breeding or energy production?

    International Nuclear Information System (INIS)

    Piera, Mireia; Lafuente, Antonio; Abanades, Alberto; Martinez-Val, J.M.

    2010-01-01

    After reviewing the long-standing tradition on hybrid research, an assessment model is presented in order to characterize the hybrid performance under different objectives. In hybrids, neutron multiplication in the subcritical blanket plays a major role, not only for energy production and nuclear breeding, but also for tritium breeding, which is fundamental requirement in fusion-fission hybrids. All three objectives are better achieved with high values of the neutron multiplication factor (k-eff) with the obvious and fundamental limitation that it cannot reach criticality under any event, particularly, in the case of a loss of coolant accident. This limitation will be very important in the selection of the coolant. Some general considerations will be proposed, as guidelines for assessing the hybrid potential in a given scenario. Those guidelines point out that hybrids can be of great interest for the future of nuclear energy in a framework of Sustainable Development, because they can contribute to the efficient exploitation of nuclear fuels, with very high safety features. Additionally, a proposal is presented on a blanket specially suited for fusion-fission hybrids, although this reactor concept is still under review, and new work is needed for identifying the most suitable blanket composition, which can vary depending on the main objective of the hybrid.

  14. The Federal electric and hybrid vehicle program

    Science.gov (United States)

    Schwartz, H. J.

    1980-01-01

    The commercial development and use of electric and hybrid vehicles is discussed with respect to its application as a possible alternative transportation system. A market demonstration is described that seeks to place 10,000 electric hybrid vehicles into public and private sector demonstrations.

  15. Research overview : design specifications for hybrid vehicles

    NARCIS (Netherlands)

    Hofman, T.; Druten, van R.M.

    2004-01-01

    In this paper a method is proposed for determination of the design specifications regarding the energy exchange systems for different chargesustaining hybrid vehicles of different vehicle classes. Hybrid drivetrains for vehicles combine multiple power sources in order to increase the driving

  16. Dynamics and control of hybrid mechanical systems

    NARCIS (Netherlands)

    Leonov, G.A.; Nijmeijer, H.; Pogromski, A.Y.; Fradkov, A.L.

    2010-01-01

    The papers in this edited volume aim to provide a better understanding of the dynamics and control of a large class of hybrid dynamical systems that are described by different models in different state space domains. They not only cover important aspects and tools for hybrid systems analysis and

  17. Synthesis and characterization of interspecific trigenomic hybrids ...

    African Journals Online (AJOL)

    All the triploids showed high frequency of bivalents during diakinesis and metaphase I (MI) of meiosis. The allohexaploids (FF.AABB, 2n = 52; FF.AACC, 2n = 54; BBCC.FF, 2n = 50) were synthesized by colchicine treatments of respective hybrids in vitro, which showed growth vigor and had larger stature than the hybrids, but ...

  18. Biomimetic synthesis and characterization of semiconducting hybrid

    Indian Academy of Sciences (India)

    Triple hybrid materials based on polyaniline-polyethylene glycol and cadmium sulphide have been prepared by the duffusion–limited biomimetic route and characterized by a number of spectroscopic, XRD, SEM, thermal and electrical measurements. These hybrid materials have been prepared by controlled precipitation of ...

  19. Hybrid and Electric Advanced Vehicle Systems Simulation

    Science.gov (United States)

    Beach, R. F.; Hammond, R. A.; Mcgehee, R. K.

    1985-01-01

    Predefined components connected to represent wide variety of propulsion systems. Hybrid and Electric Advanced Vehicle System (HEAVY) computer program is flexible tool for evaluating performance and cost of electric and hybrid vehicle propulsion systems. Allows designer to quickly, conveniently, and economically predict performance of proposed drive train.

  20. Hybridization, transgressive segregation and evolution of new ...

    Indian Academy of Sciences (India)

    Unknown

    This paper is dedicated to the memory of our teacher, Prof. N. B. ... of genetic variations wherein favourably interacting gene complexes are determined ... speciation. Hybrid-zone studies can yield information ... tic systems and in speciation, using an artificial hybrid ...... process of the development of reproductive isolation in.

  1. Electrokinetic acceleration of DNA hybridization in microsystems.

    Science.gov (United States)

    Lei, Kin Fong; Wang, Yun-Hsiang; Chen, Huai-Yi; Sun, Jia-Hong; Cheng, Ji-Yen

    2015-06-01

    In this work, electrokinetic acceleration of DNA hybridization was investigated by different combinations of frequencies and amplitudes of actuating electric signals. Because the frequencies from low to high can induce different kinds of electrokinetic forces, i.e., electroosmotic to electrothermal forces, this work provides an in-depth investigation of electrokinetic enhanced hybridization. Concentric circular Cr/Au microelectrodes of 350 µm in diameter were fabricated on a glass substrate and probe DNA was immobilized on the electrode surface. Target DNA labeled with fluorescent dyes suspending in solution was then applied to the electrode. Different electrokinetic forces were induced by the application of different electric signals to the circular microelectrodes. Local microfluidic vortexes were generated to increase the collision efficiency between the target DNA suspending in solution and probe DNA immobilized on the electrode surface. DNA hybridization on the electrode surface could be accelerated by the electrokinetic forces. The level of hybridization was represented by the fluorescent signal intensity ratio. Results revealed that such 5-min dynamic hybridization increased 4.5 fold of signal intensity ratio as compared to a 1-h static hybridization. Moreover, dynamic hybridization was found to have better differentiation ability between specific and non-specific target DNA. This study provides a strategy to accelerate DNA hybridization in microsystems. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Hybrid Warfare: Preparing for Future Conflict

    Science.gov (United States)

    2015-02-17

    ciceromagazine.com/?s=getting+behind+hybrid+warfare. Brown , Col Leslie F. “Twenty-First Century Warfare Will be Hybrid.” Carlisle Barracks, PA...Lebanon and Gaza.” Rand Corporation Occasional Paper. Santa Monica, CA: Rand Corporation, 2010. Jones, Gareth and Darya Korsunskaya. “U.S., EU

  3. In Pipe Robot with Hybrid Locomotion System

    Directory of Open Access Journals (Sweden)

    Cristian Miclauş

    2015-06-01

    Full Text Available The first part of the paper covers aspects concerning in pipe robots and their components, such as hybrid locomotion systems and the adapting mechanisms used. The second part describes the inspection robot that was developed, which combines tracked and wheeled locomotion (hybrid locomotion. The end of the paper presents the advantages and disadvantages of the proposed robot.

  4. Species hybridization in the genus Pinus

    Science.gov (United States)

    Peter W. Garrett

    1979-01-01

    Results of a breeding program in which a large number of pine species were tested indicate that a number of species and hybrids may be useful in the northeastern United States. Austrian black pine x Japanese black pine and hybrids containing Japanese red pine all had good growth rates. While none of the soft pines grew faster than eastern white pine, a number of...

  5. On Fractional Order Hybrid Differential Equations

    Directory of Open Access Journals (Sweden)

    Mohamed A. E. Herzallah

    2014-01-01

    Full Text Available We develop the theory of fractional hybrid differential equations with linear and nonlinear perturbations involving the Caputo fractional derivative of order 0<α<1. Using some fixed point theorems we prove the existence of mild solutions for two types of hybrid equations. Examples are given to illustrate the obtained results.

  6. Thermal stability of PMMA–clay hybrids

    Indian Academy of Sciences (India)

    Administrator

    Thermal stability of PMMA–clay hybrids. TANUSHREE CHOUDHURY* and NIRENDRA M MISRA. Department of Applied Chemistry, Indian School of Mines University, Dhanbad 826 004, India. MS received 9 December 2008. Abstract. Materials with small particle size are being extensively used in composites and hybrid ...

  7. Hybrid Therapy Regimen for Helicobacter Pylori Eradication

    Directory of Open Access Journals (Sweden)

    Zhi-Qiang Song

    2016-01-01

    Conclusions: Hybrid therapy showed wide differences in the efficacy but consistently good compliance and safety across different regions. Dual clarithromycin and metronidazole resistance were the key factor to efficacy. Hybrid therapy was similar to sequential or concomitant therapy in the efficacy, safety, and compliance.

  8. Hybrid Laminates for Application in North Conditions

    Science.gov (United States)

    Antipov, V. V.; Oreshko, E. I.; Erasov, V. S.; Serebrennikova, N. Yu.

    2016-11-01

    A hybrid aluminum-lithium alloy/SIAL laminate as a possible material for application in structures operated in North conditions is considered. The finite-element method is used for a buckling stability analysis of hybrid panels, bars, and plates. A technique allowing one to compare the buckling stability of multilayered hybrid plates is offered. Compression tests were run on a hybrid laminate wing panel as a prototype of the top panel of TU-204SM airplane made from a high-strength B95T2 aluminum alloy. It turned out that the lighter composite panel had a higher load-carrying capacity than the aluminum one. Results of investigation into the properties the hybrid aluminum-lithium alloy/SIAL laminate and an analysis of scientific-technical data on this subject showed that this composite material could be used in the elements of airframes, including those operated in north conditions.

  9. Hybrid nanostructures: synthesis, morphology and functional properties

    International Nuclear Information System (INIS)

    Povolotskaya, A V; Povolotskiy, A V; Manshina, A A

    2015-01-01

    Hybrid nanostructures representing combinations of different materials and possessing properties that are absent in separate components forming the hybrid are discussed. Particular attention is given to hybrid structures containing plasmonic and magnetic nanoparticles, methods of their synthesis and the relationship between the composition, structure and properties. The functional features of the hybrid nanomaterials of various morphology (with core–shell structures, with encapsulated metal nanoparticles and with metal nanoparticles on the surface) are considered. The unique properties of these hybrid materials are demonstrated, which are of interest for solving problems of catalysis and photocatalysis, detecting impurities in various media, in vivo visualization, bioanalysis, as well as for the design of optical labels and multifunctional diagnostic nanoplatforms. The bibliography includes 182 references

  10. Stochastic Reachability Analysis of Hybrid Systems

    CERN Document Server

    Bujorianu, Luminita Manuela

    2012-01-01

    Stochastic reachability analysis (SRA) is a method of analyzing the behavior of control systems which mix discrete and continuous dynamics. For probabilistic discrete systems it has been shown to be a practical verification method but for stochastic hybrid systems it can be rather more. As a verification technique SRA can assess the safety and performance of, for example, autonomous systems, robot and aircraft path planning and multi-agent coordination but it can also be used for the adaptive control of such systems. Stochastic Reachability Analysis of Hybrid Systems is a self-contained and accessible introduction to this novel topic in the analysis and development of stochastic hybrid systems. Beginning with the relevant aspects of Markov models and introducing stochastic hybrid systems, the book then moves on to coverage of reachability analysis for stochastic hybrid systems. Following this build up, the core of the text first formally defines the concept of reachability in the stochastic framework and then...

  11. Towards a Pattern Language for Hybrid Education

    DEFF Research Database (Denmark)

    Köppe, Christian; Nørgård, Rikke Toft; Pedersen, Alex Young

    2017-01-01

    -digital, academic-nonacademic, online-offline, formal-informal, learning-teaching and individual-collective. In doing so, hybrid education invites uncertainty, open-endedness, risk-taking, experimentation, critical creativity, disruption, dialogue and democracy (back) into the heart of education. Accordingly, we......In this paper we offer an initial framework for a pattern language of hybrid education. With the term hybrid education, we imply the use of educational design patterns that actively strive to cut across, circumventing or upheave traditional dichotomies within education such as physical...... see, within hybrid education, the promise to push against and circumvent current trends of marketization, managerialism and standardization in higher education today. Here, a pattern language for hybrid education presents an alternative way of designing for future higher education in ways...

  12. Towards a Pattern Language for Hybrid Education

    DEFF Research Database (Denmark)

    Köppe, Christian; Nørgård, Rikke Toft; Pedersen, Alex Young

    2018-01-01

    In this paper we offer an initial framework for a pattern language of hybrid education. With the term hybrid education, we imply the use of educa- tional design patterns that actively strive to cut across, circumventing or upheave traditional dichotomies within education such as physical-digital......, academic-nonacademic, online-offline, formal-informal, learning-teaching and individual-collective. In doing so, hybrid education invites uncertainty, open-endedness, risk-taking, experimentation, critical creativity, disruption, dialogue and democracy (back) into the heart of education. Accordingly we see...... on teaching to the test, playing it safe, rankings or gaming the system approaches. Rather, hybrid education focuses on open-endedness, risk-taking, relational entanglements, experimentation, exploration and empathy. In this way, designing for hybrid education is in this paper achieved, partly by taking...

  13. Space and power efficient hybrid counters array

    Science.gov (United States)

    Gara, Alan G [Mount Kisco, NY; Salapura, Valentina [Chappaqua, NY

    2009-05-12

    A hybrid counter array device for counting events. The hybrid counter array includes a first counter portion comprising N counter devices, each counter device for receiving signals representing occurrences of events from an event source and providing a first count value corresponding to a lower order bits of the hybrid counter array. The hybrid counter array includes a second counter portion comprising a memory array device having N addressable memory locations in correspondence with the N counter devices, each addressable memory location for storing a second count value representing higher order bits of the hybrid counter array. A control device monitors each of the N counter devices of the first counter portion and initiates updating a value of a corresponding second count value stored at the corresponding addressable memory location in the second counter portion. Thus, a combination of the first and second count values provide an instantaneous measure of number of events received.

  14. Shape Grammars for Innovative Hybrid Typological Design

    DEFF Research Database (Denmark)

    Al-kazzaz, Dhuha; Bridges, Alan; Chase, Scott Curland

    2010-01-01

    This paper describes a new methodology of deriving innovative hybrid designs using shape grammars of heterogeneous designs. The method is detailed within three phases of shape grammars: analysis, synthesis and evaluation. In the analysis phase, the research suggests that original rules of each...... design component are grouped in subclass rule sets to facilitate rule choices. Additionally, adding new hybrid rules to original rules expands the options available to the grammar user. In the synthesis phase, the research adopts state labels and markers to drive the design generation. The former...... is implemented with a user guide grammar to ensure hybridity in the generated design, while the latter aims to ensure feasible designs. Lastly evaluation criteria are added to measure the degree of innovation of the hybrid designs. This paper describes the derivation of hybrid minaret designs from a corpus...

  15. Hybrid processes in electrotechnology; Hybrid-Verfahren in der Elektroprozesstechnik

    Energy Technology Data Exchange (ETDEWEB)

    Neumeyer, Joerg; Schuelbe, Holger; Nacke, Bernard [Leibniz Univ. Hannover (Germany). Inst. fuer Elektroprozesstechnik

    2012-09-15

    Industrial process heat makes up the third largest sector of total German consumption of final energy, after mechanical energy in the field of transport and domestic space heating. An increasing percentage of the energy required to generate process heat is now supplied using electrothermal systems. The benefits of these methods over conventional fuel-based technology can be found in their universal usability, relatively simply handling and use, high transmissible output density, superior efficiency, and lower ecological impact. Electrical energy nowadays continues mainly to be generated in power-generating plants based on fuels such as coal and gas, but such large-scale facilities also include systems which keep pollutant emissions low, such as flue-gas desulphurisation and dedusting installations. This large bandwidth of benefits possessed by electrothermal systems can also be enlarged and adapted for other applications by means of rational and appropriate combination in the context of so-called hybrid processes. (orig.)

  16. Dark energy in hybrid inflation

    International Nuclear Information System (INIS)

    Gong, Jinn-Ouk; Kim, Seongcheol

    2007-01-01

    The situation that a scalar field provides the source of the accelerated expansion of the Universe while rolling down its potential is common in both the simple models of the primordial inflation and the quintessence-based dark energy models. Motivated by this point, we address the possibility of causing the current acceleration via the primordial inflation using a simple model based on hybrid inflation. We trigger the onset of the motion of the quintessence field via the waterfall field, and find that the fate of the Universe depends on the true vacuum energy determined by choosing the parameters. We also briefly discuss the variation of the equation of state and the possible implementation of our scenario in supersymmetric theories

  17. Permutation on hybrid natural inflation

    Science.gov (United States)

    Carone, Christopher D.; Erlich, Joshua; Ramos, Raymundo; Sher, Marc

    2014-09-01

    We analyze a model of hybrid natural inflation based on the smallest non-Abelian discrete group S3. Leading invariant terms in the scalar potential have an accidental global symmetry that is spontaneously broken, providing a pseudo-Goldstone boson that is identified as the inflaton. The S3 symmetry restricts both the form of the inflaton potential and the couplings of the inflaton field to the waterfall fields responsible for the end of inflation. We identify viable points in the model parameter space. Although the power in tensor modes is small in most of the parameter space of the model, we identify parameter choices that yield potentially observable values of r without super-Planckian initial values of the inflaton field.

  18. Hybrid inflation along waterfall trajectories

    International Nuclear Information System (INIS)

    Clesse, Sebastien

    2011-01-01

    We identify a new inflationary regime for which more than 60 e-folds are generated classically during the waterfall phase occurring after the usual hybrid inflation. By performing a Bayesian Monte-Carlo-Markov-Chain analysis, this scenario is shown to take place in a large part of the parameter space of the model. When this occurs, the observable perturbation modes leave the Hubble radius during waterfall inflation. The power spectrum of adiabatic perturbations is red, possibly in agreement with CMB constraints. Particular attention has been given to study only the regions for which quantum backreactions do not affect the classical dynamics. Implications concerning the preheating and the absence of topological defects in our Universe are discussed.

  19. Stellarmak a hybrid stellarator: Spheromak

    International Nuclear Information System (INIS)

    Hartman, C.W.

    1980-01-01

    This paper discusses hybridization of modified Stellarator-like transform windings (T-windings) with a Spheromak or Field-Reversed-Mirror configuration. This configuration, Stellarmak, retains the important topological advantage of the Spheromak or FRM of having no plasma linking conductors or blankets. The T-windings provide rotational transformation in toroidal angle of the outer poloidal field lines, in effect creating a reversed B/sub Toroidal/ Spheromak or adding average B/sub T/ to the FRM producing higher shear, increased limiting β, and possibly greater stability to kinks and tilt. The presence of field ripple in the toroidal direction may be sufficient to inhibit cancellation of directed ion current by electron drag to allow steady state operation with the toroidal as well as poloidal current maintained by neutral beams

  20. Hybrid photonic-crystal fiber

    DEFF Research Database (Denmark)

    Markos, Christos; Travers, John C.; Abdolvand, Amir

    2017-01-01

    This article offers an extensive survey of results obtained using hybrid photonic-crystal fibers (PCFs) which constitute one of the most active research fields in contemporary fiber optics. The ability to integrate novel and functional materials in solid- and hollow-core PCFs through various...... is reviewed from scientific and technological perspectives, focusing on how different fluids, solids, and gases can significantly extend the functionality of PCFs. The first part of this review discusses the efforts to develop tunable linear and nonlinear fiber-optic devices using PCFs infiltrated...... with various liquids, glasses, semiconductors, and metals. The second part concentrates on recent and state-of-the-art advances in the field of gas-filled hollow-core PCFs. Extreme ultrafast gas-based nonlinear optics toward light generation in the extreme wavelength regions of vacuum ultraviolet, pulse...

  1. Enhanced performance hybrid-arq

    KAUST Repository

    Fareed, Muhammad Mehboob

    2016-06-16

    Apparatuses, computer readable media, and methods are provided for enhancing hybrid automatic repeat request (ARQ) performance. In an example method, a communication device transmits a first element of a vector, where the vector is selected using the information bits to be transmitted as an index in a code book. In some embodiments, this code book is constructed using Linear Constellation Precoding (LCP). If a NACK is received, the communication device transmits a second element of the vector. The process of transmitting elements of the vector continues until an ACK is received or the maximum number of transmission attempts is reached. If an ACK is received, the communication device transmits a first element of another vector of the code book that encodes a second set of information bits. This procedure may continue until all information bits have been transmitted successfully.

  2. Hybrid model of steam boiler

    International Nuclear Information System (INIS)

    Rusinowski, Henryk; Stanek, Wojciech

    2010-01-01

    In the case of big energy boilers energy efficiency is usually determined with the application of the indirect method. Flue gas losses and unburnt combustible losses have a significant influence on the boiler's efficiency. To estimate these losses the knowledge of the operating parameters influence on the flue gases temperature and the content of combustible particles in the solid combustion products is necessary. A hybrid model of a boiler developed with the application of both analytical modelling and artificial intelligence is described. The analytical part of the model includes the balance equations. The empirical models express the dependence of the flue gas temperature and the mass fraction of the unburnt combustibles in solid combustion products on the operating parameters of a boiler. The empirical models have been worked out by means of neural and regression modelling.

  3. Enhanced performance hybrid-arq

    KAUST Repository

    Fareed, Muhammad Mehboob; Yang, Hong-Chuan; Alouini, Mohamed-Slim

    2016-01-01

    Apparatuses, computer readable media, and methods are provided for enhancing hybrid automatic repeat request (ARQ) performance. In an example method, a communication device transmits a first element of a vector, where the vector is selected using the information bits to be transmitted as an index in a code book. In some embodiments, this code book is constructed using Linear Constellation Precoding (LCP). If a NACK is received, the communication device transmits a second element of the vector. The process of transmitting elements of the vector continues until an ACK is received or the maximum number of transmission attempts is reached. If an ACK is received, the communication device transmits a first element of another vector of the code book that encodes a second set of information bits. This procedure may continue until all information bits have been transmitted successfully.

  4. Hybrid mask for deep etching

    KAUST Repository

    Ghoneim, Mohamed T.

    2017-08-10

    Deep reactive ion etching is essential for creating high aspect ratio micro-structures for microelectromechanical systems, sensors and actuators, and emerging flexible electronics. A novel hybrid dual soft/hard mask bilayer may be deposited during semiconductor manufacturing for deep reactive etches. Such a manufacturing process may include depositing a first mask material on a substrate; depositing a second mask material on the first mask material; depositing a third mask material on the second mask material; patterning the third mask material with a pattern corresponding to one or more trenches for transfer to the substrate; transferring the pattern from the third mask material to the second mask material; transferring the pattern from the second mask material to the first mask material; and/or transferring the pattern from the first mask material to the substrate.

  5. Quantum photonics hybrid integration platform

    Energy Technology Data Exchange (ETDEWEB)

    Murray, E.; Floether, F. F. [Cambridge Research Laboratory, Toshiba Research Europe Limited, 208 Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Ellis, D. J. P.; Meany, T.; Bennett, A. J., E-mail: anthony.bennet@crl.toshiba.co.uk; Shields, A. J. [Cambridge Research Laboratory, Toshiba Research Europe Limited, 208 Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Lee, J. P. [Cambridge Research Laboratory, Toshiba Research Europe Limited, 208 Science Park, Milton Road, Cambridge CB4 0GZ (United Kingdom); Engineering Department, University of Cambridge, 9 J. J. Thomson Avenue, Cambridge CB3 0FA (United Kingdom); Griffiths, J. P.; Jones, G. A. C.; Farrer, I.; Ritchie, D. A. [Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom)

    2015-10-26

    Fundamental to integrated photonic quantum computing is an on-chip method for routing and modulating quantum light emission. We demonstrate a hybrid integration platform consisting of arbitrarily designed waveguide circuits and single-photon sources. InAs quantum dots (QD) embedded in GaAs are bonded to a SiON waveguide chip such that the QD emission is coupled to the waveguide mode. The waveguides are SiON core embedded in a SiO{sub 2} cladding. A tuneable Mach Zehnder interferometer (MZI) modulates the emission between two output ports and can act as a path-encoded qubit preparation device. The single-photon nature of the emission was verified using the on-chip MZI as a beamsplitter in a Hanbury Brown and Twiss measurement.

  6. Contextual Validity in Hybrid Logic

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Jørgensen, Klaus Frovin

    2013-01-01

    interpretations. Moreover, such indexicals give rise to a special kind of validity—contextual validity—that interacts with ordinary logi- cal validity in interesting and often unexpected ways. In this paper we model these interactions by combining standard techniques from hybrid logic with insights from the work...... of Hans Kamp and David Kaplan. We introduce a simple proof rule, which we call the Kamp Rule, and first we show that it is all we need to take us from logical validities involving now to contextual validities involving now too. We then go on to show that this deductive bridge is strong enough to carry us...... to contextual validities involving yesterday, today and tomorrow as well....

  7. Sexual dimorphism in hybrids rats.

    Science.gov (United States)

    Garcia-Falgueras, Alicia; Pinos, Helena; Fernández, Rosa; Collado, Paloma; Pasaro, Eduardo; Segovia, Santiago; Guillamon, Antonio

    2006-12-06

    Laboratory rat strains descend from Wistar rats as a consequence of artificial selection. Previously we reported that the medial posterior division of the bed nucleus of the stria terminalis (BSTMP) was sexually dimorphic in Wistar and Long-Evans strains while the medial anterior division (BSTMA) and the locus coeruleus (LC) only showed sex differences in the ancestor Wistar strain. The lateral posterior division (BSTLP) was isomorphic in both strains. The present work studies the number of neurons in the BSTMP, BSTMA, BSTLP and LC of male and female Wistar and Long-Evans rats (F(0)) and their hybrid F(1) and F(2) generations. The BSTMP is sexually dimorphic in the F(0), F(1) and F(2) generations while sex differences in the LC are only seen in F(0) Wistar rats but not in the F(0) Long-Evans or the F(1) and F(2) hybrid generations. Sex differences in the BSTMA are seen in F(0) Wistar but not in F(0) Long-Evans rats and completely disappear in the F(2) generations. The number of neurons in the LC of both males and females decreased in heterozygotic individuals (F(1)) but increased in homozygotic (F(2)). However, the number of neurons in the BSTMP changes significantly over the generations, although the ratio of neurons (female/male) is stable and unaffected in homo- or heterozygosis. Thus, the mechanism that regulates the neuronal female/male ratio would be different from the one that controls the number of neurons. The facts that sex differences in the BSTMP are not affected by homo- or heterozygosis and that they are seen in several mammalian orders suggest the existence of a "fixed" type of brain sex differences in the Mammalia Class.

  8. Hybrid microcircuits for nuclear instrumentation

    International Nuclear Information System (INIS)

    Kulkarni, R.G.

    2005-01-01

    Hybrid microcircuits (HMCs) have distinct advantages over their rival products like printed circuit boards (PCBs) and integrated circuits (ICs), and are able to survive the onslaught of Moore's law, by retaining the niche market for themselves. The ASIC development cost is normally huge and when the volumes are small (less than ten thousand or so), the prohibitively high unit cost deters the potential customers. However the HMCs can be developed at a small fraction of an ASIC development cost and thus they are attractive when the volumes are small, as in the case of professional electronics industries like defense, broadcast, or instrumentation industries. The hybrid microcircuit (HMC) technology can involve one of the two processes: thick-film and thin- film. Broadly the thick-film process consists of printing and firing of, conductor and resistor pastes, on an Alumina substrate. The thin-film process consists of photo lithographic etching of, conductor and resistor patterns, on a metal/resistor sputtered high purity Alumina substrate. The active devices, either in die-form or in surface-mount form, are attached to the thick-film or the thin-film substrate. The passive devices like chip inductors and chip capacitors are also attached to the substrate. This paper discusses in detail the thick-film and the thin-film processes and their relative merits and demerits. The associated qualification and screening procedures followed to provide reliable HMCs to the customer are described. The existing HMC facilities and the product range available in Bharat Electronics including the HMCs developed for nuclear instrumentation are presented. (author)

  9. Hybrid chernoff tau-leap

    KAUST Repository

    Moraes, Alvaro

    2014-01-01

    Markovian pure jump processes model a wide range of phenomena, including chemical reactions at the molecular level, dynamics of wireless communication networks, and the spread of epidemic diseases in small populations. There exist algorithms such as Gillespie\\'s stochastic simulation algorithm (SSA) and Anderson\\'s modified next reaction method (MNRM) that simulate a single path with the exact distribution of the process, but this can be time consuming when many reactions take place during a short time interval. Gillespie\\'s approximated tau-leap method, on the other hand, can be used to reduce computational time, but it may lead to nonphysical values due to a positive one-step exit probability, and it also introduces a time discretization error. Here, we present a novel hybrid algorithm for simulating individual paths which adaptively switches between the SSA and the tau-leap method. The switching strategy is based on a comparison of the expected interarrival time of the SSA and an adaptive time step derived from a Chernoff-type bound for the one-step exit probability. Because this bound is nonasymptotic, we do not need to make any distributional approximation for the tau-leap increments. This hybrid method allows us (i) to control the global exit probability of any simulated path and (ii) to obtain accurate and computable estimates of the expected value of any smooth observable of the process with minimal computational work. We present numerical examples that illustrate the performance of the proposed method. © 2014 Society for Industrial and Applied Mathematics.

  10. Novel brewing yeast hybrids: creation and application.

    Science.gov (United States)

    Krogerus, Kristoffer; Magalhães, Frederico; Vidgren, Virve; Gibson, Brian

    2017-01-01

    The natural interspecies Saccharomyces cerevisiae × Saccharomyces eubayanus hybrid yeast is responsible for global lager beer production and is one of the most important industrial microorganisms. Its success in the lager brewing environment is due to a combination of traits not commonly found in pure yeast species, principally low-temperature tolerance, and maltotriose utilization. Parental transgression is typical of hybrid organisms and has been exploited previously for, e.g., the production of wine yeast with beneficial properties. The parental strain S. eubayanus has only been discovered recently and newly created lager yeast strains have not yet been applied industrially. A number of reports attest to the feasibility of this approach and artificially created hybrids are likely to have a significant impact on the future of lager brewing. De novo S. cerevisiae × S. eubayanus hybrids outperform their parent strains in a number of respects, including, but not restricted to, fermentation rate, sugar utilization, stress tolerance, and aroma formation. Hybrid genome function and stability, as well as different techniques for generating hybrids and their relative merits are discussed. Hybridization not only offers the possibility of generating novel non-GM brewing yeast strains with unique properties, but is expected to aid in unraveling the complex evolutionary history of industrial lager yeast.

  11. Sustainability assessment of a hybrid energy system

    International Nuclear Information System (INIS)

    Afgan, Nain H.; Carvalho, Maria G.

    2008-01-01

    A hybrid energy system in the form of the Object structure is the pattern for the structure of options in the evaluation of a hybrid system. The Object structure is defined as: Hybrid Energy System {[production (solar, wind, biomass, natural gas)] [utilization(electricity, heat, hydrogen)]}. In the evaluation of hybrid energy systems only several options are selected to demonstrate the sustainability assessment method application in the promotion of the specific quality of the hybrid energy system. In this analysis the following options are taken into a consideration: 1.Solar photo-voltaic power plant (PV PP), wind turbine power plant (WTPP) biomass thermal power plant (ThSTPP) for electricity, heat and hydrogen production. 2.Solar PV PP and wind power plant (WPP) for electricity and hydrogen production. 3.Biomass thermal steam turbine power plant (BThSTPP) and WPP for heat and hydrogen production. 4.Combined cycle gas turbine power plant for electricity and hydrogen production. 5.Cogeneration of electricity and water by the hybrid system. The sustainability assessment method is used for the evaluation of quality of the selected hybrid systems. In this evaluation the following indicators are used: economic indicator, environment indicator and social indicator

  12. Graphene hybridization for energy storage applications.

    Science.gov (United States)

    Li, Xianglong; Zhi, Linjie

    2018-05-08

    Graphene has attracted considerable attention due to its unique two-dimensional structure, high electronic mobility, exceptional thermal conductivity, excellent optical transmittance, good mechanical strength, and ultrahigh surface area. To meet the ever increasing demand for portable electronic products, electric vehicles, smart grids, and renewable energy integrations, hybridizing graphene with various functions and components has been demonstrated to be a versatile and powerful strategy to significantly enhance the performance of various energy storage systems such as lithium-ion batteries, supercapacitors and beyond, because such hybridization can result in synergistic effects that combine the best merits of involved components and confer new functions and properties, thereby improving the charge/discharge efficiencies and capabilities, energy/power densities, and cycle life of these energy storage systems. This review will focus on diverse graphene hybridization principles and strategies for energy storage applications, and the proposed outline is as follows. First, graphene and its fundamental properties, followed by graphene hybrids and related hybridization motivation, are introduced. Second, the developed hybridization formulas of using graphene for lithium-ion batteries are systematically categorized from the viewpoint of material structure design, bulk electrode construction, and material/electrode collaborative engineering; the latest representative progress on anodes and cathodes of lithium-ion batteries will be reviewed following such classifications. Third, similar hybridization formulas for graphene-based supercapacitor electrodes will be summarized and discussed as well. Fourth, the recently emerging hybridization formulas for other graphene-based energy storage devices will be briefed in combination with typical examples. Finally, future prospects and directions on the exploration of graphene hybridization toward the design and construction of

  13. Design Principles for Natural and Hybrid Ventilation

    DEFF Research Database (Denmark)

    Heiselberg, Per

    For many years mechanical and natural ventilation systems have developed separately. Naturally, the next step in this development is the development of ventilation concepts that utilize and combine the best features from each system to create a new type of ventilation system- Hybrid Ventilation. ....... The hybrid ventilation concepts, design challenges and principles are discussed and illustrated by four building examples.......For many years mechanical and natural ventilation systems have developed separately. Naturally, the next step in this development is the development of ventilation concepts that utilize and combine the best features from each system to create a new type of ventilation system- Hybrid Ventilation...

  14. Chemical sensors are hybrid-input memristors

    Science.gov (United States)

    Sysoev, V. I.; Arkhipov, V. E.; Okotrub, A. V.; Pershin, Y. V.

    2018-04-01

    Memristors are two-terminal electronic devices whose resistance depends on the history of input signal (voltage or current). Here we demonstrate that the chemical gas sensors can be considered as memristors with a generalized (hybrid) input, namely, with the input consisting of the voltage, analyte concentrations and applied temperature. The concept of hybrid-input memristors is demonstrated experimentally using a single-walled carbon nanotubes chemical sensor. It is shown that with respect to the hybrid input, the sensor exhibits some features common with memristors such as the hysteretic input-output characteristics. This different perspective on chemical gas sensors may open new possibilities for smart sensor applications.

  15. Advanced propulsion system concept for hybrid vehicles

    Science.gov (United States)

    Bhate, S.; Chen, H.; Dochat, G.

    1980-01-01

    A series hybrid system, utilizing a free piston Stirling engine with a linear alternator, and a parallel hybrid system, incorporating a kinematic Stirling engine, are analyzed for various specified reference missions/vehicles ranging from a small two passenger commuter vehicle to a van. Parametric studies for each configuration, detail tradeoff studies to determine engine, battery and system definition, short term energy storage evaluation, and detail life cycle cost studies were performed. Results indicate that the selection of a parallel Stirling engine/electric, hybrid propulsion system can significantly reduce petroleum consumption by 70 percent over present conventional vehicles.

  16. Powertrain system for a hybrid electric vehicle

    Science.gov (United States)

    Reed, Jr., Richard G.; Boberg, Evan S.; Lawrie, Robert E.; Castaing, Francois J.

    1999-08-31

    A hybrid electric powertrain system is provided including an electric motor/generator drivingly engaged with the drive shaft of a transmission. The electric is utilized for synchronizing the rotation of the drive shaft with the driven shaft during gear shift operations. In addition, a mild hybrid concept is provided which utilizes a smaller electric motor than typical hybrid powertrain systems. Because the electric motor is drivingly engaged with the drive shaft of the transmission, the electric motor/generator is driven at high speed even when the vehicle speed is low so that the electric motor/generator provides more efficient regeneration.

  17. DSP Control of Line Hybrid Active Filter

    DEFF Research Database (Denmark)

    Dan, Stan George; Benjamin, Doniga Daniel; Magureanu, R.

    2005-01-01

    Active Power Filters have been intensively explored in the past decade. Hybrid active filters inherit the efficiency of passive filters and the improved performance of active filters, and thus constitute a viable improved approach for harmonic compensation. In this paper a parallel hybrid filter...... is studied for current harmonic compensation. The hybrid filter is formed by a single tuned Le filter and a small-rated power active filter, which are directly connected in series without any matching transformer. Thus the required rating of the active filter is much smaller than a conventional standalone...... active filter. Simulation and experimental results obtained in laboratory confirmed the validity and effectiveness of the control....

  18. Hybrid Logical Analyses of the Ambient Calculus

    DEFF Research Database (Denmark)

    Bolander, Thomas; Hansen, René Rydhof

    2007-01-01

    In this paper, hybrid logic is used to formulate a rational reconstruction of a previously published control flow analysis for the mobile ambients calculus and we further show how a more precise flow-sensitive analysis, that takes the ordering of action sequences into account, can be formulated...... in a natural way. We show that hybrid logic is very well suited to express the semantic structure of the ambient calculus and how features of hybrid logic can be exploited to reduce the "administrative overhead" of the analysis specification and thus simplify it. Finally, we use HyLoTab, a fully automated...

  19. Hybrid Ceramic Matrix Fibrous Composites: an Overview

    Science.gov (United States)

    Naslain, R.

    2011-10-01

    Ceramic-Matrix Composites (CMCs) consist of a ceramic fiber architecture in a ceramic matrix, bonded together through a thin interphase. The present contribution is limited to non-oxide CMCs. Their constituents being oxidation-prone, they are protected by external coatings. We state here that CMCs display a hybrid feature, when at least one of their components is not homogeneous from a chemical or microstructural standpoint. Hybrid fiber architectures are used to tailor the mechanical or thermal CMC-properties whereas hybrid interphases, matrices and coatings to improve CMC resistance to aggressive environments.

  20. Fault tolerant control design for hybrid systems

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hao; Jiang, Bin [Nanjing University of Aeronautics and Astronautics, Nanjing (China); Cocquempot, Vincent [Universite des Sciences et Technologies de Lille, Villeneuve d' Ascq (France)

    2010-07-01

    This book intends to provide the readers a good understanding on how to achieve Fault Tolerant Control goal of Hybrid Systems. The book can be used as a reference for the academic research on Fault Tolerant Control and Hybrid Systems or used in Ph.D. study of control theory and engineering. The knowledge background for this monograph would be some undergraduate and graduate courses on Fault Diagnosis and Fault Tolerant Control theory, linear system theory, nonlinear system theory, Hybrid Systems theory and Discrete Event System theory. (orig.)