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Sample records for gene array studies

  1. Liver steatosis study_PFAA treated mouse gene array data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This file contains a link for Gene Expression Omnibus and the GSE designations for the publicly available gene expression data used in the study and reflected in...

  2. HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Q.; Deng, Ye; Lin, Lu; Hemme, Chris L.; He, Zhili; Zhou, Jizhong

    2010-05-17

    Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.

  3. Tandemly Arrayed Genes in Vertebrate Genomes

    Directory of Open Access Journals (Sweden)

    Deng Pan

    2008-01-01

    Full Text Available Tandemly arrayed genes (TAGs are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94% have parallel transcription orientation (i.e., they are encoded on the same strand in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

  4. DNA Array-Based Gene Profiling

    Science.gov (United States)

    Mocellin, Simone; Provenzano, Maurizio; Rossi, Carlo Riccardo; Pilati, Pierluigi; Nitti, Donato; Lise, Mario

    2005-01-01

    Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations, and diverse clinical behaviors. Traditional molecular analyses are reductionist, assessing only 1 or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes. The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously. Accordingly, DNA array, like other high-throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology. Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to carcinogenesis, tumor aggressiveness, and sensitivity to antiblastic agents. Given the revolutionary implications that the use of this technology might have in the clinical management of patients with cancer, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated. In the present work, we discuss the technical features characterizing this powerful laboratory tool and review the applications so far described in the field of oncology. PMID:15621987

  5. Array data extractor (ADE): a LabVIEW program to extract and merge gene array data.

    Science.gov (United States)

    Kurtenbach, Stefan; Kurtenbach, Sarah; Zoidl, Georg

    2013-12-01

    Large data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists. Here, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets. Although existing software allows for complex data analyses, the LabVIEW based program presented here, "Array Data Extractor (ADE)", provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge.

  6. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

    Directory of Open Access Journals (Sweden)

    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  7. Advanced cell culture technology for essential oil production and micro array studies leading to discovery of genes for fragrance compounds in Michelia alba (Cempaka Putih)

    International Nuclear Information System (INIS)

    Rusli Ibrahim; Norazlina Nordin; Edrina Azlan

    2006-01-01

    Michelia spp. is known to produce high value essential oil for perfumery industry. The essence of world's most expensive perfumes, such as JOY and Jadore, is based on the oil of Michelia spp. One major problem anticipated in this approach, based on our early experiments, is limited amount of fragrance produced in cell cultures. The appropriate strategy is to superimpose DNA micro array studies on top of the cell culture project. The study covers natural flower development phases that led to the identification of genes or sets of genes that regulate the production of the fragrance. Seven developmental stages of Michelia alba flower namely Stage 5 to 11 were investigated for their volatile constituents. The essential oil was isolated by Simultaneous Distillation Extraction technique and the oil obtained was subjected to GC-MS analysis. In total, seventy-seven compounds representing 93-98% of the overall volatiles compounds were identified on the basis of mass spectra and retention indices. Thirty-three of these compounds belonged to isoprenoids group which comprised 30-50% of the total volatile compounds whereas the remaining belonged to fatty acid derivatives, benzenoid, phenylpropanoid and other hydrocarbon compounds. Studies were conducted to optimize culture parameters for scaling-up the production of callus, suspension cell cultures and somatic and product accumulation of essential oils using bioreactor technology. (Author)

  8. A functional gene array for detection of bacterial virulence elements

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  9. NORMAL NASAL GENE EXPRESSION LEVELS USING CDNA ARRAY TECHNOLOGY

    Science.gov (United States)

    Normal Nasal Gene Expression Levels Using cDNA Array Technology. The nasal epithelium is a target site for chemically-induced toxicity and carcinogenicity. To detect and analyze genetic events which contribute to nasal tumor development, we first defined the gene expressi...

  10. Study of rectenna array connection

    Energy Technology Data Exchange (ETDEWEB)

    Miura, T.; Shinohara, N.; Matsumoto, H. [Kyoto Univ., Uji (Japan). Engineering Research Inst.

    1997-11-01

    A study was conducted in which a new rectenna working at 2.45 GHz microwave was developed for ground-to-ground microwave power transmission. The new rectenna consists of an antenna section and a rectifying section. The new design is simple and therefore more accurate than a micro-strip type patch antenna. The efficiency of conversion of microwave power to direct current depends on the mutual dependence of antenna elements and circuit conditions of rectifying sections. A series of experiments were conducted to analyze the rectenna characteristics and a method for efficiently connecting rectenna arrays was proposed. 3 refs., 2 tabs., 15 figs.

  11. Combining gene expression data from different generations of oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Kong Sek

    2004-10-01

    Full Text Available Abstract Background One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. Results We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis. Conclusions Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different

  12. Breast Carcinoma Cells in Primary Tumors and Effusions Have Different Gene Array Profiles

    Directory of Open Access Journals (Sweden)

    Sophya Konstantinovsky

    2010-01-01

    Full Text Available The detection of breast carcinoma cells in effusions is associated with rapidly fatal outcome, but these cells are poorly characterized at the molecular level. This study compared the gene array signatures of breast carcinoma cells in primary carcinomas and effusions. The genetic signature of 10 primary tumors and 10 effusions was analyzed using the Array-Ready Oligo set for the Human Genome platform. Results for selected genes were validated using PCR, Western blotting, and immunohistochemistry. Array analysis identified 255 significantly downregulated and 96 upregulated genes in the effusion samples. The majority of differentially expressed genes were part of pathways involved in focal adhesion, extracellular matrix-cell interaction, and the regulation of the actin cytoskeleton. Genes that were upregulated in effusions included KRT8, BCAR1, CLDN4, VIL2, while DCN, CLDN19, ITGA7, and ITGA5 were downregulated at this anatomic site. PCR, Western blotting, and immunohistochemistry confirmed the array findings for BCAR1, CLDN4, VIL2, and DCN. Our data show that breast carcinoma cells in primary carcinomas and effusions have different gene expression signatures, and differentially express a large number of molecules related to adhesion, motility, and metastasis. These differences may have a critical role in designing therapy and in prognostication for patients with metastatic disease localized to the serosal cavities.

  13. MARS - a multidetector array for reaction studies

    International Nuclear Information System (INIS)

    Ball, G.C.; Davies, W.G.; Forster, J.S.

    1988-03-01

    The proposal for MARS, a Multidetector Array for Reaction Studies is presented. MARS consists of a large, high-vacuum vessel enclosing an array of 128 scintillation detectors for use in studies of heavy-ion collisions at TASCC. The instrument will be funded and owned jointly by AECL and NSERC

  14. Some statistical properties of gene expression clustering for array data

    DEFF Research Database (Denmark)

    Abreu, G C G; Pinheiro, A; Drummond, R D

    2010-01-01

    DNA array data without a corresponding statistical error measure. We propose an easy-to-implement and simple-to-use technique that uses bootstrap re-sampling to evaluate the statistical error of the nodes provided by SOM-based clustering. Comparisons between SOM and parametric clustering are presented...... for simulated as well as for two real data sets. We also implement a bootstrap-based pre-processing procedure for SOM, that improves the false discovery ratio of differentially expressed genes. Code in Matlab is freely available, as well as some supplementary material, at the following address: https...

  15. GeneBins: a database for classifying gene expression data, with application to plant genome arrays

    Directory of Open Access Journals (Sweden)

    Weiller Georg

    2007-03-01

    Full Text Available Abstract Background To interpret microarray experiments, several ontological analysis tools have been developed. However, current tools are limited to specific organisms. Results We developed a bioinformatics system to assign the probe set sequences of any organism to a hierarchical functional classification modelled on KEGG ontology. The GeneBins database currently supports the functional classification of expression data from four Affymetrix arrays; Arabidopsis thaliana, Oryza sativa, Glycine max and Medicago truncatula. An online analysis tool to identify relevant functions is also provided. Conclusion GeneBins provides resources to interpret gene expression results from microarray experiments. It is available at http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/

  16. Intracellular Protein Delivery and Gene Transfection by Electroporation Using a Microneedle Electrode Array

    Science.gov (United States)

    Choi, Seong-O; Kim, Yeu-Chun; Lee, Jeong Woo; Park, Jung-Hwan

    2012-01-01

    The impact of many biopharmaceuticals, including protein- and gene-based therapies, has been limited by the need for better methods of delivery into cells within tissues. Here, we present intracellular delivery of molecules and transfection with plasmid DNA by electroporation using a novel microneedle electrode array designed for targeted treatment of skin and other tissue surfaces. The microneedle array is molded out of polylactic acid. Electrodes and circuitry required for electroporation are applied to the microneedle array surface by a new metal-transfer micromolding method. The microneedle array maintains mechanical integrity after insertion into pig cadaver skin and is able to electroporate human prostate cancer cells in vitro. Quantitative measurements show that increasing electroporation pulse voltage increases uptake efficiency of calcein and bovine serum albumin, whereas increasing pulse length has lesser effects over the range studied. Uptake of molecules by up to 50 % of cells and transfection of 12 % of cells with a gene for green fluorescent protein is demonstrated at high cell viability. We conclude that the microneedle electrode array is able to electroporate cells, resulting in intracellular uptake of molecules, and has potential applications to improve intracellular delivery of proteins, DNA and other biopharmaceuticals. PMID:22328093

  17. Study and Design of Differential Microphone Arrays

    CERN Document Server

    Benesty, Jacob

    2013-01-01

    Microphone arrays have attracted a lot of interest over the last few decades since they have the potential to solve many important problems such as noise reduction/speech enhancement, source separation, dereverberation, spatial sound recording, and source localization/tracking, to name a few. However, the design and implementation of microphone arrays with beamforming algorithms is not a trivial task when it comes to processing broadband signals such as speech. Indeed, in most sensor arrangements, the beamformer tends to have a frequency-dependent response. One exception, perhaps, is the family of differential microphone arrays (DMAs) that have the promise to form frequency-independent responses. Moreover, they have the potential to attain high directional gains with small and compact apertures. As a result, this type of microphone arrays has drawn much research and development attention recently. This book is intended to provide a systematic study of DMAs from a signal processing perspective. The primary obj...

  18. Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

    International Nuclear Information System (INIS)

    Oudes, Asa J; Roach, Jared C; Walashek, Laura S; Eichner, Lillian J; True, Lawrence D; Vessella, Robert L; Liu, Alvin Y

    2005-01-01

    Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases

  19. Development of Gene Expression Fingerprints for Identification of Environmental Contaminants Using cDNA Arrays

    National Research Council Canada - National Science Library

    Inouye, L

    2004-01-01

    ...) to develop cDNA array-based assays that map gene expression from contaminant exposures. Results substantiate that distinct gene expression profiles exist for major contaminant classes such as PARs, PCBs, and PCDD/Fs...

  20. Array2BIO: from microarray expression data to functional annotation of co-regulated genes

    Directory of Open Access Journals (Sweden)

    Rasley Amy

    2006-06-01

    Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

  1. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2006-01-01

    Full Text Available Abstract Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be. Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. Results The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes. It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene

  2. Study of Plasma Flow Modes in Imploding Nested Arrays

    Science.gov (United States)

    Mitrofanov, K. N.; Aleksandrov, V. V.; Gritsuk, A. N.; Branitsky, A. V.; Frolov, I. N.; Grabovski, E. V.; Sasorov, P. V.; Ol'khovskaya, O. G.; Zaitsev, V. I.

    2018-02-01

    Results from experimental studies of implosion of nested wire and fiber arrays at currents of up to 4 MA at the Angara-5-1 facility are presented. Depending on the ratio between the radii of the inner and outer arrays, different modes of the plasma flow in the space between the inner and outer arrays were implemented: the sub-Alfvénic ( V r V A ) modes and a mode with the formation of the transition shock wave (SW) region between the cascades. By varying the material of the outer array (tungsten wires or kapron fibers), it is shown that the plasma flow mode between the inner and outer arrays depends on the ratio between the plasma production rates ṁ in / ṁ out in the inner and outer arrays. The obtained experimental results are compared with the results of one-dimensional MHD simulation of the plasma flow between the arrays. Stable implosion of the inner array plasma was observed in experiments with combined nested arrays consisting of a fiber outer array and a tungsten inner array. The growth rates of magnetic Rayleigh-Taylor (MRT) instability in the inner array plasma at different numbers of fibers in the outer array and different ratios between the radii of the inner and outer arrays are compared. Suppression of MRT instability during the implosion of the inner array plasma results in the formation of a stable compact Z-pinch and generation of a soft X-ray pulse. A possible scenario of interaction between the plasmas of the inner and outer arrays is offered. The stability of the inner array plasma in the stage of final compression depends on the character of interaction of plasma jets from the outer array with the magnetic field of the inner array.

  3. Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays

    Directory of Open Access Journals (Sweden)

    Xiaoling Zhang

    2013-01-01

    Full Text Available We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs at a false discovery rate (FDR <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.

  4. GENE ARRAY ANALYSIS OF THE VENTRAL PROSTATE IN RATS EXPOSED TO EITHER VINCLOZOLIN OR PROCYMIDONE

    Science.gov (United States)

    GENE ARRAY ANALYSIS OF THE VENTRAL PROSTATE IN RATS EXPOSED TO EITHER VINCLOZOLIN OR PROCYMIDONE. MB Rosen, VS Wilson, JE Schmid, and LE Gray Jr. US EPA, ORD, NHEERL, RTP, NC.Vinclozolin (Vi) and procymidone (Pr) are antiandrogenic fungicides. While changes in gene expr...

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

    Science.gov (United States)

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

    2012-11-01

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

  6. A statistical method for predicting splice variants between two groups of samples using GeneChip® expression array data

    Directory of Open Access Journals (Sweden)

    Olson James M

    2006-04-01

    medulloblastomas to non-metastatic ones. We checked the consistency of some of our findings with information in UCSC Human Genome Browser. Conclusion The two-step approach described in this paper is capable of predicting some alternative splicing from multiple oligonucleotide-based gene expression array data with GeneChip® technology. Our method employs the extensive repositories of gene expression array data available and generates alternative splicing hypotheses, which can be further validated by experimental studies.

  7. Integrated strain array for cellular mechanobiology studies

    International Nuclear Information System (INIS)

    Simmons, C S; Sim, J Y; Baechtold, P; Chung, C; Borghi, N; Pruitt, B L; Gonzalez, A

    2011-01-01

    We have developed an integrated strain array for cell culture enabling high-throughput mechano-transduction studies. Biocompatible cell culture chambers were integrated with an acrylic pneumatic compartment and microprocessor-based control system. Each element of the array consists of a deformable membrane supported by a cylindrical pillar within a well. For user-prescribed waveforms, the annular region of the deformable membrane is pulled into the well around the pillar under vacuum, causing the pillar-supported region with cultured cells to be stretched biaxially. The optically clear device and pillar-based mechanism of operation enables imaging on standard laboratory microscopes. Straightforward fabrication utilizes off-the-shelf components, soft lithography techniques in polydimethylsiloxane and laser ablation of acrylic sheets. Proof of compatibility with basic biological assays and standard imaging equipment were accomplished by straining C2C12 skeletal myoblasts on the device for 6 h. At higher strains, cells and actin stress fibers realign with a circumferential preference

  8. Linear Array Ultrasonic Transducers: Sensitivity and Resolution Study

    International Nuclear Information System (INIS)

    Kramb, V.A.

    2005-01-01

    The University of Dayton Research Institute (UDRI) under contract by the US Air Force has designed and integrated a fully automated inspection system for the inspection of turbine engines that incorporates linear phased array ultrasonic transducers. Phased array transducers have been successfully implemented into weld and turbine blade root inspections where the defect types are well known and characterized. Embedded defects in aerospace turbine engine components are less well defined, however. In order to determine the applicability of linear arrays to aerospace inspections the sensitivity of array transducers to embedded defects in engine materials must be characterized. In addition, the implementation of array transducers into legacy inspection procedures must take into account any differences in sensitivity between the array transducer and that of the single element transducer currently used. This paper discusses preliminary results in a study that compares the sensitivity of linear array and conventional single element transducers to synthetic hard alpha defects in a titanium alloy

  9. Tumour metastasis-associated gene profiling using one-dimensional microfluidic beads array

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Great efforts have been made on the early diagnosis and molecular mechanism research of tumour metastasis in recent years. In this paper, based on the one-dimensional microfluidic beads array, a novel platform for tumour metastasis-associated genes profiling has been developed by depositing nucleic acids functional beads in the microchannel. This platform is sensitive (limit of detection: 0.02 nmol/L) and can perform mRNAs analysis without PCR. Two human colon cancer cell lines (primary and metastatic) from the same patient were used as a model, and transcriptional expression profiling of multiple tumour metastasis-associated genes in these two cell lines was successfully achieved. Furthermore, the results obtained on the beads array were validated by RT-PCR. This novel beads array has advantages of high sensitivity, little sample consumption, short assay time, low cost and high throughput capability. It holds the potential in early diagnosis and mechanism research of tumour metastasis.

  10. Targeting 160 candidate genes for blood pressure regulation with a genome-wide genotyping array.

    Directory of Open Access Journals (Sweden)

    Siim Sõber

    2009-06-01

    Full Text Available The outcome of Genome-Wide Association Studies (GWAS has challenged the field of blood pressure (BP genetics as previous candidate genes have not been among the top loci in these scans. We used Affymetrix 500K genotyping data of KORA S3 cohort (n = 1,644; Southern-Germany to address (i SNP coverage in 160 BP candidate genes; (ii the evidence for associations with BP traits in genome-wide and replication data, and haplotype analysis. In total, 160 gene regions (genic region+/-10 kb covered 2,411 SNPs across 11.4 Mb. Marker densities in genes varied from 0 (n = 11 to 0.6 SNPs/kb. On average 52.5% of the HAPMAP SNPs per gene were captured. No evidence for association with BP was obtained for 1,449 tested SNPs. Considerable associations (P50% of HAPMAP SNPs were tagged. In general, genes with higher marker density (>0.2 SNPs/kb revealed a better chance to reach close to significance associations. Although, none of the detected P-values remained significant after Bonferroni correction (P<0.05/2319, P<2.15 x 10(-5, the strength of some detected associations was close to this level: rs10889553 (LEPR and systolic BP (SBP (P = 4.5 x 10(-5 as well as rs10954174 (LEP and diastolic BP (DBP (P = 5.20 x 10(-5. In total, 12 markers in 7 genes (ADRA2A, LEP, LEPR, PTGER3, SLC2A1, SLC4A2, SLC8A1 revealed considerable association (P<10(-3 either with SBP, DBP, and/or hypertension (HYP. None of these were confirmed in replication samples (KORA S4, HYPEST, BRIGHT. However, supportive evidence for the association of rs10889553 (LEPR and rs11195419 (ADRA2A with BP was obtained in meta-analysis across samples stratified either by body mass index, smoking or alcohol consumption. Haplotype analysis highlighted LEPR and PTGER3. In conclusion, the lack of associations in BP candidate genes may be attributed to inadequate marker coverage on the genome-wide arrays, small phenotypic effects of the loci and/or complex interaction with life-style and metabolic parameters.

  11. A pilot trial assessing urinary gene expression profiling with an mRNA array for diabetic nephropathy.

    Directory of Open Access Journals (Sweden)

    Min Zheng

    Full Text Available BACKGROUND: The initiation and progression of diabetic nephropathy (DN is complex. Quantification of mRNA expression in urinary sediment has emerged as a novel strategy for studying renal diseases. Considering the numerous molecules involved in DN development, a high-throughput platform with parallel detection of multiple mRNAs is needed. In this study, we constructed a self-assembling mRNA array to analyze urinary mRNAs in DN patients with aims to reveal its potential in searching novel biomarkers. METHODS: mRNA array containing 88 genes were fabricated and its performance was evaluated. A pilot study with 9 subjects including 6 DN patients and 3 normal controls were studied with the array. DN patients were assigned into two groups according to their estimate glomerular rate (eGFR: DNI group (eGFR>60 ml/min/1.73 m(2, n = 3 and DNII group (eGFR<60 ml/min/1.73 m(2, n = 3. Urinary cell pellet was collected from each study participant. Relative abundance of these target mRNAs from urinary pellet was quantified with the array. RESULTS: The array we fabricated displayed high sensitivity and specificity. Moreover, the Cts of Positive PCR Controls in our experiments were 24±0.5 which indicated high repeatability of the array. A total of 29 mRNAs were significantly increased in DN patients compared with controls (p<0.05. Among these genes, α-actinin4, CDH2, ACE, FAT1, synaptopodin, COL4α, twist, NOTCH3 mRNA expression were 15-fold higher than those in normal controls. In contrast, urinary TIMP-1 mRNA was significantly decreased in DN patients (p<0.05. It was shown that CTGF, MCP-1, PAI-1, ACE, CDH1, CDH2 mRNA varied significantly among the 3 study groups, and their mRNA levels increased with DN progression (p<0.05. CONCLUSION: Our pilot study demonstrated that mRNA array might serve as a high-throughput and sensitive tool for detecting mRNA expression in urinary sediment. Thus, this primary study indicated that mRNA array probably could be a

  12. Study of Implosion of Combined Nested Arrays

    Science.gov (United States)

    Mitrofanov, K. N.; Aleksandrov, V. V.; Grabovski, E. V.; Sasorov, P. V.; Branitsky, A. V.; Gritsuk, A. N.; Frolov, I. N.; Laukhin, Ya. N.

    2017-12-01

    New experimental data on the implosion of plasma of nested kapron-tungsten arrays are obtained at the Angara-5-1 facility. The mode of plasma implosion is implemented in which a shock wave region forms in the space between the inner and outer arrays where a transition from the super-Alfvénic ( V r > V A ) to sub-Alfvénic ( V r Z-pinch and generation of a soft X-ray pulse with a peak power of 4 TW and duration of about 5 ns.

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  14. Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

    Science.gov (United States)

    Xu, Y; Ehringer, M; Yang, F; Sikela, J M

    2001-06-01

    Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and

  15. Hybrid Enrichment Verification Array: Module Characterization Studies

    Energy Technology Data Exchange (ETDEWEB)

    Zalavadia, Mital A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Leon E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McDonald, Benjamin S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kulisek, Jonathan A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mace, Emily K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Deshmukh, Nikhil S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-01

    The work presented in this report is focused on the characterization and refinement of the Hybrid Enrichment Verification Array (HEVA) approach, which combines the traditional 186-keV 235U signature with high-energy prompt gamma rays from neutron capture in the detector and surrounding collimator material, to determine the relative enrichment and 235U mass of the cylinder. The design of the HEVA modules (hardware and software) deployed in the current field trial builds on over seven years of study and evolution by PNNL, and consists of a ø3''×3'' NaI(Tl) scintillator coupled to an Osprey digital multi-channel analyzer tube base from Canberra. The core of the HEVA methodology, the high-energy prompt gamma-ray signature, serves as an indirect method for the measurement of total neutron emission from the cylinder. A method for measuring the intrinsic efficiency of this “non-traditional” neutron signature and the results from a benchmark experiment are presented. Also discussed are potential perturbing effects on the non-traditional signature, including short-lived activation of materials in the HEVA module. Modeling and empirical results are presented to demonstrate that such effects are expected to be negligible for the envisioned implementation scenario. In comparison to previous versions, the new design boosts the high-energy prompt gamma-ray signature, provides more flexible and effective collimation, and improves count-rate management via commercially available pulse-processing electronics with a special modification prompted by PNNL.

  16. Subclassification and Detection of New Markers for the Discrimination of Primary Liver Tumors by Gene Expression Analysis Using Oligonucleotide Arrays.

    Science.gov (United States)

    Hass, Holger G; Vogel, Ulrich; Scheurlen, Michael; Jobst, Jürgen

    2017-12-26

    The failure to correctly differentiate between intrahepatic cholangiocarcinoma [CC] and hepatocellular carcinoma [HCC] is a significant clinical problem, particularly in terms of the different treatment goals for both cancers. In this study a specific gene expression profile to discriminate these two subgroups of liver cancer was established and potential diagnostic markers for clinical use were analyzed. To evaluate the gene expression profiles of HCC and intrahepatic CC, Oligonucleotide arrays ( Affymetrix U133A) were used. Overexpressed genes were checked for their potential use as new markers for discrimination and their expression values were validated by reverse transcription polymerase chain reaction and immunohistochemistry analyses. 695 genes/expressed sequence tags (ESTs) in HCC (245 up-/450 down-regulated) and 552 genes/ESTs in CC (221 up-/331 down-regulated) were significantly dysregulated (p〈0.05, fold change >2, ≥70%). Using a supervised learning method, and one-way analysis of variance a specific 270-gene expression profile that enabled rapid, reproducible differentiation between both tumors and non-malignant liver tissues was established. A panel of 12 genes (e.g. HSP90β, ERG1, GPC3, TKT, ACLY, and NME1 for HCC; SPT2, T4S3, CNX43, TTD1, HBD01 for CC) were detected and partly described for the first time as potential discrimination markers. A specific gene expression profile for discrimination of primary liver cancer was identified and potential marker genes with feasible clinical impact were described.

  17. Nitrate-induced genes in tomato roots. Array analysis reveals novel genes that may play a role in nitrogen nutrition.

    Science.gov (United States)

    Wang, Y H; Garvin, D F; Kochian, L V

    2001-09-01

    A subtractive tomato (Lycopersicon esculentum) root cDNA library enriched in genes up-regulated by changes in plant mineral status was screened with labeled mRNA from roots of both nitrate-induced and mineral nutrient-deficient (-nitrogen [N], -phosphorus, -potassium [K], -sulfur, -magnesium, -calcium, -iron, -zinc, and -copper) tomato plants. A subset of cDNAs was selected from this library based on mineral nutrient-related changes in expression. Additional cDNAs were selected from a second mineral-deficient tomato root library based on sequence homology to known genes. These selection processes yielded a set of 1,280 mineral nutrition-related cDNAs that were arrayed on nylon membranes for further analysis. These high-density arrays were hybridized with mRNA from tomato plants exposed to nitrate at different time points after N was withheld for 48 h, for plants that were grown on nitrate/ammonium for 5 weeks prior to the withholding of N. One hundred-fifteen genes were found to be up-regulated by nitrate resupply. Among these genes were several previously identified as nitrate responsive, including nitrate transporters, nitrate and nitrite reductase, and metabolic enzymes such as transaldolase, transketolase, malate dehydrogenase, asparagine synthetase, and histidine decarboxylase. We also identified 14 novel nitrate-inducible genes, including: (a) water channels, (b) root phosphate and K(+) transporters, (c) genes potentially involved in transcriptional regulation, (d) stress response genes, and (e) ribosomal protein genes. In addition, both families of nitrate transporters were also found to be inducible by phosphate, K, and iron deficiencies. The identification of these novel nitrate-inducible genes is providing avenues of research that will yield new insights into the molecular basis of plant N nutrition, as well as possible networking between the regulation of N, phosphorus, and K nutrition.

  18. Study of LCP based flexible patch antenna array

    KAUST Repository

    Ghaffar, Farhan A.; Shamim, Atif; Roy, Langis

    2012-01-01

    Wrapping of a two element LCP based patch antenna array is studied in this work. For the first time, the designed array is bent in both E and H planes to observe the effect on the radiation and impedance performance of the antenna. The 38 GHz

  19. Blood Pressure Loci Identified with a Gene-Centric Array

    NARCIS (Netherlands)

    Johnson, Toby; Gaunt, Tom R.; Newhouse, Stephen J.; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W.; Tzoulaki, Ioanna; O'Brien, Eoin T.; Poulter, Neil R.; Sever, Peter; Shields, Denis C.; Thom, Simon; Wannamethee, Sasiwarang G.; Whincup, Peter H.; Brown, Morris J.; Connell, John M.; Dobson, Richard J.; Howard, Philip J.; Mein, Charles A.; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Smith, George Davey; Day, Ian N. M.; Lawlor, Debbie A.; Goodall, Alison H.; Fowkes, F. Gerald; Abecasis, Goncalo R.; Elliott, Paul; Gateva, Vesela; Braund, Peter S.; Burton, Paul R.; Nelson, Christopher P.; Tobin, Martin D.; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A.; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-Francois; Tichet, Jean; Juhanson, Peeter; Org, Elin; Westra, Harm-Jan; Wolfs, Marcel G. M.; Franke, Lude

    2011-01-01

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a

  20. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

    Science.gov (United States)

    Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

    2015-02-02

    There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.

  1. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

    Directory of Open Access Journals (Sweden)

    Settles Matthew L

    2009-05-01

    Full Text Available Abstract Background Natural antisense transcripts (NATs are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded or a different locus (trans-encoded. They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept. Results By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense

  2. Genetic diversity of K-antigen gene clusters of Escherichia coli and their molecular typing using a suspension array.

    Science.gov (United States)

    Yang, Shuang; Xi, Daoyi; Jing, Fuyi; Kong, Deju; Wu, Junli; Feng, Lu; Cao, Boyang; Wang, Lei

    2018-04-01

    Capsular polysaccharides (CPSs), or K-antigens, are the major surface antigens of Escherichia coli. More than 80 serologically unique K-antigens are classified into 4 groups (Groups 1-4) of capsules. Groups 1 and 4 contain the Wzy-dependent polymerization pathway and the gene clusters are in the order galF to gnd; Groups 2 and 3 contain the ABC-transporter-dependent pathway and the gene clusters consist of 3 regions, regions 1, 2 and 3. Little is known about the variations among the gene clusters. In this study, 9 serotypes of K-antigen gene clusters (K2ab, K11, K20, K24, K38, K84, K92, K96, and K102) were sequenced and correlated with their CPS chemical structures. On the basis of sequence data, a K-antigen-specific suspension array that detects 10 distinct CPSs, including the above 9 CPSs plus K30, was developed. This is the first report to catalog the genetic features of E. coli K-antigen variations and to develop a suspension array for their molecular typing. The method has a number of advantages over traditional bacteriophage and serum agglutination methods and lays the foundation for straightforward identification and detection of additional K-antigens in the future.

  3. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

    Energy Technology Data Exchange (ETDEWEB)

    Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

    2009-06-15

    To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

  4. Microwell Arrays for Studying Many Individual Cells

    Science.gov (United States)

    Folch, Albert; Kosar, Turgut Fettah

    2009-01-01

    "Laboratory-on-a-chip" devices that enable the simultaneous culturing and interrogation of many individual living cells have been invented. Each such device includes a silicon nitride-coated silicon chip containing an array of micromachined wells sized so that each well can contain one cell in contact or proximity with a patch clamp or other suitable single-cell-interrogating device. At the bottom of each well is a hole, typically 0.5 m wide, that connects the well with one of many channels in a microfluidic network formed in a layer of poly(dimethylsiloxane) on the underside of the chip. The microfluidic network makes it possible to address wells (and, thus, cells) individually to supply them with selected biochemicals. The microfluidic channels also provide electrical contact to the bottoms of the wells.

  5. Gene array analysis of PD-1H overexpressing monocytes reveals a pro-inflammatory profile

    Directory of Open Access Journals (Sweden)

    Preeti Bharaj

    2018-02-01

    Full Text Available We have previously reported that overexpression of Programmed Death -1 Homolog (PD-1H in human monocytes leads to activation and spontaneous secretion of multiple pro inflammatory cytokines. Here we evaluate changes in monocytes gene expression after enforced PD-1H expression by gene array. The results show that there are significant alterations in 51 potential candidate genes that relate to immune response, cell adhesion and metabolism. Genes corresponding to pro-inflammatory cytokines showed the highest upregulation, 7, 3.2, 3.0, 5.8, 4.4 and 3.1 fold upregulation of TNF-α, IL-1 β, IFN-α, γ, λ and IL-27 relative to vector control. The data are in agreement with cytometric bead array analysis showing induction of proinflammatory cytokines, IL-6, IL-1β and TNF-α by PD-1H. Other genes related to inflammation, include transglutaminase 2 (TG2, NF-κB (p65 and p50 and toll like receptors (TLR 3 and 4 were upregulated 5, 4.5 and 2.5 fold, respectively. Gene set enrichment analysis (GSEA also revealed that signaling pathways related to inflammatory response, such as NFκB, AT1R, PYK2, MAPK, RELA, TNFR1, MTOR and proteasomal degradation, were significantly upregulated in response to PD-1H overexpression. We validated the results utilizing a standard inflammatory sepsis model in humanized BLT mice, finding that PD-1H expression was highly correlated with proinflammatory cytokine production. We therefore conclude that PD-1H functions to enhance monocyte activation and the induction of a pro-inflammatory gene expression profile.

  6. Loci influencing blood pressure identified using a cardiovascular gene-centric array.

    Science.gov (United States)

    Ganesh, Santhi K; Tragante, Vinicius; Guo, Wei; Guo, Yiran; Lanktree, Matthew B; Smith, Erin N; Johnson, Toby; Castillo, Berta Almoguera; Barnard, John; Baumert, Jens; Chang, Yen-Pei Christy; Elbers, Clara C; Farrall, Martin; Fischer, Mary E; Franceschini, Nora; Gaunt, Tom R; Gho, Johannes M I H; Gieger, Christian; Gong, Yan; Isaacs, Aaron; Kleber, Marcus E; Mateo Leach, Irene; McDonough, Caitrin W; Meijs, Matthijs F L; Mellander, Olle; Molony, Cliona M; Nolte, Ilja M; Padmanabhan, Sandosh; Price, Tom S; Rajagopalan, Ramakrishnan; Shaffer, Jonathan; Shah, Sonia; Shen, Haiqing; Soranzo, Nicole; van der Most, Peter J; Van Iperen, Erik P A; Van Setten, Jessica; Van Setten, Jessic A; Vonk, Judith M; Zhang, Li; Beitelshees, Amber L; Berenson, Gerald S; Bhatt, Deepak L; Boer, Jolanda M A; Boerwinkle, Eric; Burkley, Ben; Burt, Amber; Chakravarti, Aravinda; Chen, Wei; Cooper-Dehoff, Rhonda M; Curtis, Sean P; Dreisbach, Albert; Duggan, David; Ehret, Georg B; Fabsitz, Richard R; Fornage, Myriam; Fox, Ervin; Furlong, Clement E; Gansevoort, Ron T; Hofker, Marten H; Hovingh, G Kees; Kirkland, Susan A; Kottke-Marchant, Kandice; Kutlar, Abdullah; Lacroix, Andrea Z; Langaee, Taimour Y; Li, Yun R; Lin, Honghuang; Liu, Kiang; Maiwald, Steffi; Malik, Rainer; Murugesan, Gurunathan; Newton-Cheh, Christopher; O'Connell, Jeffery R; Onland-Moret, N Charlotte; Ouwehand, Willem H; Palmas, Walter; Penninx, Brenda W; Pepine, Carl J; Pettinger, Mary; Polak, Joseph F; Ramachandran, Vasan S; Ranchalis, Jane; Redline, Susan; Ridker, Paul M; Rose, Lynda M; Scharnag, Hubert; Schork, Nicholas J; Shimbo, Daichi; Shuldiner, Alan R; Srinivasan, Sathanur R; Stolk, Ronald P; Taylor, Herman A; Thorand, Barbara; Trip, Mieke D; van Duijn, Cornelia M; Verschuren, W Monique; Wijmenga, Cisca; Winkelmann, Bernhard R; Wyatt, Sharon; Young, J Hunter; Boehm, Bernhard O; Caulfield, Mark J; Chasman, Daniel I; Davidson, Karina W; Doevendans, Pieter A; Fitzgerald, Garret A; Gums, John G; Hakonarson, Hakon; Hillege, Hans L; Illig, Thomas; Jarvik, Gail P; Johnson, Julie A; Kastelein, John J P; Koenig, Wolfgang; März, Winfried; Mitchell, Braxton D; Murray, Sarah S; Oldehinkel, Albertine J; Rader, Daniel J; Reilly, Muredach P; Reiner, Alex P; Schadt, Eric E; Silverstein, Roy L; Snieder, Harold; Stanton, Alice V; Uitterlinden, André G; van der Harst, Pim; van der Schouw, Yvonne T; Samani, Nilesh J; Johnson, Andrew D; Munroe, Patricia B; de Bakker, Paul I W; Zhu, Xiaofeng; Levy, Daniel; Keating, Brendan J; Asselbergs, Folkert W

    2013-04-15

    Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped ∼50 000 single-nucleotide polymorphisms (SNPs) that capture variation in ∼2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 × 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.

  7. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

    Directory of Open Access Journals (Sweden)

    Sugnet Charles

    2006-12-01

    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  8. Correlation of Dynamic PET and Gene Array Data in Patients with Gastrointestinal Stromal Tumors

    Directory of Open Access Journals (Sweden)

    Ludwig G. Strauss

    2012-01-01

    Full Text Available Introduction. The results obtained with dynamic PET (dPET were compared to gene expression data obtained in patients with gastrointestinal stromal tumors (GIST. The primary aim was to assess the association of the dPET results and gene expression data. Material and Methods. dPET was performed following the injection of F-18-fluorodeoxyglucose (FDG in 22 patients with GIST. All patients were examined prior to surgery for staging purpose. Compartment and noncompartment models were used for the quantitative evaluation of the dPET examinations. Gene array data were based on tumor specimen obtained by surgery after the PET examinations. Results. The data analysis revealed significant correlations for the dPET parameters and the expression of zinc finger genes (znf43, znf85, znf91, znf189. Furthermore, the transport of FDG (k1 was associated with VEGF-A. The cell cycle gene cyclin-dependent kinase inhibitor 1C was correlated with the maximum tracer uptake (SUVmax in the tumors. Conclusions. The data demonstrate a dependency of the tracer kinetics on genes associated with prognosis in GIST. Furthermore, angiogenesis and cell proliferation have an impact on the tracer uptake.

  9. Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array

    Directory of Open Access Journals (Sweden)

    Yick Ching Wong

    2014-11-01

    Full Text Available Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA and triacylglycerol (TAG assembly, along with the tricarboxylic acid cycle (TCA and glycolysis pathway at 16 Weeks After Anthesis (WAA exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01, and rice (p-value < 0.01 arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01 throughout mesocarp development to transcriptome (RNA sequencing data, and improved correlation over quantitative real-time PCR (qPCR (r2 = 0.721, p < 0.01 of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.

  10. Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array

    Science.gov (United States)

    Wong, Yick Ching; Kwong, Qi Bin; Lee, Heng Leng; Ong, Chuang Kee; Mayes, Sean; Chew, Fook Tim; Appleton, David R.; Kulaveerasingam, Harikrishna

    2014-01-01

    Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r2 = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield. PMID:27600348

  11. Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments

    Directory of Open Access Journals (Sweden)

    Gyöngyi Munkácsy

    2016-01-01

    Full Text Available No independent cross-validation of success rate for studies utilizing small interfering RNA (siRNA for gene silencing has been completed before. To assess the influence of experimental parameters like cell line, transfection technique, validation method, and type of control, we have to validate these in a large set of studies. We utilized gene chip data published for siRNA experiments to assess success rate and to compare methods used in these experiments. We searched NCBI GEO for samples with whole transcriptome analysis before and after gene silencing and evaluated the efficiency for the target and off-target genes using the array-based expression data. Wilcoxon signed-rank test was used to assess silencing efficacy and Kruskal–Wallis tests and Spearman rank correlation were used to evaluate study parameters. All together 1,643 samples representing 429 experiments published in 207 studies were evaluated. The fold change (FC of down-regulation of the target gene was above 0.7 in 18.5% and was above 0.5 in 38.7% of experiments. Silencing efficiency was lowest in MCF7 and highest in SW480 cells (FC = 0.59 and FC = 0.30, respectively, P = 9.3E−06. Studies utilizing Western blot for validation performed better than those with quantitative polymerase chain reaction (qPCR or microarray (FC = 0.43, FC = 0.47, and FC = 0.55, respectively, P = 2.8E−04. There was no correlation between type of control, transfection method, publication year, and silencing efficiency. Although gene silencing is a robust feature successfully cross-validated in the majority of experiments, efficiency remained insufficient in a significant proportion of studies. Selection of cell line model and validation method had the highest influence on silencing proficiency.

  12. Experimental Study of Arcing on High-voltage Solar Arrays

    Science.gov (United States)

    Vayner, Boris; Galofaro, Joel; Ferguson, Dale

    2005-01-01

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

  13. AnovArray: a set of SAS macros for the analysis of variance of gene expression data

    Directory of Open Access Journals (Sweden)

    Renard Jean-Paul

    2005-06-01

    Full Text Available Abstract Background Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility to evaluate multiple sources of variation in an experiment. Results AnovArray is a package implementing ANOVA for gene expression data using SAS® statistical software. The originality of the package is 1 to quantify the different sources of variation on all genes together, 2 to provide a quality control of the model, 3 to propose two models for a gene's variance estimation and to perform a correction for multiple comparisons. Conclusion AnovArray is freely available at http://www-mig.jouy.inra.fr/stat/AnovArray and requires only SAS® statistical software.

  14. Spallation reactions studied with 4-detector arrays

    Indian Academy of Sciences (India)

    Recently there has been a renewed interest in the study of spallation reactions in basic nuclear physics as well as in potential applications. Spallation reactions induced by light projectiles (protons, antiprotons, pions, etc.) in the GeV range allow the formation of hot nuclei which do not suffer the collective excitations ...

  15. Spallation reactions studied with 4 -detector arrays

    Indian Academy of Sciences (India)

    of inert or biological materials, these neutrons can be used to study details of the material ... ping zone- or neck-built up with part of projectile- and target-nuclei). ..... also been designed to complement the set of tools at our disposal [40].

  16. Studying Functions of All Yeast Genes Simultaneously

    Science.gov (United States)

    Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

    2006-01-01

    A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

  17. Studying the Complex Expression Dependences between Sets of Coexpressed Genes

    Directory of Open Access Journals (Sweden)

    Mario Huerta

    2014-01-01

    Full Text Available Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. The use of clustering methods to obtain sets of coexpressed genes from expression arrays is very common; nevertheless there are no appropriate tools to study the expression networks among these sets of coexpressed genes. The aim of the developed tools is to allow studying the complex expression dependences that exist between sets of coexpressed genes. For this purpose, we start detecting the nonlinear expression relationships between pairs of genes, plus the coexpressed genes. Next, we form networks among sets of coexpressed genes that maintain nonlinear expression dependences between all of them. The expression relationship between the sets of coexpressed genes is defined by the expression relationship between the skeletons of these sets, where this skeleton represents the coexpressed genes with a well-defined nonlinear expression relationship with the skeleton of the other sets. As a result, we can study the nonlinear expression relationships between a target gene and other sets of coexpressed genes, or start the study from the skeleton of the sets, to study the complex relationships of activation and deactivation between the sets of coexpressed genes that carry out the different cellular processes present in the expression experiments.

  18. DNA array analysis of gene expression changes by Choto-san in the ischemic rat brain

    OpenAIRE

    Tohda, Michihisa; Matsumoto, Kinzo; Hayashi, Hisae; Murakami, Yukihisa; Watanabe, Hiroshi

    2004-01-01

    The effects of Choto-san on gene expression in the dementia model rat brain were studied using a DNA microarray system. Choto-san inhibited the expression of 181 genes that has been enhanced by permanent occlusion of the bilateral common carotid arteries (2VO). Choto-san also reversed the expression inhibition of 32 genes induced by 2VO. These results may suggest that Choto-san, which has been therapeutically used as an antidementive drug, shows therapeutic effects through gene expression cha...

  19. A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

    Directory of Open Access Journals (Sweden)

    Maider Ibarrola-Villava

    Full Text Available As the incidence of Malignant Melanoma (MM reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2 and rs2069398 (SILV/CKD2, were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls. A novel SNP located on the SLC45A2 gene (rs35414 was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001. None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls. Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.

  20. The National NeuroAIDS Tissue Consortium brain gene array: two types of HIV-associated neurocognitive impairment.

    Directory of Open Access Journals (Sweden)

    Benjamin B Gelman

    Full Text Available The National NeuroAIDS Tissue Consortium (NNTC performed a brain gene expression array to elucidate pathophysiologies of Human Immunodeficiency Virus type 1 (HIV-1-associated neurocognitive disorders.Twenty-four human subjects in four groups were examined A Uninfected controls; B HIV-1 infected subjects with no substantial neurocognitive impairment (NCI; C Infected with substantial NCI without HIV encephalitis (HIVE; D Infected with substantial NCI and HIVE. RNA from neocortex, white matter, and neostriatum was processed with the Affymetrix® array platform.With HIVE the HIV-1 RNA load in brain tissue was three log(10 units higher than other groups and over 1,900 gene probes were regulated. Interferon response genes (IFRGs, antigen presentation, complement components and CD163 antigen were strongly upregulated. In frontal neocortex downregulated neuronal pathways strongly dominated in HIVE, including GABA receptors, glutamate signaling, synaptic potentiation, axon guidance, clathrin-mediated endocytosis and 14-3-3 protein. Expression was completely different in neuropsychologically impaired subjects without HIVE. They had low brain HIV-1 loads, weak brain immune responses, lacked neuronally expressed changes in neocortex and exhibited upregulation of endothelial cell type transcripts. HIV-1-infected subjects with normal neuropsychological test results had upregulation of neuronal transcripts involved in synaptic transmission of neostriatal circuits.Two patterns of brain gene expression suggest that more than one pathophysiological process occurs in HIV-1-associated neurocognitive impairment. Expression in HIVE suggests that lowering brain HIV-1 replication might improve NCI, whereas NCI without HIVE may not respond in kind; array results suggest that modulation of transvascular signaling is a potentially promising approach. Striking brain regional differences highlighted the likely importance of circuit level disturbances in HIV/AIDS. In

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

    Directory of Open Access Journals (Sweden)

    Lo Fang-Yi

    2012-06-01

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  3. Jet arrays in supersonic crossflow — An experimental study

    Science.gov (United States)

    Ali, Mohd Yousuf; Alvi, Farrukh

    2015-12-01

    Jet injection into a supersonic crossflow is a classical fluid dynamics problem with many engineering applications. Several experimental and numerical studies have been taken up to analyze the interaction of a single jet with the incoming crossflow. However, there is a dearth of the literature on the interaction of multiple jets with one another and with the crossflow. Jets in a supersonic crossflow are known to produce a three-dimensional bow-shock structure due to the blockage of the flow. Multiple jets in a streamwise linear array interact with both one another and the incoming supersonic flow. In this paper, a parametric study is carried out to analyze the effect of microjet (sub-mm diameter) injection in a Mach 1.5 supersonic crossflow using flow visualization and velocity field measurements. The variation of the microjet orifice diameter and spacing within an array is used to study the three-dimensional nature of the flow field around the jets. The strength of the microjet-generated shock, scaling of the shock wave angle with the momentum coefficient, averaged streamwise, spanwise, and cross-stream velocity fields, and microjet array trajectories are detailed in the paper. It was found that shock angles of the microjet-generated shocks scale with the momentum coefficient for the three actuator configurations tested. As the microjets issue in the crossflow, a pair of longitudinal counter-rotating vortices (CVPs) are formed. The vortex pairs remain coherent for arrays with larger spanwise spacing between the micro-orifices and exhibit significant three-dimensionality similar to that of a single jet in crossflow. As the spacing between the jets is reduced, the CVPs merge resulting in a more two-dimensional flow field. The bow shock resulting from microjet injection also becomes nearly two-dimensional as the spacing between the micro-orifices is reduced. Trajectory estimations yield that microjets in an array have similar penetration as single jets. A notional

  4. The Array for Nuclear Astrophysics Studies with Exotic Nuclei

    Science.gov (United States)

    Linhardt, L. E.; Blackmon, J. C.; Matos, M.; Mondello, L. L.; Zganjar, E. F.; Johnson, E.; Rogachev, G.; Wiedenhover, I.

    2010-11-01

    The Array for Nuclear Astrophysics Studies with Exotic Nuclei (ANASEN) is a charged-particle detector array that is targeted primarily towards reaction studies with radioactive ion beams at FSU and the NSCL. ANASEN consists of 40 double-sided silicon-strip detectors backed with CsI scintillators and an innovative gas counter design that allows operation in a gas target/detector mode and experiments covering a broad range of center-of-mass energies simultaneously. Electronics based on ASIC components are being implemented to achieve a high channel count at low cost. Prototypes of all the detector components have been fabricated and are currently being tested. Performance of the individual components and plans for the first experiments that aim to improve our knowledge of the nuclear reactions important in stellar explosions will be reported.

  5. Digital quantification of gene methylation in stool DNA by emulsion-PCR coupled with hydrogel immobilized bead-array.

    Science.gov (United States)

    Liu, Yunlong; Wu, Haiping; Zhou, Qiang; Song, Qinxin; Rui, Jianzhong; Zou, Bingjie; Zhou, Guohua

    2017-06-15

    Aberrations of gene methylation in stool DNA (sDNA) is an effective biomarker for non-invasive colorectal cancer diagnosis. However, it is challenging to accurately quantitate the gene methylation levels in sDNA due to the low abundance and degradation of sDNA. In this study, a digital quantification strategy was proposed by combining emulsion PCR (emPCR) with hydrogel immobilized bead-array. The assay includes following steps: bisulfite conversion of sDNA, pre-amplification by PCR with specific primers containing 5' universal sequences, emPCR of pre-amplicons with beaded primers to achieve single-molecular amplification and identification of hydrogel embedding beads coated with amplicons. The sensitivity and the specificity of the method are high enough to pick up 0.05% methylated targets from unmethylated DNA background. The successful detection of hypermethylated vimentin gene in clinical stool samples suggests that the proposed method should be a potential tool for non-invasive colorectal cancer screening. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. ArraySolver: an algorithm for colour-coded graphical display and Wilcoxon signed-rank statistics for comparing microarray gene expression data.

    Science.gov (United States)

    Khan, Haseeb Ahmad

    2004-01-01

    The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t-test, analysis of variance, Pearson test and Mann-Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed-rank test, which is an appropriate test for two-groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour-coded graphical display and comparison of gene expression data using the Wilcoxon signed-rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs (n < or = 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform.

  7. Study of LCP based flexible patch antenna array

    KAUST Repository

    Ghaffar, Farhan A.

    2012-07-01

    Wrapping of a two element LCP based patch antenna array is studied in this work. For the first time, the designed array is bent in both E and H planes to observe the effect on the radiation and impedance performance of the antenna. The 38 GHz simulation results reveal better performance for H plane bending as compared to E plane bending. A 100 um thick substrate is used for the design which is best suited for flexible antenna applications. Gain variations of 1.1 dB and 1.4 dB are observed for the two orientations while a significantly increased impedance bandwidth of 3 % is obtained with H plane wrapping. The design is highly suitable for broadband micro-cellular backhaul applications. © 2012 IEEE.

  8. The pressure distribution for biharmonic transmitting array: theoretical study

    Science.gov (United States)

    Baranowska, A.

    2005-03-01

    The aim of the paper is theoretical analysis of the finite amplitude waves interaction problem for the biharmonic transmitting array. We assume that the array consists of 16 circular pistons of the same dimensions that regrouped in two sections. Two different arrangements of radiating elements were considered. In this situation the radiating surface is non-continuous without axial symmetry. The mathematical model was built on the basis of the Khokhlov - Zabolotskaya - Kuznetsov (KZK) equation. To solve the problem the finite-difference method was applied. On-axis pressure amplitude for different frequency waves as a function of distance from the source, transverse pressure distribution of these waves at fixed distances from the source and pressure amplitude distribution for them at fixed planes were examined. Especially changes of normalized pressure amplitude for difference frequency were studied. The paper presents mathematical model and some results of theoretical investigations obtained for different values of source parameters.

  9. Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood

    Directory of Open Access Journals (Sweden)

    Turner Renee J

    2009-08-01

    Full Text Available Abstract Background Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization. Methods Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT, 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms. Results Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder. Conclusion The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.

  10. [Obesity studies in candidate genes].

    Science.gov (United States)

    Ochoa, María del Carmen; Martí, Amelia; Martínez, J Alfredo

    2004-04-17

    There are more than 430 chromosomic regions with gene variants involved in body weight regulation and obesity development. Polymorphisms in genes related to energy expenditure--uncoupling proteins (UCPs), related to adipogenesis and insulin resistance--hormone-sensitive lipase (HLS), peroxisome proliferator-activated receptor gamma (PPAR gamma), beta adrenergic receptors (ADRB2,3), and alfa tumor necrosis factor (TNF-alpha), and related to food intake--ghrelin (GHRL)--appear to be associated with obesity phenotypes. Obesity risk depends on two factors: a) genetic variants in candidate genes, and b) biographical exposure to environmental risk factors. It is necessary to perform new studies, with appropriate control groups and designs, in order to reach relevant conclusions with regard to gene/environmental (diet, lifestyle) interactions.

  11. Study of Implosion of Twisted Nested Arrays at the Angara-5-1 Facility

    Science.gov (United States)

    Mitrofanov, K. N.; Zukakishvili, G. G.; Aleksandrov, V. V.; Grabovski, E. V.; Frolov, I. N.; Gribov, A. N.

    2018-01-01

    Results are presented from experimental studies of the implosion of twisted nested arrays in which the wires of the outer and inner arrays are twisted about the array axis in opposite directions (clockwise and counterclockwise). Experiments with twisted arrays were carried out at the Angara-5-1 facility at currents of up to 4 MA. The currents through the arrays were switched either simultaneously or the current pulse through the outer array was delayed by 10-15 ns with the help of an anode spark gap. It is shown that, in such arrays, the currents flow along the inclined wires and, accordingly, there are both the azimuthal and axial components of the discharge current. The process of plasma implosion in twisted arrays depends substantially on the value of the axial (longitudinal) magnetic field generated inside the array by the azimuthal currents. Two-dimensional simulations of the magnetic field in twisted nested arrays were performed in the ( r, z) geometry with allowance for the skin effect in the discharge electrodes. It is shown that, depending on the geometry of the discharge electrodes, different configurations of the magnetic field can be implemented inside twisted nested arrays. The calculated magnetic configurations are compared with the results of measurements of the magnetic field inside such arrays. It is shown that the configuration of the axial magnetic field inside a twisted nested array depends substantially on the distribution of the azimuthal currents between the inner and outer arrays.

  12. Sex-linked pheromone receptor genes of the European corn borer, Ostrinia nubilalis, are in tandem arrays.

    Directory of Open Access Journals (Sweden)

    Yuji Yasukochi

    Full Text Available BACKGROUND: Tuning of the olfactory system of male moths to conspecific female sex pheromones is crucial for correct species recognition; however, little is known about the genetic changes that drive speciation in this system. Moths of the genus Ostrinia are good models to elucidate this question, since significant differences in pheromone blends are observed within and among species. Odorant receptors (ORs play a critical role in recognition of female sex pheromones; eight types of OR genes expressed in male antennae were previously reported in Ostrinia moths. METHODOLOGY/PRINCIPAL FINDINGS: We screened an O. nubilalis bacterial artificial chromosome (BAC library by PCR, and constructed three contigs from isolated clones containing the reported OR genes. Fluorescence in situ hybridization (FISH analysis using these clones as probes demonstrated that the largest contig, which contained eight OR genes, was located on the Z chromosome; two others harboring two and one OR genes were found on two autosomes. Sequence determination of BAC clones revealed the Z-linked OR genes were closely related and tandemly arrayed; moreover, four of them shared 181-bp direct repeats spanning exon 7 and intron 7. CONCLUSIONS/SIGNIFICANCE: This is the first report of tandemly arrayed sex pheromone receptor genes in Lepidoptera. The localization of an OR gene cluster on the Z chromosome agrees with previous findings for a Z-linked locus responsible for O. nubilalis male behavioral response to sex pheromone. The 181-bp direct repeats might enhance gene duplications by unequal crossovers. An autosomal locus responsible for male response to sex pheromone in Heliothis virescens and H. subflexa was recently reported to contain at least four OR genes. Taken together, these findings support the hypothesis that generation of additional copies of OR genes can increase the potential for male moths to acquire altered specificity for pheromone components, and accordingly

  13. Feasibility study of patient motion monitoring using tactile array sensor

    International Nuclear Information System (INIS)

    Kim, Tae Ho; Kang, Seong Hee; Kim, Dong Su; Cho, Min Seok; Kim, Kyeong Hyeon; Suh, Tae Suk; Kim, Si Yong

    2014-01-01

    The aim of this study is to evaluate patient pretreatment set-up error and intra-fraction motion using the tactile array sensors (Pressure Profile Systems Inc, Los Angeles, CA) which could measure distributed pressure profiles along the contacting surface and to check a feasibility of the sensor (tactile array sensor) in the patient motion monitoring. Laser alignment and optical camera based monitoring system are very useful for reduce patient set-up error but these systems could not monitor the blind area like patient's back position. Actually after patient alignment using laser or optical monitoring system, it was assumed that there is no error in the patient's back position (pressure profile distribution). But if an error occurs in the patient's back position, it will affect the radiation therapy accuracy. In spite of optical motion monitoring or using the immobilization tool, distributed pressure profiles of patient's back position was changed during inter and intra-fraction. For more accurate patient set-up, blind area (patient's back) monitoring was necessary. We expect that the proposed method will be very useful for make up for the weakness of optical monitoring method

  14. Feasibility study of patient motion monitoring using tactile array sensor

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Ho; Kang, Seong Hee; Kim, Dong Su; Cho, Min Seok; Kim, Kyeong Hyeon; Suh, Tae Suk [Dept. of Biomedical Engineering, Research Institute of Biomedical Engineering, the Catholic University of Korea, Seoul (Korea, Republic of); Kim, Si Yong [Dept. of Radiation Oncology, Virginia Commonwealth University, Richmond (United States)

    2014-11-15

    The aim of this study is to evaluate patient pretreatment set-up error and intra-fraction motion using the tactile array sensors (Pressure Profile Systems Inc, Los Angeles, CA) which could measure distributed pressure profiles along the contacting surface and to check a feasibility of the sensor (tactile array sensor) in the patient motion monitoring. Laser alignment and optical camera based monitoring system are very useful for reduce patient set-up error but these systems could not monitor the blind area like patient's back position. Actually after patient alignment using laser or optical monitoring system, it was assumed that there is no error in the patient's back position (pressure profile distribution). But if an error occurs in the patient's back position, it will affect the radiation therapy accuracy. In spite of optical motion monitoring or using the immobilization tool, distributed pressure profiles of patient's back position was changed during inter and intra-fraction. For more accurate patient set-up, blind area (patient's back) monitoring was necessary. We expect that the proposed method will be very useful for make up for the weakness of optical monitoring method.

  15. Multiplex preamplification of specific cDNA targets prior to gene expression analysis by TaqMan Arrays

    Directory of Open Access Journals (Sweden)

    Ribal María

    2008-06-01

    Full Text Available Abstract Background An accurate gene expression quantification using TaqMan Arrays (TA could be limited by the low RNA quantity obtained from some clinical samples. The novel cDNA preamplification system, the TaqMan PreAmp Master Mix kit (TPAMMK, enables a multiplex preamplification of cDNA targets and therefore, could provide a sufficient amount of specific amplicons for their posterior analysis on TA. Findings A multiplex preamplification of 47 genes was performed in 22 samples prior to their analysis by TA, and relative gene expression levels of non-preamplified (NPA and preamplified (PA samples were compared. Overall, the mean cycle threshold (CT decrement in the PA genes was 3.85 (ranging from 2.07 to 5.01. A high correlation (r between the gene expression measurements of NPA and PA samples was found (mean r = 0.970, ranging from 0.937 to 0.994; p Conclusion We demonstrate that cDNA preamplification using the TPAMMK before TA analysis is a reliable approach to simultaneously measure gene expression of multiple targets in a single sample. Moreover, this procedure was validated in genes from degraded RNA samples and low abundance expressed genes. This combined methodology could have wide applications in clinical research, where scarce amounts of degraded RNA are usually obtained and several genes need to be quantified in each sample.

  16. Identification of transcription coactivator OCA-B-dependent genes involved in antigen-dependent B cell differentiation by cDNA array analyses.

    Science.gov (United States)

    Kim, Unkyu; Siegel, Rachael; Ren, Xiaodi; Gunther, Cary S; Gaasterland, Terry; Roeder, Robert G

    2003-07-22

    The tissue-specific transcriptional coactivator OCA-B is required for antigen-dependent B cell differentiation events, including germinal center formation. However, the identity of OCA-B target genes involved in this process is unknown. This study has used large-scale cDNA arrays to monitor changes in gene expression patterns that accompany mature B cell differentiation. B cell receptor ligation alone induces many genes involved in B cell expansion, whereas B cell receptor and helper T cell costimulation induce genes associated with B cell effector function. OCA-B expression is induced by both B cell receptor ligation alone and helper T cell costimulation, suggesting that OCA-B is involved in B cell expansion as well as B cell function. Accordingly, several genes involved in cell proliferation and signaling, such as Lck, Kcnn4, Cdc37, cyclin D3, B4galt1, and Ms4a11, have been identified as OCA-B-dependent genes. Further studies on the roles played by these genes in B cells will contribute to an understanding of B cell differentiation.

  17. Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

    International Nuclear Information System (INIS)

    Celen, Burcu; Piskin, Erhan; Demirel, Goekhan

    2011-01-01

    The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

  18. Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

    Science.gov (United States)

    Celen, Burcu; Demirel, Gökhan; Piskin, Erhan

    2011-04-01

    The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

  19. National array of neutron detectors (NAND) a versatile setup for studies on reaction dynamics

    International Nuclear Information System (INIS)

    Golda, K.S.; Singh, R.P.; Zacharias, J.; Archunan, M.; Kothari, A.; Barua, P.; Gupta, Arti; Venkataramanan, S.; Suman, S.K.; Kumar, Rajesh; Kumar, Pankaj; Jhingan, A.; Sugathan, P.; Datta, S.K.; Chatterjee, Mihir; Bhowmik, R.K.; Singh, Hardev; Behera, B.; Kumar, A.; Singh, G.; Ranjit; Mandal, S.

    2006-01-01

    National Array of Neutron Detectors (NAND) is a large array of neutron detectors being setup at Inter University Accelerator Centre. The primary motive behind the development of this array, is the study of reaction dynamics in the energy domain near the Coulomb barrier

  20. Commercial/industrial photovoltaic module and array requirement study. Low-cost solar array project engineering area

    Science.gov (United States)

    1981-01-01

    Design requirements for photovoltaic modules and arrays used in commercial and industrial applications were identified. Building codes and referenced standards were reviewed for their applicability to commercial and industrial photovoltaic array installation. Four general installation types were identified - integral (replaces roofing), direct (mounted on top of roofing), stand-off (mounted away from roofing), and rack (for flat or low slope roofs, or ground mounted). Each of the generic mounting types can be used in vertical wall mounting systems. This implies eight mounting types exist in the commercial/industrial sector. Installation costs were developed for these mounting types as a function of panel/module size. Cost drivers were identified. Studies were performed to identify optimum module shapes and sizes and operating voltage cost drivers. The general conclusion is that there are no perceived major obstacles to the use of photovoltaic modules in commercial/industrial arrays.

  1. Altered Gene Expression by Low-Dose Arsenic Exposure in Humans and Cultured Cardiomyocytes: Assessment by Real-Time PCR Arrays

    Directory of Open Access Journals (Sweden)

    Judy Mumford

    2011-06-01

    Full Text Available Chronic arsenic exposure results in higher risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. The purpose of this study was to investigate the effects on expression of selected genes in the blood lymphocytes from 159 people exposed chronically to arsenic in their drinking water using a novel RT-PCR TaqMan low-density array (TLDA. We found that expression of tumor necrosis factor-α (TNF-α, which activates both inflammation and NF-κB-dependent survival pathways, was strongly associated with water and urinary arsenic levels. Expression of KCNA5, which encodes a potassium ion channel protein, was positively associated with water and toe nail arsenic levels. Expression of 2 and 11 genes were positively associated with nail and urinary arsenic, respectively. Because arsenic exposure has been reported to be associated with long QT intervals and vascular disease in humans, we also used this TLDA for analysis of gene expression in human cardiomyocytes exposed to arsenic in vitro. Expression of the ion-channel genes CACNA1, KCNH2, KCNQ1 and KCNE1 were down-regulated by 1-mM arsenic. Alteration of some common pathways, including those involved in oxidative stress, inflammatory signaling, and ion-channel function, may underlay the seemingly disparate array of arsenic-associated diseases, such as cancer, cardiovascular disease, and diabetes.

  2. Gene array and real time PCR analysis of the adrenal sensitivity to adrenocorticotropic hormone in pig

    Directory of Open Access Journals (Sweden)

    SanCristobal Magali

    2008-02-01

    Full Text Available Abstract Background Variability in hypothalamic-pituitary-adrenal (HPA axis activity has been shown to be influenced by genetic factors and related to great metabolic differences such as obesity. The aim of this study was to investigate molecular bases of genetic variability of the adrenal sensitivity to ACTH, a major source of variability, in Meishan (MS and Large White (LW pigs, MS being reported to exhibit higher basal cortisol levels, response to ACTH and fatness than LW. A pig cDNA microarray was used to identify changes in gene expression in basal conditions and in response to ACTH stimulation. Results Genotype and/or ACTH affected the expression of 211 genes related to transcription, cell growth/maintenance, signal transduction, cell structure/adhesion/extra cellular matrix and protein kinase/phosphatase activity. No change in the expression of known key regulator proteins of the ACTH signaling pathway or of steroidogenic enzymes was found. However, Mdh2, Sdha, Suclg2, genes involved in the tricarboxylic acid (TCA pathway, were over-expressed in MS pigs. Higher TCA cycle activity in MS than in LW may thus result in higher steroidogenic activity and thus explain the typically higher cortisol levels in MS compared to LW. Moreover, up-regulation of Star and Ldlr genes in MS and/or in response to ACTH suggest that differences in the adrenal function between MS and LW may also involve mechanisms requisite for cholesterol supply to steroidogenesis. Conclusion The present study provides new potential candidate genes to explain genetic variations in the adrenal sensitivity to ACTH and better understand relationship between HPA axis activity and obesity.

  3. Polycistronic transcription of fused cassettes and identification of translation initiation signals in an unusual gene cassette array from Pseudomonas aeruginosa [version 3; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Érica L. Fonseca

    2015-11-01

    Full Text Available The gene cassettes found in class 1 integrons are generally promoterless units composed by an open reading frame (ORF, a short 5’ untranslated region (UTR and a 3’ recombination site (attC. Fused gene cassettes are generated by partial or total loss of the attC from the first cassette in an array, creating, in some cases, a fusion with the ORF from the next cassette. These structures are rare and little is known about their mechanisms of mobilization and expression. The aim of this study was to evaluate the dynamic of mobilization and transcription of the gcu14-blaGES-1/aacA4 gene cassette array, which harbours a fused gene cassette represented by blaGES-1/aacA4. The cassette array was analyzed by Northern blot and real-time reverse transcription-polymerase chain reaction (RT-PCR in order to assess the transcription mechanism of blaGES-1/aacA4 fused cassette. Also, inverse polymerase chain reactions (PCR were performed to detect the free circular forms of gcu14, blaGES-1 and aacA4. The Northern blot and real time RT-PCR revealed a polycistronic transcription, in which the fused cassette blaGES-1/aacA4 is transcribed as a unique gene, while gcu14 (with a canonical attC recombination site has a monocistronic transcription. The gcu14 cassette, closer to the weak configuration of cassette promoter (PcW, had a higher transcription level than blaGES-1/aacA4, indicating that the cassette position affects the transcript amounts. The presence of ORF-11 at attI1, immediately preceding gcu14, and of a Shine-Dalgarno sequence upstream blaGES-1/aacA4 composes a scenario for the occurrence of array translation. Inverse PCR generated amplicons corresponding to gcu14, gcu14-aacA4 and gcu14-blaGES-1/aacA4 free circular forms, but not to blaGES-1 and aacA4 alone, indicating that the GES-1 truncated attC is not substrate of integrase activity and that these genes are mobilized together as a unique cassette. This study was original in showing the transcription

  4. Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays

    Directory of Open Access Journals (Sweden)

    Heather D. Kissel

    2013-01-01

    Full Text Available Identifying molecular markers of endometrial hyperplasia (neoplasia progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE hysterectomy specimens (benign indications from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87% FF and 50/51 (98% FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.

  5. Engineering development studies for integrated evacuated CPC arrays

    Science.gov (United States)

    Winston, R.

    1982-04-01

    An evacuated tube concentrator which achieves respectable high temperature performance (100 C to 300 C) was developed. The design concept utilizes nonimaging CPC type concentration integrated into each tube by shaping the outer glass vacuum envelope. The detailed design, prototype fabrication and preliminary test measurements are reviewed. In addition the results of this first study specifically devoted to engineering development questions related to practical applications of this collector concept are summarized. Questions having to do with the deployment of medium to large area arrays, optimizations of the manifolding of individual tube panels, selected near term applications (with an emphasis on residential cooling based on Rankine driven chillers) and long term performance projections are addressed.

  6. Transcript profiling of common bean (Phaseolus vulgaris L. using the GeneChip® Soybean Genome Array: optimizing analysis by masking biased probes

    Directory of Open Access Journals (Sweden)

    Gronwald John W

    2010-05-01

    Full Text Available Abstract Background Common bean (Phaseolus vulgaris L. and soybean (Glycine max both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip® Soybean Genome Array (soybean GeneChip may be used for gene expression studies using common bean. Results To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent. Conclusions The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In

  7. Can intrinsic human tissue radiosensitivity be correlated with late responding gene RNA expression in white blood cells using a 96 gene micro-array?

    International Nuclear Information System (INIS)

    Schmidt, D.; Streeter, O.; Dagliyan, G.; Hill, C.K.; Williams-Hill, D.M.

    2003-01-01

    Radiation is widely used in the treatment of cancers. It is generally believed there is a sigmoid relationship between radiation dose and probability of cure. There is also a sigmoid relationship between radiation dose and normal tissue response. Generally total radiation dose to a tumor is limited by normal tissue tolerance. It has been postulated that up to 70% of inter-individual differences in radiosensitivity may be due to genetic predisposition (Tureson I. Et al, IJROBP, 1996;36:1065). However, to date, clinicians have no way of estimating or predicting an individual's normal tissue response to radiation exposure. Thus the prescribed dose cannot be tailored to an individuals actual expected response but is an empirically derived compromise based on experience. Although a number of studies using cellular techniques have shown that human cell radiosensitivity can be measured, none of these can be performed quick enough to be used in the clinic. In this study we are looking at gene expression that occurs some 24 hours after an exposure compared to expression before any exposure in peripheral white blood cells from patients undergoing radiotherapy for various tumors. The patients will be followed for overt radiation sensitivity by standard criteria by clinicians in the Department. The main aims are: does RNA expression level in a 96 gene micro-array vary before and after radiation and do these changes in RNA expression correlate with the objective measurements of acute radiation response observed by the clinicians in the patients. The USC IRB recently approved the protocol and human consent for this study to enter 50 patients in the next 12 months using mostly head and neck and endometrial cancer patients where we can get a normal tissue sample to examine as well as the blood sample. We will present the rationale, protocol, methods and early results in detail

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

    International Nuclear Information System (INIS)

    Gunn, Shelly; Gorre, Mercedes; Mohammed, Mansoor; Yeh, I-Tien; Lytvak, Irina; Tirtorahardjo, Budi; Dzidic, Natasha; Zadeh, Soheila; Kim, Jaeweon; McCaskill, Chris; Lim, Lony

    2010-01-01

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

  9. Zinc finger arrays binding human papillomavirus types 16 and 18 genomic DNA: precursors of gene-therapeutics for in-situ reversal of associated cervical neoplasia

    Directory of Open Access Journals (Sweden)

    Wayengera Misaki

    2012-07-01

    Full Text Available Abstract Background Human papillomavirus (HPV types 16 and 18 are the high-risk, sexually transmitted infectious causes of most cervical intraepithelial neoplasias (CIN or cancers. While efficacious vaccines to reduce the sexual acquisition of these high-risk HPVs have recently been introduced, no virus-targeted therapies exist for those already exposed and infected. Considering the oncogenic role of the transforming (E6 and E7 genes of high-risk HPVs in the slow pathogenesis of cervical cancer, we hypothesize that timely disruption or abolition of HPV genome expression within pre-cancerous lesions identified at screening may reverse neoplasia. We aimed to derive model zinc finger nucleases (ZFNs for mutagenesis of the genomes of two high-risk HPV (types 16 & 18. Methods and results Using ZiFiT software and the complete genomes of HPV types16 and 18, we computationally generated the consensus amino acid sequences of the DNA-binding domains (F1, F2, & F3 of (i 296 & 327 contextually unpaired (or single three zinc-finger arrays (sZFAs and (ii 9 & 13 contextually paired (left and right three- zinc-finger arrays (pZFAs that bind genomic DNA of HPV-types 16 and 18 respectively, inclusive of the E7 gene (s/pZFAHpV/E7. In the absence of contextually paired three-zinc-finger arrays (pZFAs that bind DNA corresponding to the genomic context of the E6 gene of either HPV type, we derived the DNA binding domains of another set of 9 & 14 contextually unpaired E6 gene-binding ZFAs (sZFAE6 to aid the future quest for paired ZFAs to target E6 gene sequences in both HPV types studied (pZFAE6. This paper presents models for (i synthesis of hybrid ZFNs that cleave within the genomic DNA of either HPV type, by linking the gene sequences of the DNA-cleavage domain of the FokI endonuclease FN to the gene sequences of a member of the paired-HPV-binding ZFAs (pZFAHpV/E7 + FN, and (ii delivery of the same into precancerous lesions using HPV-derived viral plasmids or

  10. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.

    Directory of Open Access Journals (Sweden)

    Guy C J Abell

    Full Text Available Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively, combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

  11. Space solar array reliability: A study and recommendations

    Science.gov (United States)

    Brandhorst, Henry W., Jr.; Rodiek, Julie A.

    2008-12-01

    Providing reliable power over the anticipated mission life is critical to all satellites; therefore solar arrays are one of the most vital links to satellite mission success. Furthermore, solar arrays are exposed to the harshest environment of virtually any satellite component. In the past 10 years 117 satellite solar array anomalies have been recorded with 12 resulting in total satellite failure. Through an in-depth analysis of satellite anomalies listed in the Airclaim's Ascend SpaceTrak database, it is clear that solar array reliability is a serious, industry-wide issue. Solar array reliability directly affects the cost of future satellites through increased insurance premiums and a lack of confidence by investors. Recommendations for improving reliability through careful ground testing, standardization of testing procedures such as the emerging AIAA standards, and data sharing across the industry will be discussed. The benefits of creating a certified module and array testing facility that would certify in-space reliability will also be briefly examined. Solar array reliability is an issue that must be addressed to both reduce costs and ensure continued viability of the commercial and government assets on orbit.

  12. Wire Array Solar Cells: Fabrication and Photoelectrochemical Studies

    Science.gov (United States)

    Spurgeon, Joshua Michael

    Despite demand for clean energy to reduce our addiction to fossil fuels, the price of these technologies relative to oil and coal has prevented their widespread implementation. Solar energy has enormous potential as a carbon-free resource but is several times the cost of coal-produced electricity, largely because photovoltaics of practical efficiency require high-quality, pure semiconductor materials. To produce current in a planar junction solar cell, an electron or hole generated deep within the material must travel all the way to the junction without recombining. Radial junction, wire array solar cells, however, have the potential to decouple the directions of light absorption and charge-carrier collection so that a semiconductor with a minority-carrier diffusion length shorter than its absorption depth (i.e., a lower quality, potentially cheaper material) can effectively produce current. The axial dimension of the wires is long enough for sufficient optical absorption while the charge-carriers are collected along the shorter radial dimension in a massively parallel array. This thesis explores the wire array solar cell design by developing potentially low-cost fabrication methods and investigating the energy-conversion properties of the arrays in photoelectrochemical cells. The concept was initially investigated with Cd(Se, Te) rod arrays; however, Si was the primary focus of wire array research because its semiconductor properties make low-quality Si an ideal candidate for improvement in a radial geometry. Fabrication routes for Si wire arrays were explored, including the vapor-liquid-solid growth of wires using SiCl4. Uniform, vertically aligned Si wires were demonstrated in a process that permits control of the wire radius, length, and spacing. A technique was developed to transfer these wire arrays into a low-cost, flexible polymer film, and grow multiple subsequent arrays using a single Si(111) substrate. Photoelectrochemical measurements on Si wire array

  13. Gene Silencing in Skin After Deposition of Self-Delivery siRNA With a Motorized Microneedle Array Device

    Directory of Open Access Journals (Sweden)

    Robyn P Hickerson

    2013-01-01

    Full Text Available Despite the development of potent siRNAs that effectively target genes responsible for skin disorders, translation to the clinic has been hampered by inefficient delivery through the stratum corneum barrier and into the live cells of the epidermis. Although hypodermic needles can be used to transport siRNA through the stratum corneum, this approach is limited by pain caused by the injection and the small volume of tissue that can be accessed by each injection. The use of microneedle arrays is a less painful method for siRNA delivery, but restricted payload capacity limits this approach to highly potent molecules. To address these challenges, a commercially available motorized microneedle array skin delivery device was evaluated. This device combines the positive elements of both hypodermic needles and microneedle array technologies with little or no pain to the patient. Application of fluorescently tagged self-delivery (sd-siRNA to both human and murine skin resulted in distribution throughout the treated skin. In addition, efficient silencing (78% average reduction of reporter gene expression was achieved in a transgenic fluorescent reporter mouse skin model. These results indicate that this device effectively delivers functional sd-siRNA with an efficiency that predicts successful clinical translation.

  14. An array-based study of increased system lifetime probability

    DEFF Research Database (Denmark)

    Nesgaard, Carsten

    2003-01-01

    Society's increased dependence on electronic systems calls for highly reliable power supplies comprised of multiple converters working in parallel. This paper describes a redundancy control scheme, based on the array technology that increases the overall reliability quite considerably and thereby...

  15. An array-based study of increased system lifetime probability

    DEFF Research Database (Denmark)

    Nesgaard, Carsten

    2002-01-01

    Society's increased dependence on electronic systems calls for highly reliable power supplies comprised of multiple converters working in parallel. This paper describes a redundancy control scheme, based on the array technology that increases the overall reliability quite considerably and thereby...

  16. Studies on coaxial circular array for underwater transducer applications

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.

    of the coaxial array from the next stage of investigation during which a hybrid formulation is developed to provide a computationally efficient method of calculating impedance. Different sidelobe suppression techniques including uniform and nonuniform excitations...

  17. An Empirical Study of Precise Interprocedural Array Analysis

    Directory of Open Access Journals (Sweden)

    Michael Hind

    1994-01-01

    Full Text Available In this article we examine the role played by the interprocedural analysis of array accesses in the automatic parallelization of Fortran programs. We use the PTRAN system to provide measurements of several benchmarks to compare different methods of representing interprocedurally accessed arrays. We examine issues concerning the effectiveness of automatic parallelization using these methods and the efficiency of a precise summarization method.

  18. Residential photovoltaic module and array requirement study. Low-Cost Solar Array Project engineering area. Final report appendices

    Energy Technology Data Exchange (ETDEWEB)

    1979-06-01

    This volume contains the appendices to a study to identify design requirements for photovoltaic modules and arrays used in residential applications. Appendices include: (1) codes, standards, and manuals of accepted practice-definition and importance; (2) regional code variations-impact; (3) model and city codes-review; (4) National Electric Code (NEC)-review; (5) types of standards-definition and importance; (6) federal standards-review; (7) standards review method; (8) manuals of accepted practice; (9) codes and referenced standards-summary; (10) public safety testing laboratories; (11) insurance review; (12) studies approach; (13) mounting configurations; (14) module/panel size and shape cost analysis; (15) grounding, wiring, terminal and voltage studies; (16) array installation cost summary; (17) photovoltaic shingle/module comparison; (18) retrofit application; (19) residential photovoltaic module performance criteria; (20) critique of JPL's solar cell module design and test specifications for residential applications; and (21) CSI format specification. (WHK)

  19. Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci

    NARCIS (Netherlands)

    Saxena, Richa; Elbers, Clara C.; Guo, Yiran; Peter, Inga; Gaunt, Tom R.; Mega, Jessica L.; Lanktree, Matthew B.; Tare, Archana; Almoguera Castillo, Berta; Li, Yun R.; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F.; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Boehm, Bernhard O.; Braund, Peter S.; Burton, Paul R.; Chandrupatla, Hareesh R.; Clarke, Robert; Cooper-DeHoff, Rhonda M.; Crook, Errol D.; Davey-Smith, George; Day, Ian N.; de Boer, Anthonius; de Groot, Mark C. H.; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S.; Furlong, Clement E.; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A.; Glessner, Joseph T.; Goel, Anuj; Gong, Yan; Grant, Struan F. A.; Kumari, Meena; van der Harst, Pim; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Wolffenbuttel, Bruce H. R.; Hofker, Marten H.; Asselbergs, Folkert W.; Wijmenga, Cisca

    2012-01-01

    To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom similar to 50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with similar to 2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and

  20. ExonMiner: Web service for analysis of GeneChip Exon array data

    Directory of Open Access Journals (Sweden)

    Imoto Seiya

    2008-11-01

    Full Text Available Abstract Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1 data normalization, (2 statistical analysis based on two-way ANOVA, (3 finding transcripts with significantly different splice patterns, (4 efficient visualization based on heatmaps and barplots, and (5 meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.

  1. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M

    2007-01-01

    neuroblastoma cell line SK-N-AS. Using this strategy, we identify thousands of human candidate RNA genes. To further verify the expression of these genes, we focused on candidate genes that had a stable hairpin structures or a high level of covariance. Using northern blotting, we verify the expression of 2 out...

  2. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

    Science.gov (United States)

    Geraldes, A; Difazio, S P; Slavov, G T; Ranjan, P; Muchero, W; Hannemann, J; Gunter, L E; Wymore, A M; Grassa, C J; Farzaneh, N; Porth, I; McKown, A D; Skyba, O; Li, E; Fujita, M; Klápště, J; Martin, J; Schackwitz, W; Pennacchio, C; Rokhsar, D; Friedmann, M C; Wasteneys, G O; Guy, R D; El-Kassaby, Y A; Mansfield, S D; Cronk, Q C B; Ehlting, J; Douglas, C J; Tuskan, G A

    2013-03-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids. © 2013 Blackwell Publishing Ltd.

  3. Ultrasound cylindrical phased array for transoesophageal thermal therapy: initial studies

    International Nuclear Information System (INIS)

    Melodelima, David; Lafon, Cyril; Prat, Frederic; Birer, Alain; Cathignol, Dominique

    2002-01-01

    This work was undertaken to investigate the feasibility of constructing a cylindrical phased array composed of 64 elements spread around the periphery (OD 10.6 mm) for transoesophageal ultrasound thermotherapy. The underlying operating principle of this applicator is to rotate a plane ultrasound beam electronically. For this purpose, eight adjacent transducers were successively excited with appropriate delay times so as to generate a plane wave. The exposure direction was changed by exciting a different set of eight elements. For these feasibility studies, we used a cylindrical prototype (OD 10.6 mm) composed of 16 elementary transducers distributed over a quarter of the cylinder, all operating at 4.55 MHz. The active part was mechanically reinforced by a rigid damper structure behind the transducers. It was shown that an ultrasound field similar to that emitted by a plane transducer could be generated. Ex vivo experiments on pig's liver demonstrated that the ultrasound beam could be accurately rotated to generate sector-based lesions to a suitable depth (up to 19 mm). Throughout these experiments, exposures lasting 20 s were delivered at an acoustic intensity of 17 W cm -2 . By varying the power from exposure to exposure, the depth of the lesion at different angles could be controlled

  4. Studying Room Acoustics using a Monopole-Dipole Microphone Array

    Science.gov (United States)

    Begault, Durand R.; Abel, Jonathan S.; Gills, Stephen R. (Technical Monitor)

    1997-01-01

    The use of a soundfield microphone for examining the directional nature of a room impulse response was reported recently. By cross-correlating monopole and co-located dipole microphone signals aligned with left-right, up-down, and front-back axes, a sense of signal direction of arrival is revealed. The current study is concerned with the array's ability to detect individual reflections and directions of arrival, as a function of the cross-correlation window duration. If is window is too long, weak reflections are overlooked; if too short, spurious detections result. Guidelines are presented for setting the window width according to perceptual criteria. Formulas are presented describing the accuracy with which direction of arrival can be estimated as a function of room specifics and measurement noise. The direction of arrival of early reflections is more accurately determined than that of later reflections which are quieter and more numerous. The transition from a fairly directional sound field at the beginning of the room impulse response to a uni-directional diffuse field is examined. Finally, it is shown that measurements from additional dipole orientations can significantly improve the ability to detect reflections and estimate their directions of arrival.

  5. Responses of murine and human macrophages to leptospiral infection: a study using comparative array analysis.

    Directory of Open Access Journals (Sweden)

    Feng Xue

    Full Text Available Leptospirosis is a re-emerging tropical infectious disease caused by pathogenic Leptospira spp. The different host innate immune responses are partially related to the different severities of leptospirosis. In this study, we employed transcriptomics and cytokine arrays to comparatively calculate the responses of murine peritoneal macrophages (MPMs and human peripheral blood monocytes (HBMs to leptospiral infection. We uncovered a series of different expression profiles of these two immune cells. The percentages of regulated genes in several biological processes of MPMs, such as antigen processing and presentation, membrane potential regulation, and the innate immune response, etc., were much greater than those of HBMs (>2-fold. In MPMs and HBMs, the caspase-8 and Fas-associated protein with death domain (FADD-like apoptosis regulator genes were significantly up-regulated, which supported previous results that the caspase-8 and caspase-3 pathways play an important role in macrophage apoptosis during leptospiral infection. In addition, the key component of the complement pathway, C3, was only up-regulated in MPMs. Furthermore, several cytokines, e.g. interleukin 10 (IL-10 and tumor necrosis factor alpha (TNF-alpha, were differentially expressed at both mRNA and protein levels in MPMs and HBMs. Some of the differential expressions were proved to be pathogenic Leptospira-specific regulations at mRNA level or protein level. Though it is still unclear why some animals are resistant and others are susceptible to leptospiral infection, this comparative study based on transcriptomics and cytokine arrays partially uncovered the differences of murine resistance and human susceptibility to leptospirosis. Taken together, these findings will facilitate further molecular studies on the innate immune response to leptospiral infection.

  6. Responses of Murine and Human Macrophages to Leptospiral Infection: A Study Using Comparative Array Analysis

    Science.gov (United States)

    Yang, Yingchao; Zhao, Jinping; Yang, Yutao; Cao, Yongguo; Hong, Cailing; Liu, Yuan; Sun, Lan; Huang, Minjun; Gu, Junchao

    2013-01-01

    Leptospirosis is a re-emerging tropical infectious disease caused by pathogenic Leptospira spp. The different host innate immune responses are partially related to the different severities of leptospirosis. In this study, we employed transcriptomics and cytokine arrays to comparatively calculate the responses of murine peritoneal macrophages (MPMs) and human peripheral blood monocytes (HBMs) to leptospiral infection. We uncovered a series of different expression profiles of these two immune cells. The percentages of regulated genes in several biological processes of MPMs, such as antigen processing and presentation, membrane potential regulation, and the innate immune response, etc., were much greater than those of HBMs (>2-fold). In MPMs and HBMs, the caspase-8 and Fas-associated protein with death domain (FADD)-like apoptosis regulator genes were significantly up-regulated, which supported previous results that the caspase-8 and caspase-3 pathways play an important role in macrophage apoptosis during leptospiral infection. In addition, the key component of the complement pathway, C3, was only up-regulated in MPMs. Furthermore, several cytokines, e.g. interleukin 10 (IL-10) and tumor necrosis factor alpha (TNF-alpha), were differentially expressed at both mRNA and protein levels in MPMs and HBMs. Some of the differential expressions were proved to be pathogenic Leptospira-specific regulations at mRNA level or protein level. Though it is still unclear why some animals are resistant and others are susceptible to leptospiral infection, this comparative study based on transcriptomics and cytokine arrays partially uncovered the differences of murine resistance and human susceptibility to leptospirosis. Taken together, these findings will facilitate further molecular studies on the innate immune response to leptospiral infection. PMID:24130911

  7. Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization.

    Science.gov (United States)

    Fister, Andrew S; Mejia, Luis C; Zhang, Yufan; Herre, Edward Allen; Maximova, Siela N; Guiltinan, Mark J

    2016-05-17

    The pathogenesis-related (PR) group of proteins are operationally defined as polypeptides that increase in concentration in plant tissues upon contact with a pathogen. To date, 17 classes of highly divergent proteins have been described that act through multiple mechanisms of pathogen resistance. Characterizing these families in cacao, an economically important tree crop, and comparing the families to those in other species, is an important step in understanding cacao's immune response. Using publically available resources, all members of the 17 recognized pathogenesis-related gene families in the genome of Theobroma cacao were identified and annotated resulting in a set of ~350 members in both published cacao genomes. Approximately 50 % of these genes are organized in tandem arrays scattered throughout the genome. This feature was observed in five additional plant taxa (three dicots and two monocots), suggesting that tandem duplication has played an important role in the evolution of the PR genes in higher plants. Expression profiling captured the dynamics and complexity of PR genes expression at basal levels and after induction by two cacao pathogens (the oomycete, Phytophthora palmivora, and the fungus, Colletotrichum theobromicola), identifying specific genes within families that are more responsive to pathogen challenge. Subsequent qRT-PCR validated the induction of several PR-1, PR-3, PR-4, and PR-10 family members, with greater than 1000 fold induction detected for specific genes. We describe candidate genes that are likely to be involved in cacao's defense against Phytophthora and Colletotrichum infection and could be potentially useful for marker-assisted selection for breeding of disease resistant cacao varieties. The data presented here, along with existing cacao-omics resources, will enable targeted functional genetic screening of defense genes likely to play critical functions in cacao's defense against its pathogens.

  8. Study and operating conditions of HTS Josephson arrays for metrological application

    International Nuclear Information System (INIS)

    Sosso, A.; Lacquaniti, V.; Andreone, D.; Cerri, R.; Klushin, A.M.

    2006-01-01

    We report an experimental study of metrological properties of high-temperature superconductor arrays, made of shunted bicrystal YBCO Josephson junctions. The work is mainly based on a direct comparison against a low temperature array. Owing to the high sensitivity of the measurements, we observed at nanovolt level the changes in the HTS array voltage on a step. A precise estimate of the dependence of the HTS array step width on operating conditions was obtained. Differences were observed with respect to the results of low sensitivity techniques, confirming that our method is necessary in the study of HTS arrays for metrology. The high sensitivity analysis was also applied in the derivation of the temperature dependence of the critical current, providing insights on the behavior of the HTS array

  9. A Study of Array Direction HDPE Fiber Reinforced Mortar

    Science.gov (United States)

    Kamsuwan, Trithos

    2018-02-01

    This paper presents the effect of array direction HDPE fiber using as the reinforced material in cement mortar. The experimental data were created reference to the efficiency of using HDPE fiber reinforced on the tensile properties of cement mortar with different high drawn ratio of HDPE fibers. The fiber with the different drawn ratio 25x (d25 with E xx), and 35x (d35 with E xx) fiber volume fraction (0%, 1.0%, 1.5%) and fiber length 20 mm. were used to compare between random direction and array direction of HDPE fibers and the stress - strain displacement relationship behavior of HDPE short fiber reinforced cement mortar were investigated. It was found that the array direction with HDPE fibers show more improved in tensile strength and toughness when reinforced in cement mortar.

  10. Study of solar array switching power management technology for space power system

    Science.gov (United States)

    Cassinelli, J. E.

    1982-01-01

    This report documents work performed on the Solar Array Switching Power Management Study. Mission characteristics for three missions were defined to the depth necessary to determine their power management requirements. Solar array switching concepts which could satisfy the mission requirements were identified. The switching concepts were compared with a conventional buck regulator system for cost, weight and volume, reliability, efficiency and thermal control. Solar array switching provided significant advantages in all areas of comparison for the reviewed missions.

  11. Development of multitissue microfluidic dynamic array for assessing changes in gene expression associated with channel catfish appetite, growth, metabolism, and intestinal health

    Science.gov (United States)

    Large-scale, gene expression methods allow for high throughput analysis of physiological pathways at a fraction of the cost of individual gene expression analysis. Systems, such as the Fluidigm quantitative PCR array described here, can provide powerful assessments of the effects of diet, environme...

  12. Empirical study of supervised gene screening

    Directory of Open Access Journals (Sweden)

    Ma Shuangge

    2006-12-01

    Full Text Available Abstract Background Microarray studies provide a way of linking variations of phenotypes with their genetic causations. Constructing predictive models using high dimensional microarray measurements usually consists of three steps: (1 unsupervised gene screening; (2 supervised gene screening; and (3 statistical model building. Supervised gene screening based on marginal gene ranking is commonly used to reduce the number of genes in the model building. Various simple statistics, such as t-statistic or signal to noise ratio, have been used to rank genes in the supervised screening. Despite of its extensive usage, statistical study of supervised gene screening remains scarce. Our study is partly motivated by the differences in gene discovery results caused by using different supervised gene screening methods. Results We investigate concordance and reproducibility of supervised gene screening based on eight commonly used marginal statistics. Concordance is assessed by the relative fractions of overlaps between top ranked genes screened using different marginal statistics. We propose a Bootstrap Reproducibility Index, which measures reproducibility of individual genes under the supervised screening. Empirical studies are based on four public microarray data. We consider the cases where the top 20%, 40% and 60% genes are screened. Conclusion From a gene discovery point of view, the effect of supervised gene screening based on different marginal statistics cannot be ignored. Empirical studies show that (1 genes passed different supervised screenings may be considerably different; (2 concordance may vary, depending on the underlying data structure and percentage of selected genes; (3 evaluated with the Bootstrap Reproducibility Index, genes passed supervised screenings are only moderately reproducible; and (4 concordance cannot be improved by supervised screening based on reproducibility.

  13. Radiation-induced adaptive response in fetal mice: a micro-array study

    International Nuclear Information System (INIS)

    Vares, G.; Bing, Wang; Mitsuru, Nenoi; Tetsuo, Nakajima; Kaoru, Tanaka; Isamu, Hayata

    2006-01-01

    Exposure of sublethal doses of ionizing radiation can induce protective mechanisms against a subsequent higher dose irradiation. This phenomenon called radio-adaptation (or adaptive response - AR), has been described in a wide range of biological models. In a series of studies, we demonstrated the existence of a radiation-induced AR in mice during late organogenesis. For better understanding of molecular mechanisms underlying AR in our model, we performed a global analysis of transcriptome regulations in cells collected from whole mouse fetuses. Using cDNA micro-arrays, we studied gene expression in these cells after in utero priming exposure to irradiation. Several combinations of radiation dose and dose-rate were applied to induce or not an AR in our system. Gene regulation was observed after exposure to priming radiation in each condition. Student's t-test was performed in order to identify genes whose expression modulation was specifically different in AR-inducing an( non-AR-inducing conditions. Genes were ranked according to their ability in discriminating AR-specific modulations. Since AR genes were implicated in variety of functions and cellular processes, we applied a functional classification algorithm, which clustered genes in a limited number of functionally related group: We established that AR genes are significantly enriched for specific keywords. Our results show a significant modulation of genes implicated in signal transduction pathways. No AR-specific alteration of DNA repair could be observed. Nevertheless, it is likely that modulation of DNA repair activity results, at least partly, from post-transcriptional regulation. One major hypothesis is that de-regulations of signal transduction pathways and apoptosis may be responsible for AR phenotype. In previous work, we demonstrated that radiation-induced AR in mice during organogenesis is related to Trp53 gene status and to the occurrence of radiation-induced apoptosis. Other work proposed that p53

  14. ArrayVigil: a methodology for statistical comparison of gene signatures using segregated-one-tailed (SOT) Wilcoxon's signed-rank test.

    Science.gov (United States)

    Khan, Haseeb Ahmad

    2005-01-28

    Due to versatile diagnostic and prognostic fidelity molecular signatures or fingerprints are anticipated as the most powerful tools for cancer management in the near future. Notwithstanding the experimental advancements in microarray technology, methods for analyzing either whole arrays or gene signatures have not been firmly established. Recently, an algorithm, ArraySolver has been reported by Khan for two-group comparison of microarray gene expression data using two-tailed Wilcoxon signed-rank test. Most of the molecular signatures are composed of two sets of genes (hybrid signatures) wherein up-regulation of one set and down-regulation of the other set collectively define the purpose of a gene signature. Since the direction of a selected gene's expression (positive or negative) with respect to a particular disease condition is known, application of one-tailed statistics could be a more relevant choice. A novel method, ArrayVigil, is described for comparing hybrid signatures using segregated-one-tailed (SOT) Wilcoxon signed-rank test and the results compared with integrated-two-tailed (ITT) procedures (SPSS and ArraySolver). ArrayVigil resulted in lower P values than those obtained from ITT statistics while comparing real data from four signatures.

  15. Study and characterization of arrays of detectors for dosimetric verification of radiotherapy, analysis of business solutions

    International Nuclear Information System (INIS)

    Gago Arias, A.; Brualla Gonzalez, L.; Gomez Rodriguez, F.; Gonzalez Castano, D. M.; Pardo Montero, J.; Luna Vega, V.; Mosquera Sueiro, J.; Sanchez Garcia, M.

    2011-01-01

    This paper presents a comparative study of the detector arrays developed by different business houses to the demand for devices that speed up the verification process. Will analyze the effect of spatial response of individual detectors in the measurement of dose distributions, modeling the same and analyzing the ability of the arrays to detect variations in a treatment yield.

  16. Numerical study of the properties of optical vortex array laser tweezers.

    Science.gov (United States)

    Kuo, Chun-Fu; Chu, Shu-Chun

    2013-11-04

    Chu et al. constructed a kind of Ince-Gaussian modes (IGM)-based vortex array laser beams consisting of p x p embedded optical vortexes from Ince-Gaussian modes, IG(e)(p,p) modes [Opt. Express 16, 19934 (2008)]. Such an IGM-based vortex array laser beams maintains its vortex array profile during both propagation and focusing, and is applicable to optical tweezers. This study uses the discrete dipole approximation (DDA) method to study the properties of the IGM-based vortex array laser tweezers while it traps dielectric particles. This study calculates the resultant force exerted on the spherical dielectric particles of different sizes situated at the IGM-based vortex array laser beam waist. Numerical results show that the number of trapping spots of a structure light (i.e. IGM-based vortex laser beam), is depended on the relation between the trapped particle size and the structure light beam size. While the trapped particle is small comparing to the beam size of the IGM-based vortex array laser beams, the IGM-based vortex array laser beams tweezers are suitable for multiple traps. Conversely, the tweezers is suitable for single traps. The results of this study is useful to the future development of the vortex array laser tweezers applications.

  17. Large Aperture Acoustic Arrays in Support of Reverberation Studies

    Science.gov (United States)

    1990-04-01

    t pesur. enr~turblwtislvl h outputP is fmlteedboasx oe o-ps ity~~~~~~~~rg vaiaio acroas aeo freqecc baDofiaog00Hz hrm prheso hyreivingl arve aipt...34Lov frequency 4a 20K I digital acoustic array,’" in Current Practices and New Technology 4C N 4RACVl0 1 in Ocean Engineering-1988, G. K. Wolfe and P

  18. A study into the design of steerable microphone arrays

    CERN Document Server

    Lai, Chiong Ching; Leung, Yee Hong

    2017-01-01

    The book covers the design formulations for broadband beamformer targeting nearfield and farfield sources. The book content includes background information on the acoustic environment, including propagation medium, the array geometries, signal models and basic beamformer designs. Subsequently it introduces design formulation for nearfield, farfield and mixed nearfield-farfield beamformers and extends the design formulation into electronically steerable beamformers. In addition, a robust formulation is introduced for all the designs mentioned.

  19. Study on Influence of Tube Arrays on Fluid Elastic Instability

    Science.gov (United States)

    Ishihara, Kunihiko; Kitayama, Gen

    The tube bank is used in boilers, heat exchangers in power plants and steam generators in nuclear plants. These tubes sometimes vibrate violently and come to the fatigue failure due to the flow induced vibration which is caused by the cross flow. This phenomenon is that the large vibrations arise at the critical flow velocity and it is called fluid elastic instability. However the relation between the onset velocity of fluid elastic instability and the tube array's geometry has not been clarified sufficiently. There is a few reference related to the relation between the pitch to diameter ratio and the onset velocity even in the lattice arrays. In this paper, the influence of tube arrays on fluid elastic instability is examined by experiments. As a result, it is clarified that the tube vibrations become large as T/D increases and L/D decreases, and the tube vibrations strongly depend on the dynamic characteristics of tubes such as the natural frequency and the damping ability.

  20. Experimental studies of Z-pinches of mixed wire array with aluminum and tungsten

    International Nuclear Information System (INIS)

    Ning Cheng; Li Zhenghong; Hua Xinsheng; Xu Rongkun; Peng Xianjue; Xu Zeping; Yang Jianlun; Guo Cun; Jiang Shilun; Feng Shuping; Yang Libing; Yan Chengli; Song Fengjun; Smirnov, V.P.; Kalinin, Yu.G.; Kingsep, A.S.; Chernenko, A.S.; Grabovsky, E.V.

    2004-01-01

    In the form of joint experiment between China and Russia, the experimental studies of Z-pinches of mixed wire array of aluminum (A1) and tungsten (W) were carried out on S-300 generator, which was located on Kurchatov Institute of Russia. The experimental results were compared with those of single A1 array and single W array, respectively. There are obvious difference between mixed one and single one in their photon spectral distributions. The intensity of K-series emission lines from the mixed wire array Z-pinch is lower than that from single A1 array. The radiated lines with wavelengths less than 1.6 nm were not found in single W array Z-pinches. In the Z-pinch processes, the area radiating x-rays in mixed wire array is smaller than that of single A1 array, but is slightly lower than that from single W array. The FWHM of x-ray pulse with a maximal power 0.3-0.5 TW and total energy 10-20 kJ is about 25 ns, which radiated from Z-pinches with a radial convergence of 4-5 on S-300 generator. The shadow photograph of the mixed wire-array Z-pinch plasma by laser probe shows that the core-corona configuration was formed and the corona was moving toward the center axis during the wire-array plasma formation, that the interface of the plasma is not clear, and that there are a number structures inside. They also suggests that there was an obvious development of Magneto Rayleigh-Taylor instability in the Z-pinch process as well

  1. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  2. A Study on Techniques for Focusing Circumferential Array Guided Waves for Long Range Inspection of Pipes

    International Nuclear Information System (INIS)

    Kang, To; Kim, Hak Joon; Song, Sung Jin; Cho, Young Do; Lee, Dong Hoon; Cho, Hyun Joon

    2009-01-01

    Ultrasonic guided waves have been widely utilized for long range inspection of structures. Especially, development of array guided waves techniques and its application for long range gas pipe lines(length of from hundreds meters to few km) were getting increased. In this study, focusing algorithm for array guided waves was developed in order to improve long range inspectability and accuracy of the array guided waves techniques for long range inspection of gas pipes, and performance of the developed techniques was verified by experiments using the developed array guided wave system. As a result, S/N ratio of array guided wave signals obtained with the focusing algorithm was increased higher than that of signals without focusing algorithm

  3. [Studies on transdermal delivery of ferulic acid through rat skin treated by microneedle arrays].

    Science.gov (United States)

    Yang, Bing; Du, Shou-ying; Bai, Jie; Shang, Ke-xin; Lu, Yang; Li, Peng-yue

    2014-12-01

    In order to investigate the characteristics of transdermal delivery of ferulic acid under the treated of microneedle arrays and the influence on permeability of rat skin capillaries, improved Franz-cells were used in the transdermal delivery experiment with the rat skin of abdominal wall and the length of microneedle arrays, different insertion forces, retention time were studied in the influence of characteristics of transdermal delivery of FA. The amount of FA was determined by HPLC system. Intravenous injection Evans blue and FA was added after microneedle arrays treated. Established inflammation model was built by daubing dimethylbenzene. The amount of Evans blue in the rat skin was read at 590 nm wavelength with a Multiskan Go microplate reader. Compared with passive diffusion group the skin pretreated with microneedle arrays had a remarkable enhancement of FA transport (P Microneedle arrays with different length had a remarkable enhancement of FA transport, but was not related to the increase of the length. The research of FA on the reduce of permeability of rat skin capillaries indicated that the skin pretreated with microneedle arrays could reduce the content of Evans blue in the skins of rat significantly compared with the untreated group. The permeation rate of ferulic acid transdermal delivery had remarkable increase under the treated of microneedle arrays and the length of microneedle arrays ,the retention time so as to the insertion force were important to the transdermal delivery of ferulic acid.

  4. Candidate gene studies and the quest for the entrepreneurial gene

    NARCIS (Netherlands)

    M.J.H.M. van der Loos (Matthijs); Ph.D. Koellinger (Philipp); P.J.F. Groenen (Patrick); C.A. Rietveld (Niels); F. Rivadeneira Ramirez (Fernando); F.J.A. van Rooij (Frank); A.G. Uitterlinden (André); A. Hofman (Albert); A.R. Thurik (Roy)

    2011-01-01

    textabstractCandidate gene studies of human behavior are gaining interest in economics and entrepreneurship research. Performing and interpreting these studies is not straightforward because the selection of candidates influences the interpretation of the results. As an example, Nicolaou et al.

  5. Study of Hydrokinetic Turbine Arrays with Large Eddy Simulation

    Science.gov (United States)

    Sale, Danny; Aliseda, Alberto

    2014-11-01

    Marine renewable energy is advancing towards commercialization, including electrical power generation from ocean, river, and tidal currents. The focus of this work is to develop numerical simulations capable of predicting the power generation potential of hydrokinetic turbine arrays-this includes analysis of unsteady and averaged flow fields, turbulence statistics, and unsteady loadings on turbine rotors and support structures due to interaction with rotor wakes and ambient turbulence. The governing equations of large-eddy-simulation (LES) are solved using a finite-volume method, and the presence of turbine blades are approximated by the actuator-line method in which hydrodynamic forces are projected to the flow field as a body force. The actuator-line approach captures helical wake formation including vortex shedding from individual blades, and the effects of drag and vorticity generation from the rough seabed surface are accounted for by wall-models. This LES framework was used to replicate a previous flume experiment consisting of three hydrokinetic turbines tested under various operating conditions and array layouts. Predictions of the power generation, velocity deficit and turbulence statistics in the wakes are compared between the LES and experimental datasets.

  6. Expression Study of Banana Pathogenic Resistance Genes

    Directory of Open Access Journals (Sweden)

    Fenny M. Dwivany

    2016-10-01

    Full Text Available Banana is one of the world's most important trade commodities. However, infection of banana pathogenic fungi (Fusarium oxysporum race 4 is one of the major causes of decreasing production in Indonesia. Genetic engineering has become an alternative way to control this problem by isolating genes that involved in plant defense mechanism against pathogens. Two of the important genes are API5 and ChiI1, each gene encodes apoptosis inhibitory protein and chitinase enzymes. The purpose of this study was to study the expression of API5 and ChiI1 genes as candidate pathogenic resistance genes. The amplified fragments were then cloned, sequenced, and confirmed with in silico studies. Based on sequence analysis, it is showed that partial API5 gene has putative transactivation domain and ChiI1 has 9 chitinase family GH19 protein motifs. Data obtained from this study will contribute in banana genetic improvement.

  7. Study of dependence of DC output of rectenna array on the method of inter-connection of its array element; Rectenna array chokuryu shutsuryoku no array yoso sogo setsuzokuho izonsei no kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Shinohara, M.; Matsumoto, H. [Kyoto University, Kyoto (Japan). Radio Atmospheric Science Center

    1997-08-20

    In 1994 and 1995, a ground-to-ground microwave power transmission (MPT) experiment was carried out by a group of Kyoto University, Kobe University and Kansai Electric Power Company. Among the MPT technologies, which are one of the most important key issues for the realization of the Solar Power Satellite (SPS), studies of `rectenna` (rectifying antenna) have been pursued to archive higher efficiency of conversion from microwave to DC. We had developed a new rectenna panel which can effectively rectify a microwave power of 2.5 W at 2.45 GHz before the ground-to ground MPT field experiment. We examine the sum of the outputs of two or three rectenna panels in which are connected ether in parallel or in series or in the hybrid connection under the same microwave circumstances. The experiment leads us to conclude: (1) The sum of the DC outputs from two rectenna panels connected in parallel is larger than that from those connected in series. (2) The sum of the DC outputs of two rectenna panels is generally smaller than the sum of the DC output of the individual panels unless their output is equal to each other. (3) The total output DC power of a rectenna array increases when we connect the array element with consideration of the `element balance`. Based on the experiment, we propose an optimum method for connection of individual rectenna elements to form an rectenna array. 12 refs., 9 figs., 4 tabs.

  8. Studies of implosion processes of nested tungsten wire-array Z-pinch

    International Nuclear Information System (INIS)

    Ning Cheng; Ding Ning; Liu Quan; Yang Zhenhua

    2006-01-01

    Nested wire-array is a kind of promising structured-load because it can improve the quality of Z-pinch plasma and enhance the radiation power of X-ray source. Based on the zero-dimensional model, the assumption of wire-array collision, and the criterion of optimized load (maximal load kinetic energy), optimization of the typical nested wire-array as a load of Z machine at Sandia Laboratory was carried out. It was shown that the load has been basically optimized. The Z-pinch process of the typical load was numerically studied by means of one-dimensional three-temperature radiation magneto-hydrodynamics (RMHD) code. The obtained results reproduce the dynamic process of the Z-pinch and show the implosion trajectory of nested wire-array and the transfer process of drive current between the inner and outer array. The experimental and computational X-ray pulse was compared, and it was suggested that the assumption of wire-array collision was reasonable in nested wire-array Z-pinch at least for the current level of Z machine. (authors)

  9. Experimental Study of Heat Transfer Enhancements from Array of Alternate Rectangular Dwarf Fins at Different Inclinations

    Science.gov (United States)

    Awasarmol, Umesh Vandeorao; Pise, Ashok T.

    2018-02-01

    The main objective of this experimental work is to investigate and compare heat transfer enhancement of alternate dwarf fin array at different angles of inclination. In this study, the steady state heat transfer from the full length fin arrays and alternate dwarf fin arrays are measured in natural convection and radiation environment. Largest increase in the Nusselt number was achieved with alternate dwarf fin at angle of orientation 90°, which shows about 28% enhanced heat transfer coefficient as opposed to the full-length fin array with 25% saving in material. In case of non-black FAB, contribution of radiation heat transfer is found to be very small nearly within 1% of the heater input. After coating lamp black contribution of radiation heat transfer is found to increase to about 3-4% of the heater input in the range of temperatures considered in this study.

  10. Array capabilities and future arrays

    International Nuclear Information System (INIS)

    Radford, D.

    1993-01-01

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

  11. A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH

    DEFF Research Database (Denmark)

    Becher, Naja; Gjørup, Vibike; Christensen, Rikke

    2012-01-01

    A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH......A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH...

  12. CRISPR-Cas9 directed knock-out of a constitutively expressed gene using lance array nanoinjection.

    Science.gov (United States)

    Sessions, John W; Skousen, Craig S; Price, Kevin D; Hanks, Brad W; Hope, Sandra; Alder, Jonathan K; Jensen, Brian D

    2016-01-01

    CRISPR-Cas9 genome editing and labeling has emerged as an important tool in biologic research, particularly in regards to potential transgenic and gene therapy applications. Delivery of CRISPR-Cas9 plasmids to target cells is typically done by non-viral methods (chemical, physical, and/or electrical), which are limited by low transfection efficiencies or with viral vectors, which are limited by safety and restricted volume size. In this work, a non-viral transfection technology, named lance array nanoinjection (LAN), utilizes a microfabricated silicon chip to physically and electrically deliver genetic material to large numbers of target cells. To demonstrate its utility, we used the CRISPR-Cas9 system to edit the genome of isogenic cells. Two variables related to the LAN process were tested which include the magnitude of current used during plasmid attraction to the silicon lance array (1.5, 4.5, or 6.0 mA) and the number of times cells were injected (one or three times). Results indicate that most successful genome editing occurred after injecting three times at a current control setting of 4.5 mA, reaching a median level of 93.77 % modification. Furthermore, we found that genome editing using LAN follows a non-linear injection-dose response, meaning samples injected three times had modification rates as high as nearly 12 times analogously treated single injected samples. These findings demonstrate the LAN's ability to deliver genetic material to cells and indicate that successful alteration of the genome is influenced by a serial injection method as well as the electrical current settings.

  13. Using macro-arrays to study routes of infection of Helicobacter pylori in three families.

    Directory of Open Access Journals (Sweden)

    Josette Raymond

    Full Text Available BACKGROUND: Analysis of the evolutionary dynamics of Helicobacter pylori allowed tracing the spread of infection through populations on different continents but transmission pathways between individual humans have not been clearly described. MATERIALS AND METHODS: To investigate person-to-person transmission, we studied three families each including one child with persistence of symptoms after antibiotic treatment. Ten isolates from the antrum and corpus of stomach of each family member were analyzed both by sequencing of two housekeeping genes and macroarray tests. RESULTS: A total of 134 (8.4% out of the 1590 coding sequences (CDSs tested, including cag PAI and insertion sequences, were present in some but not all isolates (and are therefore defined as variable CDSs. Most of the variable CDSs encoded proteins of unknown function (76/134 or were selfish DNA including that encoding restriction/modification enzymes (13/134. Isolates colonizing the stomach of one individual can vary by point mutations, as seen in hspA, or by the gain or loss of one to five CDSs. They were considered as (genetic variants. The phylogenetic clustering of gene profiles obtained on macro-arrays allowed identifying the different strains infecting families. Two to five strains circulated within a family. Identical strains were present in at least two members of all three families supporting the accepted model of intrafamilial transmission. Surprisingly, the mother was not implicated in the transmission of H. pylori in the two French families. Sibling-to-sibling transmission and acquisition of H. pylori from outside the family appeared to be probable in the transmission pathways. CONCLUSION: Macroarray analysis based on previously selected CDSs gives a comprehensive view of the genome diversity of a pathogen. This approach combined with information on the origin of the hspA and glmM alleles revealed that Helicobacter pylori infection may be acquired by more diverse routes

  14. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2) as a predisposing candidate gene in neuroblastoma.

    Science.gov (United States)

    Romania, Paolo; Castellano, Aurora; Surace, Cecilia; Citti, Arianna; De Ioris, Maria Antonietta; Sirleto, Pietro; De Mariano, Marilena; Longo, Luca; Boldrini, Renata; Angioni, Adriano; Locatelli, Franco; Fruci, Doriana

    2013-01-01

    Neuroblastoma (NB), the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH) analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2) locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.

  15. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2 as a predisposing candidate gene in neuroblastoma.

    Directory of Open Access Journals (Sweden)

    Paolo Romania

    Full Text Available Neuroblastoma (NB, the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2 locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.

  16. MISSION-ORIENTED SENSOR ARRAYS AND UAVs – A CASE STUDY ON ENVIRONMENTAL MONITORING

    Directory of Open Access Journals (Sweden)

    N. M. Figueira

    2015-08-01

    Full Text Available This paper presents a new concept of UAV mission design in geomatics, applied to the generation of thematic maps for a multitude of civilian and military applications. We discuss the architecture of Mission-Oriented Sensors Arrays (MOSA, proposed in Figueira et Al. (2013, aimed at splitting and decoupling the mission-oriented part of the system (non safety-critical hardware and software from the aircraft control systems (safety-critical. As a case study, we present an environmental monitoring application for the automatic generation of thematic maps to track gunshot activity in conservation areas. The MOSA modeled for this application integrates information from a thermal camera and an on-the-ground microphone array. The use of microphone arrays technology is of particular interest in this paper. These arrays allow estimation of the direction-of-arrival (DOA of the incoming sound waves. Information about events of interest is obtained by the fusion of the data provided by the microphone array, captured by the UAV, fused with information from the termal image processing. Preliminary results show the feasibility of the on-the-ground sound processing array and the simulation of the main processing module, to be embedded into an UAV in a future work. The main contributions of this paper are the proposed MOSA system, including concepts, models and architecture.

  17. electrode array

    African Journals Online (AJOL)

    PROF EKWUEME

    A geoelectric investigation employing vertical electrical soundings (VES) using the Ajayi - Makinde Two-Electrode array and the ... arrangements used in electrical D.C. resistivity survey. These include ..... Refraction Tomography to Study the.

  18. National Array of Neutron Detectors (NAND): A versatile tool for nuclear reaction studies

    Energy Technology Data Exchange (ETDEWEB)

    Golda, K.S., E-mail: goldaks@gmail.com [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Jhingan, A.; Sugathan, P. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Singh, Hardev [Department of Physics, Kurukshetra University, Kurukshetra 136119 (India); Singh, R.P. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Behera, B.R. [Department of Physics, Panjab University, Chandigarh 160014 (India); Mandal, S. [Department of Physics and Astrophysics, Delhi University, New Delhi 110007 (India); Kothari, A.; Gupta, Arti; Zacharias, J.; Archunan, M.; Barua, P.; Venkataramanan, S.; Bhowmik, R.K. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Govil, I.M. [Department of Physics, Panjab University, Chandigarh 160014 (India); Datta, S.K.; Chatterjee, M.B. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India)

    2014-11-01

    The first phase of the National Array of Neutron Detectors (NAND) consisting of 26 neutron detectors has been commissioned at the Inter University Accelerator Centre (IUAC), New Delhi. The motivation behind setting up of such a detector system is the need for more accurate and efficient study of reaction mechanisms in the projectile energy range of 5–8 MeV/n using heavy ion beams from a 15 UD Pelletron and an upgraded LINAC booster facility at IUAC. The above detector array can be used for inclusive as well as exclusive measurements of reaction products of which at least one product is a neutron. While inclusive measurements can be made using only the neutron detectors along with the time of flight technique and a pulsed beam, exclusive measurements can be performed by detecting neutrons in coincidence with charged particles and/or fission fragments detected with ancillary detectors. The array can also be used for neutron tagged gamma-ray spectroscopy in (HI, xn) reactions by detecting gamma-rays in coincidence with the neutrons in a compact geometrical configuration. The various features and the performance of the different aspects of the array are described in the present paper. -- Highlights: •We report the design, fabrication and installation of a 26 element modular neutron detection system (NAND). •The array has been designed for the fusion–fission studies at near and above the barrier energies. •The relevant characteristics of the array are studied exhaustively and reported. •The efficiency of the detectors are measured and compared with the monte carlo simulations. •The second phase of the array will be augmented with 80 more neutron detectors which will enable the system to measure the neutron multiplicity distribution.

  19. National Array of Neutron Detectors (NAND): A versatile tool for nuclear reaction studies

    International Nuclear Information System (INIS)

    Golda, K.S.; Jhingan, A.; Sugathan, P.; Singh, Hardev; Singh, R.P.; Behera, B.R.; Mandal, S.; Kothari, A.; Gupta, Arti; Zacharias, J.; Archunan, M.; Barua, P.; Venkataramanan, S.; Bhowmik, R.K.; Govil, I.M.; Datta, S.K.; Chatterjee, M.B.

    2014-01-01

    The first phase of the National Array of Neutron Detectors (NAND) consisting of 26 neutron detectors has been commissioned at the Inter University Accelerator Centre (IUAC), New Delhi. The motivation behind setting up of such a detector system is the need for more accurate and efficient study of reaction mechanisms in the projectile energy range of 5–8 MeV/n using heavy ion beams from a 15 UD Pelletron and an upgraded LINAC booster facility at IUAC. The above detector array can be used for inclusive as well as exclusive measurements of reaction products of which at least one product is a neutron. While inclusive measurements can be made using only the neutron detectors along with the time of flight technique and a pulsed beam, exclusive measurements can be performed by detecting neutrons in coincidence with charged particles and/or fission fragments detected with ancillary detectors. The array can also be used for neutron tagged gamma-ray spectroscopy in (HI, xn) reactions by detecting gamma-rays in coincidence with the neutrons in a compact geometrical configuration. The various features and the performance of the different aspects of the array are described in the present paper. -- Highlights: •We report the design, fabrication and installation of a 26 element modular neutron detection system (NAND). •The array has been designed for the fusion–fission studies at near and above the barrier energies. •The relevant characteristics of the array are studied exhaustively and reported. •The efficiency of the detectors are measured and compared with the monte carlo simulations. •The second phase of the array will be augmented with 80 more neutron detectors which will enable the system to measure the neutron multiplicity distribution

  20. Whole genome expression array profiling highlights differences in mucosal defense genes in Barrett's esophagus and esophageal adenocarcinoma.

    Directory of Open Access Journals (Sweden)

    Derek J Nancarrow

    Full Text Available Esophageal adenocarcinoma (EAC has become a major concern in Western countries due to rapid rises in incidence coupled with very poor survival rates. One of the key risk factors for the development of this cancer is the presence of Barrett's esophagus (BE, which is believed to form in response to repeated gastro-esophageal reflux. In this study we performed comparative, genome-wide expression profiling (using Illumina whole-genome Beadarrays on total RNA extracted from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC and those with normal squamous epithelium. We combined these data with publically accessible raw data from three similar studies to investigate key gene and ontology differences between these three tissue states. The results support the deduction that BE is a tissue with enhanced glycoprotein synthesis machinery (DPP4, ATP2A3, AGR2 designed to provide strong mucosal defenses aimed at resisting gastro-esophageal reflux. EAC exhibits the enhanced extracellular matrix remodeling (collagens, IGFBP7, PLAU effects expected in an aggressive form of cancer, as well as evidence of reduced expression of genes associated with mucosal (MUC6, CA2, TFF1 and xenobiotic (AKR1C2, AKR1B10 defenses. When our results are compared to previous whole-genome expression profiling studies keratin, mucin, annexin and trefoil factor gene groups are the most frequently represented differentially expressed gene families. Eleven genes identified here are also represented in at least 3 other profiling studies. We used these genes to discriminate between squamous epithelium, BE and EAC within the two largest cohorts using a support vector machine leave one out cross validation (LOOCV analysis. While this method was satisfactory for discriminating squamous epithelium and BE, it demonstrates the need for more detailed investigations into profiling changes between BE and EAC.

  1. Performance study of solar cell arrays based on a Trough Concentrating Photovoltaic/Thermal system

    International Nuclear Information System (INIS)

    Li, Ming; Ji, Xu; Li, Guoliang; Wei, Shengxian; Li, YingFeng; Shi, Feng

    2011-01-01

    Highlights: → The performances of solar cell arrays based on a Trough Concentrating Photovoltaic/Thermal (TCPV/T) system have been studied. → The optimum concentration ratios for the single crystalline silicon cell, the Super cells and the GaAs cells were studied by experiments. → The influences between the solar cell's performance and the series resistances, the working temperature, solar irradiation intensity were explored. - Abstract: The performances of solar cell arrays based on a Trough Concentrating Photovoltaic/Thermal (TCPV/T) system have been studied via both experiment and theoretical calculation. The I-V characteristics of the solar cell arrays and the output performances of the TCPV/T system demonstrated that among the investigated four types of solar cell arrays, the triple junction GaAs cells possessed good performance characteristics and the polysilicon cells exhibited poor performance characteristics under concentrating conditions. The optimum concentration ratios for the single crystalline silicon cell, the Super cells and the GaAs cells were also studied by experiments. The optimum concentration ratios for the single crystalline silicon cells and Super cells were 4.23 and 8.46 respectively, and the triple junction GaAs cells could work well at higher concentration ratio. Besides, some theoretical calculations and experiments were performed to explore the influences of the series resistances and the working temperature. When the series resistances R s changed from 0 Ω to 1 Ω, the maximum power P m of the single crystalline silicon, the polycrystalline silicon, the Super cell and the GaAs cell arrays decreased by 67.78%, 74.93%, 77.30% and 58.07% respectively. When the cell temperature increased by 1 K, the short circuit current of the four types of solar cell arrays decreased by 0.11818 A, 0.05364 A, 0.01387 A and 0.00215 A respectively. The research results demonstrated that the output performance of the solar cell arrays with lower

  2. Advances in study of reporter gene imaging for monitoring gene therapy

    International Nuclear Information System (INIS)

    Mu Chuanjie; Zhou Jiwen

    2003-01-01

    To evaluate the efficiency of gene therapy, it is requisite to monitor localization and expression of the therapeutic gene in vivo. Monitoring expression of reporter gene using radionuclide reporter gene technique is the best method. Adenoviral vectors expressing reporter gene are constructed using gene fusion, bicistronic, double promoter or bidirectional transcriptional recombination techniques, and transferred into target cells and tissues, then injected radiolabeled reporter probes which couple to the reporter genes. The reporter genes can be imaged invasively, repeatedly, quantitatively with γ-camera, PET and SPECT. Recently, several reporter gene and reporter probe systems have been used in studies of gene therapy. The part of them has been used for clinic trials

  3. A modified analytical model to study the sensing performance of a flexible capacitive tactile sensor array

    International Nuclear Information System (INIS)

    Liang, Guanhao; Wang, Yancheng; Mei, Deqing; Xi, Kailun; Chen, Zichen

    2015-01-01

    This paper presents a modified analytical model to study the sensing performance of a flexible capacitive tactile sensor array, which utilizes solid polydimethylsiloxane (PDMS) film as the dielectric layer. To predict the deformation of the sensing unit and capacitance changes, each sensing unit is simplified into a three-layer plate structure and divided into central, edge and corner regions. The plate structure and the three regions are studied by the general and modified models, respectively. For experimental validation, the capacitive tactile sensor array with 8  ×  8 (= 64) sensing units is fabricated. Experiments are conducted by measuring the capacitance changes versus applied external forces and compared with the general and modified models’ predictions. For the developed tactile sensor array, the sensitivity predicted by the modified analytical model is 1.25%/N, only 0.8% discrepancy from the experimental measurement. Results demonstrate that the modified analytical model can accurately predict the sensing performance of the sensor array and could be utilized for model-based optimal capacitive tactile sensor array design. (paper)

  4. An OSSE Study for Deep Argo Array using the GFDL Ensemble Coupled Data Assimilation System

    Science.gov (United States)

    Chang, You-Soon; Zhang, Shaoqing; Rosati, Anthony; Vecchi, Gabriel A.; Yang, Xiaosong

    2018-03-01

    An observing system simulation experiment (OSSE) using an ensemble coupled data assimilation system was designed to investigate the impact of deep ocean Argo profile assimilation in a biased numerical climate system. Based on the modern Argo observational array and an artificial extension to full depth, "observations" drawn from one coupled general circulation model (CM2.0) were assimilated into another model (CM2.1). Our results showed that coupled data assimilation with simultaneous atmospheric and oceanic constraints plays a significant role in preventing deep ocean drift. However, the extension of the Argo array to full depth did not significantly improve the quality of the oceanic climate estimation within the bias magnitude in the twin experiment. Even in the "identical" twin experiment for the deep Argo array from the same model (CM2.1) with the assimilation model, no significant changes were shown in the deep ocean, such as in the Atlantic meridional overturning circulation and the Antarctic bottom water cell. The small ensemble spread and corresponding weak constraints by the deep Argo profiles with medium spatial and temporal resolution may explain why the deep Argo profiles did not improve the deep ocean features in the assimilation system. Additional studies using different assimilation methods with improved spatial and temporal resolution of the deep Argo array are necessary in order to more thoroughly understand the impact of the deep Argo array on the assimilation system.

  5. A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

    Science.gov (United States)

    Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

    2015-06-30

    Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

  6. Application of high-resolution capillary array electrophoresis with automated fraction collection for GeneCalling analysis of the yeast genomic DNA

    Czech Academy of Sciences Publication Activity Database

    Berka, J.; Ruiz-Martinez, M. C.; Hammond, R.; Minarik, M.; Foret, František; Sosic, Z.; Klepárník, Karel; Karger, B. L.

    2003-01-01

    Roč. 24, č. 4 (2003), s. 639-647 ISSN 0173-0835 R&D Projects: GA ČR GA203/00/0772; GA ČR GA303/00/0928 Institutional research plan: CEZ:AV0Z4031919 Keywords : capillary array * fraction collection * gene expression profiling Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.040, year: 2003

  7. Experimental Study of Boundary Layer Flow Control Using an Array of Ramp-Shaped Vortex Generators

    Science.gov (United States)

    Hirt, Stefanie M.; Zaman, Khairul B.M.Q.; Bencic, Tomothy J.

    2012-01-01

    The objective of this study was to obtain a database on the flowfield past an array of vortex generators (VGs) in a turbulent boundary layer. All testing was carried out in a low speed wind tunnel with a flow velocity of 29 ft/sec, giving a Reynolds number of 17,500 based on the width of the VG. The flowfield generated by an array of five ramp-shaped vortex generators was examined with hot wire anemometry and smoke flow visualization. The magnitude and extent of the velocity increase near the wall, the penetration of the velocity deficit into the core flow, and the peak streamwise vorticity are examined. Influence of various parameters on the effectiveness of the array is considered on the basis of the ability to pull high momentum fluid into the near wall region.

  8. Gene set analysis for interpreting genetic studies

    DEFF Research Database (Denmark)

    Pers, Tune H

    2016-01-01

    Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways...

  9. Human cell-based micro electrode array platform for studying neurotoxicity

    Directory of Open Access Journals (Sweden)

    Laura eYlä-Outinen

    2010-09-01

    Full Text Available At present, most of the neurotoxicological analyses are based on in vitro and in vivo models utilizing animal cells or animal models. In addition, the used in vitro models are mostly based on molecular biological end-point analyses. Thus, for neurotoxicological screening, human cell-based analysis platforms in which the functional neuronal networks responses for various neurotoxicants can be also detected real-time are highly needed. Microelectrode array (MEA is a method which enables the measurement of functional activity of neuronal cell networks in vitro for long periods of time. Here, we utilize MEA to study the neurotoxicity of methyl mercury chloride (MeHgCl, concentrations 0.5-500 nM to human embryonic stem cell (hESC-derived neuronal cell networks exhibiting spontaneous electrical activity. The neuronal cell cultures were matured on MEAs into networks expressing spontaneous spike train-like activity before exposing the cells to MeHgCl for 72 hours. MEA measurements were performed acutely and 24, 48, and 72 hours after the onset of the exposure. Finally, exposed cells were analyzed with traditional molecular biological methods for cell proliferation, cell survival, and gene and protein expression. Our results show that 500 nM MeHgCl decreases the electrical signaling and alters the pharmacologic response of hESC-derived neuronal networks in delayed manner whereas effects can not be detected with qRT-PCR, immunostainings, or proliferation measurements. Thus, we conclude that human cell-based MEA-platform is a sensitive online method for neurotoxicological screening.

  10. Study on dynamic behavior analysis of towed line array sensor

    Directory of Open Access Journals (Sweden)

    Hyun Kyoung Shin

    2012-03-01

    Full Text Available A set of equations of motion is derived for vibratory motions of an underwater cable connected to a moving vehicle at one end and with drogues at the other end. From the static analysis, cable configurations are obtained for different vehicle speeds and towing pretensions are determined by fluid resistance of drogues. Also the dynamic analysis is required to predict its vibratory motion. Nonlinear fluid drag forces greatly influence the dynamic tension. In this study, a numerical analysis program was developed to find out the characteristic of cable behaviour. The motion is described in terms of space and time coordinates based on Chebyshev polynomial expansions. For the spatial integration the collocation method is employed and the Newmark method is applied for the time integration. Dynamic tensions, displacements, velocities, accelerations were predicted in the time domain while natural frequencies and transfer functions were obtained in the frequency domain.

  11. Synthesis Study of a 6-Element Non-Uniform Array with Tilted Elements for CLARREO Project

    Science.gov (United States)

    Jamnejad, Vahraz; Hoorfar, Ahmad

    2012-01-01

    This paper presents the results of a preliminary study of the gain/pattern properties of a 6-element Radio Occultation (RO) array for the proposed CLARREO (Climate Absolute Radiance and Refractivity Observatory (CLARREO) Project. CLARREO is one of the 4 highest priority missions recommended in the National Research Council Earth Science Decadal Survey.

  12. Genomewide Analysis of Aryl Hydrocarbon Receptor Binding Targets Reveals an Extensive Array of Gene Clusters that Control Morphogenetic and Developmental Programs

    Science.gov (United States)

    Sartor, Maureen A.; Schnekenburger, Michael; Marlowe, Jennifer L.; Reichard, John F.; Wang, Ying; Fan, Yunxia; Ma, Ci; Karyala, Saikumar; Halbleib, Danielle; Liu, Xiangdong; Medvedovic, Mario; Puga, Alvaro

    2009-01-01

    Background The vertebrate aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates cellular responses to environmental polycyclic and halogenated compounds. The naive receptor is believed to reside in an inactive cytosolic complex that translocates to the nucleus and induces transcription of xenobiotic detoxification genes after activation by ligand. Objectives We conducted an integrative genomewide analysis of AHR gene targets in mouse hepatoma cells and determined whether AHR regulatory functions may take place in the absence of an exogenous ligand. Methods The network of AHR-binding targets in the mouse genome was mapped through a multipronged approach involving chromatin immunoprecipitation/chip and global gene expression signatures. The findings were integrated into a prior functional knowledge base from Gene Ontology, interaction networks, Kyoto Encyclopedia of Genes and Genomes pathways, sequence motif analysis, and literature molecular concepts. Results We found the naive receptor in unstimulated cells bound to an extensive array of gene clusters with functions in regulation of gene expression, differentiation, and pattern specification, connecting multiple morphogenetic and developmental programs. Activation by the ligand displaced the receptor from some of these targets toward sites in the promoters of xenobiotic metabolism genes. Conclusions The vertebrate AHR appears to possess unsuspected regulatory functions that may be potential targets of environmental injury. PMID:19654925

  13. Evaluation of suitable reference genes for gene expression studies ...

    Indian Academy of Sciences (India)

    2011-12-14

    Dec 14, 2011 ... MADS family of TFs control floral organ identity within each whorl of the flower by activating downstream genes. Measuring gene expression in different tissue types and developmental stages is of fundamental importance in TFs functional research. In last few years, quantitative real-time. PCR (qRT-PCR) ...

  14. Gene selection heuristic algorithm for nutrigenomics studies.

    Science.gov (United States)

    Valour, D; Hue, I; Grimard, B; Valour, B

    2013-07-15

    Large datasets from -omics studies need to be deeply investigated. The aim of this paper is to provide a new method (LEM method) for the search of transcriptome and metabolome connections. The heuristic algorithm here described extends the classical canonical correlation analysis (CCA) to a high number of variables (without regularization) and combines well-conditioning and fast-computing in "R." Reduced CCA models are summarized in PageRank matrices, the product of which gives a stochastic matrix that resumes the self-avoiding walk covered by the algorithm. Then, a homogeneous Markov process applied to this stochastic matrix converges the probabilities of interconnection between genes, providing a selection of disjointed subsets of genes. This is an alternative to regularized generalized CCA for the determination of blocks within the structure matrix. Each gene subset is thus linked to the whole metabolic or clinical dataset that represents the biological phenotype of interest. Moreover, this selection process reaches the aim of biologists who often need small sets of genes for further validation or extended phenotyping. The algorithm is shown to work efficiently on three published datasets, resulting in meaningfully broadened gene networks.

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

    Science.gov (United States)

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

    2015-04-01

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

  16. Online charge calibration of LHAASO-WCDA—a study with the engineering array

    Science.gov (United States)

    Gao, Bo; Chen, Ming-Jun; Gu, Min-Hao; Hao, Xin-Jun; Li, Hui-Cai; Wu, Han-Rong; Yao, Zhi-Guo; You, Xiao-Hao; Zhou, Bin

    2014-02-01

    LHAASO-WCDA is a large ground-based water Cherenkov detector array planned to be built at Shangri-La, Yunnan Province, China. As a major component of the LHAASO project, the main purpose of LHAASO-WCDA is to survey the northern sky for very-high-energy (above 100 GeV) gamma ray sources and measure the spectrum. To gain full knowledge of the water Cherenkov technique and to investigate the engineering issues, a 9-cell detector array has been built at the Yang-Ba-Jing site, neighboring the ARGO-YBJ experiment. With the array, charge calibration methods for both low and high ranges of the PMT readout are studied, whose result shows that a precision at several percentages can be reached, which can satisfy the requirement of the detector array. During the long term operation, the charge calibration stability and environmental affection are studied; in this paper, the results are discussed. These calibration methods are proposed to be applied in the future LHAASO-WCDA project.

  17. Online charge calibration of LHASSO-WCDA-2 study with the engineering array

    International Nuclear Information System (INIS)

    Gao Bo; Chen Mingjun; Gu Minhao; Wu Hanrong; Yao Zhiguo; Zhou Bin; Hao Xinjun; Li Huicai; You Xiaohao

    2014-01-01

    LHAASO-WCDA is a large ground-based water Cherenkov detector array planned to be built at Shangri-La, Yunnan Province, China. As a major component of the LHAASO project, the main purpose of LHAASO-WCDA is to survey the northern sky for very-high-energy (above 100 GeV) gamma ray sources and measure the spectrum. To gain full knowledge of the water Cherenkov technique and to investigate the engineering issues, a 9-cell detector array has been built at the Yangbajing site, neighboring the ARGO-YBJ experiment. With the array, charge calibration methods for both low and high ranges of the PMT readout are studied, whose result shows that a precision at several percentages can be reached, which can satisfy the requirement of the detector array. During the long term operation, the charge calibration stability and environmental affection are studied; in this paper, the results are discussed. These calibration methods are proposed to be applied in the future LHAASO-WCDA project. (authors)

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

    Directory of Open Access Journals (Sweden)

    Goldstein Alisa M

    2006-11-01

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

  19. National Array of Neutron Detectors (NAND): A versatile tool for nuclear reaction studies

    Science.gov (United States)

    Golda, K. S.; Jhingan, A.; Sugathan, P.; Singh, Hardev; Singh, R. P.; Behera, B. R.; Mandal, S.; Kothari, A.; Gupta, Arti; Zacharias, J.; Archunan, M.; Barua, P.; Venkataramanan, S.; Bhowmik, R. K.; Govil, I. M.; Datta, S. K.; Chatterjee, M. B.

    2014-11-01

    The first phase of the National Array of Neutron Detectors (NAND) consisting of 26 neutron detectors has been commissioned at the Inter University Accelerator Centre (IUAC), New Delhi. The motivation behind setting up of such a detector system is the need for more accurate and efficient study of reaction mechanisms in the projectile energy range of 5-8 MeV/n using heavy ion beams from a 15 UD Pelletron and an upgraded LINAC booster facility at IUAC. The above detector array can be used for inclusive as well as exclusive measurements of reaction products of which at least one product is a neutron. While inclusive measurements can be made using only the neutron detectors along with the time of flight technique and a pulsed beam, exclusive measurements can be performed by detecting neutrons in coincidence with charged particles and/or fission fragments detected with ancillary detectors. The array can also be used for neutron tagged gamma-ray spectroscopy in (HI, xn) reactions by detecting gamma-rays in coincidence with the neutrons in a compact geometrical configuration. The various features and the performance of the different aspects of the array are described in the present paper.

  20. Study on radiation-inducible genes

    International Nuclear Information System (INIS)

    Lim, Sang Yong; Kim, Dong Ho; Joe, Min Ho; Park, Hae Jun; Song, Hyu Npa

    2012-01-01

    Radiation-inducible genes of E. coli, which is a model strain for bacterial study, and Salmonella, which is a typical strain for pathogenic bacteria were compared through omic analysis. Heat shock response genes and prophage genes were induced by radiation in Salmonella, not in E. coli. Among prophage genes tested, STM2628 showed the highest activation by radiation, and approximately 1 kb promoter region was turned out to be necessary for radiation response. To screen an artificial promoter showing activation by 2 Gy, the high-throughput screening method using fluorescent MUG substrate was established. The use of bacteria as anticancer agents has attracted interest. In this study, we tried to develop tumor targeting bacteria in which the radiation-inducible promoter activate a transgene encoding a cytotoxic protein. To do this, a tumor-targeting hfq Salmonella mutant strain was constructed, and we found that its virulence decreased. For outward secretion of anticancer protein produced inside bacteria, the signal peptide of SspH1 was determined and the signal peptide was proven to be able to secrete an anticancer protein. Tumor xenograft mouse model was secured, which can be used for efficiency evaluation of bacterial tumor therapy

  1. Study on radiation-inducible genes

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Sang Yong; Kim, Dong Ho; Joe, Min Ho; Park, Hae Jun; Song, Hyu Npa

    2012-01-15

    Radiation-inducible genes of E. coli, which is a model strain for bacterial study, and Salmonella, which is a typical strain for pathogenic bacteria were compared through omic analysis. Heat shock response genes and prophage genes were induced by radiation in Salmonella, not in E. coli. Among prophage genes tested, STM2628 showed the highest activation by radiation, and approximately 1 kb promoter region was turned out to be necessary for radiation response. To screen an artificial promoter showing activation by 2 Gy, the high-throughput screening method using fluorescent MUG substrate was established. The use of bacteria as anticancer agents has attracted interest. In this study, we tried to develop tumor targeting bacteria in which the radiation-inducible promoter activate a transgene encoding a cytotoxic protein. To do this, a tumor-targeting hfq Salmonella mutant strain was constructed, and we found that its virulence decreased. For outward secretion of anticancer protein produced inside bacteria, the signal peptide of SspH1 was determined and the signal peptide was proven to be able to secrete an anticancer protein. Tumor xenograft mouse model was secured, which can be used for efficiency evaluation of bacterial tumor therapy.

  2. Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.

    Science.gov (United States)

    Schaid, Daniel J; Sinnwell, Jason P; Jenkins, Gregory D; McDonnell, Shannon K; Ingle, James N; Kubo, Michiaki; Goss, Paul E; Costantino, Joseph P; Wickerham, D Lawrence; Weinshilboum, Richard M

    2012-01-01

    Gene-set analyses have been widely used in gene expression studies, and some of the developed methods have been extended to genome wide association studies (GWAS). Yet, complications due to linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs), and variable numbers of SNPs per gene and genes per gene-set, have plagued current approaches, often leading to ad hoc "fixes." To overcome some of the current limitations, we developed a general approach to scan GWAS SNP data for both gene-level and gene-set analyses, building on score statistics for generalized linear models, and taking advantage of the directed acyclic graph structure of the gene ontology when creating gene-sets. However, other types of gene-set structures can be used, such as the popular Kyoto Encyclopedia of Genes and Genomes (KEGG). Our approach combines SNPs into genes, and genes into gene-sets, but assures that positive and negative effects of genes on a trait do not cancel. To control for multiple testing of many gene-sets, we use an efficient computational strategy that accounts for LD and provides accurate step-down adjusted P-values for each gene-set. Application of our methods to two different GWAS provide guidance on the potential strengths and weaknesses of our proposed gene-set analyses. © 2011 Wiley Periodicals, Inc.

  3. With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies.

    Science.gov (United States)

    Chapman, Joanne R; Waldenström, Jonas

    2015-01-01

    The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.

  4. Camera trap arrays improve detection probability of wildlife: Investigating study design considerations using an empirical dataset.

    Science.gov (United States)

    O'Connor, Kelly M; Nathan, Lucas R; Liberati, Marjorie R; Tingley, Morgan W; Vokoun, Jason C; Rittenhouse, Tracy A G

    2017-01-01

    Camera trapping is a standard tool in ecological research and wildlife conservation. Study designs, particularly for small-bodied or cryptic wildlife species often attempt to boost low detection probabilities by using non-random camera placement or baited cameras, which may bias data, or incorrectly estimate detection and occupancy. We investigated the ability of non-baited, multi-camera arrays to increase detection probabilities of wildlife. Study design components were evaluated for their influence on wildlife detectability by iteratively parsing an empirical dataset (1) by different sizes of camera arrays deployed (1-10 cameras), and (2) by total season length (1-365 days). Four species from our dataset that represented a range of body sizes and differing degrees of presumed detectability based on life history traits were investigated: white-tailed deer (Odocoileus virginianus), bobcat (Lynx rufus), raccoon (Procyon lotor), and Virginia opossum (Didelphis virginiana). For all species, increasing from a single camera to a multi-camera array significantly improved detection probability across the range of season lengths and number of study sites evaluated. The use of a two camera array increased survey detection an average of 80% (range 40-128%) from the detection probability of a single camera across the four species. Species that were detected infrequently benefited most from a multiple-camera array, where the addition of up to eight cameras produced significant increases in detectability. However, for species detected at high frequencies, single cameras produced a season-long (i.e, the length of time over which cameras are deployed and actively monitored) detectability greater than 0.75. These results highlight the need for researchers to be critical about camera trap study designs based on their intended target species, as detectability for each focal species responded differently to array size and season length. We suggest that researchers a priori identify

  5. Camera trap arrays improve detection probability of wildlife: Investigating study design considerations using an empirical dataset.

    Directory of Open Access Journals (Sweden)

    Kelly M O'Connor

    Full Text Available Camera trapping is a standard tool in ecological research and wildlife conservation. Study designs, particularly for small-bodied or cryptic wildlife species often attempt to boost low detection probabilities by using non-random camera placement or baited cameras, which may bias data, or incorrectly estimate detection and occupancy. We investigated the ability of non-baited, multi-camera arrays to increase detection probabilities of wildlife. Study design components were evaluated for their influence on wildlife detectability by iteratively parsing an empirical dataset (1 by different sizes of camera arrays deployed (1-10 cameras, and (2 by total season length (1-365 days. Four species from our dataset that represented a range of body sizes and differing degrees of presumed detectability based on life history traits were investigated: white-tailed deer (Odocoileus virginianus, bobcat (Lynx rufus, raccoon (Procyon lotor, and Virginia opossum (Didelphis virginiana. For all species, increasing from a single camera to a multi-camera array significantly improved detection probability across the range of season lengths and number of study sites evaluated. The use of a two camera array increased survey detection an average of 80% (range 40-128% from the detection probability of a single camera across the four species. Species that were detected infrequently benefited most from a multiple-camera array, where the addition of up to eight cameras produced significant increases in detectability. However, for species detected at high frequencies, single cameras produced a season-long (i.e, the length of time over which cameras are deployed and actively monitored detectability greater than 0.75. These results highlight the need for researchers to be critical about camera trap study designs based on their intended target species, as detectability for each focal species responded differently to array size and season length. We suggest that researchers a priori

  6. The application of radiobiological study by gene chip technique

    International Nuclear Information System (INIS)

    Li Yu; Li Yao

    2002-01-01

    The responses to ionizing radiation are complex and are regulated by a number of overlapping molecular pathways. One such stress-signaling pathway involves p53, which regulates the expression of over 100 genes already identified. It is also becoming increasingly apparent that the pattern of stress gene expression has some cell type specificity. It may be possible to exploit these differences in stress gene responsiveness as molecular markers through the use of a combined informatics and functional genomic approach. The techniques of micro-array analysis potentially offer the opportunity to monitor changes in gene expression across the entire set of expressed genes in a cell or organism. It again highlights the importance of a cellular context to genotoxic stress responses; it also raises the prospect of expression profiling of cell lines, tissues, and tumors. Such profiles may have a predictive value in cancer therapy regimens, or identification of exposures to environmental toxins

  7. The utility of sparse 2D fully electronically steerable focused ultrasound phased arrays for thermal surgery: a simulation study

    International Nuclear Information System (INIS)

    Ellens, Nicholas; Pulkkinen, Aki; Song Junho; Hynynen, Kullervo

    2011-01-01

    Sparse arrays are widely used in diagnostic ultrasound for their strong performance and relative technical simplicity. This simulation study assessed the efficacy of phased arrays of varied sparseness for thermal surgery, especially with regard to power consumption and near-field heating. It employs a linear ultrasound propagation model and a semi-analytical solution to the Pennes' bioheat transfer equation. The basic design had 4912 cylindrical transducers (500 kHz) arranged on a flat 12 cm disk (1.5 mm spacing). This array was compared to randomly-thinned sparse arrays with 75%, 50% and 25% populations. Temperature elevations of 60 and 70 deg. C were induced in sonication times of 5-20 s, at foci spanning depths of 50-150 mm and radii of 0-60 mm. The sparse arrays produced nearly indistinguishable focal patterns but, averaged across the foci, required 132%, 200% and 393% of the power of the full array, respectively, applied through fewer transducer elements. Comparable results were found at 1 MHz from equivalent arrays. Simulated lesions were formed (thermal dose ≥ 240 equivalent minutes at 43 deg. C (T 43 )) and 'transition' and 'unsafe' regions (both defined as 5 min 43 < 240 min) were identified, the former immediately surrounding the lesion and the latter anywhere else. At a depth of 100 mm, sparse arrays were found to produce comparable lesions to the full array at the focus, but 'unsafe', over-heated near-field regions after some ablated lesion volume: about 12 mL for the 25% array, around 100 mL for the 50% array, while the 75% and full arrays produced 150 mL lesions safely.

  8. Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study

    Directory of Open Access Journals (Sweden)

    Muhie Seid Y

    2009-12-01

    Full Text Available Abstract Background Preterm delivery (PTD is a significant public health problem associated with greater risk of mortality and morbidity in infants and mothers. Pathophysiologic processes that may lead to PTD start early in pregnancy. We investigated early pregnancy peripheral blood global gene expression and PTD risk. Methods As part of a prospective study, ribonucleic acid was extracted from blood samples (collected at 16 weeks gestational age from 14 women who had PTD (cases and 16 women who delivered at term (controls. Gene expressions were measured using the GeneChip® Human Genome U133 Plus 2.0 Array. Student's T-test and fold change analysis were used to identify differentially expressed genes. We used hierarchical clustering and principle components analysis to characterize signature gene expression patterns among cases and controls. Pathway and promoter sequence analyses were used to investigate functions and functional relationships as well as regulatory regions of differentially expressed genes. Results A total of 209 genes, including potential candidate genes (e.g. PTGDS, prostaglandin D2 synthase 21 kDa, were differentially expressed. A set of these genes achieved accurate pre-diagnostic separation of cases and controls. These genes participate in functions related to immune system and inflammation, organ development, metabolism (lipid, carbohydrate and amino acid and cell signaling. Binding sites of putative transcription factors such as EGR1 (early growth response 1, TFAP2A (transcription factor AP2A, Sp1 (specificity protein 1 and Sp3 (specificity protein 3 were over represented in promoter regions of differentially expressed genes. Real-time PCR confirmed microarray expression measurements of selected genes. Conclusions PTD is associated with maternal early pregnancy peripheral blood gene expression changes. Maternal early pregnancy peripheral blood gene expression patterns may be useful for better understanding of PTD

  9. A novel deletion in the thyrotropin Beta-subunit gene identified by array comparative genomic hybridization analysis causes central congenital hypothyroidism in a boy originating from Turkey.

    Science.gov (United States)

    Hermanns, Pia; Couch, Robert; Leonard, Norma; Klotz, Cherise; Pohlenz, Joachim

    2014-01-01

    Isolated central congenital hypothyroidism (ICCH) is rare but important. Most ICCH patients are diagnosed later, which results in severe growth failure and intellectual disability. We describe a boy with ICCH due to a large homozygous TSHβ gene deletion. A 51-day-old male Turkish infant, whose parents were first cousins, was admitted for evaluation of prolonged jaundice. His clinical appearance was compatible with hypothyroidism. Venous thyrotropin (TSH) was undetectably low, with a subsequent low free T4 and a low free T3, suggestive of central hypothyroidism. Using different PCR protocols, we could not amplify both coding exons of the boy's TSHβ gene, which suggested a deletion. An array comparative genomic hybridization (aCGH) using specific probes around the TSHβ gene locus showed him to be homozygous for a 6-kb deletion spanning all exons and parts of the 5' untranslated region of the gene. Infants who are clinically suspected of having hypothyroidism should be evaluated thoroughly, even if their TSH-based screening result is normal. In cases with ICCH and undetectably low TSH serum concentrations, a TSHβ gene deletion should be considered; aCGH should be performed when gene deletions are suspected. In such cases, PCR-based sequencing techniques give negative results.

  10. Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens.

    Science.gov (United States)

    de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas

    2018-01-23

    High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine-learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in-depth characterization of gene perturbation effects. This approach enables genome-scale image-based multivariate gene perturbation profiling using CRISPR-Cas9. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  11. Study of the Interaction User Head-Ultrawideband MIMO Antenna Array for Mobile Terminals

    DEFF Research Database (Denmark)

    Zhekov, Stanislav Stefanov; Tatomirescu, Alexandru; Franek, Ondrej

    2016-01-01

    aspects of the interaction are considered: 1) the influence of the user head on the antenna operation, and 2) the exposure of the human head tissue to antenna electromagnetic radiation. The first aspect is related to the degradation of the antenna performance in a proximity to the user which is evaluated......This paper presents a numerical study of the interaction between the user head and MIMO antenna array for mobile phones. The antenna array is composed of two identical antennas and covers the frequency ranges 698-990 MHz and 1710-5530 MHz with a good radiation efficiency in free space. The two...... by the reduction of the antenna radiation efficiency. The second aspect refers to the antenna operation effect on the human and the exposure of the user head is studied by Specific Absorption Ratio (SAR)....

  12. The KCNE genes in hypertrophic cardiomyopathy: a candidate gene study

    DEFF Research Database (Denmark)

    Hedley, Paula L; Haundrup, Ole; Andersen, Paal S

    2011-01-01

    The gene family KCNE1-5, which encode modulating β-subunits of several repolarising K+-ion channels, has been associated with genetic cardiac diseases such as long QT syndrome, atrial fibrillation and Brugada syndrome. The minK peptide, encoded by KCNE1, is attached to the Z-disc of the sarcomere...... as well as the T-tubules of the sarcolemma. It has been suggested that minK forms part of an "electro-mechanical feed-back" which links cardiomyocyte stretching to changes in ion channel function. We examined whether mutations in KCNE genes were associated with hypertrophic cardiomyopathy (HCM), a genetic...

  13. The Effect of Scala Tympani Morphology on Basilar Membrane Contact With a Straight Electrode Array: A Human Temporal Bone Study.

    Science.gov (United States)

    Verberne, Juul; Risi, Frank; Campbell, Luke; Chambers, Scott; O'Leary, Stephen

    2017-01-01

    Scala tympani morphology influences the insertion dynamics and intra-scalar position of straight electrode arrays. Hearing preservation is the goal of cochlear implantation with current thin straight electrode arrays. These hug the lateral wall, facilitating full, atraumatic insertions. However, most studies still report some postoperative hearing loss. This study explores the influence of scala tympani morphology on array position relative to the basilar membrane and its possible contribution to postoperative hearing loss. Twenty-six fresh-frozen human temporal bones implanted with a straight electrode array were three-dimensionally reconstructed from micro-photographic histological sections. Insertion depth and the proximity between the array and basilar membrane were recorded. Lateral wall shape was quantified as a curvature ratio. Insertion depths ranged from 233 to 470 degrees. The mean first point of contact between the array and basilar membrane was 185 degrees; arrays tended to remain in contact with the membrane after first contacting it. Eighty-nine and 93% of arrays that reached the upper basal (>240-360 degrees) and second (>360-720 degrees) turns respectively contacted the basilar membrane in these regions. Scalar wall curvature ratio decreased significantly (the wall became steeper) from the basal to second turns. This shift correlated with a reduced distance between the array and basilar membrane. Scala tympani morphology influences the insertion dynamics and intra-scalar position of a straight electrode array. In addition to gross trauma of cochlear structures, contact between the array and basilar membrane and how this impacts membrane function should be considered in hearing preservation cases.

  14. Fiscal 2000 regional consortium research and development project - regional new technology creation research and development. Development of micro-array for next generation gene analysis (1st fiscal year); 2000 nendo chiiki consortium kenkyu kaihatsu jigyo - chiiki shingijutsu soshutsu kenkyu kaihatsu seika hokokusho. Jisedai idenshi kaiseki micro array no kaihatsu (daiichi nendo)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    Efforts are under way to construct a novel DNA (deoxyribonucleic acid) micro-array for gene diagnosis on the basis of technologies of laser scan type manipulation, nanometric position detection, and micro-machining. Using these technologies, structural changes to accompany reactions induced in the probe DNA deposited on an array are detected for the identification of the DNA. Activities are conducted in the four fields of (1) the study of probe DNA fixation technology, (2) development of an optical detection system, (3) detailed check of DNA micro-array performance evaluation technologies, and (4) a comprehensive survey. In field (1), gold colloid modified DNA molecules are designed and evaluated, and the fixation of DNA to substrates and technologies for integration are studied. In field (2), the gold colloid modified DNA is fixed on a thin gold film, and then a surface plasmon resonance (SPR) is observed in the wake of hybridization. Furthermore, a Brownian motion is observed of the metal particles fixed on a glass substrate via DNA. (NEDO)

  15. A Study on a Crack Evaluation Technique for Turbine Blade Root Using Phased Array Ultrasonics

    International Nuclear Information System (INIS)

    Cho, Yong Sang; Jung, Gye Jo; Park, Sang Ki; Kim, Jae Hoon

    2004-01-01

    Ultrasonic testing is a kind of nondestructive test to detect a crack or discontinuity in materials or on material surfaces by sending ultrasound to it. This conventional ultrasonic technique has some limitations in reliably detecting crack or accurately assessing materials in the case of complex-shaped power plant components such as a turbine blade root. An alternative method for such a difficult inspection is highly needed. In this study, application of a phased array ultrasonic testing (UT) system to a turbine blade, one of the critical power plant components, has been considered, and the particular incident angle has been determined so that the greatest track detectability and the most accurate crack length evaluation nay be achieved. The response of ultrasonic phased array was also analyzed to establish a special method to determine the track length without moving the transducer. The result showed that the developed method for crack length assessment is a more accurate and effective method, compared with the conventional method

  16. Cryogenic deuterium Z-pinch and wire array Z-pinch studies at Imperial College

    International Nuclear Information System (INIS)

    Haines, M.G.; Aliaga-Rossel, R.; Beg, N.F.

    2001-01-01

    Z-pinch experiments using cryogenic deuterium fibre loads have been carried out on the MAGPIE generator at currents up to 1.4MA. M=0 instabilities in the corona caused plasma expansion and disruption before the plasma could enter the collisionless Large ion Larmor radius regime. For the last 12 months we have studied Aluminium wire array implosions using laser probing, optical streaks and gated X-ray images. Plasma from the wires in accelerated to the axis as radial plasma streams with uncorrelated m=0 instabilities superimposed. Later in the discharge a global Rayleigh-Taylor (R-T) instability develops. Single and double aluminium and tungsten wire shots were conducted at 150kA. 2-D and 3-D simulations and a heuristic model of wire arrays will be presented along with theories on the combined MHD/R-T instability and sheared axial flow generation by large ion Larmor radius effects. (author)

  17. Cryogenic deuterium Z-pinch and wire array Z-pinch studies at imperial college

    International Nuclear Information System (INIS)

    Haines, M.G.; Aliaga-Rossel, R.; Beg, F.N.

    1999-01-01

    Z-pinch experiments using cryogenic deuterium fibre loads have been carried out on the MAGPIE generator at currents up to 1.4MA. M=0 instabilities in the corona caused plasma expansion and disruption before the plasma could enter the collisionless Large ion Larmor radius regime. For the last 12 months we have studied Aluminium wire array implosions using laser probing, optical streaks and gated X-ray images. Plasma from the wires in accelerated to the axis as radial plasma streams with uncorrelated m=0 instabilities superimposed. Later in the discharge a global Rayleigh-Taylor (R-T) instability develops. Single and double aluminium and tungsten wire shots were conducted at 150kA. 2-D and 3-D simulations and a heuristic model of wire arrays will be presented along with theories on the combined MHD/R-T instability and sheared axial flow generation by large ion Larmor radius effects. (author)

  18. Stationary chest tomosynthesis using a carbon nanotube x-ray source array: a feasibility study

    International Nuclear Information System (INIS)

    Shan, Jing; Lee, Yueh Z; Lu, Jianping; Zhou, Otto; Tucker, Andrew W; Heath, Michael D; Wang, Xiaohui; Foos, David H

    2015-01-01

    Chest tomosynthesis is a low-dose, quasi-3D imaging modality that has been demonstrated to improve the detection sensitivity for small lung nodules, compared to 2D chest radiography. The purpose of this study is to investigate the feasibility and system requirements of stationary chest tomosynthesis (s-DCT) using a spatially distributed carbon nanotube (CNT) x-ray source array, where the projection images are collected by electronically activating individual x-ray focal spots in the source array without mechanical motion of the x-ray source, detector, or the patient. A bench-top system was constructed using an existing CNT field emission source array and a flat panel detector. The tube output, beam quality, focal spot size, system in-plane and in-depth resolution were characterized. Tomosynthesis slices of an anthropomorphic chest phantom were reconstructed for image quality assessment. All 75 CNT sources in the source array were shown to operate reliably at 80 kVp and 5 mA tube current. Source-to-source consistency in the tube current and focal spot size was observed. The incident air kerma reading per mAs was measured as 74.47 uGy mAs −1 at 100 cm. The first half value layer of the beam was 3 mm aluminum. An average focal spot size of 2.5  ×  0.5 mm was measured. The system MTF was measured to be 1.7 cycles mm −1 along the scanning direction, and 3.4 cycles mm −1 perpendicular to the scanning direction. As the angular coverage of 11.6°–34°, the full width at half maximum of the artifact spread function improved greatly from 9.5 to 5.2 mm. The reconstructed tomosynthesis slices clearly show airways and pulmonary vascular structures in the anthropomorphic lung phantom. The results show the CNT source array is capable of generating sufficient dose for chest tomosynthesis imaging. The results obtained so far suggest an s-DCT using a distributed CNT x-ray source array is feasible. (paper)

  19. Cross-flow turbines: physical and numerical model studies towards improved array simulations

    Science.gov (United States)

    Wosnik, M.; Bachant, P.

    2015-12-01

    Cross-flow, or vertical-axis turbines, show potential in marine hydrokinetic (MHK) and wind energy applications. As turbine designs mature, the research focus is shifting from individual devices towards improving turbine array layouts for maximizing overall power output, i.e., minimizing wake interference for axial-flow turbines, or taking advantage of constructive wake interaction for cross-flow turbines. Numerical simulations are generally better suited to explore the turbine array design parameter space, as physical model studies of large arrays at large model scale would be expensive. However, since the computing power available today is not sufficient to conduct simulations of the flow in and around large arrays of turbines with fully resolved turbine geometries, the turbines' interaction with the energy resource needs to be parameterized, or modeled. Most models in use today, e.g. actuator disk, are not able to predict the unique wake structure generated by cross-flow turbines. Experiments were carried out using a high-resolution turbine test bed in a large cross-section tow tank, designed to achieve sufficiently high Reynolds numbers for the results to be Reynolds number independent with respect to turbine performance and wake statistics, such that they can be reliably extrapolated to full scale and used for model validation. To improve parameterization in array simulations, an actuator line model (ALM) was developed to provide a computationally feasible method for simulating full turbine arrays inside Navier--Stokes models. The ALM predicts turbine loading with the blade element method combined with sub-models for dynamic stall and flow curvature. The open-source software is written as an extension library for the OpenFOAM CFD package, which allows the ALM body force to be applied to their standard RANS and LES solvers. Turbine forcing is also applied to volume of fluid (VOF) models, e.g., for predicting free surface effects on submerged MHK devices. An

  20. Advances in study of molecular imaging reporte gene systems

    International Nuclear Information System (INIS)

    Wu Tao; An Rui

    2010-01-01

    The use of molecular imaging reporter gene systems has allowed gene therapy to move from the laboratory to the clinical application, which provides methodology to monitor the expression of therapeutic gene noninvasively and achieve quantitative outcome in vivo. Recently, the radionuclide reporter gene still is the focus many studies, but MRI and optical reporter gene have gradually played a important part in reporter gene systems. On the basis of combination of multi-subject, for example applied chemistry and molecular biology, more and more new modified reporter genes and molecular probes have spread out. This paper mainly introduces the advantages and disadvantages of reporter gene system and development trends. (authors)

  1. Classification across gene expression microarray studies

    Directory of Open Access Journals (Sweden)

    Kuner Ruprecht

    2009-12-01

    Full Text Available Abstract Background The increasing number of gene expression microarray studies represents an important resource in biomedical research. As a result, gene expression based diagnosis has entered clinical practice for patient stratification in breast cancer. However, the integration and combined analysis of microarray studies remains still a challenge. We assessed the potential benefit of data integration on the classification accuracy and systematically evaluated the generalization performance of selected methods on four breast cancer studies comprising almost 1000 independent samples. To this end, we introduced an evaluation framework which aims to establish good statistical practice and a graphical way to monitor differences. The classification goal was to correctly predict estrogen receptor status (negative/positive and histological grade (low/high of each tumor sample in an independent study which was not used for the training. For the classification we chose support vector machines (SVM, predictive analysis of microarrays (PAM, random forest (RF and k-top scoring pairs (kTSP. Guided by considerations relevant for classification across studies we developed a generalization of kTSP which we evaluated in addition. Our derived version (DV aims to improve the robustness of the intrinsic invariance of kTSP with respect to technologies and preprocessing. Results For each individual study the generalization error was benchmarked via complete cross-validation and was found to be similar for all classification methods. The misclassification rates were substantially higher in classification across studies, when each single study was used as an independent test set while all remaining studies were combined for the training of the classifier. However, with increasing number of independent microarray studies used in the training, the overall classification performance improved. DV performed better than the average and showed slightly less variance. In

  2. Improved SNR of phased-array PERES coils via simulation study

    International Nuclear Information System (INIS)

    RodrIguez, Alfredo O; Medina, LucIa

    2005-01-01

    A computational comparison of signal-to-noise ratio (SNR) was performed between a conventional phased array of two circular-shaped coils and a petal resonator surface array. The quasi-static model and phased-array optimum SNR were combined to derive an SNR formula for each array. Analysis of mutual inductance between coil petals was carried out to compute the optimal coil separation and optimum number of petal coils. Mutual interaction between coil arrays was not included in the model because this does not drastically affect coil performance. Phased arrays of PERES coils show a 114% improvement in SNR over that of the simplest circular configuration. (note)

  3. Studies of Polar Current Systems Using the IMS Scandinavian Magnetometer Array

    Science.gov (United States)

    Untiedt, J.; Baumjohann, W.

    1993-09-01

    As a contribution to the International Magnetospheric Study (IMS, 1976 1979) a two-dimensional array of 42 temporary magnetometer stations was run in Scandinavia, supplementary to the permanent observatories and concentrated in the northern part of the region. This effort aimed at the time-dependent (periods above about 100 s) determination of the two-dimensional structure of substorm-related magnetic fields at the Earth's surface with highest reasonable spatial resolution (about 100 km, corresponding to the height of the ionosphere) near the footpoints of field-aligned electric currents that couple the disturbed magnetosphere to the ionosphere at auroral latitudes. It has been of particular advantage for cooperative studies that not only simultaneous data were available from all-sky cameras, riometers, balloons, rockets, and satellites, but also from the STARE radar facility yielding colocated two-dimensional ionospheric electric field distributions. In many cases it therefore was possible to infer the three-dimensional regional structure of substorm-related ionospheric current systems. The first part of this review outlines the basic relationships and methods that have been used or have been developed for such studies. The second short part presents typical equivalent current patterns observed by the magnetometer array in the course of substorms. Finally we review main results of studies that have been based on the magnetometer array observations and on additional data, omitting studies on geomagnetic pulsations. These studies contributed to a clarification of the nature of auroral electrojets including the Harang discontinuity and of ionospheric current systems related to auroral features such as the break-up at midnight, the westward traveling surge, eastward drifting omega bands, and spirals.

  4. Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

    Science.gov (United States)

    Vathipadiekal, Vinod; Wang, Victoria; Wei, Wei; Waldron, Levi; Drapkin, Ronny; Gillette, Michael; Skates, Steven; Birrer, Michael

    2015-11-01

    To generate a comprehensive "Secretome" of proteins potentially found in the blood and derive a virtual Affymetrix array. To validate the utility of this database for the discovery of novel serum-based biomarkers using ovarian cancer transcriptomic data. The secretome was constructed by aggregating the data from databases of known secreted proteins, transmembrane or membrane proteins, signal peptides, G-protein coupled receptors, or proteins existing in the extracellular region, and the virtual array was generated by mapping them to Affymetrix probeset identifiers. Whole-genome microarray data from ovarian cancer, normal ovarian surface epithelium, and fallopian tube epithelium were used to identify transcripts upregulated in ovarian cancer. We established the secretome from eight public databases and a virtual array consisting of 16,521 Affymetrix U133 Plus 2.0 probesets. Using ovarian cancer transcriptomic data, we identified candidate blood-based biomarkers for ovarian cancer and performed bioinformatic validation by demonstrating rediscovery of known biomarkers including CA125 and HE4. Two novel top biomarkers (FGF18 and GPR172A) were validated in serum samples from an independent patient cohort. We present the secretome, comprising the most comprehensive resource available for protein products that are potentially found in the blood. The associated virtual array can be used to translate gene-expression data into cancer biomarker discovery. A list of blood-based biomarkers for ovarian cancer detection is reported and includes CA125 and HE4. FGF18 and GPR172A were identified and validated by ELISA as being differentially expressed in the serum of ovarian cancer patients compared with controls. ©2015 American Association for Cancer Research.

  5. The Use of High-Density SNP Array to Map Homozygosity in Consanguineous Families to Efficiently Identify Candidate Genes: Application to Woodhouse-Sakati Syndrome

    Directory of Open Access Journals (Sweden)

    Molly B. Sheridan

    2015-01-01

    Full Text Available Two consanguineous Qatari siblings presented for evaluation: a 17-4/12-year-old male with hypogonadotropic hypogonadism, alopecia, intellectual disability, and microcephaly and his 19-year-old sister with primary amenorrhea, alopecia, and normal cognition. Both required hormone treatment to produce secondary sex characteristics and pubertal development beyond Tanner 1. SNP array analysis of both probands was performed to detect shared regions of homozygosity which may harbor homozygous mutations in a gene causing their common features of abnormal pubertal development, alopecia, and variable cognitive delay. Our patients shared multiple homozygous genomic regions; ten shared regions were >1 Mb in length and constituted 0.99% of the genome. DCAF17, encoding a transmembrane nuclear protein of uncertain function, was the only gene identified in a homozygous region known to cause hypogonadotropic hypogonadism. DCAF17 mutations are associated with Woodhouse-Sakati syndrome, a rare disorder characterized by alopecia, hypogonadotropic hypogonadism, sensorineural hearing loss, diabetes mellitus, and extrapyramidal movements. Sequencing of the coding exons and flanking intronic regions of DCAF17 in the proband revealed homozygosity for a previously described founder mutation (c.436delC. Targeted DCAF17 sequencing of his affected sibling revealed the same homozygous mutation. This family illustrates the utility of SNP array testing in consanguineous families to efficiently and inexpensively identify regions of genomic homozygosity in which genetic candidates for recessive conditions can be identified.

  6. The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits

    DEFF Research Database (Denmark)

    Voight, Benjamin F; Kang, Hyun Min; Ding, Jun

    2012-01-01

    Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands...... dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping...

  7. Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

    Science.gov (United States)

    Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

  8. PATTERN RECOGNITION STUDIES OF HALOGENATED ORGANIC COMPOUNDS USING CONDUCTING POLYMER SENSOR ARRAYS. (R825323)

    Science.gov (United States)

    Direct measurement of volatile and semivolatile halogenated organic compounds of environmental interest was carried out using arrays of conducting polymer sensors. Mathematical expressions of the sensor arrays using microscopic polymer network model is described. A classical, non...

  9. Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies.

    Science.gov (United States)

    Powers, John M; Trobridge, Grant D

    2013-09-01

    Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.

  10. Feasibility study of patient motion monitoring by using tactile array sensors

    Science.gov (United States)

    Kim, Tae-Ho; Kang, Seong-Hee; Kim, Dong-Su; Cho, Min-Seok; Kim, Kyeong-Hyeon; Suh, Tae-Suk; Kim, Siyong

    2015-07-01

    An ideal alignment method based on the external anatomical surface of the patient should consider the entire region of interest. However, optical-camera-based systems cannot blindly monitor such areas as the patient's back, for example. Furthermore, collecting enough information to correct the associated deformation error is impossible. The study aim is to propose a new patient alignment method using tactile array sensors that can measure the distributed pressure profiles along the contact surface. The TactArray system includes one sensor, a signal-conditioning device (USB drive/interface electronics, power supply, and cables), and a PC. The tactile array sensor was placed between the patient's back and the treatment couch, and the deformations at different location on the patient's back were evaluated. Three healthy male volunteers were enrolled in this study, and pressure profile distributions (PPDs) were obtained with and without immobilization. After the initial pretreatment setup using the laser alignment system, the PPD of the patient's back was acquired. The results were obtained at four different times and included a reference PPD dataset. The contact area and the center-of-pressure value were also acquired based on the PPD data for a more elaborate quantitative data analysis. To evaluate the clinical feasibility of using the proposed alignment method for reducing the deformation error, we implemented a real-time self-correction procedure. Despite the initial alignment, we confirmed that PPD variations existed in both cases of the volunteer studies (with and without the use of the immobilization tool). Additionally, we confirmed that the contact area and the center of pressure varied in both cases, and those variations were observed in all three volunteers. With the proposed alignment method and the real-time selfcorrection procedure, the deformation error was significantly reduced. The proposed alignment method can be used to account for the limitation of

  11. Demonstration of diet-induced decoupling of fatty acid and cholesterol synthesis by combining gene expression array and 2H2O quantification.

    Science.gov (United States)

    Jensen, Kristian K; Previs, Stephen F; Zhu, Lei; Herath, Kithsiri; Wang, Sheng-Ping; Bhat, Gowri; Hu, Guanghui; Miller, Paul L; McLaren, David G; Shin, Myung K; Vogt, Thomas F; Wang, Liangsu; Wong, Kenny K; Roddy, Thomas P; Johns, Douglas G; Hubbard, Brian K

    2012-01-15

    The liver is a crossroad for metabolism of lipid and carbohydrates, with acetyl-CoA serving as an important metabolic intermediate and a precursor for fatty acid and cholesterol biosynthesis pathways. A better understanding of the regulation of these pathways requires an experimental approach that provides both quantitative metabolic flux measurements and mechanistic insight. Under conditions of high carbohydrate availability, excess carbon is converted into free fatty acids and triglyceride for storage, but it is not clear how excessive carbohydrate availability affects cholesterol biosynthesis. To address this, C57BL/6J mice were fed either a low-fat, high-carbohydrate diet or a high-fat, carbohydrate-free diet. At the end of the dietary intervention, the two groups received (2)H(2)O to trace de novo fatty acid and cholesterol synthesis, and livers were collected for gene expression analysis. Expression of lipid and glucose metabolism genes was determined using a custom-designed pathway focused PCR-based gene expression array. The expression analysis showed downregulation of cholesterol biosynthesis genes and upregulation of fatty acid synthesis genes in mice receiving the high-carbohydrate diet compared with the carbohydrate-free diet. In support of these findings, (2)H(2)O tracer data showed that fatty acid synthesis was increased 10-fold and cholesterol synthesis was reduced by 1.6-fold in mice fed the respective diets. In conclusion, by applying gene expression analysis and tracer methodology, we show that fatty acid and cholesterol synthesis are differentially regulated when the carbohydrate intake in mice is altered.

  12. Curvilinear 3-D Imaging Using Row--Column-Addressed 2-D Arrays with a Diverging Lens: Feasibility Study

    DEFF Research Database (Denmark)

    Bouzari, Hamed; Engholm, Mathias; Beers, Christopher

    2017-01-01

    imaging. Extended FOV and low channel count of double-curved RCA 2-D arrays make 3-D imaging possible with equipment in the price range of conventional 2-D imaging. This study proposes a delay-and-sum beamformation scheme specific to double-curved RCA 2-D arrays and validates its focusing ability based...... of this study demonstrate that the proposed beamforming approach is accurate for achieving correct time-of-flight calculations, and hence avoids geometrical distortions....

  13. The concentration principle applied to spaceborne solar arrays. AGORA mission: Studies synthesis

    Science.gov (United States)

    Laget, R.

    1986-01-01

    Studies that led to selection of the distributed 25 kW SARA LOUVRE concept for the solar cell generator to be flown on the AGORA asteroid mission, and the major characteristics of such a spaceborne solar array are summarized. In the SARA LOUVRE concept, a parabolic cross section reflector concentrates incident light over the rear face of the identical, preceding reflector dish. The whole set of reflectors is pivotally commanded, thus compensating the effects of depointing. Geometric concentration factor is 10. End of life power level at 2.5 AU is 4.5 kW.

  14. Digitalized Mirror Array and Its Application in Large Telescope: Principle and Case Studies

    International Nuclear Information System (INIS)

    Chen Yingtian; Zhang Yang; Lim, Boon Ham; Lim, Chen Sin; Hu Sen; Ho, Tso-Hsiu; Chong, Kok Keong; Tan, Boon Kok

    2009-01-01

    In this article, we report the principle and conceptual design of a fundamentally different technology in fabricating high precision aberration free optical devices. The tip-tilt of facet in a mirror array is produced by digitally controlled line-tilts of rows and columns. It has not only provided a cost-effective designing methodology in optical physics but also led to a much finer precision of 1 mili arc sec or less. As examples of the application of the proposed digitalised optics, two case studies have been given: a 10 m Schmidt telescope (off-axis) and an 8 m Cassegrain telescope (on-axis). (geophysics, astronomy, and astrophysics)

  15. Study on radiation-inducible genes

    International Nuclear Information System (INIS)

    Lim, Sang Yong; Kim, Dong Ho; Joe, Min Ho; Song, Hyu Npa

    2012-01-01

    Transcription of previously identified radiation-inducible genes, uscA and cyoA, was examined responding to radiation. The putative promoter regions of both genes were cloned into pRS415 vector containing lacZ, and the core promoter region necessary for radiation response were determined through promoter deletion method. To investigate the role of uscA, which is assumed to be small RNA related with radiation response, a deletion mutant strain of uscA was constructed. However, uscA deletion did not affect bacterial survival against radiation exposure. The use of bacteria as anticancer agents has attracted interest. In this study, we tried to develop tumor targeting bacteria in which the radiation-inducible promoter activate a transgene encoding a cytotoxic protein. For outward secretion of anticancer protein produced inside bacteria, the N-terminal 140 amino acid of SspH1 was found to function as a secretion signal peptide. To create an attenuated tumor-targeting bacteria, Salmonella ptsI mutant strain was constructed, and we found that its virulence decreased. Finally, the tumor-targeting ability of ptsI mutant was verified by the use of in-vivo imaging analysis

  16. Study on radiation-inducible genes

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Sang Yong; Kim, Dong Ho; Joe, Min Ho; Song, Hyu Npa

    2012-01-15

    Transcription of previously identified radiation-inducible genes, uscA and cyoA, was examined responding to radiation. The putative promoter regions of both genes were cloned into pRS415 vector containing lacZ, and the core promoter region necessary for radiation response were determined through promoter deletion method. To investigate the role of uscA, which is assumed to be small RNA related with radiation response, a deletion mutant strain of uscA was constructed. However, uscA deletion did not affect bacterial survival against radiation exposure. The use of bacteria as anticancer agents has attracted interest. In this study, we tried to develop tumor targeting bacteria in which the radiation-inducible promoter activate a transgene encoding a cytotoxic protein. For outward secretion of anticancer protein produced inside bacteria, the N-terminal 140 amino acid of SspH1 was found to function as a secretion signal peptide. To create an attenuated tumor-targeting bacteria, Salmonella ptsI mutant strain was constructed, and we found that its virulence decreased. Finally, the tumor-targeting ability of ptsI mutant was verified by the use of in-vivo imaging analysis.

  17. Studying gene regulation in methanogenic archaea.

    Science.gov (United States)

    Rother, Michael; Sattler, Christian; Stock, Tilmann

    2011-01-01

    Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. KRAS mutation detection in colorectal cancer by a commercially available gene chip array compares well with Sanger sequencing.

    Science.gov (United States)

    French, Deborah; Smith, Andrew; Powers, Martin P; Wu, Alan H B

    2011-08-17

    Binding of a ligand to the epidermal growth factor receptor (EGFR) stimulates various intracellular signaling pathways resulting in cell cycle progression, proliferation, angiogenesis and apoptosis inhibition. KRAS is involved in signaling pathways including RAF/MAPK and PI3K and mutations in this gene result in constitutive activation of these pathways, independent of EGFR activation. Seven mutations in codons 12 and 13 of KRAS comprise around 95% of the observed human mutations, rendering monoclonal antibodies against EGFR (e.g. cetuximab and panitumumab) useless in treatment of colorectal cancer. KRAS mutation testing by two different methodologies was compared; Sanger sequencing and AutoGenomics INFINITI® assay, on DNA extracted from colorectal cancers. Out of 29 colorectal tumor samples tested, 28 were concordant between the two methodologies for the KRAS mutations that were detected in both assays with the INFINITI® assay detecting a mutation in one sample that was indeterminate by Sanger sequencing and a third methodology; single nucleotide primer extension. This study indicates the utility of the AutoGenomics INFINITI® methodology in a clinical laboratory setting where technical expertise or access to equipment for DNA sequencing does not exist. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.

    Directory of Open Access Journals (Sweden)

    Benjamin F Voight

    Full Text Available Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.

  20. ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

    Directory of Open Access Journals (Sweden)

    Krasnogor Natalio

    2009-10-01

    Full Text Available Abstract Background Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

  1. Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

    Directory of Open Access Journals (Sweden)

    Calogero Raffaele A

    2008-11-01

    Full Text Available Abstract Background A new microarray platform (GeneChip® Exon 1.0 ST has recently been developed by Affymetrix http://www.affymetrix.com. This microarray platform changes the conventional view of transcript analysis since it allows the evaluation of the expression level of a transcript by querying each exon component. The Exon 1.0 ST platform does however raise some issues regarding the approaches to be used in identifying genome-wide alternative splicing events (ASEs. In this study an exon-level data analysis workflow is dissected in order to detect limit and strength of each step, thus modifying the overall workflow and thereby optimizing the detection of ASEs. Results This study was carried out using a semi-synthetic exon-skipping benchmark experiment embedding a total of 268 exon skipping events. Our results point out that summarization methods (RMA, PLIER do not affect the efficacy of statistical tools in detecting ASEs. However, data pre-filtering is mandatory if the detected number of false ASEs are to be reduced. MiDAS and Rank Product methods efficiently detect true ASEs but they suffer from the lack of multiple test error correction. The intersection of MiDAS and Rank Product results efficiently moderates the detection of false ASEs. Conclusion To optimize the detection of ASEs we propose the following workflow: i data pre-filtering, ii statistical selection of ASEs using both MiDAS and Rank Product, iii intersection of results derived from the two statistical analyses in order to moderate family-wise errors (FWER.

  2. Studies of Neurofibromatosis-1 Modifier Genes

    Science.gov (United States)

    2005-06-01

    characterize patients of the FANCD1 complementation group (Howlett et al., 2002), and FANCA , which is the most frequently mutated FA gene , maps to a 650 kb...associations, we genotyped a total of 16 SNPs in FANCA and three immediately adjacent genes and collaborated with statistical geneticist Dr. Mark Daly at MIT to...across 15 SNPs in FANCA and the adjacent FLJ12547, CDKIO, and SPG7 genes . Red/pink coloration indicates statistical significance (LOD=3). The number in

  3. Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population

    Directory of Open Access Journals (Sweden)

    Tae-Joon Park

    2015-01-01

    Full Text Available Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip.

  4. The Study of a Beam Profile Monitor based on Faraday Cup Array

    Energy Technology Data Exchange (ETDEWEB)

    Park, K. M.; Park, S. H.; Kim, S. G.; Kwon, H. J.; Cho, Y. S. [KAERI, Daejeon (Korea, Republic of)

    2015-05-15

    The metal can then be discharged to measure a small current equivalent to the number of impinging ions. The beam current can be measured and used to determine the number of ions or electrons hitting the cup. Recently, beam profile monitor (BPM) based on Faraday cup array (FCA), which represented beam position through the spatial and temporal distribution of the beam current, has been studied due to advantages of measure of wide-range ion beam current. FCA system is divided into a FC, an electrical circuit and display parts. We have studied FCA to monitor beam profile on an electrostatic accelerator with wide-range ion current. In this paper, we represented basic characteristics and designs for the fabricated FCA. FCA system, which consisted of FC system, electronic readout system, and output display, was suggested to measure ion beam current, efficiently. FC system consisted of a collimator, suppressor, tiny FC, insulator frame, and circuit board divided into elec PCB, cap PCB, and con PCB. FC size was 4 mm diameters and FCA system was considered as 8 x 8 array and whole size of 8 x 8 mm''2. FCA system was set-up in vacuum chamber and an integrator and output display parts were formed out of chamber to minimize number of feed-through.

  5. Study of the structure of light neutron rich nucleus with the Tonnerre array

    International Nuclear Information System (INIS)

    Pietri, St.

    2003-06-01

    This work concern the technical development made on the multidetector TONNERRE and the study of the 34 Si nucleus by a complete beta-neutron-gamma spectroscopy. In the first part various tests performed on modules of the detector in the 'Centre d'Etude de Bruyere le Chatel' are presented. A modification of the embassies of the photomultipliers tubes allows to gain more than 50% in the neutron efficiency and to obtain a threshold lower than 300 keV for the neutron energy. A complete C++ simulation of the neutron propagation in the array was carried out. It explains that the slow component of the light output of the scintillator may be responsible of the shape of the time-of-flight spectrum. The second part of these report presents the experiment devoted to the study of the structure of the 34 Si from the beta decay of the 34 Al. It was performed at the GANIL facility using the TONNERRE array and germanium of ENOGAM. The 34 Al was produced by projectile fragmentation of a 36 S beam of 50 MeV/A in a target of 9 Be. A complete beta scheme of the 34 Al is proposed. Eight neutron lines following the 34 Al decay were observed for the first time. Finally we suggest that a monopolar transition could occur in the 34 Si nucleus signing a O + 2 state at 2133 keV. (author)

  6. In Vivo Experimental Study of Noninvasive Insulin Microinjection through Hollow Si Microneedle Array

    Directory of Open Access Journals (Sweden)

    Drago Resnik

    2018-01-01

    Full Text Available An experimental study of in vivo insulin delivery through microinjection by using hollow silicon microneedle array is presented. A case study was carried out on a healthy human subject in vivo to determine the influence of delivery parameters on drug transfer efficiency. As a microinjection device, a hollow microneedle array (13 × 13 mm2 having 100 microneedles (220 µm high, 130 µm-outer diameter and 50 µm-inner diameter was designed and fabricated using classical microfabrication techniques. The efficiency of the delivery process was first characterized using methylene blue and a saline solution. Based on these results, the transfer efficiency was found to be predominantly limited by the inability of viable epidermis to absorb and allow higher drug transport toward the capillary-rich region. Two types of fast-acting insulin were used to provide evidence of efficient delivery by hollow MNA to a human subject. By performing blood analyses, infusion of more-concentrated insulin (200 IU/mL, international units (IU exhibited similar blood glucose level drop (5–7% compared to insulin of standard concentration (100 IU/mL, however, significant increase of serum insulin (40–50% with respect to the preinfusion values was determined. This was additionally confirmed by a distinctive increase of insulin to C-peptide ratio as compared to preinfusion ratio. Moreover, we noticed that this route of administration mimics a multiple dose regimen, able to get a “steady state” for insulin plasma concentration.

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

    Directory of Open Access Journals (Sweden)

    Siggberg Linda

    2012-09-01

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

  8. Histone and ribosomal RNA repetitive gene clusters of the boll weevil are linked in a tandem array.

    Science.gov (United States)

    Roehrdanz, R; Heilmann, L; Senechal, P; Sears, S; Evenson, P

    2010-08-01

    Histones are the major protein component of chromatin structure. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and the clusters are tandemly repeated. Ribosomal DNA contains a cluster of the rRNA sequences 18S, 5.8S and 28S. The rRNA genes are separated by the spacers ITS1, ITS2 and IGS. This cluster is also tandemly repeated. We found that the ribosomal RNA repeat unit of at least two species of Anthonomine weevils, Anthonomus grandis and Anthonomus texanus (Coleoptera: Curculionidae), is interspersed with a block containing the histone gene quintet. The histone genes are situated between the rRNA 18S and 28S genes in what is known as the intergenic spacer region (IGS). The complete reiterated Anthonomus grandis histone-ribosomal sequence is 16,248 bp.

  9. Application of oligonucleotide array CGH to the simultaneous detection of a deletion in the nuclear TK2 gene and mtDNA depletion.

    Science.gov (United States)

    Zhang, Shulin; Li, Fang-Yuan; Bass, Harold N; Pursley, Amber; Schmitt, Eric S; Brown, Blaire L; Brundage, Ellen K; Mardach, Rebecca; Wong, Lee-Jun

    2010-01-01

    Thymidine kinase 2 (TK2), encoded by the TK2 gene on chromosome 16q22, is one of the deoxyribonucleoside kinases responsible for the maintenance of mitochondrial deoxyribonucleotide pools. Defects in TK2 mainly cause a myopathic form of the mitochondrial DNA depletion syndrome (MDDS). Currently, only point mutations and small insertions and deletions have been reported in TK2 gene; gross rearrangements of TK2 gene and possible hepatic involvement in patients with TK2 mutations have not been described. We report a non-consanguineous Jordanian family with three deceased siblings due to mtDNA depletion. Sequence analysis of the father detected a heterozygous c.761T>A (p.I254N) mutation in his TK2 gene; however, point mutations in the mother were not detected. Subsequent gene dosage analysis using oligonucleotide array CGH identified an intragenic approximately 5.8-kb deletion encompassing the 5'UTR to intron 2 of her TK2 gene. Sequence analysis confirmed that the deletion spans c.1-495 to c.283-2899 of the TK2 gene (nucleotide 65,136,256-65,142,086 of chromosome 16). Analysis of liver and muscle specimens from one of the deceased infants in this family revealed compound heterozygosity for the paternal point mutation and maternal intragenic deletion. In addition, a significant reduction of the mtDNA content in liver and muscle was detected (10% and 20% of age- and tissue-matched controls, respectively). Prenatal diagnosis was performed in the third pregnancy. The fetus was found to carry both the point mutation and the deletion. This child died 6months after birth due to myopathy. A serum specimen demonstrated elevated liver transaminases in two of the infants from whom results were available. This report expands the mutation spectrum associated with TK2 deficiency. While the myopathic form of MDDS appears to be the main phenotype of TK2 mutations, liver dysfunction may also be a part of the mitochondrial depletion syndrome caused by TK2 gene defects.

  10. In situ Raman scattering study on a controllable plasmon-driven surface catalysis reaction on Ag nanoparticle arrays

    International Nuclear Information System (INIS)

    Dai, Z G; Xiao, X H; Zhang, Y P; Ren, F; Wu, W; Zhang, S F; Zhou, J; Jiang, C Z; Mei, F

    2012-01-01

    Control of the plasmon-driven chemical reaction for the transformation of 4-nitrobenzenethiol to p,p′-dimercaptoazobenzene by Ag nanoparticle arrays was studied. The Ag nanoparticle arrays were fabricated by means of nanosphere lithography. By changing the PS particle size, the localized surface plasmon resonance (LSPR) peaks of the Ag nanoparticle arrays can be tailored from 460 to 560 nm. The controlled reaction process was monitored by in situ surface-enhanced Raman scattering. The reaction can be dramatically influenced by varying the duration of laser exposure, Ag nanoparticle size, laser power and laser excitation wavelength. The maximum reaction speed was achieved when the LSPR wavelength of the Ag nanoparticle arrays matched the laser excitation wavelength. The experimental results reveal that the strong LSPR can effectively drive the transfer of the ‘hot’ electrons that decay from the plasmon to the reactants. The experimental results were confirmed by theoretical calculations. (paper)

  11. A scintillating bolometer array for double beta decay studies: The LUCIFER experiment

    Energy Technology Data Exchange (ETDEWEB)

    Gironi, L., E-mail: luca.gironi@mib.infn.it [Università degli Studi di Milano-Bicocca, Milano (Italy); INFN – Sezione di Milano-Bicocca, Milano (Italy)

    2016-07-11

    The main goal of the LUCIFER experiment is to study the neutrinoless double beta decay, a rare process allowed if neutrinos are Majorana particles. Although aiming at a discovery, in the case of insufficient sensitivity the LUCIFER technique will be the demonstrator for a higher mass experiment able to probe the entire inverted hierarchy region of the neutrino mass. In order to achieve this challenging result, high resolution detectors with active background discrimination capability are required. This very interesting possibility can be largely fulfilled by scintillating bolometers thanks to the simultaneous read-out of heat and light emitted by the interactions in the detector or by pulse shape analysis. - Highlights: • The LUCIFER technique will be the demonstrator for a higher mass experiment. • Scintillating bolometers allow high energy resolution and background discrimination. • The first choice for the LUCIFER tower are ZnSe crystals. • The LUCIFER setup will consist of an array of 30 individual single module detectors. • An array of ZnMoO4 crystals allowed the bolometric observation of the 2vDBD of {sup 100}Mo.

  12. The design of a focused ultrasound transducer array for the treatment of stroke: a simulation study

    International Nuclear Information System (INIS)

    Pajek, Daniel; Hynynen, Kullervo

    2012-01-01

    High intensity focused ultrasound (HIFU) is capable of mechanically disintegrating blood clots at high pressures. Safe thrombolysis may require frequencies higher than those currently utilized by transcranial HIFU. Since the attenuation and focal distortion of ultrasound in bone increases at higher frequencies, resulting focal pressures are diminished. This study investigated the feasibility of using transcranial HIFU for the non-invasive treatment of ischemic stroke. The use of large aperture, 1.1–1.5 MHz phased arrays in targeting four clinically relevant vessel locations was simulated. Resulting focal sizes decreased with frequency, producing a maximum –3 dB depth of field and lateral width of 2.0 and 1.2 mm, respectively. Mean focal gains above an order of magnitude were observed in three of four targets and transducer intensities required to achieve thrombolysis were determined. Required transducer element counts are about an order of magnitude higher than what currently exists and so, although technically feasible, new arrays would need to be developed to realize this as a treatment modality for stroke. (paper)

  13. GISAXS and SAXS studies on the spatial structures of Co nanowire arrays

    International Nuclear Information System (INIS)

    Cheng Weidong; Xing Xueqing; Wang Dehong; Gong Yu; Mo Guang; Cai Quan; Chen Zhongjun; Wu Zhonghua

    2011-01-01

    The spatial structures of magnetic Co nanowire array embedded in anodic aluminium membranes were investigated by grazing incidence small angle X-ray scattering (GISAXS) and conventional small angle X-ray scattering (SAXS) techniques. Compared with SEM observation, the GISAXS and SAXS measurements can get more overall structural information in a large-area scale. In this study, the two-dimensional GISAXS pattern was well reconstructed by using the IsGISAXS program. The results demonstrate that the hexagonal lattice formed by the Co nanowires is distorted (a≈105 nm, b≈95 nm). These Co nanowires are isolated into many structure domains with different orientations with a size of about 2 μm. The SAXS results have also confirmed that the nanopore structures in the AAM can be retained after depositing Co nanowires although the Co nanowires can not completely but only just fill up the nanopores. These results are helpful for understanding the global structure of the Co nanowire array. (authors)

  14. Experimental study of mixing in a square array rod bundle with grid spacer

    International Nuclear Information System (INIS)

    Zong Guifang; Cai Zuti; Zhang Demei

    1989-01-01

    This paper describes the experimental study of mixing in a full scale 15x15 square array rod bundle fuel assembly with 10 mm diameter and 13.3 mm pitch. The experiment was carried out in an open water loop, K 2 CrO 4 was used as tracer. Each subchannel was sampled at the open bundle outlet. Titration, spectrophotometry and fibreoptic methods were used to measure the concentration. The Reynolds numbers ranged from 2.12x10 4 to 4.37x10 4 . For the turbulent mixing of the bare rod bundle, the results of this study agreed with the formulas recommended by other authors. Both flow visualisation studies and the quantitative analysis indicated that flow scattering caused by the grid has a little effect on the mixing. The cause has been examined in this paper. (orig.)

  15. Optimization study on the magnetic field of superconducting Halbach Array magnet

    Science.gov (United States)

    Shen, Boyang; Geng, Jianzhao; Li, Chao; Zhang, Xiuchang; Fu, Lin; Zhang, Heng; Ma, Jun; Coombs, T. A.

    2017-07-01

    This paper presents the optimization on the strength and homogeneity of magnetic field from superconducting Halbach Array magnet. Conventional Halbach Array uses a special arrangement of permanent magnets which can generate homogeneous magnetic field. Superconducting Halbach Array utilizes High Temperature Superconductor (HTS) to construct an electromagnet to work below its critical temperature, which performs equivalently to the permanent magnet based Halbach Array. The simulations of superconducting Halbach Array were carried out using H-formulation based on B-dependent critical current density and bulk approximation, with the FEM platform COMSOL Multiphysics. The optimization focused on the coils' location, as well as the geometry and numbers of coils on the premise of maintaining the total amount of superconductor. Results show Halbach Array configuration based superconducting magnet is able to generate the magnetic field with intensity over 1 Tesla and improved homogeneity using proper optimization methods. Mathematical relation of these optimization parameters with the intensity and homogeneity of magnetic field was developed.

  16. Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue

    Directory of Open Access Journals (Sweden)

    Dunner Susana

    2008-09-01

    Full Text Available Abstract Background Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR is a technique used to measure mRNA species copy number as a way to determine key genes involved in different biological processes. However, the expression level of these key genes may vary among tissues or cells not only as a consequence of differential expression but also due to different factors, including choice of reference genes to normalize the expression levels of the target genes; thus the selection of reference genes is critical for expression studies. For this purpose, ten candidate reference genes were investigated in bovine muscular tissue. Results The value of stability of ten candidate reference genes included in three groups was estimated: the so called 'classical housekeeping' genes (18S, GAPDH and ACTB, a second set of genes used in expression studies conducted on other tissues (B2M, RPII, UBC and HMBS and a third set of novel genes (SF3A1, EEF1A2 and CASC3. Three different statistical algorithms were used to rank the genes by their stability measures as produced by geNorm, NormFinder and Bestkeeper. The three methods tend to agree on the most stably expressed genes and the least in muscular tissue. EEF1A2 and HMBS followed by SF3A1, ACTB, and CASC3 can be considered as stable reference genes, and B2M, RPII, UBC and GAPDH would not be appropriate. Although the rRNA-18S stability measure seems to be within the range of acceptance, its use is not recommended because its synthesis regulation is not representative of mRNA levels. Conclusion Based on geNorm algorithm, we propose the use of three genes SF3A1, EEF1A2 and HMBS as references for normalization of real-time RTqPCR in muscle expression studies.

  17. Histone and Ribosomal RNA Repetitive Gene Clusters of the Boll Weevil are Linked in a Tandem Array

    Science.gov (United States)

    Histones are the major protein component of chromatin structure. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and ...

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

    Science.gov (United States)

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

    2015-03-01

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

  19. Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity.

    Science.gov (United States)

    Thiel, Cora S; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Unverdorben, Felix; Buttron, Isabell; Lauber, Beatrice; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E; Ullrich, Oliver

    2015-01-01

    Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

  20. Genome-wide gene expression array identifies novel genes related to disease severity and excessive daytime sleepiness in patients with obstructive sleep apnea.

    Directory of Open Access Journals (Sweden)

    Yung-Che Chen

    Full Text Available We aimed to identify novel molecular associations between chronic intermittent hypoxia with re-oxygenation and adverse consequences in obstructive sleep apnea (OSA. We analyzed gene expression profiles of peripheral blood mononuclear cells from 48 patients with sleep-disordered breathing stratified into four groups: primary snoring (PS, moderate to severe OSA (MSO, very severe OSA (VSO, and very severe OSA patients on long-term continuous positive airway pressure treatment (VSOC. Comparisons of the microarray gene expression data identified eight genes up-regulated with OSA and down-regulated with CPAP treatment, and five genes down-regulated with OSA and up-regulated with CPAP treatment. Protein expression levels of two genes related to endothelial tight junction (AMOT P130, and PLEKHH3, and three genes related to anti-or pro-apoptosis (BIRC3, ADAR1 P150, and LGALS3 were all increased in the VSO group, while AMOT P130 was further increased, and PLEKHH3, BIRC3, and ADAR1 P150 were all decreased in the VSOC group. Subgroup analyses revealed that AMOT P130 protein expression was increased in OSA patients with excessive daytime sleepiness, BIRC3 protein expression was decreased in OSA patients with hypertension, and LGALS3 protein expression was increased in OSA patients with chronic kidney disease. In vitro short-term intermittent hypoxia with re-oxygenation experiment showed immediate over-expression of ADAR1 P150. In conclusion, we identified a novel association between AMOT/PLEKHH3/BIRC3/ADAR1/LGALS3 over-expressions and high severity index in OSA patients. AMOT and GALIG may constitute an important determinant for the development of hypersomnia and kidney injury, respectively, while BIRC3 may play a protective role in the development of hypertension.

  1. Numerical study of self-field effects on dynamics of Josephson-junction arrays

    International Nuclear Information System (INIS)

    Phillips, J.R.; Van der Zant, H.S.J.; White, J.; Orlando, T.P.

    1994-01-01

    We consider the influence of self-induced magnetic fields on dynamic properties of arrays of resistively and capacitively shunted Josephson junctions. Self-field effects are modeled by including mutual inductance interactions between every cell in the array. We find that it is important to include all mutual inductance interactions in order to understand the dynamic properties of the array, in particular subharmonic structure arising under AC current bias. (orig.)

  2. a Study of Ultrasonic Wave Propagation Through Parallel Arrays of Immersed Tubes

    Science.gov (United States)

    Cocker, R. P.; Challis, R. E.

    1996-06-01

    Tubular array structures are a very common component in industrial heat exchanging plant and the non-destructive testing of these arrays is essential. Acoustic methods using microphones or ultrasound are attractive but require a thorough understanding of the acoustic properties of tube arrays. This paper details the development and testing of a small-scale physical model of a tube array to verify the predictions of a theoretical model for acoustic propagation through tube arrays developed by Heckl, Mulholland, and Huang [1-5] as a basis for the consideration of small-scale physical models in the development of non-destructive testing procedures for tube arrays. Their model predicts transmission spectra for plane waves incident on an array of tubes arranged in straight rows. Relative transmission is frequency dependent with bands of high and low attenuation caused by resonances within individual tubes and between tubes in the array. As the number of rows in the array increases the relative transmission spectrum becomes more complex, with increasingly well-defined bands of high and low attenuation. Diffraction of acoustic waves with wavelengths less than the tube spacing is predicted and appears as step reductions in the transmission spectrum at frequencies corresponding to integer multiples of the tube spacing. Experiments with the physical model confirm the principle features of the theoretical treatment.

  3. Systematic identification of human housekeeping genes possibly useful as references in gene expression studies.

    Science.gov (United States)

    Caracausi, Maria; Piovesan, Allison; Antonaros, Francesca; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara

    2017-09-01

    The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes. Recent advancements in the quality and completeness of human expression microarray data and in their statistical analysis may provide new clues toward the quantitative standardization of human gene expression studies in biology and medicine, both cross‑ and within‑tissue. The systematic approach used by the present study is based on the Transcriptome Mapper tool and exploits the automated reassignment of probes to corresponding genes, intra‑ and inter‑sample normalization, elaboration and representation of gene expression values in linear form within an indexed and searchable database with a graphical interface recording quantitative levels of expression, expression variability and cross‑tissue width of expression for more than 31,000 transcripts. The present study conducted a meta‑analysis of a pool of 646 expression profile data sets from 54 different human tissues and identified actin γ 1 as the HK gene that best fits the combination of all the traditional criteria to be used as a reference gene for general use; two ribosomal protein genes, RPS18 and RPS27, and one aquaporin gene, POM121 transmembrane nucleporin C, were also identified. The present study provided a list of tissue‑ and organ‑specific genes that may be most suited for the following individual tissues/organs: Adipose tissue, bone marrow, brain, heart, kidney, liver, lung, ovary, skeletal muscle and testis; and also provides in these cases a representative

  4. Studies to single subassembly flow monitoring with a complete 7 element array under sodium

    International Nuclear Information System (INIS)

    Hess, B.; Ruppert, E.; Stehle, H.; Vinzens, K.

    1975-01-01

    As part of the SNR-300 R and D programme a complete clamped array, consisting of 4 full size fuel elements and 3 blanket elements was tested for more than 4000 hours at 600 deg C in the AKB sodium loop at Interatom, Bensberg. The test was split into two phases and the total cluster was prestrained in the second phase to simulate 15 mm subassembly displacement at the level of the upper bearing pads. Although this test was mainly considered as an endurance test to demonstrate the integrity of prestrained core elements, efforts were made to study the feasibility of single subassembly flow monitoring with this full size model of a core section. The results of these investigations are presented and discussed in this paper

  5. Nanoindentation study of the mechanical behavior of TiO{sub 2} nanotube arrays

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Y. N.; Wang, M. C.; Oloyede, A.; Bell, J. M.; Yan, C., E-mail: c2.yan@qut.edu.au [School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Queensland 4001 (Australia); Liu, M. N. [i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Science, Suzhou (China)

    2015-10-14

    Titanium dioxide (TiO{sub 2}) nanotube arrays are attracting increasing attention for use in solar cells, lithium-ion batteries, and biomedical implants. To take full advantage of their unique physical properties, such arrays need to maintain adequate mechanical integrity in applications. However, the mechanical performance of TiO{sub 2} nanotube arrays is not well understood. In this work, we investigate the deformation and failure of TiO{sub 2} nanotube arrays using the nanoindentation technique. We found that the load–displacement response of the arrays strongly depends on the indentation depth and indenter shape. Substrate-independent elastic modulus and hardness can be obtained when the indentation depth is less than 2.5% of the array height. The deformation mechanisms of TiO{sub 2} nanotube arrays by Berkovich and conical indenters are closely associated with the densification of TiO{sub 2} nanotubes under compression. A theoretical model for deformation of the arrays under a large-radius conical indenter is also proposed.

  6. Nanoindentation study of the mechanical behavior of TiO2 nanotube arrays

    International Nuclear Information System (INIS)

    Xu, Y. N.; Wang, M. C.; Oloyede, A.; Bell, J. M.; Yan, C.; Liu, M. N.

    2015-01-01

    Titanium dioxide (TiO 2 ) nanotube arrays are attracting increasing attention for use in solar cells, lithium-ion batteries, and biomedical implants. To take full advantage of their unique physical properties, such arrays need to maintain adequate mechanical integrity in applications. However, the mechanical performance of TiO 2 nanotube arrays is not well understood. In this work, we investigate the deformation and failure of TiO 2 nanotube arrays using the nanoindentation technique. We found that the load–displacement response of the arrays strongly depends on the indentation depth and indenter shape. Substrate-independent elastic modulus and hardness can be obtained when the indentation depth is less than 2.5% of the array height. The deformation mechanisms of TiO 2 nanotube arrays by Berkovich and conical indenters are closely associated with the densification of TiO 2 nanotubes under compression. A theoretical model for deformation of the arrays under a large-radius conical indenter is also proposed

  7. Study of attenuation structure for central Anatolia region, Turkey based on Keskin seismic array data

    Science.gov (United States)

    Semin, K. U.; Ozel, N. M.

    2011-12-01

    Central Anatolia is bounded in the north by the well-known north Anatolian fault system (NAFS) and on the south-southwest is bounded by the east Anatolian fault system (EAFS). The central area does not have major faults and acts as a single block moving westward. This region is not considered as seismically active as the NAFS or EAFS but the recent moderate-size Bala earthquakes (Ml=5.7, Ml= 5.5) on 20 and 27 December 2007 near the Tuz golu fault may be an indication of future seismic activity. In order to get a better picture of the crustal structure of this region we applied Coda Normalization method for the measurement of Qs-1 as a function of frequency for the frequencies 1.5, 3, 6, 8 Hz. 20 and 27 December 2007 Bala earthquakes (Ml magnitude 5.6 an 5.5) and their aftershocks recorded by the Keskin seismic array (International Monitoring System code BRTR) is analyzed in this study. Keskin seismic array has a small aperture circular design with 6 vertical short period and 1 broadband borehole seismometers. In addition, Multiple Lapse Time Window Analysis (MLTWA) method was applied to the data for the separation of intrinsic and scattering attenuation inm the region at the same frequencies. MLTWA method allowed a separation between the intrinsic attenuation and scattering attenuation. Preliminary results show a relatively low attenuation compared to western and eastern anatolia regions. This might be explained by the less seismicity in the region. A study of the regional and site attenuation of seismic waves of earthquakes in this area will contribute in predicting earthquake generated ground-motion and becomes vital in making decisions for earthquake regulations, building codes and to monitoring nuclear explosions.

  8. A study on the crack inspection signal characteristics for power plant components by phased array UT

    International Nuclear Information System (INIS)

    Cho, Yong Sang; Lim, Sang Gyu; Kil, Du Song

    2001-01-01

    Phased array ultrasonic testing system has become available for practical application in complicated geometry such as turbine blade root, tenon, disc in power industry. This research describes the characteristics of phased array UT signal for various type of blade roots in thermal Power Plant turbines. This application of Phased array ultrasonic testing system has been promoted mainly to save inspection time and labor cost of turbine inspection. The characteristic of phase array UT signal for power plant component is very simple to understand but to difficult for perform the inspection. Since our sophisticated inspection technique and systems are essential for the inspection of steam turbine blade roots that require high reliability, we intend to develop new technology and improve phased array technique based on the wide and much experience for the inspection of turbine components.

  9. Numerical study of read scheme in one-selector one-resistor crossbar array

    Science.gov (United States)

    Kim, Sungho; Kim, Hee-Dong; Choi, Sung-Jin

    2015-12-01

    A comprehensive numerical circuit analysis of read schemes of a one selector-one resistance change memory (1S1R) crossbar array is carried out. Three schemes-the ground, V/2, and V/3 schemes-are compared with each other in terms of sensing margin and power consumption. Without the aid of a complex analytical approach or SPICE-based simulation, a simple numerical iteration method is developed to simulate entire current flows and node voltages within a crossbar array. Understanding such phenomena is essential in successfully evaluating the electrical specifications of selectors for suppressing intrinsic drawbacks of crossbar arrays, such as sneaky current paths and series line resistance problems. This method provides a quantitative tool for the accurate analysis of crossbar arrays and provides guidelines for developing an optimal read scheme, array configuration, and selector device specifications.

  10. A kernel regression approach to gene-gene interaction detection for case-control studies.

    Science.gov (United States)

    Larson, Nicholas B; Schaid, Daniel J

    2013-11-01

    Gene-gene interactions are increasingly being addressed as a potentially important contributor to the variability of complex traits. Consequently, attentions have moved beyond single locus analysis of association to more complex genetic models. Although several single-marker approaches toward interaction analysis have been developed, such methods suffer from very high testing dimensionality and do not take advantage of existing information, notably the definition of genes as functional units. Here, we propose a comprehensive family of gene-level score tests for identifying genetic elements of disease risk, in particular pairwise gene-gene interactions. Using kernel machine methods, we devise score-based variance component tests under a generalized linear mixed model framework. We conducted simulations based upon coalescent genetic models to evaluate the performance of our approach under a variety of disease models. These simulations indicate that our methods are generally higher powered than alternative gene-level approaches and at worst competitive with exhaustive SNP-level (where SNP is single-nucleotide polymorphism) analyses. Furthermore, we observe that simulated epistatic effects resulted in significant marginal testing results for the involved genes regardless of whether or not true main effects were present. We detail the benefits of our methods and discuss potential genome-wide analysis strategies for gene-gene interaction analysis in a case-control study design. © 2013 WILEY PERIODICALS, INC.

  11. Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

    Directory of Open Access Journals (Sweden)

    Ozge Cebeci

    2009-01-01

    Full Text Available Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate application at 1.58 mM and 6.32 mM, representing 5% and 20%, respectively, of the recommended rate. Differences highlighted categories of general metabolic processes, such as photosynthesis, protein synthesis, stress responses, and a larger number of transcripts responded to 20% glyphosate application. Differential expression of genes encoding proteins involved in the shikimic acid pathway could not be identified by cross hybridization. Microarray data were confirmed by RT-PCR and qRT-PCR analyses. This is the first report to analyze the potential of cross species hybridization in Fescue species and the data and analyses will help extend our knowledge on the cellular processes affected by glyphosate.

  12. Recent studies on the ATM gene

    International Nuclear Information System (INIS)

    Lavin, M.F.; Khanna, K.K.; Waters, D.

    1996-01-01

    Full text: Radiosensitivity is a universal characteristic of ataxia-telangiectasia (A-T), observed after exposure of patients and of cells in culture to radiation. This sensitivity is manifested as higher levels of radiation-induced chromosomal aberrations and reduced survival compared to controls. The gene for A-T was mapped to chromosome 11q 22-23 seven years ago and more recently we have been involved in the cloning of a single gene, ATM (ataxia-telangiectasia mutated), mutated in this syndrome. ATM is a large gene, approximately 150 kb in size, composed of 66 exons and codes for a major mRNA of 13 kb with a predicted open reading frame of 9.135 kb. It is not yet known what activity the ATM gene product possesses, but the ralatedness of this gene sequence to the phosphatidylinositol 3-kinase gene family supports a role for ATM in intracellular signalling. Considerable information is already available on defective signalling through the p53 damage-inducible pathway in A-T. This includes failure to arrest at either the G1/S or G2/M checkpoints as well as radioresistant DNA synthesis. A reduced and/or delayed response in the induction of p53 after exposure of A-T cells to ionizing radiation can account for the defective G1/S checkpoint. More recently we have demonstrated that the ATM gene product is involved in the control of multiple cell cycle checkpoints. Antibodies prepared against ATM peptides demonstrate the presence of a protein 350 kDa in size, which is the predicted size for this protein based on open reading frame of 9 kb. This protein is present both in the nucleus and in the cytoplasm where it is present in vesicular structures. As expected from mutation data the ATM protein is absent in cells from some patients with A-T. The cloning of the ATM gene will allow for screening of radiosensitive patients for mutations in this gene and will provide a means of identifying interacting proteins and thus an understanding of how it functions

  13. Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean.

    Directory of Open Access Journals (Sweden)

    Aldrin Kay-Yuen Yim

    Full Text Available Differential gene expression profiles often provide important clues for gene functions. While reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR is an important tool, the validity of the results depends heavily on the choice of proper reference genes. In this study, we employed new and published RNA-sequencing (RNA-Seq datasets (26 sequencing libraries in total to evaluate reference genes reported in previous soybean studies. In silico PCR showed that 13 out of 37 previously reported primer sets have multiple targets, and 4 of them have amplicons with different sizes. Using a probabilistic approach, we identified new and improved candidate reference genes. We further performed 2 validation tests (with 26 RNA samples on 8 commonly used reference genes and 7 newly identified candidates, using RT-qPCR. In general, the new candidate reference genes exhibited more stable expression levels under the tested experimental conditions. The three newly identified candidate reference genes Bic-C2, F-box protein2, and VPS-like gave the best overall performance, together with the commonly used ELF1b. It is expected that the proposed probabilistic model could serve as an important tool to identify stable reference genes when more soybean RNA-Seq data from different growth stages and treatments are used.

  14. Selection of reference genes for gene expression studies in heart failure for left and right ventricles.

    Science.gov (United States)

    Li, Mengmeng; Rao, Man; Chen, Kai; Zhou, Jianye; Song, Jiangping

    2017-07-15

    Real-time quantitative reverse transcriptase-PCR (qRT-PCR) is a feasible tool for determining gene expression profiles, but the accuracy and reliability of the results depends on the stable expression of selected housekeeping genes in different samples. By far, researches on stable housekeeping genes in human heart failure samples are rare. Moreover the effect of heart failure on the expression of housekeeping genes in right and left ventricles is yet to be studied. Therefore we aim to provide stable housekeeping genes for both ventricles in heart failure and normal heart samples. In this study, we selected seven commonly used housekeeping genes as candidates. By using the qRT-PCR, the expression levels of ACTB, RAB7A, GAPDH, REEP5, RPL5, PSMB4 and VCP in eight heart failure and four normal heart samples were assessed. The stability of candidate housekeeping genes was evaluated by geNorm and Normfinder softwares. GAPDH showed the least variation in all heart samples. Results also indicated the difference of gene expression existed in heart failure left and right ventricles. GAPDH had the highest expression stability in both heart failure and normal heart samples. We also propose using different sets of housekeeping genes for left and right ventricles respectively. The combination of RPL5, GAPDH and PSMB4 is suitable for the right ventricle and the combination of GAPDH, REEP5 and RAB7A is suitable for the left ventricle. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Genome-wide association study identifies candidate genes for starch content regulation in maize kernels

    Directory of Open Access Journals (Sweden)

    Na Liu

    2016-07-01

    Full Text Available Kernel starch content is an important trait in maize (Zea mays L. as it accounts for 65% to 75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60% to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001, among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437 is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops.

  16. Evidence for plasticity genotypes in a gene-gene-environment interaction : the TRAILS study

    NARCIS (Netherlands)

    Nederhof, E; Bouma, Esther; Riese, Harriette; Laceulle, Odilia; Ormel, J.; Oldehinkel, A.J.

    2010-01-01

    The purpose was to study how functional polymorphisms in the brain derived neurotrophic factor gene (BDNF val66met) and the serotonin transporter gene linked promotor region (5-HTTLPR) interact with childhood adversities in predicting Effortful Control. Effortful Control refers to the ability to

  17. Study of nuclei far from stability with AYE-Ball array

    International Nuclear Information System (INIS)

    Carpenter, M.P.

    1996-01-01

    The coupling of a Compton-suppressed Ge (CsGe) detector array to a recoil mass separator (RMS) has seen limited use in the past due to the low efficiency for measuring recoil-γ ray coincidences (< 0.1%). With the building of new generation recoil separators and gamma-ray arrays, a substantial increase in detection efficiency has been achieved. This allows for the opportunity to measure excited states in nuclei with cross-sections approaching 100 nb. In this paper, results from the coupling of a modest array of CsGe detectors (AYE-Ball) with a recoil separator (FMA) will be presented

  18. Studies of Hot Spots in Imploding Wire Arrays at 1 MA on COBRA

    International Nuclear Information System (INIS)

    Pikuz, Sergey A.; Shelkovenko, Tatiana A.; McBride, Ryan D.; Hammer, David A.

    2009-01-01

    We present recent results from hot spot investigations in imploding Al wire array z-pinches on the COBRA generator at Cornell University using x-ray diagnostics. Measurements of the temporal and spatial distribution of hot spots in stagnating plasmas by an x-ray streak-camera are included. Experiments show that hot spots have nanosecond lifetime and appear randomly along the array axis after plasma stagnation in secondary pinches in 8 mm diameter and during plasma stagnation in the arrays with 4 mm diameter.

  19. A complex array of Hpr consensus DNA recognition sequences proximal to the enterotoxin gene in Clostridium perfringens type A.

    Science.gov (United States)

    Brynestad, S; Iwanejko, L A; Stewart, G S; Granum, P E

    1994-01-01

    Enterotoxin production in Clostridium perfringens is both strain dependent and sporulation associated. Underlying these phenotypic observations must lie a genetic and molecular explanation and the principal keys will be held within the DNA sequence both upstream and downstream of the structural gene cpe. In accordance with the above we have sequenced 4.1 kbp of DNA upstream of cpe in the type strain NCTC 8239. A region of DNA extending up to 1.5 kb 5' to cpe is conserved in all enterotoxin-positive strains. This region contains a putative ORF with substantial homology to an ORF in the Salmonella typhimurium IS200 insertion element and, in addition, contains multiple perfect consensus DNA-binding sequences for the Bacillus subtilis transition state regulator Hpr. The detailed structural elements revealed by the sequence analysis are presented and used to develop a new perspective on the molecular basis of enterotoxin production in this important food-poisoning bacterium.

  20. Reveal genes functionally associated with ACADS by a network study.

    Science.gov (United States)

    Chen, Yulong; Su, Zhiguang

    2015-09-15

    Establishing a systematic network is aimed at finding essential human gene-gene/gene-disease pathway by means of network inter-connecting patterns and functional annotation analysis. In the present study, we have analyzed functional gene interactions of short-chain acyl-coenzyme A dehydrogenase gene (ACADS). ACADS plays a vital role in free fatty acid β-oxidation and regulates energy homeostasis. Modules of highly inter-connected genes in disease-specific ACADS network are derived by integrating gene function and protein interaction data. Among the 8 genes in ACADS web retrieved from both STRING and GeneMANIA, ACADS is effectively conjoined with 4 genes including HAHDA, HADHB, ECHS1 and ACAT1. The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with ACADS are HAHDA, HADHB, ECHS1 and ACAT1. Interestingly, the ontological aspect of genes in the ACADS network reveals that ACADS, HAHDA and HADHB play equally vital roles in fatty acid metabolism. The gene ACAT1 together with ACADS indulges in ketone metabolism. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of ACADS, HAHDA, HADHB, ECHS1 and ACAT1 not only with lipid metabolism but also with infant death syndrome, skeletal myopathy, acute hepatic encephalopathy, Reye-like syndrome, episodic ketosis, and metabolic acidosis. The current study presents a comprehensible layout of ACADS network, its functional strategies and candidate disease approach associated with ACADS network. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Thermal therapy for breast tumors by using a cylindrical ultrasound phased array with multifocus pattern scanning: a preliminary numerical study

    International Nuclear Information System (INIS)

    Ho, C-S; Ju, K-C; Cheng, T-Y; Chen, Y-Y; Lin, W-L

    2007-01-01

    The purpose of this study is to investigate the feasibility of using a 1 MHz cylindrical ultrasound phased array with multifocus pattern scanning to produce uniform heating for breast tumor thermal therapy. The breast was submerged in water and surrounded by the cylindrical ultrasound phased array. A multifocus pattern was generated and electrically scanned by the phased array to enlarge the treatment lesion in single heating. To prevent overheating normal tissues, a large planning target volume (PTV) would be divided into several planes with several subunits on each plane and sequentially treated with a cooling phase between two successive heatings of the subunit. Heating results for different target temperatures (T tgt ), blood perfusion rates and sizes of the PTV have been studied. Furthermore, a superficial breast tumor with different water temperatures was also studied. Results indicated that a higher target temperature would produce a slightly larger thermal lesion, and a higher blood perfusion rate would not affect the heating lesion size but increase the heating time significantly. The acoustic power deposition and temperature elevations in ribs can be minimized by orienting the acoustic beam from the ultrasound phased array approximately parallel to the ribs. In addition, a large acoustic window on the convex-shaped breast surface for the proposed ultrasound phased array and the cooling effect of water would prevent the skin overheating for the production of a lesion at any desired location. This study demonstrated that the proposed cylindrical ultrasound phased array can provide effective heating for breast tumor thermal therapy without overheating the skin and ribs within a reasonable treatment time

  2. Nonlinear dynamics of solitary and optically injected two-element laser arrays with four different waveguide structures: a numerical study.

    Science.gov (United States)

    Li, Nianqiang; Susanto, H; Cemlyn, B R; Henning, I D; Adams, M J

    2018-02-19

    We study the nonlinear dynamics of solitary and optically injected two-element laser arrays with a range of waveguide structures. The analysis is performed with a detailed direct numerical simulation, where high-resolution dynamic maps are generated to identify regions of dynamic instability in the parameter space of interest. Our combined one- and two-parameter bifurcation analysis uncovers globally diverse dynamical regimes (steady-state, oscillation, and chaos) in the solitary laser arrays, which are greatly influenced by static design waveguiding structures, the amplitude-phase coupling factor of the electric field, i.e. the linewidth-enhancement factor, as well as the control parameter, e.g. the pump rate. When external optical injection is introduced to one element of the arrays, we show that the whole system can be either injection-locked simultaneously or display rich, different dynamics outside the locking region. The effect of optical injection is to significantly modify the nature and the regions of nonlinear dynamics from those found in the solitary case. We also show similarities and differences (asymmetry) between the oscillation amplitude of the two elements of the array in specific well-defined regions, which hold for all the waveguiding structures considered. Our findings pave the way to a better understanding of dynamic instability in large arrays of lasers.

  3. Study of Defect Sizing in Carbon Steel Butt Welds using Conventional Ultrasonic Technique and Phased Array Ultrasonic

    International Nuclear Information System (INIS)

    Amry Amin Abas; Noorhazleena Azaman; Mohd Yusnisyam Mohd Yusoff

    2016-01-01

    Ultrasonic testing is a proven reliable method which is able to detect and measure the size of defects in butt welds with acceptable tolerance. Recent advancement of technology has introduced a computerized technique which is phased array. Phased array employs focal law that enable focusing and steering of beam at the active aperture axis. This enables one line scanning but covering the whole weld volume as compared to conventional technique which employs aster scan and multiple probes to completely cover the whole weld volume. Phased array also gives multiple data view which assist the interpreter. This paper is about the study of these two techniques and technical analysis of comparison between the two. The conventional technique is performed using GE USM GO with 4 MHz 45 degrees shear wave probe. The phased array technique uses OLYMPUS OMNISCAN MX2 with 5L64 linear array probe with 16 elements aperture and 55 degrees wedge emitting shear wave into the specimen. Sensitivity of both techniques are based on 1.5 mm Side Drilled Hole. The results are compared and analysis such as defect sizing and defect type determination are performed. (author)

  4. Probabilistic Neural Networks for Chemical Sensor Array Pattern Recognition: Comparison Studies, Improvements and Automated Outlier Rejection

    National Research Council Canada - National Science Library

    Shaffer, Ronald E

    1998-01-01

    For application to chemical sensor arrays, the ideal pattern recognition is accurate, fast, simple to train, robust to outliers, has low memory requirements, and has the ability to produce a measure...

  5. The Experience of Using Innovative Artificial Filter Arrays on South Kuzbass Open Pit: Case Study

    Directory of Open Access Journals (Sweden)

    Tyulenev Maxim

    2017-01-01

    Full Text Available The article describes the detailed example of placement of artificial filter arrays in one of Kuzbass open pits. It is proved that the use of the existing rock dump as an artificial filter array allows cleaning the quarry wastewater to the required parameters. Therefore, for water purification, it is possible to pile a new array as well as to use the existing dump, which will reduce the operating costs and the land consumption of open pit mining operations. Also, a brief methodology for determining the parameters of the artificial filter array is given in the article, taking into account the volume of contaminated water, the degree of its contamination and the location of the filter. The proposed complex of measures significantly improves the geo-ecological situation of mining region.

  6. In situ x-ray diffraction study on AgI nanowire arrays

    International Nuclear Information System (INIS)

    Wang Yinhai; Ye Changhui; Wang Guozhong; Zhang Lide; Liu Yanmei; Zhao Zhongyan

    2003-01-01

    The AgI nanowire arrays were prepared in the ordered porous alumina membrane by an electrochemical method. Transmission electron microscopy observation shows that the AgI nanowires are located in the channels of the alumina membrane. In situ x-ray diffractions show that the nanowire arrays possess hexagonal close-packed structure (β-AgI) at 293 K, orienting along the (002) plane, whereas at 473 K, the nanowire arrays possess a body-centered cubic structure (α-AgI), orienting along the (110) plane. The AgI nanowire arrays exhibit a negative thermal expansion property from 293 to 433 K, and a higher transition temperature from the β to α phase. We ascribe the negative thermal expansion behavior to the phase transition from the β to α phase, and the elevated transition temperature to the radial restriction by the channels of alumina membrane

  7. Screening for the Most Suitable Reference Genes for Gene Expression Studies in Equine Milk Somatic Cells.

    Directory of Open Access Journals (Sweden)

    Jakub Cieslak

    Full Text Available Apart from the well-known role of somatic cell count as a parameter reflecting the inflammatory status of the mammary gland, the composition of cells isolated from milk is considered as a valuable material for gene expression studies in mammals. Due to its unique composition, in recent years an increasing interest in mare's milk consumption has been observed. Thus, investigating the genetic background of horse's milk variability presents and interesting study model. Relying on 39 milk samples collected from mares representing three breeds (Polish Primitive Horse, Polish Cold-blooded Horse, Polish Warmblood Horse we aimed to investigate the utility of equine milk somatic cells as a source of mRNA and to screen the best reference genes for RT-qPCR using geNorm and NormFinder algorithms. The results showed that despite relatively low somatic cell counts in mare's milk, the amount and the quality of the extracted RNA are sufficient for gene expression studies. The analysis of the utility of 7 potential reference genes for RT-qPCR experiments for the normalization of equine milk somatic cells revealed some differences between the outcomes of the applied algorithms, although in both cases the KRT8 and TOP2B genes were pointed as the most stable. Analysis by geNorm showed that the combination of 4 reference genes (ACTB, GAPDH, TOP2B and KRT8 is required for apropriate RT-qPCR experiments normalization, whereas NormFinder algorithm pointed the combination of KRT8 and RPS9 genes as the most suitable. The trial study of the relative transcript abundance of the beta-casein gene with the use of various types and numbers of internal control genes confirmed once again that the selection of proper reference gene combinations is crucial for the final results of each real-time PCR experiment.

  8. Josephson junction arrays

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  9. Identification of suitable reference genes for gene expression studies of shoulder instability.

    Directory of Open Access Journals (Sweden)

    Mariana Ferreira Leal

    Full Text Available Shoulder instability is a common shoulder injury, and patients present with plastic deformation of the glenohumeral capsule. Gene expression analysis may be a useful tool for increasing the general understanding of capsule deformation, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR has become an effective method for such studies. Although RT-qPCR is highly sensitive and specific, it requires the use of suitable reference genes for data normalization to guarantee meaningful and reproducible results. In the present study, we evaluated the suitability of a set of reference genes using samples from the glenohumeral capsules of individuals with and without shoulder instability. We analyzed the expression of six commonly used reference genes (ACTB, B2M, GAPDH, HPRT1, TBP and TFRC in the antero-inferior, antero-superior and posterior portions of the glenohumeral capsules of cases and controls. The stability of the candidate reference gene expression was determined using four software packages: NormFinder, geNorm, BestKeeper and DataAssist. Overall, HPRT1 was the best single reference gene, and HPRT1 and B2M composed the best pair of reference genes from different analysis groups, including simultaneous analysis of all tissue samples. GenEx software was used to identify the optimal number of reference genes to be used for normalization and demonstrated that the accumulated standard deviation resulting from the use of 2 reference genes was similar to that resulting from the use of 3 or more reference genes. To identify the optimal combination of reference genes, we evaluated the expression of COL1A1. Although the use of different reference gene combinations yielded variable normalized quantities, the relative quantities within sample groups were similar and confirmed that no obvious differences were observed when using 2, 3 or 4 reference genes. Consequently, the use of 2 stable reference genes for normalization, especially

  10. Human reporter genes: potential use in clinical studies

    Energy Technology Data Exchange (ETDEWEB)

    Serganova, Inna [Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States); Ponomarev, Vladimir [Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States); Blasberg, Ronald [Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States); Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States)], E-mail: blasberg@neuro1.mskcc.org

    2007-10-15

    The clinical application of positron-emission-tomography-based reporter gene imaging will expand over the next several years. The translation of reporter gene imaging technology into clinical applications is the focus of this review, with emphasis on the development and use of human reporter genes. Human reporter genes will play an increasingly more important role in this development, and it is likely that one or more reporter systems (human gene and complimentary radiopharmaceutical) will take leading roles. Three classes of human reporter genes are discussed and compared: receptors, transporters and enzymes. Examples of highly expressed cell membrane receptors include specific membrane somatostatin receptors (hSSTrs). The transporter group includes the sodium iodide symporter (hNIS) and the norepinephrine transporter (hNET). The endogenous enzyme classification includes human mitochondrial thymidine kinase 2 (hTK2). In addition, we also discuss the nonhuman dopamine 2 receptor and two viral reporter genes, the wild-type herpes simplex virus 1 thymidine kinase (HSV1-tk) gene and the HSV1-tk mutant (HSV1-sr39tk). Initial applications of reporter gene imaging in patients will be developed within two different clinical disciplines: (a) gene therapy and (b) adoptive cell-based therapies. These studies will benefit from the availability of efficient human reporter systems that can provide critical monitoring information for adenoviral-based, retroviral-based and lenteviral-based gene therapies, oncolytic bacterial and viral therapies, and adoptive cell-based therapies. Translational applications of noninvasive in vivo reporter gene imaging are likely to include: (a) quantitative monitoring of gene therapy vectors for targeting and transduction efficacy in clinical protocols by imaging the location, extent and duration of transgene expression; (b) monitoring of cell trafficking, targeting, replication and activation in adoptive T-cell and stem/progenitor cell therapies

  11. Human reporter genes: potential use in clinical studies

    International Nuclear Information System (INIS)

    Serganova, Inna; Ponomarev, Vladimir; Blasberg, Ronald

    2007-01-01

    The clinical application of positron-emission-tomography-based reporter gene imaging will expand over the next several years. The translation of reporter gene imaging technology into clinical applications is the focus of this review, with emphasis on the development and use of human reporter genes. Human reporter genes will play an increasingly more important role in this development, and it is likely that one or more reporter systems (human gene and complimentary radiopharmaceutical) will take leading roles. Three classes of human reporter genes are discussed and compared: receptors, transporters and enzymes. Examples of highly expressed cell membrane receptors include specific membrane somatostatin receptors (hSSTrs). The transporter group includes the sodium iodide symporter (hNIS) and the norepinephrine transporter (hNET). The endogenous enzyme classification includes human mitochondrial thymidine kinase 2 (hTK2). In addition, we also discuss the nonhuman dopamine 2 receptor and two viral reporter genes, the wild-type herpes simplex virus 1 thymidine kinase (HSV1-tk) gene and the HSV1-tk mutant (HSV1-sr39tk). Initial applications of reporter gene imaging in patients will be developed within two different clinical disciplines: (a) gene therapy and (b) adoptive cell-based therapies. These studies will benefit from the availability of efficient human reporter systems that can provide critical monitoring information for adenoviral-based, retroviral-based and lenteviral-based gene therapies, oncolytic bacterial and viral therapies, and adoptive cell-based therapies. Translational applications of noninvasive in vivo reporter gene imaging are likely to include: (a) quantitative monitoring of gene therapy vectors for targeting and transduction efficacy in clinical protocols by imaging the location, extent and duration of transgene expression; (b) monitoring of cell trafficking, targeting, replication and activation in adoptive T-cell and stem/progenitor cell therapies

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

    Directory of Open Access Journals (Sweden)

    Guan-Nan Tan

    2016-01-01

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

  13. A study for soundness of turbine blade root using ultrasonic and phased array

    International Nuclear Information System (INIS)

    Gil, Doo Song; Park, Sang Ki; Cho, Yong Sang; Lee, Sang Gug; Huh, Kuang Bum

    2003-01-01

    Power plant is consisted of many component parts for the generation of the electricity, and occasionally, turbine equipment may be caused in break-down because of the damage of the blade root. Phased array ultrasonic testing system has become available for practical application in complicated geometry such as turbine blade root, tenon, disc in power industry. This research describes the characteristics of phased array ultrasonic testing signal for various type of blade roots in thermal Power Plant turbines. This application of Phased array ultrasonic testing system has been promoted mainly to save inspection time and labor cost of turbine inspection. The characteristic of phased array ultrasonic testing signal for power plant component in very simple to understand but to difficult for perform the inspection. This paper is focused on the safety of the turbine equipment by the ultrasonic measurement and phased array analysis. As a result of the test through ultrasonic and phased array method, we have concluded that the main damage in these turbine blade root parts could be generated by the concentrated stress and centrifugal force.

  14. A study for soundness of turbine blade root using ultrasonic and phased array

    International Nuclear Information System (INIS)

    Gil, Doo Song; Park, Sang Ki; Cho, Yong Sang; Lee, Sang Gug; Huh, Kuang Bum

    2003-01-01

    Power plant is consisted of many component parts for the generation of the electricity and occasionally, turbine equipment may be caused in break-down because of the damage of the blade root. Phased array ultrasonic testing system has become available for power industry. This research describes the characteristics of phased array ultrasonic testing signal for various type of blade roots in thermal power plant turbines. This application of Phased array ultrasonic testing system has been promoted mainly to save inspection time and labor cost of turbine inspection. The characteristic of phased array ultrasonic testing signal for power plant component in very simple to understand but to difficult for perform the inspection. This paper is focused on the safety of the turbine equipment by the ultrasonic measurement and phased array analysis. As a result of the test through ultrasonic and phased array method, we have concluded that the main damage in these turbine blade roots parts could be generated by the concentrated stress and centrifugal force.

  15. Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don.

    Science.gov (United States)

    Xiao, Zheng; Sun, Xiaobo; Liu, Xiaoqing; Li, Chang; He, Lisi; Chen, Shangping; Su, Jiale

    2016-01-01

    The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper. The results showed that EF1- α (elongation factor 1-alpha), 18S (18s ribosomal RNA), and RPL3 (ribosomal protein L3) were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin ( TUB ) was the least stable. ACT5 (actin), RPL3 , 18S , and EF1- α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle . Furthermore, the expression profiles of RmPSY (phytoene synthase) and RmPDS (phytoene dehydrogenase) were assessed using EF1- α, 18S , ACT5 , RPL3 , and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle .

  16. Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don

    Directory of Open Access Journals (Sweden)

    Zheng Xiao

    2016-10-01

    Full Text Available The quantitative real-time polymerase chain reaction (qRT-PCR approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder and BestKeeper. The results showed that EF1-α (elongation factor 1-alpha, 18S (18s ribosomal RNA and RPL3 (ribosomal protein L3 were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin (TUB was the least stable. ACT5 (actin, RPL3, 18S and EF1-α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle. Furthermore, the expression profiles of RmPSY (phytoene synthase and RmPDS (phytoene dehydrogenase were assessed using EF1-α, 18S, ACT5, and RPL3 and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle.

  17. Correlation of gene expression and contaminat concentrations in wild largescale suckers: a field-based study

    Science.gov (United States)

    Christiansen, Helena E.; Mehinto, Alvine C.; Yu, Fahong; Perry, Russell W.; Denslow, Nancy D.; Maule, Alec G.; Mesa, Matthew G.

    2014-01-01

    Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use food resources from within the river. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant concentration suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin. The array developed in this study could also be a useful tool for studies involving endangered sucker species and other sucker species used in contaminant research.

  18. Genes and gene expression: Localization, damage and control -- A multilevel and inter-disciplinary study

    International Nuclear Information System (INIS)

    Ts'o, P.O.P.

    1990-09-01

    All projects are working toward a goal for describing the three dimensional nuclear topography in terms of relative spatial relationships among genes (specific DNA sequence). Methods are now being perfected to detect these genes, quantitatively and spatially, to perturb these genes specifically, and to measure the perturbation in order to assure specificity. We are developing methods to assay, after perturbation of the target DNA within living cells, whether or not only the target sequence are attacked while other sequences remain unharmed. We are now at the stage to do chemical gene modification or masking within living cells in a strictly sequence-specific manner. Soon, we will be able to study the function and the physical location of each gene in living cells with exquisite specificity. 25 refs., 15 figs

  19. Identification of reference genes and validation for gene expression studies in diverse axolotl (Ambystoma mexicanum) tissues.

    Science.gov (United States)

    Guelke, Eileen; Bucan, Vesna; Liebsch, Christina; Lazaridis, Andrea; Radtke, Christine; Vogt, Peter M; Reimers, Kerstin

    2015-04-10

    For the precise quantitative RT-PCR normalization a set of valid reference genes is obligatory. Moreover have to be taken into concern the experimental conditions as they bias the regulation of reference genes. Up till now, no reference targets have been described for the axolotl (Ambystoma mexicanum). In a search in the public database SalSite for genetic information of the axolotl we identified fourteen presumptive reference genes, eleven of which were further tested for their gene expression stability. This study characterizes the expressional patterns of 11 putative endogenous control genes during axolotl limb regeneration and in an axolotl tissue panel. All 11 reference genes showed variable expression. Strikingly, ACTB was to be found most stable expressed in all comparative tissue groups, so we reason it to be suitable for all different kinds of axolotl tissue-type investigations. Moreover do we suggest GAPDH and RPLP0 as suitable for certain axolotl tissue analysis. When it comes to axolotl limb regeneration, a validated pair of reference genes is ODC and RPLP0. With these findings, new insights into axolotl gene expression profiling might be gained. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Experimental study of the retention properties of a cyclo olefin polymer pillar array column in reversed-phase mode

    NARCIS (Netherlands)

    Illa, Xavi; de Malsche, Wim; Gardeniers, Johannes G.E.; Desmet, Gert; Romano-Rodriguez, Albert

    2010-01-01

    Experimental measurements to study the retention capacity and band broadening under retentive conditions using micromachined non-porous pillar array columns fabricated in cyclo olefin polymer are presented. In particular, three columns with different depths but with the same pillar structure have

  1. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

    Science.gov (United States)

    Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

    2016-03-01

    A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

  2. Imputation across genotyping arrays for genome-wide association studies: assessment of bias and a correction strategy.

    Science.gov (United States)

    Johnson, Eric O; Hancock, Dana B; Levy, Joshua L; Gaddis, Nathan C; Saccone, Nancy L; Bierut, Laura J; Page, Grier P

    2013-05-01

    A great promise of publicly sharing genome-wide association data is the potential to create composite sets of controls. However, studies often use different genotyping arrays, and imputation to a common set of SNPs has shown substantial bias: a problem which has no broadly applicable solution. Based on the idea that using differing genotyped SNP sets as inputs creates differential imputation errors and thus bias in the composite set of controls, we examined the degree to which each of the following occurs: (1) imputation based on the union of genotyped SNPs (i.e., SNPs available on one or more arrays) results in bias, as evidenced by spurious associations (type 1 error) between imputed genotypes and arbitrarily assigned case/control status; (2) imputation based on the intersection of genotyped SNPs (i.e., SNPs available on all arrays) does not evidence such bias; and (3) imputation quality varies by the size of the intersection of genotyped SNP sets. Imputations were conducted in European Americans and African Americans with reference to HapMap phase II and III data. Imputation based on the union of genotyped SNPs across the Illumina 1M and 550v3 arrays showed spurious associations for 0.2 % of SNPs: ~2,000 false positives per million SNPs imputed. Biases remained problematic for very similar arrays (550v1 vs. 550v3) and were substantial for dissimilar arrays (Illumina 1M vs. Affymetrix 6.0). In all instances, imputing based on the intersection of genotyped SNPs (as few as 30 % of the total SNPs genotyped) eliminated such bias while still achieving good imputation quality.

  3. Development of a novel ozone- and photo-stable HyPer5 red fluorescent dye for array CGH and microarray gene expression analysis with consistent performance irrespective of environmental conditions

    Directory of Open Access Journals (Sweden)

    Kille Peter

    2008-11-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (CGH and gene expression profiling have become vital techniques for identifying molecular defects underlying genetic diseases. Regardless of the microarray platform, cyanine dyes (Cy3 and Cy5 are one of the most widely used fluorescent dye pairs for microarray analysis owing to their brightness and ease of incorporation, enabling high level of assay sensitivity. However, combining both dyes on arrays can become problematic during summer months when ozone levels rise to near 25 parts per billion (ppb. Under such conditions, Cy5 is known to rapidly degrade leading to loss of signal from either "homebrew" or commercial arrays. Cy5 can also suffer disproportionately from dye photobleaching resulting in distortion of (Cy5/Cy3 ratios used in copy number analysis. Our laboratory has been active in fluorescent dye research to find a suitable alternative to Cy5 that is stable to ozone and resistant to photo-bleaching. Here, we report on the development of such a dye, called HyPer5, and describe its' exceptional ozone and photostable properties on microarrays. Results Our results show HyPer5 signal to be stable to high ozone levels. Repeated exposure of mouse arrays hybridized with HyPer5-labeled cDNA to 300 ppb ozone at 5, 10 and 15 minute intervals resulted in no signal loss from the dye. In comparison, Cy5 arrays showed a dramatic 80% decrease in total signal during the same interval. Photobleaching experiments show HyPer5 to be resistant to light induced damage with 3- fold improvement in dye stability over Cy5. In high resolution array CGH experiments, HyPer5 is demonstrated to detect chromosomal aberrations at loci 2p21-16.3 and 15q26.3-26.2 from three patient sample using bacterial artificial chromosome (BAC arrays. The photostability of HyPer5 is further documented by repeat array scanning without loss of detection. Additionally, HyPer5 arrays are shown to preserve sensitivity and

  4. Superior Cross-Species Reference Genes: A Blueberry Case Study

    Science.gov (United States)

    Die, Jose V.; Rowland, Lisa J.

    2013-01-01

    The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well. PMID:24058469

  5. Superior cross-species reference genes: a blueberry case study.

    Directory of Open Access Journals (Sweden)

    Jose V Die

    Full Text Available The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well.

  6. In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

    Directory of Open Access Journals (Sweden)

    Kristiansen Glen

    2007-06-01

    Full Text Available Abstract Background Housekeeping genes are commonly used as endogenous reference genes for the relative quantification of target genes in gene expression studies. No conclusive systematic study comparing the suitability of different candidate reference genes in clear cell renal cell carcinoma has been published to date. To remedy this situation, 10 housekeeping genes for normalizing purposes of RT-PCR measurements already recommended in various studies were examined with regard to their usefulness as reference genes. Results The expression of the potential reference genes was examined in matched malignant and non-malignant tissue specimens from 25 patients with clear cell renal cell carcinoma. Quality assessment of isolated RNA performed with a 2100 Agilent Bioanalyzer showed a mean RNA integrity number of 8.7 for all samples. The between-run variations related to the crossing points of PCR reactions of a control material ranged from 0.17% to 0.38%. The expression of all genes did not depend on age, sex, and tumour stage. Except the genes TATA box binding protein (TBP and peptidylprolyl isomerase A (PPIA, all genes showed significant differences in expression between malignant and non-malignant pairs. The expression stability of the candidate reference genes was additionally controlled using the software programs geNorm and NormFinder. TBP and PPIA were validated as suitable reference genes by normalizing the target gene ADAM9 using these two most stably expressed genes in comparison with up- and down-regulated housekeeping genes of the panel. Conclusion Our study demonstrated the suitability of the two housekeeping genes PPIA and TBP as endogenous reference genes when comparing malignant tissue samples with adjacent normal tissue samples from clear cell renal cell carcinoma. Both genes are recommended as reference genes for relative gene quantification in gene profiling studies either as single gene or preferably in combination.

  7. Study on the Performance of the “Pendulor” Wave Energy Converter in an Array Configuration

    Directory of Open Access Journals (Sweden)

    Sudath Prasanna Gunawardane

    2016-04-01

    Full Text Available For over three decades the “Pendulor” wave energy device has had a significant influence in this field, triggering several research endeavours. It includes a top-hinged flap propelled by the standing waves produced in a caisson with a back wall on the leeward side. However, one of the main disadvantages which impedes its progress is the enormous expense involved in the construction of the custom made typical caisson structure, about a little more than one-quarter of the wave length. In this study, the influence of such design parameters on the performance of the device is investigated, via numerical modelling for a device arranged in an array configuration, for irregular waves. The potential wave theory is applied to derive the frequency-dependent hydrodynamic parameters by making a distinction in the fluid domain into a separate sea side and lee side. The Cummins equation was utilised for the development of the time domain equation of motion while the transfer function estimation methods were used to solve the convolution integrals. Finally, the device was tested numerically for irregular wave conditions for a 50 kW class unit. It was observed that in irregular wave operating conditions, the caisson chamber length could be reduced by 40% of the value estimated for the regular waves. Besides, the device demonstrated around 80% capture efficiency for irregular waves thus allowing provision for avoiding the employment of any active control.

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

    International Nuclear Information System (INIS)

    Casini, G.; Barlini, S.; Pasquali, G.; Pastore, G.; Bini, M.; Carboni, S.; Olmi, A.; Piantelli, S.; Poggi, G.; Stefanini, A.; Valdre, S.; Bonnet, E.; Chbihi, A.; Frankland, J.D.; Gruyer, D.; Marini, P.; Borderie, B.; Edelbruck, P.; Rivet, M.F.; Salomon, F.; Bougault, R.; Le Neindre, N.; Lopez, O.; Parlog, M.; Vient, E.; Bruno, M.; Guerzoni, M.; Morelli, L.; Cinausero, M.; Gramegna, F.; Degerlier, M.; Kordjasz, A.; Twarog, T.; Kozik, T.; Marchi, T.; Ordine, A.; Rosato, E.; Spadaccini, G.; Vigilante, M.

    2014-01-01

    A modular array of 192 Si-Si-CsI(Tl) telescopes is under construction by the european FAZIA collaboration for charged product identification in heavy-ion studies. Thanks to an intense development phase, the ion identification capability of such modules has been improved both adopting specific solutions for the detectors and using fast digital electronics channels featuring high resolution. The silicons have been cut to present almost random orientation and have uniform doping homogeneity. To improve pulse shape analysis (PSA), they are reverse mounted in the telescopes. Full charge separation has been obtained up to over Z=54 also for ions stopping in the first silicon layer via PSA, with a threshold of 2.5 MeV/u for Carbon (Tin) ions. Isotopes are separated up to the iron region by the ΔE - E method for ions stopped in second silicon or in the CsI crystal. For slower particles, the PSA allows for isotopic resolution up to Z ∼ 14 with thresholds corresponding to ∼ 50 μm of (fully depleted) silicon detector. Preliminary results for partially depleted detectors indicate a strong improvement of mass separation with respect to the full depletion case at the cost of somewhat higher thresholds

  9. Feasibility study of a unilateral RF array coil for MR-scintimammography

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Seunghoon; Hamamura, Mark J; Roeck, Werner W; Nalcioglu, Orhan [Tu and Yuen Center for Functional Onco-Imaging, University of California, Irvine, CA (United States); Hugg, James; Wagenaar, Douglas J; Patt, Bradley E [Gamma Medica, Inc. (Clinical Division), Northridge, CA (United States); Meier, Dirk, E-mail: seunghoh@uci.edu [Gamma Medica, Inc. (Industrial Division), Fornebu (Norway)

    2011-11-07

    Despite its high sensitivity, the variable specificity of magnetic resonance imaging (MRI) in breast cancer diagnosis can lead to unnecessary biopsies and over-treatment. Scintimammography (SMM) could potentially supplement MRI to improve the diagnostic specificity. The synergistic combination of MRI and SMM (MRSMM) could result in both high sensitivity from MRI and high specificity from SMM. Development of such a dual-modality system requires the integration of a radio frequency (RF) coil and radiation detector in a strong magnetic field without significant mutual interference. In this study, we developed and tested a unilateral breast array coil specialized for MRSMM imaging. The electromagnetic field, specific absorption ratio and RF coil parameters with cadmium-zinc-telluride detectors encapsulated in specialized RF and gamma-ray shielding mounted within the RF coil were investigated through simulation and experimental measurements. Simultaneous MR and SMM images of a breast phantom were also acquired using the integrated MRSMM system. This work, we feel, represents an important step toward the fabrication of a working MRSMM system.

  10. Feasibility study of a unilateral RF array coil for MR-scintimammography

    International Nuclear Information System (INIS)

    Ha, Seunghoon; Hamamura, Mark J; Roeck, Werner W; Nalcioglu, Orhan; Hugg, James; Wagenaar, Douglas J; Patt, Bradley E; Meier, Dirk

    2011-01-01

    Despite its high sensitivity, the variable specificity of magnetic resonance imaging (MRI) in breast cancer diagnosis can lead to unnecessary biopsies and over-treatment. Scintimammography (SMM) could potentially supplement MRI to improve the diagnostic specificity. The synergistic combination of MRI and SMM (MRSMM) could result in both high sensitivity from MRI and high specificity from SMM. Development of such a dual-modality system requires the integration of a radio frequency (RF) coil and radiation detector in a strong magnetic field without significant mutual interference. In this study, we developed and tested a unilateral breast array coil specialized for MRSMM imaging. The electromagnetic field, specific absorption ratio and RF coil parameters with cadmium-zinc-telluride detectors encapsulated in specialized RF and gamma-ray shielding mounted within the RF coil were investigated through simulation and experimental measurements. Simultaneous MR and SMM images of a breast phantom were also acquired using the integrated MRSMM system. This work, we feel, represents an important step toward the fabrication of a working MRSMM system.

  11. Studies to single subassembly flow monitoring with a complete 7 element array under sodium

    International Nuclear Information System (INIS)

    Hess, B.; Ruppert, E.; Stehle, H.; Vinzens, K.

    1975-01-01

    A core restraint system in a fast reactor serves to limit fuel element movement leading to reactivity changes and misalignment of control rod drives and instrumentation. To guarantee proper control rod function the upper ring of the passive restraint system for the SNR-300 should keep subassembly displacement below 20 mm, whereas a free bowing up to 25 mm does not impair subassembly handling. With respect to single subassembly instrumentation the influences of subassembly displacement on temperature and flow monitoring were not exactly known. As part of the SNR-300 R and D programme a complete clamped array, consisting of 4 full size fuel elements and 3 blanket elements was tested for more than 4000 hours at 600 0 C in the AKB sodium loop at Interatom, Bensberg. The test was split into two phases and the total cluster was prestrained in the second phase to simulate 15 mm subassembly displacement at the level of the upper pads. Although this test was mainly considered as an endurance test to demonstrate the integrity of prestrained core elements, effort were made to study the feasibility of single subassembly flow monitoring with this full size model of a core section. (Auth.)

  12. A high resolution germanium detector array for hypernuclear studies at PANDA

    Energy Technology Data Exchange (ETDEWEB)

    Bleser, Sebastian; Sanchez Lorente, Alicia; Steinen, Marcell [Helmholtz-Institut Mainz (Germany); Gerl, Juergen; Kojouharov, Ivan [GSI, Darmstadt (Germany); Iazzi, Felice [Politecnico, Torino, Turin (Italy); INFN, Torino, Turin (Italy); Pochodzalla, Josef; Rittgen, Kai; Sahin, Cihan [Institute for Nuclear Physics, JGU Mainz (Germany); Collaboration: PANDA-Collaboration

    2013-07-01

    The PANDA experiment, planned at the FAIR facility in Darmstadt, aims at the high resolution γ-spectroscopy of double Λ hypernuclei. For this purpose a devoted detector setup is required, consisting of a primary nuclear target, an active secondary target and a germanium detector array for the γ-spectroscopy. Due to the limited space within the PANDA detector a compact design is required. In particular the conventional LN{sub 2} cooling system must be replaced by an electro-mechanical device and a new arrangement of the crystals is needed. This poster shows the ongoing development of the germanium detectors. Test measurements of a single crystal prototype with an improved cooling concept are shown. Thermal simulations for a triple crystal detector are presented. Aditionally studies of the optimization of the detector arrangement inside the PANDA barrel spectrometer are shown. Finally the status on digital pulse shape analysis is presented which will be necessary to deal with high counting rates and to recover the high original energy resolution in case of neutron damage.

  13. NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

    Directory of Open Access Journals (Sweden)

    Ivan Merelli

    Full Text Available Long-range chromosomal associations between genomic regions, and their repositioning in the 3D space of the nucleus, are now considered to be key contributors to the regulation of gene expression and important links have been highlighted with other genomic features involved in DNA rearrangements. Recent Chromosome Conformation Capture (3C measurements performed with high throughput sequencing (Hi-C and molecular dynamics studies show that there is a large correlation between colocalization and coregulation of genes, but these important researches are hampered by the lack of biologists-friendly analysis and visualisation software. Here, we describe NuChart, an R package that allows the user to annotate and statistically analyse a list of input genes with information relying on Hi-C data, integrating knowledge about genomic features that are involved in the chromosome spatial organization. NuChart works directly with sequenced reads to identify the related Hi-C fragments, with the aim of creating gene-centric neighbourhood graphs on which multi-omics features can be mapped. Predictions about CTCF binding sites, isochores and cryptic Recombination Signal Sequences are provided directly with the package for mapping, although other annotation data in bed format can be used (such as methylation profiles and histone patterns. Gene expression data can be automatically retrieved and processed from the Gene Expression Omnibus and ArrayExpress repositories to highlight the expression profile of genes in the identified neighbourhood. Moreover, statistical inferences about the graph structure and correlations between its topology and multi-omics features can be performed using Exponential-family Random Graph Models. The Hi-C fragment visualisation provided by NuChart allows the comparisons of cells in different conditions, thus providing the possibility of novel biomarkers identification. NuChart is compliant with the Bioconductor standard and it is freely

  14. Functionally enigmatic genes: a case study of the brain ignorome.

    Directory of Open Access Journals (Sweden)

    Ashutosh K Pandey

    Full Text Available What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.

  15. Functionally enigmatic genes: a case study of the brain ignorome.

    Science.gov (United States)

    Pandey, Ashutosh K; Lu, Lu; Wang, Xusheng; Homayouni, Ramin; Williams, Robert W

    2014-01-01

    What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.

  16. Validation of commonly used reference genes for sleep-related gene expression studies

    Directory of Open Access Journals (Sweden)

    Castro Rosa MRPS

    2009-05-01

    Full Text Available Abstract Background Sleep is a restorative process and is essential for maintenance of mental and physical health. In an attempt to understand the complexity of sleep, multidisciplinary strategies, including genetic approaches, have been applied to sleep research. Although quantitative real time PCR has been used in previous sleep-related gene expression studies, proper validation of reference genes is currently lacking. Thus, we examined the effect of total or paradoxical sleep deprivation (TSD or PSD on the expression stability of the following frequently used reference genes in brain and blood: beta-actin (b-actin, beta-2-microglobulin (B2M, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, and hypoxanthine guanine phosphoribosyl transferase (HPRT. Results Neither TSD nor PSD affected the expression stability of all tested genes in both tissues indicating that b-actin, B2M, GAPDH and HPRT are appropriate reference genes for the sleep-related gene expression studies. In order to further verify these results, the relative expression of brain derived neurotrophic factor (BDNF and glycerol-3-phosphate dehydrogenase1 (GPD1 was evaluated in brain and blood, respectively. The normalization with each of four reference genes produced similar pattern of expression in control and sleep deprived rats, but subtle differences in the magnitude of expression fold change were observed which might affect the statistical significance. Conclusion This study demonstrated that sleep deprivation does not alter the expression stability of commonly used reference genes in brain and blood. Nonetheless, the use of multiple reference genes in quantitative RT-PCR is required for the accurate results.

  17. Rotatable Small Permanent Magnet Array for Ultra-Low Field Nuclear Magnetic Resonance Instrumentation: A Concept Study.

    Science.gov (United States)

    Vogel, Michael W; Giorni, Andrea; Vegh, Viktor; Pellicer-Guridi, Ruben; Reutens, David C

    2016-01-01

    We studied the feasibility of generating the variable magnetic fields required for ultra-low field nuclear magnetic resonance relaxometry with dynamically adjustable permanent magnets. Our motivation was to substitute traditional electromagnets by distributed permanent magnets, increasing system portability. The finite element method (COMSOL®) was employed for the numerical study of a small permanent magnet array to calculate achievable magnetic field strength, homogeneity, switching time and magnetic forces. A manually operated prototype was simulated and constructed to validate the numerical approach and to verify the generated magnetic field. A concentric small permanent magnet array can be used to generate strong sample pre-polarisation and variable measurement fields for ultra-low field relaxometry via simple prescribed magnet rotations. Using the array, it is possible to achieve a pre-polarisation field strength above 100 mT and variable measurement fields ranging from 20-50 μT with 200 ppm absolute field homogeneity within a field-of-view of 5 x 5 x 5 cubic centimetres. A dynamic small permanent magnet array can generate multiple highly homogeneous magnetic fields required in ultra-low field nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) instruments. This design can significantly reduce the volume and energy requirements of traditional systems based on electromagnets, improving portability considerably.

  18. Study on single-channel signals of water Cherenkov detector array for the LHAASO project

    Energy Technology Data Exchange (ETDEWEB)

    Li, H.C., E-mail: lihuicai@ihep.ac.cn [University of Nankai, Tianjin 300071 (China); Yao, Z.G.; Chen, M.J. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Yu, C.X. [University of Nankai, Tianjin 300071 (China); Zha, M.; Wu, H.R.; Gao, B.; Wang, X.J. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Liu, J.Y.; Liao, W.Y. [University of Nankai, Tianjin 300071 (China); Huang, D.Z. [Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)

    2017-05-11

    The Large High Altitude Air Shower Observatory (LHAASO) is planned to be built at Daocheng, Sichuan Province, China. The water Cherenkov detector array (WCDA), with an area of 78,000 m{sup 2} and capacity of 350,000 tons of purified water, is one of the major components of the LHAASO project. A 9-cell detector prototype array has been built at the Yangbajing site, Tibet, China to comprehensively understand the water Cherenkov technique and investigate the engineering issues of WCDA. In this paper, the rate and charge distribution of single-channel signals are evaluated using a full detail Monte Carlo simulation. The results are discussed and compared with the results obtained with prototype array.

  19. Study on data acquisition circuit used in SSPA linear array detector X-ray detection

    CERN Document Server

    Wei Biao; Che Zhen Ping

    2002-01-01

    After SSPA used as X-ray array detector is developed, the authors take a research on the data acquisition circuit applied to the detector. The experiment designed has verified the feasibility of application of this array detector and its data acquisition circuit to X-ray computed tomography (X-CT). The preliminary test results indicate that the method of the X-ray detection is feasible for industry X-CT nondestructive testing, which brings about advantage for detecting and measuring with high resolution, good efficiency and low cost

  20. Transparently wrap-gated semiconductor nanowire arrays for studies of gate-controlled photoluminescence

    Energy Technology Data Exchange (ETDEWEB)

    Nylund, Gustav; Storm, Kristian; Torstensson, Henrik; Wallentin, Jesper; Borgström, Magnus T.; Hessman, Dan; Samuelson, Lars [Solid State Physics, Nanometer Structure Consortium, Lund University, Box 118, S-221 00 Lund (Sweden)

    2013-12-04

    We present a technique to measure gate-controlled photoluminescence (PL) on arrays of semiconductor nanowire (NW) capacitors using a transparent film of Indium-Tin-Oxide (ITO) wrapping around the nanowires as the gate electrode. By tuning the wrap-gate voltage, it is possible to increase the PL peak intensity of an array of undoped InP NWs by more than an order of magnitude. The fine structure of the PL spectrum reveals three subpeaks whose relative peak intensities change with gate voltage. We interpret this as gate-controlled state-filling of luminescing quantum dot segments formed by zincblende stacking faults in the mainly wurtzite NW crystal structure.

  1. Experimental study of implosion dynamics of multi-material nested wire-arrays on S-300 pulsed power generator

    International Nuclear Information System (INIS)

    Chernenko, A.S.; Smirnov, V.P.; Kingsep, A.S.

    2004-01-01

    On 'S-300' generator (700 kV, 4 MA, 70 ns) at the Kurchatov Institute, the experimental studies with multi-material wire array units are carried on aimed at creating the powerful X-ray source. The development of new diagnostic methods would definitely contribute to attain new data, which could help in explanation of X-ray emission mechanism of imploding multi-wire arrays that has not well understood yet. The experimental study of soft X-ray emission of different wire sets, different in both mass and composition, has been carried on in the same geometry. One of the purposes of these experiments was investigation of the wire array chemical composition influence on the implosion dynamics and stability. Study of the nested (cascade) liner dynamics shows that the minimal liner radius at the stagnation moment of time (2r ∼ 3 - 3.5 mm) recorded in the visible range by the streak camera fairly coincides with the outer diameter of the inner tungsten array of 4 mm. The same size is shown by the integral pinhole pictures obtained in the SXR range, without a filter. Unlike all these pictures, images obtained in the range E > 2 keV demonstrate the resulting state of Z-pinch in the form of a thin (∼ 0.2 mm) twisting filament. In addition, small space scales are typical of the liner pictures taken in the range of He- and H-like aluminum ions by means of a spectrograph. Thus, one may conclude that Al plasma of the outer liner passes into the inner space of the almost immovable W array where becomes trapped and compressed by the magnetic field. (author)

  2. Environmental confounding in gene-environment interaction studies.

    Science.gov (United States)

    Vanderweele, Tyler J; Ko, Yi-An; Mukherjee, Bhramar

    2013-07-01

    We show that, in the presence of uncontrolled environmental confounding, joint tests for the presence of a main genetic effect and gene-environment interaction will be biased if the genetic and environmental factors are correlated, even if there is no effect of either the genetic factor or the environmental factor on the disease. When environmental confounding is ignored, such tests will in fact reject the joint null of no genetic effect with a probability that tends to 1 as the sample size increases. This problem with the joint test vanishes under gene-environment independence, but it still persists if estimating the gene-environment interaction parameter itself is of interest. Uncontrolled environmental confounding will bias estimates of gene-environment interaction parameters even under gene-environment independence, but it will not do so if the unmeasured confounding variable itself does not interact with the genetic factor. Under gene-environment independence, if the interaction parameter without controlling for the environmental confounder is nonzero, then there is gene-environment interaction either between the genetic factor and the environmental factor of interest or between the genetic factor and the unmeasured environmental confounder. We evaluate several recently proposed joint tests in a simulation study and discuss the implications of these results for the conduct of gene-environment interaction studies.

  3. Gene array analysis of neural crest cells identifies transcription factors necessary for direct conversion of embryonic fibroblasts into neural crest cells

    Directory of Open Access Journals (Sweden)

    Tsutomu Motohashi

    2016-03-01

    Full Text Available Neural crest cells (NC cells are multipotent cells that emerge from the edge of the neural folds and migrate throughout the developing embryo. Although the gene regulatory network for generation of NC cells has been elucidated in detail, it has not been revealed which of the factors in the network are pivotal to directing NC identity. In this study we analyzed the gene expression profile of a pure NC subpopulation isolated from Sox10-IRES-Venus mice and investigated whether these genes played a key role in the direct conversion of Sox10-IRES-Venus mouse embryonic fibroblasts (MEFs into NC cells. The comparative molecular profiles of NC cells and neural tube cells in 9.5-day embryos revealed genes including transcription factors selectively expressed in developing trunk NC cells. Among 25 NC cell-specific transcription factor genes tested, SOX10 and SOX9 were capable of converting MEFs into SOX10-positive (SOX10+ cells. The SOX10+ cells were then shown to differentiate into neurons, glial cells, smooth muscle cells, adipocytes and osteoblasts. These SOX10+ cells also showed limited self-renewal ability, suggesting that SOX10 and SOX9 directly converted MEFs into NC cells. Conversely, the remaining transcription factors, including well-known NC cell specifiers, were unable to convert MEFs into SOX10+ NC cells. These results suggest that SOX10 and SOX9 are the key factors necessary for the direct conversion of MEFs into NC cells.

  4. A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion

    Science.gov (United States)

    Mitsios, Nick; Saka, Mohamad; Krupinski, Jerzy; Pennucci, Roberta; Sanfeliu, Coral; Wang, Qiuyu; Rubio, Francisco; Gaffney, John; Kumar, Pat; Kumar, Shant; Sullivan, Matthew; Slevin, Mark

    2007-01-01

    Background Altered gene expression is an important feature of ischemic cerebral injury and affects proteins of many functional classes. We have used microarrays to investigate the changes in gene expression at various times after middle cerebral artery occlusion in human and rat brain. Results Our results demonstrated a significant difference in the number of genes affected and the time-course of expression between the two cases. The total number of deregulated genes in the rat was 335 versus 126 in the human, while, of 393 overlapping genes between the two array sets, 184 were changed only in the rat and 36 in the human with a total of 41 genes deregulated in both cases. Interestingly, the mean fold changes were much higher in the human. The expression of novel genes, including p21-activated kinase 1 (PAK1), matrix metalloproteinase 11 (MMP11) and integrase interactor 1, was further analyzed by RT-PCR, Western blotting and immunohistochemistry. Strong neuronal staining was seen for PAK1 and MMP11. Conclusion Our findings confirmed previous studies reporting that gene expression screening can detect known and unknown transcriptional features of stroke and highlight the importance of research using human brain tissue in the search for novel therapeutic agents. PMID:17997827

  5. A longitudinal study of gene expression in healthy individuals

    Directory of Open Access Journals (Sweden)

    Tessier Michel

    2009-06-01

    Full Text Available Abstract Background The use of gene expression in venous blood either as a pharmacodynamic marker in clinical trials of drugs or as a diagnostic test requires knowledge of the variability in expression over time in healthy volunteers. Here we defined a normal range of gene expression over 6 months in the blood of four cohorts of healthy men and women who were stratified by age (22–55 years and > 55 years and gender. Methods Eleven immunomodulatory genes likely to play important roles in inflammatory conditions such as rheumatoid arthritis and infection in addition to four genes typically used as reference genes were examined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR, as well as the full genome as represented by Affymetrix HG U133 Plus 2.0 microarrays. Results Gene expression levels as assessed by qRT-PCR and microarray were relatively stable over time with ~2% of genes as measured by microarray showing intra-subject differences over time periods longer than one month. Fifteen genes varied by gender. The eleven genes examined by qRT-PCR remained within a limited dynamic range for all individuals. Specifically, for the seven most stably expressed genes (CXCL1, HMOX1, IL1RN, IL1B, IL6R, PTGS2, and TNF, 95% of all samples profiled fell within 1.5–2.5 Ct, the equivalent of a 4- to 6-fold dynamic range. Two subjects who experienced severe adverse events of cancer and anemia, had microarray gene expression profiles that were distinct from normal while subjects who experienced an infection had only slightly elevated levels of inflammatory markers. Conclusion This study defines the range and variability of gene expression in healthy men and women over a six-month period. These parameters can be used to estimate the number of subjects needed to observe significant differences from normal gene expression in clinical studies. A set of genes that varied by gender was also identified as were a set of genes with elevated

  6. A large-eddy simulation study of wake propagation and power production in an array of tidal-current turbines.

    Science.gov (United States)

    Churchfield, Matthew J; Li, Ye; Moriarty, Patrick J

    2013-02-28

    This paper presents our initial work in performing large-eddy simulations of tidal turbine array flows. First, a horizontally periodic precursor simulation is performed to create turbulent flow data. Then those data are used as inflow into a tidal turbine array two rows deep and infinitely wide. The turbines are modelled using rotating actuator lines, and the finite-volume method is used to solve the governing equations. In studying the wakes created by the turbines, we observed that the vertical shear of the inflow combined with wake rotation causes lateral wake asymmetry. Also, various turbine configurations are simulated, and the total power production relative to isolated turbines is examined. We found that staggering consecutive rows of turbines in the simulated configurations allows the greatest efficiency using the least downstream row spacing. Counter-rotating consecutive downstream turbines in a non-staggered array shows a small benefit. This work has identified areas for improvement. For example, using a larger precursor domain would better capture elongated turbulent structures, and including salinity and temperature equations would account for density stratification and its effect on turbulence. Additionally, the wall shear stress modelling could be improved, and more array configurations could be examined.

  7. A tool based on Ligation Detection Reaction-Universal Array (LDR-UA) for the characterization of VTEC by identification of virulence-associated and serogroup-specific genes.

    Science.gov (United States)

    Lauri, Andrea; Castiglioni, Bianca; Morabito, Stefano; Tozzoli, Rosangela; Consolandi, Clarissa; Mariani, Paola

    2011-02-01

    Verocytoxigenic Escherichia coli (VTEC) are zoonotic pathogens whose natural reservoir is represented by ruminants, particularly cattle. Infections are mainly acquired by consumption of undercooked contaminated food of animal origin, contact with infected animals and contaminated environment. VTEC O157 is the most frequently isolated serogroup from cases of human disease, however, other VTEC serogroups, such as O26, O111, O145 and O103, are increasingly reported as causing Hemolytic Uremic Syndrome (HUS) worldwide. The identification of VTEC is troublesome, hindering the development of effective prevention strategies. In fact, VTEC are morphologically indistinguishable from harmless E. coli and their pathogenic potential is not strictly dependent on the serogroup, but relies on the presence of a collection of virulence genes. We developed a diagnostic tool for VTEC based on the Ligation Detection Reaction coupled to Universal Array (LDR-UA) for the simultaneous identification of virulence factors and serogroup-associated genes. The method includes the investigation of 40 sites located in 13 fragments from 12 genes (sodCF1/F2, adfO, terB, ehxA, eae, vtx1, vtx2, ihp1, wzx, wbdI, rfbE, dnaK) and was evaluated by performing a trial on a collection of 67 E. coli strains, both VTEC and VT-negative E. coli, as well as on 25 isolates belonging to other related species. Results of this study showed that the LDR-UA technique was specific in identifying the target microorganism. Moreover, due to its higher throughput, the LDR-UA can be a valid and cheaper alternative to real time PCR-based (rt-PCR) methods for VTEC identification. Copyright © 2010 Elsevier Ltd. All rights reserved.

  8. Report on achievements in fiscal 1998. Research on acceleration of improving the base for biological resource information, and development of a technology to measure gene information (development of the DNA measuring technology using bead arrays); 1998 nendo seibutsu shigen joho kiban seibi kasokuka kenkyu idenshi joho no keisoku gijutsu no kaihatsu seika hokokusho. Bizu array wo mochiita DNA keisoku gijutsu no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    It is necessary in the field of post-genoms to know statistical correlation between DNA orientation information and clinical data, which helped growth of DNA probe arrays (DNA chips). However, it is difficult in patent point of view to develop chips in Japan. On the other hand, a movement has begun to use beads fixed with DNA probes in place of DNA chips demarcated on the surface of solids. This is a method to investigate hybridized DNA by means of fluorescent detection, in which each bead retaining the DNA probes is colored to make identification of the retained probes possible, and hybridizing reaction is performed in aqueous solution. Hitachi has developed a DNA measuring technology using bead arrays. The bead array has probe fixing beads of about 100 {mu} m laid sequentially inside a capillary, wherein the array can be used to inspect a large number of genes. Thus, this method can be a DNA measuring technology which is inexpensive, and high in reproducibility. These features lead to a belief that the technology is suitable for gene inspection devices used in the process of medicine development and at the clinical sites. (NEDO)

  9. SNP Arrays

    Directory of Open Access Journals (Sweden)

    Jari Louhelainen

    2016-10-01

    Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

  10. Theoretical study of 2χ2 element planar array of equilateral ...

    Indian Academy of Sciences (India)

    Microstrip planar array antennas mounted on such aerospace vehicles encounter plasma medium during their travel in space, as a result of which radiation prop- ... and Eφt are the components of total electric field vectors for EM-mode, Ept is the total electric field vector for P-mode, Fx and Fy are the vector electric potentials.

  11. Microwave Synthesized ZnO Nanorod Arrays for UV Sensors: A Seed Layer Annealing Temperature Study.

    Science.gov (United States)

    Pimentel, Ana; Ferreira, Sofia Henriques; Nunes, Daniela; Calmeiro, Tomas; Martins, Rodrigo; Fortunato, Elvira

    2016-04-20

    The present work reports the influence of zinc oxide (ZnO) seed layer annealing temperature on structural, optical and electrical properties of ZnO nanorod arrays, synthesized by hydrothermal method assisted by microwave radiation, to be used as UV sensors. The ZnO seed layer was produced using the spin-coating method and several annealing temperatures, ranging from 100 to 500 °C, have been tested. X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and spectrophotometry measurements have been used to investigate the structure, morphology, and optical properties variations of the produced ZnO nanorod arrays regarding the seed layer annealing temperatures employed. After the growth of ZnO nanorod arrays, the whole structure was tested as UV sensors, showing an increase in the sensitivity with the increase of seed layer annealing temperature. The UV sensor response of ZnO nanorod arrays produced with the seed layer annealed temperature of 500 °C was 50 times superior to the ones produced with a seed layer annealed at 100 °C.

  12. The water Cherenkov detector array for studies of cosmic rays at the University of Puebla

    International Nuclear Information System (INIS)

    Cotzomi, J.; Moreno, E.; Murrieta, T.; Palma, B.; Perez, E.; Salazar, H.; Villasenor, L.

    2005-01-01

    We describe the design and performance of a hybrid extensive air shower detector array built on the Campus of the University of Puebla (19 - bar N, 90 - bar W, 800g/cm 2 ) to measure the energy, arrival direction and composition of primary cosmic rays with energies around 1PeV, i.e., around the knee of the cosmic ray spectrum. The array consists of 3 water Cherenkov detectors of 1.86m 2 cross-section and 12 liquid scintillator detectors of 1m 2 distributed in a square grid with a detector spacing of 20m over an area of 4000m 2 . We discuss the calibration and stability of the array for both sets of detectors and report on preliminary measurements and reconstruction of the lateral distributions for the electromagnetic (EM) and muonic components of extensive air showers. We also discuss how the hybrid character of the array can be used to measure mass composition of the primary cosmic rays by estimating the relative contents of muons with respect to the EM component of extensive air showers. This facility is also used to train students interested in the field of cosmic rays

  13. Studying DAC capacitor-array degradation in charge-redistribution SAR ADCs

    NARCIS (Netherlands)

    Khan, M.A.; Kerkhoff, Hans G.

    2014-01-01

    In this paper, system-level behavioural models are used to simulate the aging-related degradation effects in the DAC capacitor array of a charge-redistribution successive approximation register (SAR) ADC because of the large calculation time of transistor-level aging simulators. A

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

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.; Schenke, H.W.

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

  15. Reaction selectivity studies on nanolithographically-fabricated platinum model catalyst arrays

    Energy Technology Data Exchange (ETDEWEB)

    Grunes, Jeffrey Benjamin [Univ. of California, Berkeley, CA (United States)

    2004-05-01

    In an effort to understand the molecular ingredients of catalytic activity and selectivity toward the end of tuning a catalyst for 100% selectivity, advanced nanolithography techniques were developed and utilized to fabricate well-ordered two-dimensional model catalyst arrays of metal nanostructures on an oxide support for the investigation of reaction selectivity. In-situ and ex-situ surface science techniques were coupled with catalytic reaction data to characterize the molecular structure of the catalyst systems and gain insight into hydrocarbon conversion in heterogeneous catalysis. Through systematic variation of catalyst parameters (size, spacing, structure, and oxide support) and catalytic reaction conditions (hydrocarbon chain length, temperature, pressures, and gas composition), the data presented in this dissertation demonstrate the ability to direct a reaction by rationally adjusting, through precise control, the design of the catalyst system. Electron beam lithography (EBL) was employed to create platinum nanoparticles on an alumina (Al2O3) support. The Pt nanoparticle spacing (100-150-nm interparticle distance) was varied in these samples, and they were characterized using x-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and atomic force microscopy (AFM), both before and after reactions. The TEM studies showed the 28-nm Pt nanoparticles with 100 and 150-nm interparticle spacing on alumina to be polycrystalline in nature, with crystalline sizes of 3-5 nm. The nanoparticle crystallites increased significantly after heat treatment. The nanoparticles were still mostly polycrystalline in nature, with 2-3 domains. The 28-nm Pt nanoparticles deposited on alumina were removed by the AFM tip in contact mode with a normal force of approximately 30 nN. After heat treatment at 500 C in vacuum for 3 hours, the AFM tip, even at 4000 nN, could not remove the platinum

  16. Recent advances in human gene-longevity association studies

    DEFF Research Database (Denmark)

    De Benedictis, G; Tan, Q; Jeune, B

    2001-01-01

    This paper reviews the recent literature on genes and longevity. The influence of genes on human life span has been confirmed in studies of life span correlation between related individuals based on family and twin data. Results from major twin studies indicate that approximately 25......% of the variation in life span is genetically determined. Taking advantage of recent developments in molecular biology, researchers are now searching for candidate genes that might have an influence on life span. The data on unrelated individuals emerging from an ever-increasing number of centenarian studies makes...... this possible. This paper summarizes the rich literature dealing with the various aspects of the influence of genes on individual survival. Common phenomena affecting the development of disease and longevity are discussed. The major methodological difficulty one is confronted with when studying the epidemiology...

  17. Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication

    Directory of Open Access Journals (Sweden)

    Kilpinen Sami

    2010-05-01

    Full Text Available Abstract Background Neuroblastoma has successfully served as a model system for the identification of neuroectoderm-derived oncogenes. However, in spite of various efforts, only a few clinically useful prognostic markers have been found. Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma. Methods A single-gene resolution aCGH profiling was integrated with microarray-based gene expression profiling data to distinguish genetic copy number alterations that were strongly associated with transcriptional changes in two neuroblastoma cell lines. FISH analysis using a hotspot tumor tissue microarray of 37 paraffin-embedded neuroblastoma samples and in silico data mining for gene expression information obtained from previously published studies including up to 445 healthy nervous system samples and 123 neuroblastoma samples were used to evaluate the clinical significance and transcriptional consequences of the detected alterations and to identify subsequently activated gene(s. Results In addition to the anticipated high-level amplification and subsequent overexpression of MYCN, MEIS1, CDK4 and MDM2 oncogenes, the aCGH analysis revealed numerous other genetic alterations, including microamplifications at 2p and 12q24.11. Most interestingly, we identified and investigated the clinical relevance of a previously poorly characterized amplicon at 12q24.31. FISH analysis showed low-level gain of 12q24.31 in 14 of 33 (42% neuroblastomas. Patients with the low-level gain had an intermediate prognosis in comparison to patients with MYCN amplification (poor prognosis and to those with no MYCN amplification or 12q24.31 gain (good prognosis (P = 0.001. Using the in silico data mining approach, we identified elevated expression of five genes located at the 12q24.31 amplicon in neuroblastoma (DIABLO, ZCCHC

  18. SLC6A1 gene involvement in susceptibility to attention-deficit/hyperactivity disorder: A case-control study and gene-environment interaction.

    Science.gov (United States)

    Yuan, Fang-Fen; Gu, Xue; Huang, Xin; Zhong, Yan; Wu, Jing

    2017-07-03

    Attention-deficit/hyperactivity disorder (ADHD) is an early onset childhood neurodevelopmental disorder with an estimated heritability of approximately 76%. We conducted a case-control study to explore the role of the SLC6A1 gene in ADHD. The genotypes of eight variants were determined using Sequenom MassARRAY technology. The participants in the study were 302 children with ADHD and 411 controls. ADHD symptoms were assessed using the Conners Parent Symptom Questionnaire. In our study, rs2944366 was consistently shown to be associated with the ADHD risk in the dominant model (odds ratio [OR]=0.554, 95% confidence interval [CI]=0.404-0.760), and nominally associated with Hyperactive index score (P=0.027). In addition, rs1170695 has been found to be associated with the ADHD risk in the addictive model (OR=1.457, 95%CI=1.173-1.809), while rs9990174 was associated with the Hyperactive index score (P=0.010). Intriguingly, gene-environmental interactions analysis consistently revealed the potential interactions of rs1170695 with blood lead (P mul =0.044) to modify the ADHD risk. Expression quantitative trait loci analysis suggested that these positive single nucleotide polymorphisms (SNPs) may mediate SLC6A1 gene expression. Therefore, our results suggest that selected SLC6A1 gene variants may have a significant effect on the ADHD risk. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Efficacy of Hummel (Modified Schlumberger Arrays of Vertical Electrical Sounding in Groundwater Exploration: Case Study of Parts of Ibadan Metropolis, Southwestern Nigeria

    Directory of Open Access Journals (Sweden)

    Micheal Oladunjoye

    2015-01-01

    Full Text Available This research compared the interpretation results of the Vertical Electrical Sounding data acquired using the conventional Schlumberger and modified Schlumberger arrays with a view to assessing the effectiveness of the modified Schlumberger arrays of vertical electrical sounding as an alternative to the conventional Schlumberger array at sites with space constraint during groundwater exploration. A total of thirty-seven (37 sounding locations were occupied and one hundred (100 sounding data for both conventional Schlumberger and modified Schlumberger arrays were collected across different rock units within Ibadan metropolis, south-western Nigeria, with electrode spacing (AB/2 ranging from 1 to 75 m. The field data were interpreted qualitatively by curve matching and computer iterative methods. Also, statistical analysis of subsurface units and the coefficient of correlation “R” of the statistical plots of the field data shows the relationship between the different arrays. The raw data plot of the different arrays shows significant similarities while statistical analysis of the geo-electric parameters obtained from the different arrays across varied lithologic units show that strong relationships exist between the different field methods. The coefficient of correlation R with values ranging from 0.7 to 0.99 implies that a good similarity exists between the different field methods employed in this study. Hence, modified Schlumberger arrays can be said to be a good alternative to the conventional Schlumberger array for groundwater exploration especially in urban settings where space constraint is a major challenge.

  20. A comparative study of three different gene expression analysis methods.

    Science.gov (United States)

    Choe, Jae Young; Han, Hyung Soo; Lee, Seon Duk; Lee, Hanna; Lee, Dong Eun; Ahn, Jae Yun; Ryoo, Hyun Wook; Seo, Kang Suk; Kim, Jong Kun

    2017-12-04

    TNF-α regulates immune cells and acts as an endogenous pyrogen. Reverse transcription polymerase chain reaction (RT-PCR) is one of the most commonly used methods for gene expression analysis. Among the alternatives to PCR, loop-mediated isothermal amplification (LAMP) shows good potential in terms of specificity and sensitivity. However, few studies have compared RT-PCR and LAMP for human gene expression analysis. Therefore, in the present study, we compared one-step RT-PCR, two-step RT-LAMP and one-step RT-LAMP for human gene expression analysis. We compared three gene expression analysis methods using the human TNF-α gene as a biomarker from peripheral blood cells. Total RNA from the three selected febrile patients were subjected to the three different methods of gene expression analysis. In the comparison of three gene expression analysis methods, the detection limit of both one-step RT-PCR and one-step RT-LAMP were the same, while that of two-step RT-LAMP was inferior. One-step RT-LAMP takes less time, and the experimental result is easy to determine. One-step RT-LAMP is a potentially useful and complementary tool that is fast and reasonably sensitive. In addition, one-step RT-LAMP could be useful in environments lacking specialized equipment or expertise.

  1. The zebrafish genome: a review and msx gene case study.

    Science.gov (United States)

    Postlethwait, J H

    2006-01-01

    Zebrafish is one of several important teleost models for understanding principles of vertebrate developmental, molecular, organismal, genetic, evolutionary, and genomic biology. Efficient investigation of the molecular genetic basis of induced mutations depends on knowledge of the zebrafish genome. Principles of zebrafish genomic analysis, including gene mapping, ortholog identification, conservation of syntenies, genome duplication, and evolution of duplicate gene function are discussed here using as a case study the zebrafish msxa, msxb, msxc, msxd, and msxe genes, which together constitute zebrafish orthologs of tetrapod Msx1, Msx2, and Msx3. Genomic analysis suggests orthologs for this difficult to understand group of paralogs.

  2. Characterization of the Gray Whale Eschrichtius robustus Genome and a Genotyping Array Based on Single-Nucleotide Polymorphisms in Candidate Genes.

    Science.gov (United States)

    DeWoody, J Andrew; Fernandez, Nadia B; Brüniche-Olsen, Anna; Antonides, Jennifer D; Doyle, Jacqueline M; San Miguel, Phillip; Westerman, Rick; Vertyankin, Vladimir V; Godard-Codding, Céline A J; Bickham, John W

    2017-06-01

    Genetic and genomic approaches have much to offer in terms of ecology, evolution, and conservation. To better understand the biology of the gray whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome and produced an assembly that contains ∼95% of the genes known to be highly conserved among eukaryotes. From this assembly, we annotated 22,711 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs). Using this assembly, we generated a curated list of candidate genes potentially subject to strong natural selection, including genes associated with osmoregulation, oxygen binding and delivery, and other aspects of marine life. From these candidate genes, we queried 92 autosomal protein-coding markers with a panel of 96 SNPs that also included 2 sexing and 2 mitochondrial markers. Genotyping error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed heterozygosity was 0.33 averaged over all autosomal markers. This level of variability provides substantial discriminatory power across loci (mean probability of identity of 1.6 × 10 -25 and mean probability of exclusion >0.999 with neither parent known), indicating that these markers provide a powerful means to assess parentage and relatedness in gray whales. We found 29 unique multilocus genotypes represented among our 36 biopsies (indicating that we inadvertently sampled 7 whales twice). In total, we compiled an individual data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray whale (EGW). The lone EGW we sampled was no more or less related to the WGWs than expected by chance alone. The gray whale genomes reported here will enable comparative studies of natural selection in cetaceans, and the SNP markers should be highly informative for future studies of gray whale evolution, population structure, demography, and relatedness.

  3. A study of angle dependent surface plasmon polaritons in nano-hole array structures

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishnan, Shankar [Department of Physics and Astronomy, University of Western Ontario, London, Ontario N6A 3K7 (Canada); Lawson Health Research Institute, St. Joseph' s Health Care, London, Ontario N6A 4V2 (Canada); Najiminaini, Mohamadreza; Carson, Jeffrey J. L. [Lawson Health Research Institute, St. Joseph' s Health Care, London, Ontario N6A 4V2 (Canada); Department of Medical Biophysics, University of Western Ontario, London, Ontario N6A 3K7 (Canada); Singh, Mahi R. [Department of Physics and Astronomy, University of Western Ontario, London, Ontario N6A 3K7 (Canada)

    2016-07-21

    We report that the light-matter interaction in metallic nano-hole array structures possess a subwavelength hole radius and periodicity. The transmission coefficient for nano-hole array structures was measured for different angles of incidence of light. Each measured transmission spectrum had several peaks due to surface plasmon polaritons. A theory of the transmission coefficient was developed based on the quantum density matrix method. It was found that the location of the surface plasmon polariton and the heights of the spectral peaks were dependent on the angle of incidence of light. Good agreement was observed between the experimental and theoretical results. This property of these structures has opened up new possibilities for sensing applications.

  4. A Case Study of Some Issues in the Optimization of Fortran 90 Array Notation

    Directory of Open Access Journals (Sweden)

    John D. McCalpin

    1996-01-01

    Full Text Available Some issues in the relationship of coding style and compiler optimization are discussed with regard to Fortran 90 array notation. A review of several important Fortran 90 array constructs and their performance on vector and scalar hardware sets the stage for a more detailed example based on the kernel of a finite difference computational fluid dynamics model, specifically the nonlinear shallow water equations. Special attention is paid to the optimization of memory use and memory traffic. It is shown that the style of coding interacts with the rules of Fortran 90 and the current state of the art of Fortran 90 compilers to produce a fairly wide range of performance levels. Although performance degradations are typically small, a few cases of more serious loss of effciency are identified and discussed.

  5. Feasibility study of flexible phased array ultrasonic technology using irregular surface specimen

    International Nuclear Information System (INIS)

    Lee, Seung Pyo; Moon, Yong Sik; Jung, Nam Du

    2015-01-01

    Nuclear power plant contain many dissimilar metal welds that connect carbon steel components with stainless steel pipes using alloy 600 welding materials. Primary water stress corrosion cracks at dissimilar metal welds have been continuously reported around the world. In periodic integrity evaluations, dissimilar metal welds are examined using a generic ultrasonic testing procedure, KPD-UT-10. In this procedure, the gap between the probe and examination surface is limited to 1/32 inch (0.8 mm). It is not easy to test some dissimilar metal welds in Korean plants applying ordinary technology because of their tapered shapes and irregular surface conditions. This paper introduces a method for applying a flexible phased array technology to improve the reliability of ultrasonic testing results for various shapes and surface conditions. The artificial flaws in specimens with irregular surfaces were completely detected using the flexible phased array ultrasonic technology. Therefore, it can be said that the technology is applicable to field examination.

  6. Feasibility study of flexible phased array ultrasonic technology using irregular surface specimen

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Pyo; Moon, Yong Sik; Jung, Nam Du [NDE Performance Demonstration Team, Korea Hydro and Nuclear Power, Central Research Institute, Daejeon (Korea, Republic of)

    2015-02-15

    Nuclear power plant contain many dissimilar metal welds that connect carbon steel components with stainless steel pipes using alloy 600 welding materials. Primary water stress corrosion cracks at dissimilar metal welds have been continuously reported around the world. In periodic integrity evaluations, dissimilar metal welds are examined using a generic ultrasonic testing procedure, KPD-UT-10. In this procedure, the gap between the probe and examination surface is limited to 1/32 inch (0.8 mm). It is not easy to test some dissimilar metal welds in Korean plants applying ordinary technology because of their tapered shapes and irregular surface conditions. This paper introduces a method for applying a flexible phased array technology to improve the reliability of ultrasonic testing results for various shapes and surface conditions. The artificial flaws in specimens with irregular surfaces were completely detected using the flexible phased array ultrasonic technology. Therefore, it can be said that the technology is applicable to field examination.

  7. 12-Channel Peltier array temperature control unit for single molecule enzymology studies using capillary electrophoresis.

    Science.gov (United States)

    Craig, Douglas B; Reinfelds, Gundars; Henderson, Anna

    2014-08-01

    Capillary electrophoresis has been used to demonstrate that individual molecules of a given enzyme support different catalytic rates. In order to determine how rate varies with temperature, and determine activation energies for individual β-galactosidase molecules, a 12-channel Peltier array temperature control device was constructed where the temperature of each cell was separately controlled. This array was used to control the temperature of the central 30 cm of a 50 cm long capillary, producing a temperature gradient along its length. Continuous flow single β-galactosidase molecule assays were performed allowing measurement of the catalytic rates at different temperatures. Arrhenius plots were produced and the distribution of activation energies for individual β-galactosidase molecules was found to be 56 ± 10 kJ/mol with a range of 34-72 kJ/mol. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Study of residual gas adsorption on GaN nanowire arrays photocathode

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Sihao; Liu, Lei, E-mail: liu1133_cn@sina.com.cn; Diao, Yu; Kong, Yike

    2017-05-01

    Highlights: • H{sub 2}O is more easily to absorb on the nanowire surface. • The work function increase after residual gas adsorption. • Bandgaps of the nanowire increase slightly. • Absorption coefficient is reduced and moves to higher energy side. - Abstract: In order to find out the influences of residual gas on GaN nanowire arrays photocathode, the optoelectronic properties of adsorption system are calculated on the basis of first principles. Results suggest that the residual gas adsorption will increase the work function and introduce a dipole moment with a direction from the nanowire to the adsorbates. The surface structures are changed and electrons transfer from nanowire to gas molecule. The bandgaps are enhanced after adsorption. Besides, the peak of absorption coefficients is reduced and moves to higher energy side. It is discovered that residual gas will drastically degrade the characteristics and lifetime of GaN nanowire arrays photocathode.

  9. Expression studies of the obesity candidate gene FTO in pig

    DEFF Research Database (Denmark)

    Madsen, Majbritt Busk; Birck, Malene Muusfeldt; Fredholm, Merete

    2010-01-01

    Obesity is an increasing problem worldwide and research on candidate genes in good animal models is highly needed. The pig is an excellent model as its metabolism, organ size, and eating habits resemble that of humans. The present study is focused on the characterization of the fat mass and obesity...... associated gene (FTO) in pig. This gene has recently been associated with increased body mass index in several human populations. To establish information on the expression profile of FTO in the pig we performed quantitative PCR in a panel of adult pig tissues and in tissues sampled at different...... and cerebellum). Additionally, in order to see the involvement of the FTO gene in obesity, the changes in expression level were investigated in a nutritional study in brain of Gottingen minipigs under a high cholesterol diet. Significantly higher (P

  10. Preliminary study of Rayleigh-Taylor instability in wire-array Z-pinch

    International Nuclear Information System (INIS)

    He Kaihui; Feng Kaiming; Li Qiang; Gao Chunming

    2000-01-01

    It is important to research into the MHD Rayleigh-Taylor instability developed in Z-pinch implosion. A snowplough model of the single wire Z-pinch is presented. The perturbation amplitude of Rayleigh-Taylor instability in the wire-array Z-pinch is analyzed quantitatively. Sheared axial flow is put forward to mitigate and reduce the Rayleigh-Taylor instability. And other approaches used to mitigate MHD instability in such a super-fast process are explored

  11. Parameter study of global and cluster synchronization in arrays of dry friction oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Marszal, Michał, E-mail: michal.marszal@p.lodz.pl; Stefański, Andrzej

    2017-04-18

    Highlights: • Synchronization properties in arrays of coupled dry friction oscillators are investigated. • Master stability function in form of two-oscillator probe is used for predicting synchronization thresholds. • Two network topologies are checked: open and closed nearest neighbor coupling. • Regions of complete and cluster synchronization are found in parameter space. - Abstract: We investigate synchronization thresholds in arrays of identical classic stick-slip dry friction oscillators connected in a nearest neighbor fashion in closed and open ring network. Friction force is modeled by smoothened Stribeck model. Arrays of different length are checked in two parameter space (i.e., coupling coefficient vs. excitation frequency) for complete synchronization as well as cluster synchronization. Synchronization thresholds obtained by brute force numerical integration are compared with possible synchronization regions using the concept called master stability function in the form of two-oscillator reference probe. The results show existence of both complete synchronization and cluster synchronization regions in the investigated systems and confirm that two-oscillator probe can be applied for prediction of synchronization thresholds in systems with stick-slip phenomenon.

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

    Science.gov (United States)

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

    2018-02-01

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

  13. Study of spin dynamics and damping on the magnetic nanowire arrays with various nanowire widths

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Jaehun [Department of Physics, Inha University, Incheon, 402-751 (Korea, Republic of); Fujii, Yuya; Konioshi, Katsunori [Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); Yoon, Jungbum [Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576 (Singapore); Kim, Nam-Hui; Jung, Jinyong [Department of Physics, Inha University, Incheon, 402-751 (Korea, Republic of); Miwa, Shinji [Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); Jung, Myung-Hwa [Department of Physics, Sogang University, Seoul, 121-742 (Korea, Republic of); Suzuki, Yoshishige [Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); You, Chun-Yeol, E-mail: cyyou@inha.ac.kr [Department of Physics, Inha University, Incheon, 402-751 (Korea, Republic of)

    2016-07-01

    We investigate the spin dynamics including Gilbert damping in the ferromagnetic nanowire arrays. We have measured the ferromagnetic resonance of ferromagnetic nanowire arrays using vector-network analyzer ferromagnetic resonance (VNA-FMR) and analyzed the results with the micromagnetic simulations. We find excellent agreement between the experimental VNA-FMR spectra and micromagnetic simulations result for various applied magnetic fields. We find that the same tendency of the demagnetization factor for longitudinal and transverse conditions, N{sub z} (N{sub y}) increases (decreases) as increasing the nanowire width in the micromagnetic simulations while N{sub x} is almost zero value in transverse case. We also find that the Gilbert damping constant increases from 0.018 to 0.051 as the increasing nanowire width for the transverse case, while it is almost constant as 0.021 for the longitudinal case. - Highlights: • We investigate the spin dynamic properties in the ferromagnetic nanowire arrays. • The demagnetization factors have similar tendency with the prism geometry results. • The Gilbert damping constant is increased from 0.018 to 0.051 as the increasing nanowire width for the transverse. • The Gilbert damping constant is almost constant as 0.021 for the longitudinal case.

  14. Numerical Study of a Crossed Loop Coil Array for Parallel Magnetic Resonance Imaging

    International Nuclear Information System (INIS)

    Hernandez, J.; Solis, S. E.; Rodriguez, A. O.

    2008-01-01

    A coil design has been recently proposed by Temnikov (Instrum Exp Tech. 2005;48;636-637), with higher experimental signal-to-noise ratio than that of the birdcage coil. It is also claimed that it is possible to individually tune it with a single chip capacitor. This coil design shows a great resemble to the gradiometer coil. These results motivated us to numerically simulate a three-coil array for parallel magnetic resonance imaging and in vivo magnetic resonance spectroscopy with multi nuclear capability. The magnetic field was numerical simulated by solving Maxwell's equations with the finite element method. Uniformity profiles were calculated at the midsection for one single coil and showed a good agreement with the experimental data. Then, two more coils were added to form two different coil arrays: coil elements were equally distributed by an angle of a 30 deg. angle. Then, uniformity profiles were calculated again for all cases at the midsection. Despite the strong interaction among all coil elements, very good field uniformity can be achieved. These numerical results indicate that this coil array may be a good choice for magnetic resonance imaging parallel imaging

  15. Correlations of gene expression with ratings of inattention and hyperactivity/impulsivity in tourette syndrome: a pilot study

    Directory of Open Access Journals (Sweden)

    Tian Yingfang

    2012-10-01

    Full Text Available Abstract Background Inattentiveness, impulsivity and hyperactivity are the primary behaviors associated with attention-deficit hyperactivity disorder (ADHD. Previous studies showed that peripheral blood gene expression signatures can mirror central nervous system disease. Tourette syndrome (TS is associated with inattention (IA and hyperactivity/impulsivity (HI symptoms over 50% of the time. This study determined if gene expression in blood correlated significantly with IA and/or HI rating scale scores in participants with TS. Methods RNA was isolated from the blood of 21 participants with TS, and gene expression measured on Affymetrix human U133 Plus 2.0 arrays. To identify the genes that correlated with Conners’ Parents Ratings of IA and HI ratings of symptoms, an analysis of covariance (ANCOVA was performed, controlling for age, gender and batch. Results There were 1201 gene probesets that correlated with IA scales, 1625 that correlated with HI scales, and 262 that correlated with both IA and HI scale scores (Prp|>0.4. Immune, catecholamine and other neurotransmitter pathways were associated with IA and HI behaviors. A number of the identified genes (n=27 have previously been reported in ADHD genetic studies. Many more genes correlated with either IA or HI scales alone compared to those that correlated with both IA and HI scales. Conclusions These findings support the concept that the pathophysiology of ADHD and/or its subtypes in TS may involve the interaction of multiple genes. These preliminary data also suggest gene expression may be useful for studying IA and HI symptoms that relate to ADHD in TS and perhaps non-TS participants. These results will need to be confirmed in future studies.

  16. Choroid plexus transport: gene deletion studies

    Directory of Open Access Journals (Sweden)

    Keep Richard F

    2011-11-01

    Full Text Available Abstract This review examines the use of transporter knockout (KO animals to evaluate transporter function at the choroid plexus (the blood-CSF barrier; BCSFB. Compared to the blood-brain barrier, there have been few such studies on choroid plexus (CP function. These have primarily focused on Pept2 (an oligopeptide transporter, ATP-binding cassette (ABC transporters, Oat3 (an organic anion transporter, Svct2 (an ascorbic acid transporter, transthyretin, ion transporters, and ion and water channels. This review focuses on the knowledge gained from such studies, both with respect to specific transporters and in general to the role of the CP and its impact on brain parenchyma. It also discusses the pros and cons of using KO animals in such studies and the technical approaches that can be used.

  17. Blood lead levels, iron metabolism gene polymorphisms and homocysteine: a gene-environment interaction study.

    Science.gov (United States)

    Kim, Kyoung-Nam; Lee, Mee-Ri; Lim, Youn-Hee; Hong, Yun-Chul

    2017-12-01

    Homocysteine has been causally associated with various adverse health outcomes. Evidence supporting the relationship between lead and homocysteine levels has been accumulating, but most prior studies have not focused on the interaction with genetic polymorphisms. From a community-based prospective cohort, we analysed 386 participants (aged 41-71 years) with information regarding blood lead and plasma homocysteine levels. Blood lead levels were measured between 2001 and 2003, and plasma homocysteine levels were measured in 2007. Interactions of lead levels with 42 genotyped single-nucleotide polymorphisms (SNPs) in five genes ( TF , HFE , CBS , BHMT and MTR ) were assessed via a 2-degree of freedom (df) joint test and a 1-df interaction test. In secondary analyses using imputation, we further assessed 58 imputed SNPs in the TF and MTHFR genes. Blood lead concentrations were positively associated with plasma homocysteine levels (p=0.0276). Six SNPs in the TF and MTR genes were screened using the 2-df joint test, and among them, three SNPs in the TF gene showed interactions with lead with respect to homocysteine levels through the 1-df interaction test (plead levels. Blood lead levels were positively associated with plasma homocysteine levels measured 4-6 years later, and three SNPs in the TF gene modified the association. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. Combining Human Epigenetics and Sleep Studies in Caenorhabditis elegans: A Cross-Species Approach for Finding Conserved Genes Regulating Sleep.

    Science.gov (United States)

    Huang, Huiyan; Zhu, Yong; Eliot, Melissa N; Knopik, Valerie S; McGeary, John E; Carskadon, Mary A; Hart, Anne C

    2017-06-01

    We aimed to test a combined approach to identify conserved genes regulating sleep and to explore the association between DNA methylation and sleep length. We identified candidate genes associated with shorter versus longer sleep duration in college students based on DNA methylation using Illumina Infinium HumanMethylation450 BeadChip arrays. Orthologous genes in Caenorhabditis elegans were identified, and we examined whether their loss of function affected C. elegans sleep. For genes whose perturbation affected C. elegans sleep, we subsequently undertook a small pilot study to re-examine DNA methylation in an independent set of human participants with shorter versus longer sleep durations. Eighty-seven out of 485,577 CpG sites had significant differential methylation in young adults with shorter versus longer sleep duration, corresponding to 52 candidate genes. We identified 34 C. elegans orthologs, including NPY/flp-18 and flp-21, which are known to affect sleep. Loss of five additional genes alters developmentally timed C. elegans sleep (B4GALT6/bre-4, DOCK180/ced-5, GNB2L1/rack-1, PTPRN2/ida-1, ZFYVE28/lst-2). For one of these genes, ZFYVE28 (also known as hLst2), the pilot replication study again found decreased DNA methylation associated with shorter sleep duration at the same two CpG sites in the first intron of ZFYVE28. Using an approach that combines human epigenetics and C. elegans sleep studies, we identified five genes that play previously unidentified roles in C. elegans sleep. We suggest sleep duration in humans may be associated with differential DNA methylation at specific sites and that the conserved genes identified here likely play roles in C. elegans sleep and in other species. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  19. Study of a 3×3 module array of the ECAL0 calorimeter with an electron beam at the ELSA

    Science.gov (United States)

    Dziewiecki, M.; Anfimov, N.; Anosov, V.; Barth, J.; Chalyshev, V.; Chirikov-Zorin, I.; Elsner, D.; Frolov, V.; Frommberger, F.; Guskov, A.; Klein, F.; Krumshteyn, Z.; Kurjata, R.; Marzec, J.; Nagaytsev, A.; Olchevski, A.; Orlov, I.; Rybnikov, A.; Rychter, A.; Selyunin, A.; Zaremba, K.; Ziembicki, M.

    2015-02-01

    ECAL0 is a new electromagnetic calorimeter designed for studying generalized parton distributions at the COMPASS II experiment at CERN. It will be located next to the target and will cover larger photon angles (up to 30 degrees). It is a modular high-granularity Shashlyk device with total number of individual channels of approx. 1700 and readout based on wavelength shifting fibers and micropixel avalanche photodiodes. Characterization of the calorimeter includes tests of particular sub-components, tests of complete modules and module arrays, as well as a pilot run of a fully-functional, quarter-size prototype in the COMPASS experiment. The main goals of the tests on low-intensity electron beam at the ELSA accelerator in Bonn were: to provide energy calibration using electrons, to measure angular response of the calorimeter and to perform an energy scan to cross-check previously collected data. A dedicated measurement setup was prepared for the tests, including a 3x3 array of the ECAL0 modules, a scintillating-fibre hodoscope and a remotely-controlled motorized movable platform. The measurements were performed using three electron energies: 3.2 GeV, 1.6 GeV and 0.8 GeV. They include a calibration of the whole detector array with a straight beam and multiple angular scans.

  20. Analysis of O-glycans as 9-fluorenylmethyl derivatives and its application to the studies on glycan array.

    Science.gov (United States)

    Yamada, Keita; Hirabayashi, Jun; Kakehi, Kazuaki

    2013-03-19

    A method is proposed for the analysis of O-glycans as 9-fluorenylmethyl (Fmoc) derivatives. After releasing the O-glycans from the protein backbone in the presence of ammonia-based media, the glycosylamines thus formed are conveniently labeled with Fmoc-Cl and analyzed by HPLC and MALDI-TOF MS after easy purification. Fmoc labeled O-glycans showed 3.5 times higher sensitivities than those labeled with 2-aminobenzoic acid in fluorescent detection. Various types of O-glycans having sialic acids, fucose, and/or sulfate residues were successfully labeled with Fmoc and analyzed by HPLC and MALDI-TOF MS. The method was applied to the comprehensive analysis of O-glycans expressed on MKN45 cells (human gastric adenocarcinoma). In addition, Fmoc-derivatized O-glycans were easily converted to free hemiacetal or glycosylamine-form glycans that are available for fabrication of glycan array and neoglycoproteins. To demonstrate the availability of our methods, we fabricate the glycan array with Fmoc labeled glycans derived from mucin samples and cancer cells. The model studies using the glycan array showed clear interactions between immobilized glycans and some lectins.

  1. Study of a 3×3 module array of the ECAL0 calorimeter with an electron beam at the ELSA

    International Nuclear Information System (INIS)

    Dziewiecki, M; Kurjata, R; Marzec, J; Rychter, A; Anfimov, N; Anosov, V; Chalyshev, V; Chirikov-Zorin, I; Frolov, V; Guskov, A; Krumshteyn, Z; Nagaytsev, A; Olchevski, A; Orlov, I; Rybnikov, A; Selyunin, A; Barth, J; Elsner, D; Frommberger, F; Klein, F

    2015-01-01

    ECAL0 is a new electromagnetic calorimeter designed for studying generalized parton distributions at the COMPASS II experiment at CERN. It will be located next to the target and will cover larger photon angles (up to 30 degrees). It is a modular high-granularity Shashlyk device with total number of individual channels of approx. 1700 and readout based on wavelength shifting fibers and micropixel avalanche photodiodes. Characterization of the calorimeter includes tests of particular sub-components, tests of complete modules and module arrays, as well as a pilot run of a fully-functional, quarter-size prototype in the COMPASS experiment. The main goals of the tests on low-intensity electron beam at the ELSA accelerator in Bonn were: to provide energy calibration using electrons, to measure angular response of the calorimeter and to perform an energy scan to cross-check previously collected data. A dedicated measurement setup was prepared for the tests, including a 3x3 array of the ECAL0 modules, a scintillating-fibre hodoscope and a remotely-controlled motorized movable platform. The measurements were performed using three electron energies: 3.2 GeV, 1.6 GeV and 0.8 GeV. They include a calibration of the whole detector array with a straight beam and multiple angular scans

  2. Filter arrays

    Science.gov (United States)

    Page, Ralph H.; Doty, Patrick F.

    2017-08-01

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

  3. A Comparative Study on Structural and Optical Properties of ZnO Micro-Nanorod Arrays Grown on Seed Layers Using Chemical Bath Deposition and Spin Coating Methods

    Directory of Open Access Journals (Sweden)

    Sibel MORKOÇ KARADENİZ

    2016-11-01

    Full Text Available In this study, Zinc Oxide (ZnO seed layers were prepared on Indium Tin Oxide (ITO substrates by using Chemical Bath Deposition (CBD method and Sol-gel Spin Coating (SC method. ZnO micro-nanorod arrays were grown on ZnO seed layers by using Hydrothermal Synthesis method. Seed layer effects of structural and optical properties of ZnO arrays were characterized. X-ray diffractometer (XRD, Scanning Electron Microscopy (SEM and Ultraviolet Visible (UV-Vis Spectrometer were used for analyses. ZnO micro-nanorod arrays consisted of a single crystalline wurtzite ZnO structure for each seed layer. Besides, ZnO rod arrays were grown smoothly and vertically on SC seed layer, while ZnO rod arrays were grown randomly and flower like structures on CBD seed layer. The optical absorbance peaks found at 422 nm wavelength in the visible region for both ZnO arrays. Optical bandgap values were determined by using UV-Vis measurements at 3.12 and 3.15 eV for ZnO micro-nanorod arrays on CBD seed layer and for ZnO micro-nanorod arrays on SC-seed layer respectively.DOI: http://dx.doi.org/10.5755/j01.ms.22.4.13443

  4. Simulation study of a high power density rectenna array for biomedical implantable devices

    Science.gov (United States)

    Day, John; Yoon, Hargsoon; Kim, Jaehwan; Choi, Sang H.; Song, Kyo D.

    2016-04-01

    The integration of wireless power transmission devices using microwaves into the biomedical field is close to a practical reality. Implanted biomedical devices need a long lasting power source or continuous power supply. Recent development of high efficiency rectenna technology enables continuous power supply to these implanted devices. Due to the size limit of most of medical devices, it is imperative to minimize the rectenna as well. The research reported in this paper reviews the effects of close packing the rectenna elements which show the potential of directly empowering the implanted devices, especially within a confined area. The rectenna array is tested in the X band frequency range.

  5. Detector block based on arrays of 144 SiPMs and monolithic scintillators: A performance study

    International Nuclear Information System (INIS)

    González, A.J.; Conde, P.; Iborra, A.; Aguilar, A.; Bellido, P.; García-Olcina, R.; Hernández, L.; Moliner, L.; Rigla, J.P.; Rodríguez-Álvarez, M.J.; Sánchez, F.; Seimetz, M.; Soriano, A.; Torres, J.; Vidal, L.F.; Benlloch, J.M.

    2015-01-01

    We have developed a detector block composed by a monolithic LYSO scintillator coupled to a custom made 12×12 SiPMs array. The design is mainly focused to applications such as Positron Emission Tomography. The readout electronics is based on 3 identical and scalable Application Specific Integrated Circuits (ASIC). We have determined the main performance of the detector block namely spatial, energy, and time resolution but also the system capability to determine the photon depth of interaction, for different crystal surface treatments. Intrinsic detector spatial resolution values as good as 1.7 mm FWHM and energies of 15% for black painted crystals were measured

  6. Performance studies of X3 silicon detectors for the future ELISSA array at ELI-NP

    Science.gov (United States)

    Chesnevskaya, S.; Balabanski, D. L.; Choudhury, D.; Constantin, P.; Filipescu, D. M.; Ghita, D. G.; Guardo, G. L.; Lattuada, D.; Matei, C.; Rotaru, A.; State, A.

    2018-05-01

    ELISSA is an array of silicon strip detectors under construction at the ELI-NP facility for measurements of photodissociation reactions using high-brilliance, quasi monoenergetic gamma beams. The detection system consists of 35 single-sided position-sensitive X3 detectors arranged in a cylindrical configuration and eight QQQ3 detectors as end-caps. A batch of forty X3 detectors have been tested at ELI-NP. The energy and position resolution, ballistic deficit, leakage currents, and depletion voltage were measured and analyzed. Measurements of the energy resolution were carried out using two read-out electronic chains, one based on multichannel preamplifiers and another based on multiplexers.

  7. 'Smoking genes': a genetic association study.

    Directory of Open Access Journals (Sweden)

    Zoraida Verde

    Full Text Available Some controversy exists on the specific genetic variants that are associated with nicotine dependence and smoking-related phenotypes. The purpose of this study was to analyse the association of smoking status and smoking-related phenotypes (included nicotine dependence with 17 candidate genetic variants: CYP2A6*1×2, CYP2A6*2 (1799T>A [rs1801272], CYP2A6*9 (-48T>G [rs28399433], CYP2A6*12, CYP2A13*2 (3375C>T [rs8192789], CYP2A13*3 (7520C>G, CYP2A13*4 (579G>A, CYP2A13*7 (578C>T [rs72552266], CYP2B6*4 (785A>G, CYP2B6*9 (516G>T, CHRNA3 546C>T [rs578776], CHRNA5 1192G>A [rs16969968], CNR1 3764C>G [rs6928499], DRD2-ANKK1 2137G>A (Taq1A [rs1800497], 5HTT LPR, HTR2A -1438A>G [rs6311] and OPRM1 118A>G [rs1799971]. We studied the genotypes of the aforementioned polymorphisms in a cohort of Spanish smokers (cases, N = 126 and ethnically matched never smokers (controls, N = 80. The results showed significant between-group differences for CYP2A6*2 and CYP2A6*12 (both PA (Taq1A polymorphisms was 3.60 (95%CI: 1.75, 7.44 and 2.63 (95%CI: 1.41, 4.89 respectively. Compared with the wild-type genotype, the OR for being a non-smoker in carriers of the minor CYP2A6*2 allele was 1.80 (95%CI: 1.24, 2.65. We found a significant genotype effect (all P≤0.017 for the following smoking-related phenotypes: (i cigarettes smoked per day and CYP2A13*3; (ii pack years smoked and CYP2A6*2, CYP2A6*1×2, CYP2A13*7, CYP2B6*4 and DRD2-ANKK1 2137G>A (Taq1A; (iii nicotine dependence (assessed with the Fagestrom test and CYP2A6*9. Overall, our results suggest that genetic variants potentially involved in nicotine metabolization (mainly, CYP2A6 polymorphisms are those showing the strongest association with smoking-related phenotypes, as opposed to genetic variants influencing the brain effects of nicotine, e.g., through nicotinic acetylcholine (CHRNA5, serotoninergic (HTR2A, opioid (OPRM1 or cannabinoid receptors (CNR1.

  8. Study on Fusion Protein and Its gene in Baculovirus Specificity

    International Nuclear Information System (INIS)

    Nemr, W.A.H.

    2012-01-01

    Baculoviruses are subdivided into two groups depending on the type of budded virus envelop fusion protein; group I utilized gp64 which include the most of nucleopolyhedroviruses (NPVs), group II utilized F protein which include the remnants of NPVs and all Granuloviruses (GVs). Recent studies reported the viral F protein coding gene as a host cellular sourced gene and may evolutionary acquired from the host genome referring to phylogeny analysis of fusion proteins. Thus, it was deduced that F protein coding gene is species- specific nucleotide sequence related to the type of the specific host and if virus could infect an unexpected host, the resulted virus may encode a vary F gene. In this regard, the present study utilized the mentioned properties of F gene in an attempt to produce a model of specific and more economic wider range granulovirus bio- pesticide able to infect both Spodoptera littoralis and Phthorimaea operculella larvae. Multiple sequence alignment and phylogeny analysis were performed on six members of group II baculovirus, novel universal PCR primers were manually designed from the conserved regions in the alignment graph, targeted to amplify species- specific sequence entire F gene open reading frame (ORF) which is useful in molecular identification of baculovirus in unknown samples. So, the PCR product of SpliGV used to prepare a specific probe for the F gene of this type of virus. Results reflected that it is possible to infect S. littoralis larvae by PhopGV if injected into larval haemocoel, the resulted virus of this infection showed by using DNA hybridization technique to be encode to F gene homologous with the F gene of Spli GV, which is revealed that the resulted virus acquired this F gene sequence from the host genome after infection. Consequently, these results may infer that if genetic aberrations occur in the host genome, this may affect in baculoviral infectivity. So, this study aimed to investigate the effect of gamma radiation at

  9. Bone marrow transplantations to study gene function in hematopoietic cells

    NARCIS (Netherlands)

    de Winther, Menno P. J.; Heeringa, Peter

    2011-01-01

    Immune cells are derived from hematopoietic stem cells in the bone marrow. Experimental replacement of bone marrow offers the unique possibility to replace immune cells, to study gene function in mouse models of disease. Over the past decades, this technique has been used extensively to study, for

  10. Serial Analysis of Gene Expression: Applications in Human Studies

    Directory of Open Access Journals (Sweden)

    Tuteja Renu

    2004-01-01

    Full Text Available Serial analysis of gene expression (SAGE is a powerful tool, which provides quantitative and comprehensive expression profile of genes in a given cell population. It works by isolating short fragments of genetic information from the expressed genes that are present in the cell being studied. These short sequences, called SAGE tags, are linked together for efficient sequencing. The frequency of each SAGE tag in the cloned multimers directly reflects the transcript abundance. Therefore, SAGE results in an accurate picture of gene expression at both the qualitative and the quantitative levels. It does not require a hybridization probe for each transcript and allows new genes to be discovered. This technique has been applied widely in human studies and various SAGE tags/SAGE libraries have been generated from different cells/tissues such as dendritic cells, lung fibroblast cells, oocytes, thyroid tissue, B-cell lymphoma, cultured keratinocytes, muscles, brain tissues, sciatic nerve, cultured Schwann cells, cord blood-derived mast cells, retina, macula, retinal pigment epithelial cells, skin cells, and so forth. In this review we present the updated information on the applications of SAGE technology mainly to human studies.

  11. Study and building of a detection array for delayed neutrons: TONNERRE

    International Nuclear Information System (INIS)

    Martin, Thierry

    1998-01-01

    This work has been undertaken within a French-Romanian collaboration in order to build a high efficiency detector array for delayed neutrons: barrel-shaped TONNERRE. Some neutron-rich nuclei decay through 1, 2 or 3 neutron emission after β - decay. More exotic nuclei will be produced by SPIRAL at GANIL. An array with high efficiency and good resolution is then required. Thirty two BC400 plastic scintillators (160 x 20 x 4 cm 3 ) allow us to get the time of flight neutron spectra. They are bent for uniform flight path and viewed by a photomultiplier tube at both ends. Simulations have allowed to establish scintillator size and to minimize light attenuation. Intrinsic efficiency and crosstalk have been measured with 252 Cf and compared to GEANT. 1 to 5 MeV neutrons are detected with good timing and position properties. Other counters will be built for neutrons from 300 keV to 1 MeV. Planned to run at several particle accelerators (GANIL, CERN, and others), TONNERRE is modular and many geometries are possible. (author)

  12. Experimental study on imploding characteristics of wire-array Z pinches on Qiangguang-1 facility

    Institute of Scientific and Technical Information of China (English)

    Wang Zhen; Xu Rong-Kun; Yang Jian-Lun; Hua Xin-Sheng; Li Lin-Bo; Xu Ze-Ping; Ning Jia-Min; Song Feng-Jun

    2007-01-01

    To investigate the imploding characteristics of cylindrical wire array,experiments with load current varying from 1.5MA to 1.7MA were carried out on the Qiangguang-1 facility.The complicated temporal-spatial distribution of x-ray radiation was measured by the one-dimensional (1D) x-ray imaging system.Other diagnostic equipments including the x-ray power meter(XRPM) and the time-integrated pinhole camera were used to record time-resolved x-ray power pulse and pinhole x-ray images.Analysis shows that the fast leading edge of the local x-ray radiation pulse is of primary importance in sharpening x-ray power pulse rather than the temporal synchrony and the spatial uniformity of implosion.Experimental results indicated that the better axial imploding synchrony,the faster the increase of X-ray power for an array consisting of 32 tungsten wires of 5μm diameter than for the others,and the higher the x-ray radiation power with maximal convergence ratio (r0/r1) of 10.5.A 'zipper-like' effect of x-ray radiation extending from the cathode Was also observed.

  13. A DNA methylation microarray-based study identifies ERG as a gene commonly methylated in prostate cancer.

    Science.gov (United States)

    Schwartzman, Jacob; Mongoue-Tchokote, Solange; Gibbs, Angela; Gao, Lina; Corless, Christopher L; Jin, Jennifer; Zarour, Luai; Higano, Celestia; True, Lawrence D; Vessella, Robert L; Wilmot, Beth; Bottomly, Daniel; McWeeney, Shannon K; Bova, G Steven; Partin, Alan W; Mori, Motomi; Alumkal, Joshi

    2011-10-01

    DNA methylation of promoter regions is a common event in prostate cancer, one of the most common cancers in men worldwide. Because prior reports demonstrating that DNA methylation is important in prostate cancer studied a limited number of genes, we systematically quantified the DNA methylation status of 1505 CpG dinucleotides for 807 genes in 78 paraffin-embedded prostate cancer samples and three normal prostate samples. The ERG gene, commonly repressed in prostate cells in the absence of an oncogenic fusion to the TMPRSS2 gene, was one of the most commonly methylated genes, occurring in 74% of prostate cancer specimens. In an independent group of patient samples, we confirmed that ERG DNA methylation was common, occurring in 57% of specimens, and cancer-specific. The ERG promoter is marked by repressive chromatin marks mediated by polycomb proteins in both normal prostate cells and prostate cancer cells, which may explain ERG's predisposition to DNA methylation and the fact that tumors with ERG DNA methylation were more methylated, in general. These results demonstrate that bead arrays offer a high-throughput method to discover novel genes with promoter DNA methylation such as ERG, whose measurement may improve our ability to more accurately detect prostate cancer.

  14. The development of a high-throughput gradient array apparatus for the study of porous polymer networks.

    Energy Technology Data Exchange (ETDEWEB)

    Majumdar, Partha (North Dakota State University, Fargo, ND); Lee, Elizabeth (North Dakota State University, Fargo, ND); Chisholm, Bret J. (North Dakota State University, Fargo, ND); Dirk, Shawn M.; Weisz, Michael (North Dakota State University, Fargo, ND); Bahr, James (North Dakota State University, Fargo, ND); Schiele, Kris (North Dakota State University, Fargo, ND)

    2010-01-01

    A gradient array apparatus was constructed for the study of porous polymers produced using the process of chemically-induced phase separation (CIPS). The apparatus consisted of a 60 element, two-dimensional array in which a temperature gradient was placed in the y-direction and composition was varied in the x-direction. The apparatus allowed for changes in opacity of blends to be monitored as a function of temperature and cure time by taking images of the array with time. The apparatus was validated by dispense a single blend composition into all 60 wells of the array and curing them for 24 hours and doing the experiment in triplicate. Variations in micron scale phase separation were readily observed as a function of both curing time and temperature and there was very good well-to-well consistency as well as trial-to-trial consistency. Poragen of samples varying with respect to cure temperature was removed and SEM images were obtained. The results obtained showed that cure temperature had a dramatic affect on sample morphology, and combining data obtained from visual observations made during the curing process with SEM data can enable a much better understanding of the CIPS process and provide predictive capability through the relatively facile generation of composition-process-morphology relationships. Data quality could be greatly enhanced by making further improvements in the apparatus. The primary improvements contemplated include the use of a more uniform light source, an optical table, and a CCD camera with data analysis software. These improvements would enable quantification of the amount of scattered light generated from individual elements as a function of cure time. In addition to the gradient array development, porous composites were produced by incorporating metal particles into a blend of poragen, epoxy resin, and crosslinker. The variables involved in the experiment were metal particle composition, primary metal particle size, metal concentration

  15. Network graph analysis of gene-gene interactions in genome-wide association study data.

    Science.gov (United States)

    Lee, Sungyoung; Kwon, Min-Seok; Park, Taesung

    2012-12-01

    Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR) is one of the powerful and efficient methods for detecting high-order gene-gene (GxG) interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE) data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI). Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.

  16. Actin gene identification from selected medicinal plants for their use as internal controls for gene expression studies

    International Nuclear Information System (INIS)

    Mufti, F.U.D.; Banaras, S.

    2015-01-01

    Internal control genes are the constitutive genes which maintain the basic cellular functions and regularly express in both normal and stressed conditions in living organisms. They are used in normalization of gene expression studies in comparative analysis of target genes, as their expression remains comparatively unchanged in all varied conditions. Among internal control genes, actin is considered as a candidate gene for expression studies due to its vital role in shaping cytoskeleton and plant physiology. Unfortunately most of such knowledge is limited to only model plants or crops, not much is known about important medicinal plants. Therefore, we selected seven important medicinal wild plants for molecular identification of actin gene. We used gene specific primers designed from the conserved regions of several known orthologues or homologues of actin genes from other plants. The amplified products of 370-380 bp were sequenced and submitted to GeneBank after their confirmation using different bioinformatics tools. All the novel partial sequences of putative actin genes were submitted to GeneBank (Parthenium hysterophorus (KJ774023), Fagonia indica (KJ774024), Rhazya stricta (KJ774025), Whithania coagulans (KJ774026), Capparis decidua (KJ774027), Verbena officinalis (KJ774028) and Aerva javanica (KJ774029)). The comparisons of these partial sequences by Basic Local Alignment Search Tool (BLAST) and phylogenetic trees demonstrated high similarity with known actin genes of other plants. Our findings illustrated highly conserved nature of actin gene among these selected plants. These novel partial fragments of actin genes from these wild medicinal plants can be used as internal controls for future gene expression studies of these important plants after precise validations of their stable expression in such plants. (author)

  17. Capturing heterogeneity in gene expression studies by surrogate variable analysis.

    Directory of Open Access Journals (Sweden)

    Jeffrey T Leek

    2007-09-01

    Full Text Available It has unambiguously been shown that genetic, environmental, demographic, and technical factors may have substantial effects on gene expression levels. In addition to the measured variable(s of interest, there will tend to be sources of signal due to factors that are unknown, unmeasured, or too complicated to capture through simple models. We show that failing to incorporate these sources of heterogeneity into an analysis can have widespread and detrimental effects on the study. Not only can this reduce power or induce unwanted dependence across genes, but it can also introduce sources of spurious signal to many genes. This phenomenon is true even for well-designed, randomized studies. We introduce "surrogate variable analysis" (SVA to overcome the problems caused by heterogeneity in expression studies. SVA can be applied in conjunction with standard analysis techniques to accurately capture the relationship between expression and any modeled variables of interest. We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.

  18. Lithium storage study on MoO3-grafted TiO2 nanotube arrays

    Directory of Open Access Journals (Sweden)

    Tauseef Anwar

    2016-03-01

    Full Text Available Abstract Titanium dioxide nanotube arrays (TNAs were fabricated via anodic ionization. Porous MoO3 was grafted on TNAs with the help of hydrothermal method. Scanning electron microscopy and X-ray powder diffraction was utilized for the confirmation of one dimensional morphology and phase identification. The porous MoO3 nanoflake-grafted TNAs (MoO3/TNAs electrode was used as anode material in lithium ion battery (LIB and it was found that the areal specific capacity of MoO3/TNAs (~797 µAh cm−2 was three times higher than those of anatase TNAs (~287 µAh cm−2 and porous MoO3 (~234 µAh cm−2 at 50 µA cm−2.

  19. Surface roughness studies with DALLAS-detector array for laser light angular scattering

    Science.gov (United States)

    Vorburger, T. V.; Teague, E. C.; Scire, F. E.; Mclay, M. J.; Gilsinn, D. E.

    1984-01-01

    An attempt is made to develop a better mathematical description of optical scattering phenomena, in order to construct an optical scattering apparatus for reliable and routine measurements of roughness parameters without resorting to comparator standards. After a brief outline of optical scattering theory, a description is presented of an experimental instrument for measuring surface roughness which incorporates optical scattering principles. The instrument has a He-Ne laser which illuminates the test surface at a variable angle of incidence. Scattered light distribution is detected by an array of 87 fiber-optic sensors positioned in a rotating semicircular yoke. The output from the detector is digitized and analyzed in a laboratory computer. For a comparison with experimental data, theoretical distributions are calculated by substituting the roughness profiles into the operand of and integral equation for electromagnetic scattering developed by Beckmann and Spizzichino (1963). A schematic diagram of the instrument is provided and the general implications of the experimental results are discussed.

  20. A Study on Group Key Agreement in Sensor Network Environments Using Two-Dimensional Arrays

    Science.gov (United States)

    Jang, Seung-Jae; Lee, Young-Gu; Lee, Kwang-Hyung; Kim, Tai-Hoon; Jun, Moon-Seog

    2011-01-01

    These days, with the emergence of the concept of ubiquitous computing, sensor networks that collect, analyze and process all the information through the sensors have become of huge interest. However, sensor network technology fundamentally has wireless communication infrastructure as its foundation and thus has security weakness and limitations such as low computing capacity, power supply limitations and price. In this paper, and considering the characteristics of the sensor network environment, we propose a group key agreement method using a keyset pre-distribution of two-dimension arrays that should minimize the exposure of key and personal information. The key collision problems are resolved by utilizing a polygonal shape’s center of gravity. The method shows that calculating a polygonal shape’s center of gravity only requires a very small amount of calculations from the users. The simple calculation not only increases the group key generation efficiency, but also enhances the sense of security by protecting information between nodes. PMID:22164072

  1. Study of the pressure drop in a rob bundle arranged in square array

    International Nuclear Information System (INIS)

    Barros Filho, J.A.

    1987-01-01

    Results of single-phase tests performed in a 3 x 3 rod bundle arranged in square array are presented and analysed. The tests were performed in adiabatic conditions and with heat transfer, covering the following range of parameters: Reynolds no.: 1,5 to 20 x 10 4 ; inlet temperature [ 0 C]: 30 to 150; pressure [bar]: 1 to 15; heat flux [kW/cm 2 ]: 0 to 1000. Correlations were determined for the friction factor, isothermal under conditions of heat transfer, spacer grids pressure drop coefficient and average heat transfer coefficient. The experimental data were compared with published data obtained by other researchers and with some theoretical models selected in the literature. (Autor) [pt

  2. Performance study of monochromatic synchrotron X-ray computed tomography using a linear array detector

    Energy Technology Data Exchange (ETDEWEB)

    Kazama, Masahiro; Takeda, Tohoru; Itai, Yuji [Tsukuba Univ., Ibaraki (Japan). Inst. of Clinical Medicine; Akiba, Masahiro; Yuasa, Tetsuya; Hyodo, Kazuyuki; Ando, Masami; Akatsuka, Takao

    1997-09-01

    Monochromatic x-ray computed tomography (CT) using synchrotron radiation (SR) is being developed for detection of non-radioactive contrast materials at low concentration for application in clinical diagnosis. A new SR-CT system with improved contrast resolution, was constructed using a linear array detector which provides wide dynamic ranges and a double monochromator. The performance of this system was evaluated in a phantom and a rat model of brain ischemia. This system consists of a silicon (111) double crystal monochromator, an x-ray shutter, an ionization chamber, x-ray slits, a scanning table for the target organ, and an x-ray linear array detector. The research was carried out at the BLNE-5A bending magnet beam line of the Tristan Accumulation Ring in KEK, Japan. In this experiment, the reconstructed image of the spatial-resolution phantom clearly showed the 1 mm holes. At 1 mm slice thickness, the above K-edge image of the phantom showed contrast resolution at the concentration of 200 {mu}g/ml iodine-based contrast materials whereas the K-edge energy subtraction image showed contrast resolution at the concentration of 500 {mu}g/ml contrast materials. The cerebral arteries filled with iodine microspheres were clearly revealed, and the ischemic regions at the right temporal lobe and frontal lobe were depicted as non-vascular regions. The measured minimal detectable concentration of iodine on the above K-edge image is about 6 times higher than the expected value of 35.3 {mu}g/ml because of the high dark current of this detector. Thus, the use of a CCD detector which is cooled by liquid nitrogen to improve the dynamic range of the detector, is being under construction. (author)

  3. Exome-wide association study reveals novel susceptibility genes to sporadic dilated cardiomyopathy.

    Directory of Open Access Journals (Sweden)

    Ulrike Esslinger

    Full Text Available Dilated cardiomyopathy (DCM is an important cause of heart failure with a strong familial component. We performed an exome-wide array-based association study (EWAS to assess the contribution of missense variants to sporadic DCM.116,855 single nucleotide variants (SNVs were analyzed in 2796 DCM patients and 6877 control subjects from 6 populations of European ancestry. We confirmed two previously identified associations with SNVs in BAG3 and ZBTB17 and discovered six novel DCM-associated loci (Q-value<0.01. The lead-SNVs at novel loci are common and located in TTN, SLC39A8, MLIP, FLNC, ALPK3 and FHOD3. In silico fine mapping identified HSPB7 as the most likely candidate at the ZBTB17 locus. Rare variant analysis (MAF<0.01 demonstrated significant association for TTN variants only (P = 0.0085. All candidate genes but one (SLC39A8 exhibit preferential expression in striated muscle tissues and mutations in TTN, BAG3, FLNC and FHOD3 are known to cause familial cardiomyopathy. We also investigated a panel of 48 known cardiomyopathy genes. Collectively, rare (n = 228, P = 0.0033 or common (n = 36, P = 0.019 variants with elevated in silico severity scores were associated with DCM, indicating that the spectrum of genes contributing to sporadic DCM extends beyond those identified here.We identified eight loci independently associated with sporadic DCM. The functions of the best candidate genes at these loci suggest that proteostasis regulation might play a role in DCM pathophysiology.

  4. Comprehensive evaluation of candidate reference genes for gene expression studies in Lysiphlebia japonica (Hymenoptera: Aphidiidae) using RT-qPCR.

    Science.gov (United States)

    Gao, Xue-Ke; Zhang, Shuai; Luo, Jun-Yu; Wang, Chun-Yi; Lü, Li-Min; Zhang, Li-Juan; Zhu, Xiang-Zhen; Wang, Li; Lu, Hui; Cui, Jin-Jie

    2017-12-30

    Lysiphlebia japonica (Ashmead) is a predominant parasitoid of cotton-melon aphids in the fields of northern China with a proven ability to effectively control cotton aphid populations in early summer. For accurate normalization of gene expression in L. japonica using quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR), reference genes with stable gene expression patterns are essential. However, no appropriate reference genes is L. japonica have been investigated to date. In the present study, 12 selected housekeeping genes from L. japonica were cloned. We evaluated the stability of these genes under various experimental treatments by RT-qPCR using four independent (geNorm, NormFinder, BestKeeper and Delta Ct) and one comparative (RefFinder) algorithm. We identified genes showing the most stable levels of expression: DIMT, 18S rRNA, and RPL13 during different stages; AK, RPL13, and TBP among sexes; EF1A, PPI, and RPL27 in different tissues, and EF1A, RPL13, and PPI in adults fed on different diets. Moreover, the expression profile of a target gene (odorant receptor 1, OR1) studied during the developmental stages confirms the reliability of the chosen selected reference genes. This study provides for the first time a comprehensive list of suitable reference genes for gene expression studies in L. japonica and will benefit subsequent genomics and functional genomics research on this natural enemy. Copyright © 2017. Published by Elsevier B.V.

  5. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  6. Selection of relatively exact reference genes for gene expression studies in goosegrass (Eleusine indica) under herbicide stress.

    Science.gov (United States)

    Chen, Jingchao; Huang, Zhaofeng; Huang, Hongjuan; Wei, Shouhui; Liu, Yan; Jiang, Cuilan; Zhang, Jie; Zhang, Chaoxian

    2017-04-21

    Goosegrass (Eleusine indica) is one of the most serious annual grassy weeds worldwide, and its evolved herbicide-resistant populations are more difficult to control. Quantitative real-time PCR (qPCR) is a common technique for investigating the resistance mechanism; however, there is as yet no report on the systematic selection of stable reference genes for goosegrass. This study proposed to test the expression stability of 9 candidate reference genes in goosegrass in different tissues and developmental stages and under stress from three types of herbicide. The results show that for different developmental stages and organs (control), eukaryotic initiation factor 4 A (eIF-4) is the most stable reference gene. Chloroplast acetolactate synthase (ALS) is the most stable reference gene under glyphosate stress. Under glufosinate stress, eIF-4 is the best reference gene. Ubiquitin-conjugating enzyme (UCE) is the most stable reference gene under quizalofop-p-ethyl stress. The gene eIF-4 is the recommended reference gene for goosegrass under the stress of all three herbicides. Moreover, pairwise analysis showed that seven reference genes were sufficient to normalize the gene expression data under three herbicides treatment. This study provides a list of reliable reference genes for transcript normalization in goosegrass, which will facilitate resistance mechanism studies in this weed species.

  7. Tomographic array

    International Nuclear Information System (INIS)

    1976-01-01

    The configuration of a tomographic array in which the object can rotate about its axis is described. The X-ray detector is a cylindrical screen perpendicular to the axis of rotation. The X-ray source has a line-shaped focus coinciding with the axis of rotation. The beam is fan-shaped with one side of this fan lying along the axis of rotation. The detector screen is placed inside an X-ray image multiplier tube

  8. Tomographic array

    International Nuclear Information System (INIS)

    1976-01-01

    A tomographic array with the following characteristics is described. An X-ray screen serving as detector is placed before a photomultiplier tube which itself is placed in front of a television camera connected to a set of image processors. The detector is concave towards the source and is replacable. Different images of the object are obtained simultaneously. Optical fibers and lenses are used for transmission within the system

  9. Study of ablation and implosion stages in wire arrays using coupled ultraviolet and X-ray probing diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, A. A.; Ivanov, V. V.; Astanovitskiy, A. L.; Wiewior, P. P.; Chalyy, O. [University of Nevada Reno, Reno, Nevada 89557 (United States); Papp, D. [University of Nevada Reno, Reno, Nevada 89557 (United States); ELI-ALPS, ELI-Hu Nkft., H-6720 Szeged (Hungary)

    2015-11-15

    Star and cylindrical wire arrays were studied using laser probing and X-ray radiography at the 1-MA Zebra pulse power generator at the University of Nevada, Reno. The Leopard laser provided backlighting, producing a laser plasma from a Si target which emitted an X-ray probing pulse at the wavelength of 6.65 Å. A spherically bent quartz crystal imaged the backlit wires onto X-ray film. Laser probing diagnostics at the wavelength of 266 nm included a 3-channel polarimeter for Faraday rotation diagnostic and two-frame laser interferometry with two shearing interferometers to study the evolution of the plasma electron density at the ablation and implosion stages. Dynamics of the plasma density profile in Al wire arrays at the ablation stage were directly studied with interferometry, and expansion of wire cores was measured with X-ray radiography. The magnetic field in the imploding plasma was measured with the Faraday rotation diagnostic, and current was reconstructed.

  10. Exome Array Analysis of Nuclear Lens Opacity.

    Science.gov (United States)

    Loomis, Stephanie J; Klein, Alison P; Lee, Kristine E; Chen, Fei; Bomotti, Samantha; Truitt, Barbara; Iyengar, Sudha K; Klein, Ronald; Klein, Barbara E K; Duggal, Priya

    2018-06-01

    Nuclear cataract is the most common subtype of age-related cataract, the leading cause of blindness worldwide. It results from advanced nuclear sclerosis, or opacity in the center of the optic lens, and is affected by both genetic and environmental risk factors, including smoking. We sought to understand the genetic factors associated with nuclear sclerosis through interrogation of rare and low frequency coding variants using exome array data. We analyzed Illumina Human Exome Array data for 1,488 participants of European ancestry in the Beaver Dam Eye Study who were without cataract surgery for association with nuclear sclerosis grade, controlling for age and sex. We performed single-variant regression analysis for 32,138 variants with minor allele frequency (MAF) ≥0.003. In addition, gene-based analysis of 11,844 genes containing at least two variants with MAF nuclear sclerosis, the possible association with the RNF149 gene highlights a potential candidate gene for future studies that aim to understand the genetic architecture of nuclear sclerosis.

  11. Studies of the seismic coda using an earthquake cluster as a deeply buried seismograph array

    Science.gov (United States)

    Spudich, Paul; Bostwick, Todd

    1987-09-01

    Loosely speaking, the principle of Green's function reciprocity means that the source and receiver positions in a seismic experiment can be exchanged without affecting the observed seismograms. Consequently, the seismograms observed at a single observation location o and caused by a cluster of microearthquakes at locations {ei} are identical to the time series that would be measured by an array of stress meters emplaced at positions {ei}, recording waves generated by a source acting at o. By applying array analysis techniques like slant stacking and frequency-wave number analysis to these seismograms, we can determine the directions and velocities of the component waves as they travel in the earthquake focal region rather than at the surface. We have developed a computationally rapid plane-wave decomposition which we have applied to single-station recordings of aftershocks of the 1984 Morgan Hill, California, earthquake. The analysis is applied to data from three seismic stations having considerably different site geologies. One is a relatively hard rock station situated on Franciscan metamorphics, one is within the Calaveras fault zone, and one is on semiconsolidated sand and gravels. We define the early coda to be the part of the coda initiating immediately after the direct S wave and ending at twice the S wave lapse time. The character of the S wave and early coda varies from being impulsive at the first station to highly reverberative at the last. We examine waves in sequential time windows starting at the S wave and continuing through the early part of the coda. At all seismic stations the early coda is dominated by a persistent signal that must be caused by multiple scattering, probably within 2 km of each seismic station. Despite clear station-to-station differences in the character of the early coda, coda Q values measured in the late coda (greater than twice the S lapse time) agree well among stations, implying that the mechanisms causing the varying

  12. Genotype-phenotype analysis of recombinant chromosome 4 syndrome: an array-CGH study and literature review.

    Science.gov (United States)

    Hemmat, Morteza; Hemmat, Omid; Anguiano, Arturo; Boyar, Fatih Z; El Naggar, Mohammed; Wang, Jia-Chi; Wang, Borris T; Sahoo, Trilochan; Owen, Renius; Haddadin, Mary

    2013-05-02

    Recombinant chromosome 4, a rare constitutional rearrangement arising from pericentric inversion, comprises a duplicated segment of 4p13~p15→4pter and a deleted segment of 4q35→4qter. To date, 10 cases of recombinant chromosome 4 have been reported. We describe the second case in which array-CGH was used to characterize recombinant chromosome 4 syndrome. The patient was a one-year old boy with consistent clinical features. Conventional cytogenetics and FISH documented a recombinant chromosome 4, derived from a paternal pericentric inversion, leading to partial trisomy 4p and partial monosomy of 4q. Array-CGH, performed to further characterize the rearranged chromosome 4 and delineate the breakpoints, documented a small (4.36 Mb) 4q35.1 terminal deletion and a large (23.81 Mb) 4p15.1 terminal duplication. Genotype-phenotype analysis of 10 previously reported cases and the present case indicated relatively consistent clinical features and breakpoints. This consistency was more evident in our case and another characterized by array-CGH, where both showed the common breakpoints of p15.1 and q35.1. A genotype-phenotype correlation study between rec(4), dup(4p), and del(4q) syndromes revealed that urogenital and cardiac defects are probably due to the deletion of 4q whereas the other clinical features are likely due to 4p duplication. Our findings support that the clinical features of patients with rec(4) are relatively consistent and specific to the regions of duplication or deletion. Recombinant chromosome 4 syndrome thus appears to be a discrete entity that can be suspected on the basis of clinical features or specific deleted and duplicated chromosomal regions.

  13. Experimental study of the retention properties of a cyclo olefin polymer pillar array column in reversed-phase mode.

    Science.gov (United States)

    Illa, Xavi; De Malsche, Wim; Gardeniers, Han; Desmet, Gert; Romano-Rodríguez, Albert

    2010-11-01

    Experimental measurements to study the retention capacity and band broadening under retentive conditions using micromachined non-porous pillar array columns fabricated in cyclo olefin polymer are presented. In particular, three columns with different depths but with the same pillar structure have been fabricated via hot embossing and pressure-assisted thermal bonding. Separations of a mixture of four coumarins using varying mobile phase compositions have been monitored to study the relation between the retention factor and the ratio of organic solvent in the aqueous mobile phase. Moreover, the linear relation between the retention and the surface/volume ratio predicted in theory has been observed, achieving retention factors up to k=2.5. Under the same retentive conditions, minimal reduced plate height values of h(min)=0.4 have been obtained at retention factors of k=1.2. These experimental results are compared with the case of non-porous and porous silicon pillars. Similar results for the plate heights are achieved while retention factors are higher than the non-porous silicon column and considerably smaller than the porous pillar column, given the non-porous nature of the used cyclo olefin polymer. The feasibility of using this polymer column as an alternative to the pillar array silicon columns is corroborated.

  14. An experimental study of the scatter correction by using a beam-stop-array algorithm with digital breast tomosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ye-Seul; Park, Hye-Suk; Kim, Hee-Joung [Yonsei University, Wonju (Korea, Republic of); Choi, Young-Wook; Choi, Jae-Gu [Korea Electrotechnology Research Institute, Ansan (Korea, Republic of)

    2014-12-15

    Digital breast tomosynthesis (DBT) is a technique that was developed to overcome the limitations of conventional digital mammography by reconstructing slices through the breast from projections acquired at different angles. In developing and optimizing DBT, The x-ray scatter reduction technique remains a significant challenge due to projection geometry and radiation dose limitations. The most common approach to scatter reduction is a beam-stop-array (BSA) algorithm; however, this method raises concerns regarding the additional exposure involved in acquiring the scatter distribution. The compressed breast is roughly symmetric, and the scatter profiles from projections acquired at axially opposite angles are similar to mirror images. The purpose of this study was to apply the BSA algorithm with only two scans with a beam stop array, which estimates the scatter distribution with minimum additional exposure. The results of the scatter correction with angular interpolation were comparable to those of the scatter correction with all scatter distributions at each angle. The exposure increase was less than 13%. This study demonstrated the influence of the scatter correction obtained by using the BSA algorithm with minimum exposure, which indicates its potential for practical applications.

  15. Improved Titanium Billet Inspection Sensitivity through Optimized Phased Array Design, Part II: Experimental Validation and Comparative Study with Multizone

    International Nuclear Information System (INIS)

    Hassan, W.; Vensel, F.; Knowles, B.; Lupien, V.

    2006-01-01

    The inspection of critical rotating components of aircraft engines has made important advances over the last decade. The development of Phased Array (PA) inspection capability for billet and forging materials used in the manufacturing of critical engine rotating components has been a priority for Honeywell Aerospace. The demonstration of improved PA inspection system sensitivity over what is currently used at the inspection houses is a critical step in the development of this technology and its introduction to the supply base as a production inspection. As described in Part I (in these proceedings), a new phased array transducer was designed and manufactured for optimal inspection of eight inch diameter Ti-6Al-4V billets. After confirming that the transducer was manufactured in accordance with the design specifications a validation study was conducted to assess the sensitivity improvement of the PAI over the current capability of Multi-zone (MZ) inspection. The results of this study confirm the significant (≅ 6 dB in FBH number sign sensitivity) improvement of the PAI sensitivity over that of MZI

  16. Study of retro reflector array for the polarimeter-interferometer system on EAST Tokamak

    Science.gov (United States)

    Lan, T.; Wang, S. X.; Liu, H. Q.; Liu, J.; Jie, Y. X.; Zou, Z. Y.; Li, W. M.; Gao, X.; Qin, H.

    2015-12-01

    In this paper, we experimentally verify the feasibility of replacing individual retro reflectors (RRs) with retro reflector array (RRA) in EAST POlarimeter/INTerferometer (POINT) system, by considering mode transformation and power wastage. Being exposed to plasma environment directly, RRs have risks of deformation, erosion and deposition. RRA is preferable because it can be installed within a smaller space and provide a gap of several centimeters for the shutter design. This protective structure can reduce the cost of device maintenance and bring down system errors. According to Helmholtz-Kirchhoff integral theorem, the optimized incident diameter for the RRA, constituted by seven hexagonal RR cells, is 40 mm in POINT system. The corresponding bench tests are carried out by measuring the propagation properties of reflected beams by plane RRA for perpendicular incidence and reflected beams by terrace RRA for oblique incidence. The experimental results illustrate that RRA can be satisfactorily applied in POINT system at the optimized incident diameter. In view of the energy wastage caused by plasma film coating, it is found that RRA has more advantages for diagnostics using shorter wavelengths, such as the case in ITER.

  17. The new mid-scala electrode array: a radiologic and histologic study in human temporal bones.

    Science.gov (United States)

    Hassepass, Frederike; Bulla, Stefan; Maier, Wolfgang; Laszig, Roland; Arndt, Susan; Beck, Rainer; Traser, Lousia; Aschendorff, Antje

    2014-09-01

    To analyze the quality of insertion of the newly developed midscala (MS) electrode, which targets a midscalar electrode position to reduce the risk of trauma to the lateral wall and the modiolus. Modern cochlear implant surgery aims for a safe intracochlear placement of electrode arrays with an ongoing debate regarding cochleostomy or round window (RW) insertion and the use of lateral wall or perimodiolar electrode placement. Intracochlear trauma after insertion of different electrodes depends on insertion mode and electrode design and may result in trauma to the delicate structures of the cochlear. We performed a temporal bone (TB) trial with insertion of the MS electrode in n = 20 TB's after a mastoidectomy and posterior tympanotomy. Insertion was performed either via the RW or a cochleostomy. Electrode positioning, length of insertion, and angle of insertion were analyzed with rotational tomography (RT). TBs were histologically analyzed. Results of RT and histology were compared. Scala tympani (ST) insertion could be accomplished reliably by both RW and via a cochleostomy approach. In 20 TBs, 1 scala vestibuli insertion, 1 incomplete (ST), and 1 elevation of basilar membrane were depicted. No trauma was found in 94.7% of all ST insertions. RT allowed determination of the intracochlear electrode position, which was specified by histologic sectioning. The new MS electrode seems to fulfill reliable atraumatic intracochlear placement via RW and cochleostomy approaches. RT is available for evaluation of intracochlear electrode position, serving as a potential quality control instrument in human implantation.

  18. A Study on Group Key Agreement in Sensor Network Environments Using Two-Dimensional Arrays

    Directory of Open Access Journals (Sweden)

    Moon-Seog Jun

    2011-08-01

    Full Text Available These days, with the emergence of the concept of ubiquitous computing, sensor networks that collect, analyze and process all the information through the sensors have become of huge interest. However, sensor network technology fundamentally has wireless communication infrastructure as its foundation and thus has security weakness and limitations such as low computing capacity, power supply limitations and price. In this paper, and considering the characteristics of the sensor network environment, we propose a group key agreement method using a keyset pre-distribution of two-dimension arrays that should minimize the exposure of key and personal information. The key collision problems are resolved by utilizing a polygonal shape’s center of gravity. The method shows that calculating a polygonal shape’s center of gravity only requires a very small amount of calculations from the users. The simple calculation not only increases the group key generation efficiency, but also enhances the sense of security by protecting information between nodes.

  19. Study on the energy response to neutrons for a new scintillating-fiber-array neutron detector

    CERN Document Server

    Zhang Qi; Wang Qun; Xie Zhong Shen

    2003-01-01

    The energy response of a new scintillating-fiber-array neutron detector to neutrons in the energy range 0.01 MeV<=E sub n<=14 MeV was modeled by combining a simplified Monte Carlo model and the MCNP 4b code. In order to test the model and get the absolute sensitivity of the detector to neutrons, one experiment was carried out for 2.5 and 14 MeV neutrons from T(p,n) sup 3 He and T(d,n) sup 4 He reactions at the Neutron Generator Laboratory at the Institute of Modern Physics, the Chinese Academy of Science. The absolute neutron fluence was obtained with a relative standard uncertainty 4.5% or 2.0% by monitoring the associated protons or sup 4 He particles, respectively. Another experiment was carried out for 0.5, 1.0, 1.5, 2.0, 2.5 MeV neutrons from T(p,n) sup 3 He reaction, and for 3.28, 3.50, 4.83, 5.74 MeV neutrons from D(d,n) sup 3 He reaction on the Model 5SDH-2 accelerator at China Institute of Atomic Energy. The absolute neutron fluence was obtained with a relative standard uncertainty 5.0% by usin...

  20. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

    Energy Technology Data Exchange (ETDEWEB)

    Lyubimov, Artem Y. [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Murray, Thomas D. [University of California, Berkeley, CA 94720 (United States); Johns Hopkins University School of Medicine, Baltimore, MD 21205 (United States); Koehl, Antoine [Stanford University, Stanford, CA 94305 (United States); Araci, Ismail Emre [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Uervirojnangkoorn, Monarin; Zeldin, Oliver B. [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Cohen, Aina E.; Soltis, S. Michael; Baxter, Elizabeth L. [SLAC National Accelerator Laboratory, Stanford, CA 94305 (United States); Brewster, Aaron S.; Sauter, Nicholas K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Brunger, Axel T., E-mail: brunger@stanford.edu [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Berger, James M., E-mail: brunger@stanford.edu [Johns Hopkins University School of Medicine, Baltimore, MD 21205 (United States); Stanford University, Stanford, CA 94305 (United States)

    2015-04-01

    A microfluidic platform has been developed for the capture and X-ray analysis of protein microcrystals, affording a means to improve the efficiency of XFEL and synchrotron experiments. X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.

  1. SUPER-RESOLUTION ULTRASOUND TOMOGRAPHY: A PRELIMINARY STUDY WITH A RING ARRAY

    Energy Technology Data Exchange (ETDEWEB)

    HUANG, LIANJIE [Los Alamos National Laboratory; SIMONETTI, FRANCESCO [NON LANL; DURIC, NEBOJSA [NON LANL; RAMA, OLSI [NON LANL

    2007-01-18

    Ultrasound tomography attempts to retrieve the structure of an objective by exploiting the interaction of acoustic waves with the object. A fundamental limit of ultrasound tomography is that features cannot be resolved if they are spaced less than {lambda}/2 apart, where {lambda} is wavelength of the probing wave, regardless of the degree of accuracy of the measurements. Therefore, since the attenuation of the probing wave with propagation distance increases as {lambda} decreases, resolution has to be traded against imaging depth. Recently, it has been shown that the {lambda}/2 limit is a consequence of the Born approximation (implicit in the imaging algorithms currently employed) which neglects the distortion of the probing wavefield as it travels through the medium to be imaged. On the other hand, such a distortion, which is due to the multiple scattering phenomenon, can encode unlimited resolution in the radiating component of the scattered field. Previously, a resolution better than {lambda}/3 has been reported in these proceedings [F. Simonetti, pp. 126 (2006)] in the case of elastic wave probing. In this paper, they demonstrate experimentally a resolution better than {lambda}/4 for objects immersed in a water bth probed by means of a ring array which excites and detects pressure waves in a full view configuration.

  2. Study of the Carrier-Aided Thin Film Electrode Array Design for Cochlear Insertion

    Directory of Open Access Journals (Sweden)

    Yuchen Xu

    2018-04-01

    Full Text Available The micro-fabricated thin film electrode array (TFEA has been a promising design for cochlear implants (CIs because of its cost-effectiveness and fabrication precision. The latest polymer-based cochlear TFEAs have faced difficulties for cochlear insertion due to the lack of structural stiffness. To stiffen the TFEA, dissolvable stiffening materials, TFEAs with different structures, and TFEAs with commercial CIs as carriers have been invested. In this work, the concept of enhancing a Parylene TFEA with Kapton tape as a simpler carrier for cochlear insertion has been proved to be feasible. The bending stiffness of the Kapton-aided TFEA was characterized with an analytical model, a finite element model, and a cantilever bending experiment, respectively. While the Kapton tape increased the bending stiffness of the Parylene TFEA by 103 times, the 6-μm-thick TFEA with a similar Young’s modulus, as a polyimide, in turn significantly increased the bending stiffness of the 170-μm-thick Kapton carrier by 60%. This result indicated that even the TFEA is ultra-flexible and that its bending stiffness should not be neglected in the design or selection of its carrier.

  3. A high resolution germanium detector array for hypernuclear studies at PANDA

    Energy Technology Data Exchange (ETDEWEB)

    Bleser, Sebastian; Sanchez Lorente, Alicia; Steinen, Marcell [Helmholtz-Institut Mainz (Germany); Gerl, Juergen; Kojouharova, Jasmina; Kojouharov, Ivan [GSI Darmstadt (Germany); Iazzi, Felice [Politecnico, Torino (Italy); INFN, Torino (Italy); Pochodzalla, Josef; Rittgen, Kai; Sahin, Cihan [Institute for Nuclear Physics, JGU Mainz (Germany)

    2014-07-01

    The PANDA experiment, planned at the FAIR facility in Darmstadt, aims at the high resolution γ-spectroscopy of double Λ hypernuclei. For this purpose a devoted detector setup is required, consisting of a primary nuclear target, an active secondary target and a germanium detector array for the γ-spectroscopy. Due to the limited space within the PANDA detector a compact design is required. In particular the conventional LN{sub 2} cooling system must be replaced by an electro mechanical device and a new arrangement of the crystals is needed. This presentation shows the progress in the development of the germanium detectors. First results of in-beam measurements at COSY with a new electro mechanically cooled single crystal prototype are presented. Digital pulse shape analysis is used to disentangle pile up events due to the high event rate. This analysis technique also allows to recover the high original energy resolution in case of neutron damage. Finally the status of the new triple crystal detector prototype is given.

  4. Network Graph Analysis of Gene-Gene Interactions in Genome-Wide Association Study Data

    Directory of Open Access Journals (Sweden)

    Sungyoung Lee

    2012-12-01

    Full Text Available Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs. For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR is one of the powerful and efficient methods for detecting high-order gene-gene (GxG interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI. Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.

  5. Analisis Mode Sistem Pembangkit Listrik Tenaga Hibrid Microhydro - Photovoltaic Array Menggunakan Homer (Studi Kasus : Kampung Bayang Janiah, Kabupaten Pesisir Selatan

    Directory of Open Access Journals (Sweden)

    Novi Kurniasih

    2015-03-01

    Full Text Available In this study discusses the optimization of the design and analysis of engineering economics Hybrid Power Plant Off-Grid Microhydro - Photovoltaic Array with the help of software HOMER 2 version 2.81. Utilization of Hybrid Power Plant System can overcome the electrical problems in Bayang Janiah village, Nagari Koto Ranah, Bayang Utara Subdistrict, Pesisir Selatan District that is far from the reach of the grid and can improve the reliability of electricity economically in which initially operated only 12 hours/day sourced from microhydro power plant only, can be upgraded to full operation 24 hours/day. From the analysis that has been conducted, obtained monthly discharge of Bayang Janiah river availability using dependable discharge F. J. Mock 90% of 102 L/s to 14 m of effective head is able to move the hydro turbine to produce power of about 11,3 kW. Meanwhile, for an array of photovoltaic systems produce power equal to 8.4 kW with a number of solar modules by 84 modules and the number of battery 6 V 1.091 Ah required 8 units and a bidirectional converter with a total capacity of 10 kW, totaling 2 units. HOMER simulation results show that the determination of the configuration of the hybrid power plant system design most optimal for application in Bayang Janiah village lowest Total NPC is based on the integration between microhydro - photovoltaic array - battery bank - bidirectional converter. On the optimal system configuration, microhydro contribution of 78.945 kWh/yr, a photovoltaic array of 11.404 kWh/yr, with a Total NPC of $ 146.041, Levelized COE of $ 0,525/kWh, while the electrical energy consumption of 30.668 kWh per year and has excess energy of 59.608 kWh/yr, so it can meet the needs of household electricity to 56 households as well as social facilities in the village.

  6. Convergent functional genomics in addiction research - a translational approach to study candidate genes and gene networks.

    Science.gov (United States)

    Spanagel, Rainer

    2013-01-01

    Convergent functional genomics (CFG) is a translational methodology that integrates in a Bayesian fashion multiple lines of evidence from studies in human and animal models to get a better understanding of the genetics of a disease or pathological behavior. Here the integration of data sets that derive from forward genetics in animals and genetic association studies including genome wide association studies (GWAS) in humans is described for addictive behavior. The aim of forward genetics in animals and association studies in humans is to identify mutations (e.g. SNPs) that produce a certain phenotype; i.e. "from phenotype to genotype". Most powerful in terms of forward genetics is combined quantitative trait loci (QTL) analysis and gene expression profiling in recombinant inbreed rodent lines or genetically selected animals for a specific phenotype, e.g. high vs. low drug consumption. By Bayesian scoring genomic information from forward genetics in animals is then combined with human GWAS data on a similar addiction-relevant phenotype. This integrative approach generates a robust candidate gene list that has to be functionally validated by means of reverse genetics in animals; i.e. "from genotype to phenotype". It is proposed that studying addiction relevant phenotypes and endophenotypes by this CFG approach will allow a better determination of the genetics of addictive behavior.

  7. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.

    Directory of Open Access Journals (Sweden)

    Ze Tian

    Full Text Available Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study.We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling. We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal.We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.

  8. Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes.

    Directory of Open Access Journals (Sweden)

    Kevin P Keegan

    2007-11-01

    Full Text Available Five independent groups have reported microarray studies that identify dozens of rhythmically expressed genes in the fruit fly Drosophila melanogaster. Limited overlap among the lists of discovered genes makes it difficult to determine which, if any, exhibit truly rhythmic patterns of expression. We reanalyzed data from all five reports and found two sources for the observed discrepancies, the use of different expression pattern detection algorithms and underlying variation among the datasets. To improve upon the methods originally employed, we developed a new analysis that involves compilation of all existing data, application of identical transformation and standardization procedures followed by ANOVA-based statistical prescreening, and three separate classes of post hoc analysis: cross-correlation to various cycling waveforms, autocorrelation, and a previously described fast Fourier transform-based technique. Permutation-based statistical tests were used to derive significance measures for all post hoc tests. We find application of our method, most significantly the ANOVA prescreening procedure, significantly reduces the false discovery rate relative to that observed among the results of the original five reports while maintaining desirable statistical power. We identify a set of 81 cycling transcripts previously found in one or more of the original reports as well as a novel set of 133 transcripts not found in any of the original studies. We introduce a novel analysis method that compensates for variability observed among the original five Drosophila circadian array reports. Based on the statistical fidelity of our meta-analysis results, and the results of our initial validation experiments (quantitative RT-PCR, we predict many of our newly found genes to be bona fide cyclers, and suggest that they may lead to new insights into the pathways through which clock mechanisms regulate behavioral rhythms.

  9. MALDI-TOF mass spectrometry for quantitative gene expression analysis of acid responses in Staphylococcus aureus.

    Science.gov (United States)

    Rode, Tone Mari; Berget, Ingunn; Langsrud, Solveig; Møretrø, Trond; Holck, Askild

    2009-07-01

    Microorganisms are constantly exposed to new and altered growth conditions, and respond by changing gene expression patterns. Several methods for studying gene expression exist. During the last decade, the analysis of microarrays has been one of the most common approaches applied for large scale gene expression studies. A relatively new method for gene expression analysis is MassARRAY, which combines real competitive-PCR and MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry. In contrast to microarray methods, MassARRAY technology is suitable for analysing a larger number of samples, though for a smaller set of genes. In this study we compare the results from MassARRAY with microarrays on gene expression responses of Staphylococcus aureus exposed to acid stress at pH 4.5. RNA isolated from the same stress experiments was analysed using both the MassARRAY and the microarray methods. The MassARRAY and microarray methods showed good correlation. Both MassARRAY and microarray estimated somewhat lower fold changes compared with quantitative real-time PCR (qRT-PCR). The results confirmed the up-regulation of the urease genes in acidic environments, and also indicated the importance of metal ion regulation. This study shows that the MassARRAY technology is suitable for gene expression analysis in prokaryotes, and has advantages when a set of genes is being analysed for an organism exposed to many different environmental conditions.

  10. Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.

    Directory of Open Access Journals (Sweden)

    Carole F S Koning-Boucoiran

    2015-04-01

    Full Text Available In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array.Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L. genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.

  11. Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).

    Science.gov (United States)

    Koning-Boucoiran, Carole F S; Esselink, G Danny; Vukosavljev, Mirjana; van 't Westende, Wendy P C; Gitonga, Virginia W; Krens, Frans A; Voorrips, Roeland E; van de Weg, W Eric; Schulz, Dietmar; Debener, Thomas; Maliepaard, Chris; Arens, Paul; Smulders, Marinus J M

    2015-01-01

    In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.

  12. Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

    Science.gov (United States)

    Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

    2007-07-01

    Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (Pschizophrenia in the Chinese population.

  13. Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects.

    Science.gov (United States)

    Shakeel, Muhammad; Rodriguez, Alicia; Tahir, Urfa Bin; Jin, Fengliang

    2018-02-01

    Whenever gene expression is being examined, it is essential that a normalization process is carried out to eliminate non-biological variations. The use of reference genes, such as glyceraldehyde-3-phosphate dehydrogenase, actin, and ribosomal protein genes, is the usual method of choice for normalizing gene expression. Although reference genes are used to normalize target gene expression, a major problem is that the stability of these genes differs among tissues, developmental stages, species, and responses to abiotic factors. Therefore, the use and validation of multiple reference genes are required. This review discusses the reasons that why RT-qPCR has become the preferred method for validating results of gene expression profiles, the use of specific and non-specific dyes and the importance of use of primers and probes for qPCR as well as to discuss several statistical algorithms developed to help the validation of potential reference genes. The conflicts arising in the use of classical reference genes in gene normalization and their replacement with novel references are also discussed by citing the high stability and low stability of classical and novel reference genes under various biotic and abiotic experimental conditions by employing various methods applied for the reference genes amplification.

  14. Molecular genetic gene-environment studies using candidate genes in schizophrenia: a systematic review.

    Science.gov (United States)

    Modinos, Gemma; Iyegbe, Conrad; Prata, Diana; Rivera, Margarita; Kempton, Matthew J; Valmaggia, Lucia R; Sham, Pak C; van Os, Jim; McGuire, Philip

    2013-11-01

    The relatively high heritability of schizophrenia suggests that genetic factors play an important role in the etiology of the disorder. On the other hand, a number of environmental factors significantly influence its incidence. As few direct genetic effects have been demonstrated, and there is considerable inter-individual heterogeneity in the response to the known environmental factors, interactions between genetic and environmental factors may be important in determining whether an individual develops the disorder. To date, a considerable number of studies of gene-environment interactions (G×E) in schizophrenia have employed a hypothesis-based molecular genetic approach using candidate genes, which have led to a range of different findings. This systematic review aims to summarize the results from molecular genetic candidate studies and to review challenges and opportunities of this approach in psychosis research. Finally, we discuss the potential of future prospects, such as new studies that combine hypothesis-based molecular genetic candidate approaches with agnostic genome-wide association studies in determining schizophrenia risk. © 2013 Elsevier B.V. All rights reserved.

  15. Field emission study from an array of hierarchical micro protrusions on stainless steel surface generated by femtosecond pulsed laser irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Singh, A.K., E-mail: anilks@barc.gov.in [Laser & Plasma Technology Division, BARC, Mumbai, 400085 (India); Suryawanshi, Sachin R.; More, M.A. [Department of Physics, Savitribai Phule Pune University, Pune, 411007 (India); Basu, S. [Solid State Physics Division, BARC, Mumbai, 40085 (India); Sinha, Sucharita [Laser & Plasma Technology Division, BARC, Mumbai, 400085 (India)

    2017-02-28

    Highlights: • Array of self assembled micro-protrusions have been generated on stainless steel surfaces by femtosecond pulsed laser irradiation. • Density of the formed micro-protrusions is ∼5.6 × 105 protrusions/cm{sup 2}. • Laser treated surface is mainly composed of iron oxide and cementite phases. • Micro-structured sample has shown good field emission properties – low turn on field, high field enhancement factor and stable emission current. - Abstract: This paper reports our results on femtosecond (fs) pulsed laser induced surface micro/nano structuring of stainless steel 304 (SS 304) samples and their characterization in terms of surface morphology, formed material phases on laser irradiation and field emission studies. Our investigations reveal that nearly uniform and dense array of hierarchical micro-protrusions (density: ∼5.6 × 10{sup 5} protrusions/cm{sup 2}) is formed upon laser treatment. Typical tip diameters of the generated protrusions are in the range of 2–5 μm and these protrusions are covered with submicron sized features. Grazing incidence X-ray diffraction (GIXRD) analysis of the laser irradiated sample surface has shown formation mainly of iron oxides and cementite (Fe{sub 3}C) phases in the treated region. These laser micro-structured samples have shown good field emission properties such as low turn on field (∼4.1 V/μm), high macroscopic field enhancement factor (1830) and stable field emission current under ultra high vacuum conditions.

  16. Structure of 10Be and 16C nuclei via break-up reactions studied with the 4π Chimera array

    Science.gov (United States)

    Dell'Aquila, D.; Acosta, L.; Amorini, F.; Andolina, R.; Auditore, L.; Berceanu, I.; Cardella, G.; Chatterjiee, M. B.; De Filippo, E.; Francalanza, L.; Gnoffo, B.; Grzeszczuk, A.; Lanzalone, G.; Lombardo, I.; Martorana, N.; Minniti, T.; Pagano, A.; Pagano, E. V.; Papa, M.; Pirrone, S.; Politi, G.; Pop, A.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Rosato, E.; Russotto, P.; Trifirò, A.; Trimarchi, M.; Verde, G.; Vigilante, M.

    2018-01-01

    The study of cluster states in neutron-rich Be and C isotopes is a subject of interest in Nuclear Physics. These states should be characterized by high deformation where α-clusters are bounded by valence neutrons. We performed a spectroscopic study of 10Be and 16C isotopes via projectile break-up reactions, by using radioactive beams produced at the INFN-LNS FRIBs facility and the Chimera 4π array. The possible evidence of a new 10Be state at 13.5 MeV excitation energy was found in the 6He+4He disintegration channel. The spectroscopy of 16C was studied via the 6He+10Be break-up channel; in this case we found the indication of a possible new state at about 20.6 MeV.

  17. The MINDView brain PET detector, feasibility study based on SiPM arrays

    Energy Technology Data Exchange (ETDEWEB)

    González, Antonio J., E-mail: agonzalez@i3m.upv.es [Institute for Instrumentation in Molecular Imaging (I3M), 46022 Valencia (Spain); Majewski, Stan [Radiology Research, Department of Radiology, University of Virginia, VA 22903 (United States); Sánchez, Filomeno [Institute for Instrumentation in Molecular Imaging (I3M), 46022 Valencia (Spain); Aussenhofer, Sebastian [NORAS MRI products GmbH, Hochberg (Germany); Aguilar, Albert; Conde, Pablo; Hernández, Liczandro; Vidal, Luis F. [Institute for Instrumentation in Molecular Imaging (I3M), 46022 Valencia (Spain); Pani, Roberto; Bettiol, Marco; Fabbri, Andrea [Department of Molecular Medicine, Sapienza University of Rome (Italy); Bert, Julien; Visvikis, Dimitris [Université de Bretagne Occidentale, Brest (France); Jackson, Carl; Murphy, John; O’Neill, Kevin [SensL Technologies, Cork (Ireland); Benlloch, Jose M. [Institute for Instrumentation in Molecular Imaging (I3M), 46022 Valencia (Spain)

    2016-05-11

    The Multimodal Imaging of Neurological Disorders (MINDView) project aims to develop a dedicated brain Positron Emission Tomography (PET) scanner with sufficient resolution and sensitivity to visualize neurotransmitter pathways and their disruptions in mental disorders for diagnosis and follow-up treatment. The PET system should be compact and fully compatible with a Magnetic Resonance Imaging (MRI) device in order to allow its operation as a PET brain insert in a hybrid imaging setup with most MRI scanners. The proposed design will enable the currently-installed MRI base to be easily upgraded to PET/MRI systems. The current design for the PET insert consists of a 3-ring configuration with 20 modules per ring and an axial field of view of ~15 cm and a geometrical aperture of ~33 cm in diameter. When coupled to the new head Radio Frequency (RF) coil, the inner usable diameter of the complete PET-RF coil insert is reduced to 26 cm. Two scintillator configurations have been tested, namely a 3-layer staggered array of LYSO with 1.5 mm pixel size, with 35×35 elements (6 mm thickness each) and a black-painted monolithic LYSO block also covering about 50×50 mm{sup 2} active area with 20 mm thickness. Laboratory test results associated with the current MINDView PET module concept are presented in terms of key parameters' optimization, such as spatial and energy resolution, sensitivity and Depth of Interaction (DOI) capability. It was possible to resolve all pixel elements from the three scintillator layers with energy resolutions as good as 10%. The monolithic scintillator showed average detector resolutions varying from 3.5 mm in the entrance layer to better than 1.5 mm near the photosensor, with average energy resolutions of about 17%.

  18. Transparent Nanopore Cavity Arrays Enable Highly Parallelized Optical Studies of Single Membrane Proteins on Chip.

    Science.gov (United States)

    Diederichs, Tim; Nguyen, Quoc Hung; Urban, Michael; Tampé, Robert; Tornow, Marc

    2018-06-13

    Membrane proteins involved in transport processes are key targets for pharmaceutical research and industry. Despite continuous improvements and new developments in the field of electrical readouts for the analysis of transport kinetics, a well-suited methodology for high-throughput characterization of single transporters with nonionic substrates and slow turnover rates is still lacking. Here, we report on a novel architecture of silicon chips with embedded nanopore microcavities, based on a silicon-on-insulator technology for high-throughput optical readouts. Arrays containing more than 14 000 inverted-pyramidal cavities of 50 femtoliter volumes and 80 nm circular pore openings were constructed via high-resolution electron-beam lithography in combination with reactive ion etching and anisotropic wet etching. These cavities feature both, an optically transparent bottom and top cap. Atomic force microscopy analysis reveals an overall extremely smooth chip surface, particularly in the vicinity of the nanopores, which exhibits well-defined edges. Our unprecedented transparent chip design provides parallel and independent fluorescent readout of both cavities and buffer reservoir for unbiased single-transporter recordings. Spreading of large unilamellar vesicles with efficiencies up to 96% created nanopore-supported lipid bilayers, which are stable for more than 1 day. A high lipid mobility in the supported membrane was determined by fluorescent recovery after photobleaching. Flux kinetics of α-hemolysin were characterized at single-pore resolution with a rate constant of 0.96 ± 0.06 × 10 -3 s -1 . Here, we deliver an ideal chip platform for pharmaceutical research, which features high parallelism and throughput, synergistically combined with single-transporter resolution.

  19. Antibody profiling using a recombinant protein-based multiplex ELISA array accelerates recombinant vaccine development: Case study on red sea bream iridovirus as a reverse vaccinology model.

    Science.gov (United States)

    Matsuyama, Tomomasa; Sano, Natsumi; Takano, Tomokazu; Sakai, Takamitsu; Yasuike, Motoshige; Fujiwara, Atushi; Kawato, Yasuhiko; Kurita, Jun; Yoshida, Kazunori; Shimada, Yukinori; Nakayasu, Chihaya

    2018-05-03

    Predicting antigens that would be protective is crucial for the development of recombinant vaccine using genome based vaccine development, also known as reverse vaccinology. High-throughput antigen screening is effective for identifying vaccine target genes, particularly for pathogens for which minimal antigenicity data exist. Using red sea bream iridovirus (RSIV) as a research model, we developed enzyme-linked immune sorbent assay (ELISA) based RSIV-derived 72 recombinant antigen array to profile antiviral antibody responses in convalescent Japanese amberjack (Seriola quinqueradiata). Two and three genes for which the products were unrecognized and recognized, respectively, by antibodies in convalescent serum were selected for recombinant vaccine preparation, and the protective effect was examined in infection tests using Japanese amberjack and greater amberjack (S. dumerili). No protection was provided by vaccines prepared from gene products unrecognized by convalescent serum antibodies. By contrast, two vaccines prepared from gene products recognized by serum antibodies induced protective immunity in both fish species. These results indicate that ELISA array screening is effective for identifying antigens that induce protective immune responses. As this method does not require culturing of pathogens, it is also suitable for identifying protective antigens to un-culturable etiologic agents. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies.

    Directory of Open Access Journals (Sweden)

    Lucie Kosinová

    Full Text Available The use of RT-qPCR provides a powerful tool for gene expression studies; however, the proper interpretation of the obtained data is crucially dependent on accurate normalization based on stable reference genes. Recently, strong evidence has been shown indicating that the expression of many commonly used reference genes may vary significantly due to diverse experimental conditions. The isolation of pancreatic islets is a complicated procedure which creates severe mechanical and metabolic stress leading possibly to cellular damage and alteration of gene expression. Despite of this, freshly isolated islets frequently serve as a control in various gene expression and intervention studies. The aim of our study was to determine expression of 16 candidate reference genes and one gene of interest (F3 in isolated rat pancreatic islets during short-term cultivation in order to find a suitable endogenous control for gene expression studies. We compared the expression stability of the most commonly used reference genes and evaluated the reliability of relative and absolute quantification using RT-qPCR during 0-120 hrs after isolation. In freshly isolated islets, the expression of all tested genes was markedly depressed and it increased several times throughout the first 48 hrs of cultivation. We observed significant variability among samples at 0 and 24 hrs but substantial stabilization from 48 hrs onwards. During the first 48 hrs, relative quantification failed to reflect the real changes in respective mRNA concentrations while in the interval 48-120 hrs, the relative expression generally paralleled the results determined by absolute quantification. Thus, our data call into question the suitability of relative quantification for gene expression analysis in pancreatic islets during the first 48 hrs of cultivation, as the results may be significantly affected by unstable expression of reference genes. However, this method could provide reliable information

  1. Systematic study of (d,n) reactions at Ed = 16 MeV using a deuterated scintillator array

    International Nuclear Information System (INIS)

    Febbraro, M.; Becchetti, F.D.; Torres-Isea, R.O.; Riggins, A.; Lawrence, C.; Howard, A.M.; Kolata, J.J.

    2014-01-01

    We have developed a multi-element deuterated liquid scintillator array for the study of reactions involving neutrons utilizing high-speed digital signal processing. The liquid organic scintillators exhibit good digital pulse shape discrimination (DPSD). Typical configuration involves the detectors fixed to adjustable aluminium mounts, secured to an 80/20 aluminium frame. This allows for quick and adaptable configurations to be made for varying experimental conditions including measurements over a large angular range. A systematic study of (d,n) reactions at E d = 16 MeV on 9 Be, 11 B, 13 C, 14 N, 15 N, and 19 F has been conducted from 10 to 160 degrees (lab). In addition to previously unmeasured back-angle cross sections, this data can complement existing and future ( 3 He,d) measurements as an analog to (p,γ) for astrophysics applications

  2. A Case Study of Array-based Early Warning System for Tsunami Offshore Ventura, California

    Science.gov (United States)

    Xie, Y.; Meng, L.

    2017-12-01

    Extreme scenarios of M 7.5+ earthquakes on the Red Mountain and Pitas Point faults can potentially generate significant local tsunamis in southern California. The maximum water elevation could be as large as 10 m in the nearshore region of Oxnard and Santa Barbara. Recent development in seismic array processing enables rapid tsunami prediction and early warning based on the back-projection approach (BP). The idea is to estimate the rupture size by back-tracing the seismic body waves recorded by stations at local and regional distances. A simplified source model of uniform slip is constructed and used as an input for tsunami simulations that predict the tsunami wave height and arrival time. We demonstrate the feasibility of this approach in southern California by implementing it in a simulated real-time environment and applying to a hypothetical M 7.7 Dip-slip earthquake scenario on the Pitas Point fault. Synthetic seismograms are produced using the SCEC broadband platform based on the 3D SoCal community velocity model. We use S-wave instead of P-wave to avoid S-minus-P travel times shorter than rupture duration. Two clusters of strong-motion stations near Bakersfield and Palmdale are selected to determine the back-azimuth of the strongest high-frequency radiations (0.5-1 Hz). The back-azimuths of the two clusters are then intersected to locate the source positions. The rupture area is then approximated by enclosing these BP radiators with an ellipse or a polygon. Our preliminary results show that the extent of 1294 square kilometers rupture area and magnitude of 7.6 obtained by this approach is reasonably close to the 1849 square kilometers and 7.7 of the input model. The average slip of 7.3 m is then estimated according to the scaling relation between slip and rupture area, which is close to the actual average dislocation amount, 8.3 m. Finally, a tsunami simulation is conducted to assess the wave height and arrival time. The errors of -3 to +9 s in arrival time

  3. A systematic study on drug-response associated genes using baseline gene expressions of the Cancer Cell Line Encyclopedia

    Science.gov (United States)

    Liu, Xiaoming; Yang, Jiasheng; Zhang, Yi; Fang, Yun; Wang, Fayou; Wang, Jun; Zheng, Xiaoqi; Yang, Jialiang

    2016-03-01

    We have studied drug-response associated (DRA) gene expressions by applying a systems biology framework to the Cancer Cell Line Encyclopedia data. More than 4,000 genes are inferred to be DRA for at least one drug, while the number of DRA genes for each drug varies dramatically from almost 0 to 1,226. Functional enrichment analysis shows that the DRA genes are significantly enriched in genes associated with cell cycle and plasma membrane. Moreover, there might be two patterns of DRA genes between genders. There are significantly shared DRA genes between male and female for most drugs, while very little DRA genes tend to be shared between the two genders for a few drugs targeting sex-specific cancers (e.g., PD-0332991 for breast cancer and ovarian cancer). Our analyses also show substantial difference for DRA genes between young and old samples, suggesting the necessity of considering the age effects for personalized medicine in cancers. Lastly, differential module and key driver analyses confirm cell cycle related modules as top differential ones for drug sensitivity. The analyses also reveal the role of TSPO, TP53, and many other immune or cell cycle related genes as important key drivers for DRA network modules. These key drivers provide new drug targets to improve the sensitivity of cancer therapy.

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

    Directory of Open Access Journals (Sweden)

    Brahmbhatt Sonal

    2008-11-01

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

  5. Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo

    International Nuclear Information System (INIS)

    Vaiphei, S. Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Sharan, R.N.; Chaubey, R.C.; Kma, L.

    2015-01-01

    In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving 60 Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of 60 Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min -1 at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. (author)

  6. Evaluation of endogenous control gene(s) for gene expression studies in human blood exposed to 60Co γ-rays ex vivo.

    Science.gov (United States)

    Vaiphei, S Thangminlal; Keppen, Joshua; Nongrum, Saibadaiahun; Chaubey, R C; Kma, L; Sharan, R N

    2015-01-01

    In gene expression studies, it is critical to normalize data using a stably expressed endogenous control gene in order to obtain accurate and reliable results. However, we currently do not have a universally applied endogenous control gene for normalization of data for gene expression studies, particularly those involving (60)Co γ-ray-exposed human blood samples. In this study, a comparative assessment of the gene expression of six widely used housekeeping endogenous control genes, namely 18S, ACTB, B2M, GAPDH, MT-ATP6 and CDKN1A, was undertaken for a range of (60)Co γ-ray doses (0.5, 1.0, 2.0 and 4.0 Gy) at 8.4 Gy min(-1) at 0 and 24 h post-irradiation time intervals. Using the NormFinder algorithm, real-time PCR data obtained from six individuals (three males and three females) were analyzed with respect to the threshold cycle (Ct) value and abundance, ΔCt pair-wise comparison, intra- and inter-group variability assessments, etc. GAPDH, either alone or in combination with 18S, was found to be the most suitable endogenous control gene and should be used in gene expression studies, especially those involving qPCR of γ-ray-exposed human blood samples. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

  7. A comprehensive family-based replication study of schizophrenia genes

    DEFF Research Database (Denmark)

    Aberg, Karolina A; Liu, Youfang; Bukszár, Jozsef

    2013-01-01

     768 control subjects from 6 databases and, after quality control 6298 individuals (including 3286 cases) from 1811 nuclear families. MAIN OUTCOMES AND MEASURES Case-control status for SCZ. RESULTS Replication results showed a highly significant enrichment of SNPs with small P values. Of the SNPs...... in an independent family-based replication study that, after quality control, consisted of 8107 SNPs. SETTING Linkage meta-analysis, brain transcriptome meta-analysis, candidate gene database, OMIM, relevant mouse studies, and expression quantitative trait locus databases. PATIENTS We included 11 185 cases and 10...

  8. Identification of valid reference genes for gene expression studies of human stomach cancer by reverse transcription-qPCR

    International Nuclear Information System (INIS)

    Rho, Hyun-Wook; Lee, Byoung-Chan; Choi, Eun-Seok; Choi, Il-Ju; Lee, Yeon-Su; Goh, Sung-Ho

    2010-01-01

    Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a powerful method for the analysis of gene expression. Target gene expression levels are usually normalized to a consistently expressed reference gene also known as internal standard, in the same sample. However, much effort has not been expended thus far in the search for reference genes suitable for the study of stomach cancer using RT-qPCR, although selection of optimal reference genes is critical for interpretation of results. We assessed the suitability of six possible reference genes, beta-actin (ACTB), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), hypoxanthine phosphoribosyl transferase 1 (HPRT1), beta-2-microglobulin (B2M), ribosomal subunit L29 (RPL29) and 18S ribosomal RNA (18S rRNA) in 20 normal and tumor stomach tissue pairs of stomach cancer patients and 6 stomach cancer cell lines, by RT-qPCR. Employing expression stability analyses using NormFinder and geNorm algorithms we determined the order of performance of these reference genes and their variation values. This RT-qPCR study showed that there are statistically significant (p < 0.05) differences in the expression levels of HPRT1 and 18S rRNA in 'normal-' versus 'tumor stomach tissues'. The stability analyses by geNorm suggest B2M-GAPDH, as best reference gene combination for 'stomach cancer cell lines'; RPL29-HPRT1, for 'all stomach tissues'; and ACTB-18S rRNA, for 'all stomach cell lines and tissues'. NormFinder also identified B2M as the best reference gene for 'stomach cancer cell lines', RPL29-B2M for 'all stomach tissues', and 18S rRNA-ACTB for 'all stomach cell lines and tissues'. The comparisons of normalized expression of the target gene, GPNMB, showed different interpretation of target gene expression depend on best single reference gene or combination. This study validated RPL29 and RPL29-B2M as the best single reference

  9. Genes and gene expression: Localization, damage and control: A multilevel and inter-disciplinary study

    Energy Technology Data Exchange (ETDEWEB)

    Ts' o, P.O.P.

    1990-09-01

    The main objectives of this Program Project is to develop strategy and technology for the study of gene structure, organization and function in a multi-disciplinary, highly coordinated manner. In Project I, Molecular Cytology, the establishment of all instrumentation for the computerized microscopic imaging system (CMIS) has been completed with the software in place, including measurement of the third dimension (along the Z-axis). The technique is now at hand to measure single copy DNA in the nucleus, single copy mRNA in the cell, and finally, we are in the process of developing mathematical approaches for the analysis of the relative spatial 3-D relationship among the chromosomes and the individual genes in the interphasal nucleus. Also, we have a sensitive and reliable method for measuring single-stranded DNA breaks which will be useful for the determination of damage to DNA caused by ionizing radiation. In Project II, the mapping of restriction fragments by 2-D enzymatic and electrophoretic analysis has been perfected for application. In Project III, a major finding is that the binding constant and effectiveness of antisense oligonucleotide analogues, Matagen, can be significantly improved by substituting 2{prime}-O-methylribos methylphosphonate backbones for the current 2{prime}-deoxyribomethylphosphonate backbones. 15 refs., 10 figs., 2 tabs.

  10. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

    DEFF Research Database (Denmark)

    Li, Yun R.; van Setten, Jessica; Verma, Shefali S.

    2015-01-01

    genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples...

  11. Gene Expression Correlation for Cancer Diagnosis: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Binbing Ling

    2014-01-01

    Full Text Available Poor prognosis for late-stage, high-grade, and recurrent cancers has been motivating cancer researchers to search for more efficient biomarkers to identify the onset of cancer. Recent advances in constructing and dynamically analyzing biomolecular networks for different types of cancer have provided a promising novel strategy to detect tumorigenesis and metastasis. The observation of different biomolecular networks associated with normal and cancerous states led us to hypothesize that correlations for gene expressions could serve as valid indicators of early cancer development. In this pilot study, we tested our hypothesis by examining whether the mRNA expressions of three randomly selected cancer-related genes PIK3C3, PIM3, and PTEN were correlated during cancer progression and the correlation coefficients could be used for cancer diagnosis. Strong correlations (0.68≤r≤1.0 were observed between PIK3C3 and PIM3 in breast cancer, between PIK3C3 and PTEN in breast and ovary cancers, and between PIM3 and PTEN in breast, kidney, liver, and thyroid cancers during disease progression, implicating that the correlations for cancer network gene expressions could serve as a supplement to current clinical biomarkers, such as cancer antigens, for early cancer diagnosis.

  12. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi.

    Science.gov (United States)

    Huang, Xuena; Gao, Yangchun; Jiang, Bei; Zhou, Zunchun; Zhan, Aibin

    2016-01-15

    As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Identification of valid reference genes for gene expression studies of human stomach cancer by reverse transcription-qPCR

    Directory of Open Access Journals (Sweden)

    Lee Yeon-Su

    2010-05-01

    Full Text Available Abstract Background Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR is a powerful method for the analysis of gene expression. Target gene expression levels are usually normalized to a consistently expressed reference gene also known as internal standard, in the same sample. However, much effort has not been expended thus far in the search for reference genes suitable for the study of stomach cancer using RT-qPCR, although selection of optimal reference genes is critical for interpretation of results. Methods We assessed the suitability of six possible reference genes, beta-actin (ACTB, glyceraldehydes-3-phosphate dehydrogenase (GAPDH, hypoxanthine phosphoribosyl transferase 1 (HPRT1, beta-2-microglobulin (B2M, ribosomal subunit L29 (RPL29 and 18S ribosomal RNA (18S rRNA in 20 normal and tumor stomach tissue pairs of stomach cancer patients and 6 stomach cancer cell lines, by RT-qPCR. Employing expression stability analyses using NormFinder and geNorm algorithms we determined the order of performance of these reference genes and their variation values. Results This RT-qPCR study showed that there are statistically significant (p Conclusion This study validated RPL29 and RPL29-B2M as the best single reference genes and combination, for RT-qPCR analysis of 'all stomach tissues', and B2M and B2M-GAPDH as the best single reference gene and combination, for 'stomach cancer cell lines'. Use of these validated reference genes should provide more exact interpretation of differential gene expressions at transcription level in stomach cancer.

  14. fabp4 is central to eight obesity associated genes: a functional gene network-based polymorphic study.

    Science.gov (United States)

    Bag, Susmita; Ramaiah, Sudha; Anbarasu, Anand

    2015-01-07

    Network study on genes and proteins offers functional basics of the complexity of gene and protein, and its interacting partners. The gene fatty acid-binding protein 4 (fabp4) is found to be highly expressed in adipose tissue, and is one of the most abundant proteins in mature adipocytes. Our investigations on functional modules of fabp4 provide useful information on the functional genes interacting with fabp4, their biochemical properties and their regulatory functions. The present study shows that there are eight set of candidate genes: acp1, ext2, insr, lipe, ostf1, sncg, usp15, and vim that are strongly and functionally linked up with fabp4. Gene ontological analysis of network modules of fabp4 provides an explicit idea on the functional aspect of fabp4 and its interacting nodes. The hierarchal mapping on gene ontology indicates gene specific processes and functions as well as their compartmentalization in tissues. The fabp4 along with its interacting genes are involved in lipid metabolic activity and are integrated in multi-cellular processes of tissues and organs. They also have important protein/enzyme binding activity. Our study elucidated disease-associated nsSNP prediction for fabp4 and it is interesting to note that there are four rsID׳s (rs1051231, rs3204631, rs140925685 and rs141169989) with disease allelic variation (T104P, T126P, G27D and G90V respectively). On the whole, our gene network analysis presents a clear insight about the interactions and functions associated with fabp4 gene network. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Simulation Study of Using High-Z EMA to Suppress Recoil Protons Crosstalk in Scintillating Fiber Array for 14.1 MeV Neutron Imaging

    Science.gov (United States)

    Jia, Qinggang; Hu, Huasi; Zhang, Fengna; Zhang, Tiankui; Lv, Wei; Zhan, Yuanpin; Liu, Zhihua

    2013-12-01

    This paper studies the effect of a high-Z extra mural absorber (EMA) to improve the spatial resolution of a plastic (polystyrene) scintillating fiber array for 14.1 MeV fusion neutron imaging. Crosstalk induced by recoil protons was studied, and platinum (Pt) was selected as EMA material, because of its excellent ability to suppress the recoil protons penetrating the fibers. Three common fiber arrays (cylindrical scintillating fibers in square and hexagonal packing arrangements and square scintillating fibers) were simulated using the Monte Carlo method for evaluating the effect of Pt-EMA in improving spatial resolution. It is found that the resolution of the 100 μm square fiber array can be improved from 1.7 to 3.4 lp/mm by using 10- μm-thick Pt-EMA; comparatively, using an array with thinner square fibers (50 μm) only obtains a resolution of 2.1 lp/mm. The packing fraction decreases with the increase of EMA thickness. Our results recommend the use of 10 μm Pt-EMA for the square and the cylindrical (hexagonal packing) scintillating fiber arrays with fibers of 50-200 μm in the cross-sectional dimension. Besides, the dead-zone material should be replaced by high-Z material for the hexagonal packing cylindrical fiber array with fibers of 50-200 μm in diameter. Tungsten (W) and gold (Au) are also used as EMA in the three fiber arrays as a comparison. The simulation results show that W can be used at a lower cost, and Au does not have any advantages in cost and resolution improvement.

  16. Selection of reliable reference genes for gene expression studies in Trichoderma afroharzianum LTR-2 under oxalic acid stress.

    Science.gov (United States)

    Lyu, Yuping; Wu, Xiaoqing; Ren, He; Zhou, Fangyuan; Zhou, Hongzi; Zhang, Xinjian; Yang, Hetong

    2017-10-01

    An appropriate reference gene is required to get reliable results from gene expression analysis by quantitative real-time reverse transcription PCR (qRT-PCR). In order to identify stable and reliable reference genes in Trichoderma afroharzianum under oxalic acid (OA) stress, six commonly used housekeeping genes, i.e., elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme, glyceraldehyde-3-phosphate dehydrogenase, α-tubulin, actin, from the effective biocontrol isolate T. afroharzianum strain LTR-2 were tested for their expression during growth in liquid culture amended with OA. Four in silico programs (comparative ΔCt, NormFinder, geNorm and BestKeeper) were used to evaluate the expression stabilities of six candidate reference genes. The elongation factor 1 gene EF-1 was identified as the most stably expressed reference gene, and was used as the normalizer to quantify the expression level of the oxalate decarboxylase coding gene OXDC in T. afroharzianum strain LTR-2 under OA stress. The result showed that the expression of OXDC was significantly up-regulated as expected. This study provides an effective method to quantify expression changes of target genes in T. afroharzianum under OA stress. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Altered Cytokine Gene Expression in Peripheral Blood Monocytes across the Menstrual Cycle in Primary Dysmenorrhea: A Case-Control Study

    Science.gov (United States)

    Ma, Hongyue; Hong, Min; Duan, Jinao; Liu, Pei; Fan, Xinsheng; Shang, Erxin; Su, Shulan; Guo, Jianming; Qian, Dawei; Tang, Yuping

    2013-01-01

    Primary dysmenorrhea is one of the most common gynecological complaints in young women, but potential peripheral immunologic features underlying this condition remain undefined. In this paper, we compared 84 common cytokine gene expression profiles of peripheral blood mononuclear cells (PBMCs) from six primary dysmenorrheic young women and three unaffected controls on the seventh day before (secretory phase), and the first (menstrual phase) and the fifth (regenerative phase) days of menstruation, using a real-time PCR array assay combined with pattern recognition and gene function annotation methods. Comparisons between dysmenorrhea and normal control groups identified 11 (nine increased and two decreased), 14 (five increased and nine decreased), and 15 (seven increased and eight decreased) genes with ≥2-fold difference in expression (Pdysmenorrhea. This first study of cytokine gene expression profiles in PBMCs from young primary dysmenorrheic women demonstrates a shift in the balance between expression patterns of pro-inflammatory cytokines and TGF-β superfamily members across the whole menstrual cycle, underlying the peripheral immunologic features of primary dysmenorrhea. PMID:23390521

  18. Intra-city Differences in Cardiac Expression of Inflammatory Genes and Inflammasomes in Young Urbanites: A Pilot Study.

    Science.gov (United States)

    Villarreal-Calderon, Rodolfo; Dale, Gary; Delgado-Chávez, Ricardo; Torres-Jardón, Ricardo; Zhu, Hongtu; Herritt, Lou; Gónzalez-Maciel, Angelica; Reynoso-Robles, Rafael; Yuan, Ying; Wang, Jiaping; Solorio-López, Edelmira; Medina-Cortina, Humberto; Calderón-Garcidueñas, Lilian

    2012-06-01

    Southwest Mexico City (SWMC) air pollution is characterized by high concentrations of ozone and particulate matter < 10 μm (PM(10)) containing lipopolysaccharides while in the North PM(2.5) is high. These intra-city differences are likely accounting for higher CD14 and IL-1β in SWMC v NMC mice myocardial expression. This pilot study was designed to investigate whether similar intra-city differences exist in the levels of myocardial inflammatory genes in young people. Inflammatory mediator genes and inflammasome arrays were measured in right and left autopsy ventricles of 6 southwest/15 north (18.5 ± 2.6 years) MC residents after fatal sudden accidental deaths. There was a significant S v N right ventricle up-regulation of IL-1β (p=0.008), TNF-α (p=0.001), IL-10 (p=0.001), and CD14 (p=0.002), and a left ventricle difference in TNF-α (p=0.007), and IL-10 (p=0.02). SW right ventricles had significant up-regulation of NLRC1, NLRP3 and of 29/84 inflammasome genes, including NOD factors and caspases. There was significant degranulation of mast cells both in myocardium and epicardial nerve fibers. Differential expression of key inflammatory myocardial genes and inflammasomes are influenced by the location of residence. Myocardial inflammation and inflammasome activation in young hearts is a plausible pathway of heart injury in urbanites and adverse effects on the cardiovascular system are expected.

  19. A comparative study of ATPase subunit 9 (Atp9) gene between ...

    African Journals Online (AJOL)

    ATPase subunit 9 gene (Atp9) is an important functional gene in mitochondria, and is closely related with energy supply. RNA editing of atp9 gene was associated with male sterility in plants. In this study, the atp9 gene in soybeans was cloned from a soybean cytoplasmic male sterile line NJCMS2A and its maintainer line ...

  20. Behavioral science and the study of gene-nutrition and gene-physical activity interactions in obesity research.

    Science.gov (United States)

    Faith, Myles S

    2008-12-01

    This report summarizes emerging opportunities for behavioral science to help advance the field of gene-environment and gene-behavior interactions, based on presentations at The National Cancer Institute (NCI) Workshop, "Gene-Nutrition and Gene-Physical Activity Interactions in the Etiology of Obesity." Three opportunities are highlighted: (i) designing potent behavioral "challenges" in experiments, (ii) determining viable behavioral phenotypes for genetics studies, and (iii) identifying specific measures of the environment or environmental exposures. Additional points are underscored, including the need to incorporate novel findings from neuroimaging studies regarding motivation and drive for eating and physical activity. Advances in behavioral science theory and methods can play an important role in advancing understanding of gene-brain-behavior relationships in obesity onset.

  1. Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset.

    Directory of Open Access Journals (Sweden)

    Eric R Gamazon

    Full Text Available Microarray gene expression data has been used in genome-wide association studies to allow researchers to study gene regulation as well as other complex phenotypes including disease risks and drug response. To reach scientifically sound conclusions from these studies, however, it is necessary to get reliable summarization of gene expression intensities. Among various factors that could affect expression profiling using a microarray platform, single nucleotide polymorphisms (SNPs in target mRNA may lead to reduced signal intensity measurements and result in spurious results. The recently released 1000 Genomes Project dataset provides an opportunity to evaluate the distribution of both known and novel SNPs in the International HapMap Project lymphoblastoid cell lines (LCLs. We mapped the 1000 Genomes Project genotypic data to the Affymetrix GeneChip Human Exon 1.0ST array (exon array, which had been used in our previous studies and for which gene expression data had been made publicly available. We also evaluated the potential impact of these SNPs on the differentially spliced probesets we had identified previously. Though the 1000 Genomes Project data allowed a comprehensive survey of the SNPs in this particular array, the same approach can certainly be applied to other microarray platforms. Furthermore, we present a detailed catalogue of SNP-containing probesets (exon-level and transcript clusters (gene-level, which can be considered in evaluating findings using the exon array as well as benefit the design of follow-up experiments and data re-analysis.

  2. A transgenic approach to study argininosuccinate synthetase gene expression

    Science.gov (United States)

    2014-01-01

    Background Argininosuccinate synthetase (ASS) participates in urea, nitric oxide and arginine production. Besides transcriptional regulation, a post-transcriptional regulation affecting nuclear precursor RNA stability has been reported. To study whether such post-transcriptional regulation underlines particular temporal and spatial ASS expression, and to investigate how human ASS gene behaves in a mouse background, a transgenic mouse system using a modified bacterial artificial chromosome carrying the human ASS gene tagged with EGFP was employed. Results Two lines of ASS-EGFP transgenic mice were generated: one with EGFP under transcriptional control similar to that of the endogenous ASS gene, another with EGFP under both transcriptional and post-transcriptional regulation as that of the endogenous ASS mRNA. EGFP expression in the liver, the organ for urea production, and in the intestine and kidney that are responsible for arginine biosynthesis, was examined. Organs taken from embryos E14.5 stage to young adult were examined under a fluorescence microscope either directly or after cryosectioning. The levels of EGFP and endogenous mouse Ass mRNAs were also quantified by S1 nuclease mapping. EGFP fluorescence and EGFP mRNA levels in both the liver and kidney were found to increase progressively from embryonic stage toward birth. In contrast, EGFP expression in the intestine was higher in neonates and started to decline at about 3 weeks after birth. Comparison between the EGFP profiles of the two transgenic lines indicated the developmental and tissue-specific regulation was mainly controlled at the transcriptional level. The ASS transgene was of human origin. EGFP expression in the liver followed essentially the mouse Ass pattern as evidenced by zonation distribution of fluorescence and the level of EGFP mRNA at birth. However, in the small intestine, Ass mRNA level declined sharply at 3 week of age, and yet substantial EGFP mRNA was still detectable at this stage

  3. Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.

    Directory of Open Access Journals (Sweden)

    Thrush Anthony

    2010-01-01

    Full Text Available Abstract Background Perennial ryegrass (Lolium perenne L. is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate normalisation strategy to control for non-specific variation between samples. Reference genes that have stable expression at different biological and physiological states can be effectively used for normalisation; however, their expression stability must be validated before use. Results Existing Serial Analysis of Gene Expression data were queried to identify six moderately expressed genes that had relatively stable gene expression throughout the year. These six candidate reference genes (eukaryotic elongation factor 1 alpha, eEF1A; TAT-binding protein homolog 1, TBP-1; eukaryotic translation initiation factor 4 alpha, eIF4A; YT521-B-like protein family protein, YT521-B; histone 3, H3; ubiquitin-conjugating enzyme, E2 were validated for qRT-PCR normalisation in 442 diverse perennial ryegrass (Lolium perenne L. samples sourced from field- and laboratory-grown plants under a wide range of experimental conditions. Eukaryotic EF1A is encoded by members of a multigene family exhibiting differential expression and necessitated the expression analysis of different eEF1A encoding genes; a highly expressed eEF1A (h, a moderately, but stably expressed eEF1A (s, and combined expression of multigene eEF1A (m. NormFinder identified eEF1A (s and YT521-B as the best combination of two genes for normalisation of gene expression data in perennial ryegrass following different defoliation management in the field. Conclusions This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples

  4. A comparative study of mutation screening of sarcomeric genes ...

    African Journals Online (AJOL)

    , TNNT2) using single gene approach versus targeted gene panel next generation sequencing in a cohort of HCM patients in Egypt. Heba Sh. Kassem, Roddy Walsh, Paul J. Barton, Besra S. Abdelghany, Remon S. Azer, Rachel Buchan, ...

  5. RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

    Directory of Open Access Journals (Sweden)

    Van L.T. Hoang

    2017-08-01

    Full Text Available Identification of appropriate reference genes (RGs is critical to accurate data interpretation in quantitative real-time PCR (qPCR experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer.

  6. AfricaArray seismological studies of the structure and evolution of the African continent

    CSIR Research Space (South Africa)

    Durrheim, RJ

    2013-10-01

    Full Text Available and Madagascar. Brandt and Mulibo elucidated the relationship between the African Superplume, Superswell and the East African Rift System by studying the seismic velocity structure of the mantle. Kgaswane jointly inverted P-wave receiver functions (PRFs...

  7. Studies of high resolution array processing algorithms for multibeam bathymetric applications

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.; Schenke, H.W.

    In this paper a study is initiated to observe the usefulness of directional spectral estimation techniques for underwater bathymetric applications. High resolution techniques like the Maximum Likelihood (ML) method and the Maximum Entropy (ME...

  8. Molecular study of the perforin gene in familial hematological malignancies

    Directory of Open Access Journals (Sweden)

    El Abed Rim

    2011-09-01

    Full Text Available Abstract Perforin gene (PRF1 mutations have been identified in some patients diagnosed with the familial form of hemophagocytic lymphohistiocytosis (HLH and in patients with lymphoma. The aim of the present study was to determine whether patients with a familial aggregation of hematological malignancies harbor germline perforin gene mutations. For this purpose, 81 unrelated families from Tunisia and France with aggregated hematological malignancies were investigated. The variants detected in the PRF1 coding region amounted to 3.7% (3/81. Two of the three variants identified were previously described: the p.Ala91Val pathogenic mutation and the p.Asn252Ser polymorphism. A new p.Ala 211Val missense substitution was identified in two related Tunisian patients. In order to assess the pathogenicity of this new variation, bioinformatic tools were used to predict its effects on the perforin protein structure and at the mRNA level. The segregation of the mutant allele was studied in the family of interest and a control population was screened. The fact that this variant was not found to occur in 200 control chromosomes suggests that it may be pathogenic. However, overexpression of mutated PRF1 in rat basophilic leukemia cells did not affect the lytic function of perforin differently from the wild type protein.

  9. Paralogous Genes as a Tool to Study the Regulation of Gene Expression

    DEFF Research Database (Denmark)

    Hoffmann, Robert D

    The genomes of plants are marked by reoccurring events of whole-genome duplication. These events are major contributors to speciation and provide the genetic material for organisms to evolve ever greater complexity. Duplicated genes, referred to as paralogs, may be retained because they acquired...... regions. These results suggest that a concurrent purifying selection acts on coding and non-coding sequences of paralogous genes in A. thaliana. Mutational analyses of the promoters from a paralogous gene pair were performed in transgenic A. thaliana plants. The results revealed a 170-bp long DNA sequence...... that forms a bifunctional cis-regulatory module; it represses gene expression in the sporophyte while activating it in pollen. This finding is important for many aspects of gene regulation and the transcriptional changes underlying gametophyte development. In conclusion, the presented thesis suggests that...

  10. Genetic Variations of COL4A1 Gene and Intracerebral Hemorrhage Outcome: A Cohort Study in a Chinese Han Population.

    Science.gov (United States)

    Xia, Chao; Lin, Sen; Yang, Jie; He, Sha; Li, Hao; Liu, Ming; You, Chao

    2018-05-01

    To investigate the relationship between single nucleotide polymorphisms or haplotypes of COL4A1 gene and the outcome of intracerebral hemorrhage (ICH). In our study, 181 patients with hypertensive ICH were enrolled and followed up at 3 and 6 months. Outcome data included any cause of death and disability. Genomic DNA was extracted by DNA extraction kit, and the 6 single nucleotide polymorphism genotyping of the COL4A1 gene was detected through MassARRAY Analyzer. Unphased 3.1.4 and SPSS 19.0 were used to analyze the association between alleles, genotypes, and haplotypes of the COL4A1 gene and the outcomes of ICH. Of the 181 patients with hypertensive ICH, 12 were lost in follow-up, which accounted for 6.6%. Our association analysis showed that the rs532625 AA genotype of the COL4A1 gene may increase risk of disability at 3 months; the rs532625 A allele and AA genotype were association factors of the risk of disability at 6 months; the rs532625 AA genotype was an association factor of the risk of death/disability at 6 months. After adjusting for gender, age, coma, and severe neurologic deficits, only the rs532625 AA genotype was independently associated with the risk of disability at 3 and 6 months and the risk of death/disability at 6 months. Our study found that the rs532625 AA genotype in the COL4A1 gene was independently associated with the risk of disability at 3 and 6 months and death/disability at 6 months in a Chinese Han population. These conclusions need to be verified in future studies with larger samples. Copyright © 2018 Elsevier Inc. All rights reserved.

  11. Genome-wide and gene-based association studies of anxiety disorders in European and African American samples.

    Directory of Open Access Journals (Sweden)

    Takeshi Otowa

    Full Text Available Anxiety disorders (ADs are common mental disorders caused by a combination of genetic and environmental factors. Since ADs are highly comorbid with each other, partially due to shared genetic basis, studying AD phenotypes in a coordinated manner may be a powerful strategy for identifying potential genetic loci for ADs. To detect these loci, we performed genome-wide association studies (GWAS of ADs. In addition, as a complementary approach to single-locus analysis, we also conducted gene- and pathway-based analyses. GWAS data were derived from the control sample of the Molecular Genetics of Schizophrenia (MGS project (2,540 European American and 849 African American subjects genotyped on the Affymetrix GeneChip 6.0 array. We applied two phenotypic approaches: (1 categorical case-control comparisons (CC based upon psychiatric diagnoses, and (2 quantitative phenotypic factor scores (FS derived from a multivariate analysis combining information across the clinical phenotypes. Linear and logistic models were used to analyse the association with ADs using FS and CC traits, respectively. At the single locus level, no genome-wide significant association was found. A trans-population gene-based meta-analysis across both ethnic subsamples using FS identified three genes (MFAP3L on 4q32.3, NDUFAB1 and PALB2 on 16p12 with genome-wide significance (false discovery rate (FDR] <5%. At the pathway level, several terms such as transcription regulation, cytokine binding, and developmental process were significantly enriched in ADs (FDR <5%. Our approaches studying ADs as quantitative traits and utilizing the full GWAS data may be useful in identifying susceptibility genes and pathways for ADs.

  12. Leakage analysis of crossbar memristor arrays

    KAUST Repository

    Zidan, Mohammed A.; Salem, Ahmed Sultan; Fahmy, Hossam Aly Hassan; Salama, Khaled N.

    2014-01-01

    the readout operation. In this work we study the trade-off between the crossbar array density and the power consumption required for its readout. Our analysis is based on simulating full memristor arrays on a SPICE platform.

  13. Studies on a 120 degrees segmented circular array for multi-beam multi-frequency bathymetric application

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.

    A theoretical analysis of the vertical for field patterns and input impedances, as well as excitation velocities of a 120 degrees segmented circular array of 40 groups of four elements each is performed. The narrowest beam widths at normal incidence...

  14. Cyclotron-Resonance-Maser Arrays

    International Nuclear Information System (INIS)

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

    1999-01-01

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

  15. The Texas-Edinburgh-Catania Silicon Array (TECSA): A detector for nuclear astrophysics and nuclear structure studies with rare isotope beams

    Energy Technology Data Exchange (ETDEWEB)

    Roeder, B.T., E-mail: broeder@comp.tamu.ed [Cyclotron Institute, Texas A and M University, College Station, TX 77843-3366 (United States); McCleskey, M.; Trache, L.; Alharbi, A.A.; Banu, A. [Cyclotron Institute, Texas A and M University, College Station, TX 77843-3366 (United States); Cherubini, S. [INFN-Laboratori Nazionali del Sud, Via S. Sofia 62, I95123 Catania (Italy); Dipartimento di Fisica e Astronomia, Universita di Catania, I95123 Catania (Italy); Davinson, T. [University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Goldberg, V.Z. [Cyclotron Institute, Texas A and M University, College Station, TX 77843-3366 (United States); Gulino, M. [INFN-Laboratori Nazionali del Sud, Via S. Sofia 62, I95123 Catania (Italy); Dipartimento di Fisica e Astronomia, Universita di Catania, I95123 Catania (Italy); Pizzone, R.G. [INFN-Laboratori Nazionali del Sud, Via S. Sofia 62, I95123 Catania (Italy); Simmons, E. [Cyclotron Institute, Texas A and M University, College Station, TX 77843-3366 (United States); Sparta, R. [INFN-Laboratori Nazionali del Sud, Via S. Sofia 62, I95123 Catania (Italy); Spiridon, A. [Cyclotron Institute, Texas A and M University, College Station, TX 77843-3366 (United States); Spitaleri, C. [INFN-Laboratori Nazionali del Sud, Via S. Sofia 62, I95123 Catania (Italy); Dipartimento di Fisica e Astronomia, Universita di Catania, I95123 Catania (Italy); Wallace, J.P. [University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Tribble, R.E. [Cyclotron Institute, Texas A and M University, College Station, TX 77843-3366 (United States); Woods, P.J. [University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom)

    2011-04-01

    We present the details of the construction and commissioning of the Texas-Edinburgh-Catania Silicon Array (TECSA). TECSA is composed of up to 16 Micron Semiconductor Ltd. type-YY1 silicon strip detectors and associated electronics, which is designed for use in studies of nuclear astrophysics and nuclear structure with rare isotope beams. TECSA was assembled at the Texas A and M University Cyclotron Institute and will be housed there for the next few years. The array was commissioned in a recent experiment where the d({sup 14}C,p){sup 15}C reaction at 11.7 MeV/u was measured in inverse kinematics. The results of the measurement and a discussion of the future use of this array are presented.

  16. The Texas-Edinburgh-Catania Silicon Array (TECSA): A detector for nuclear astrophysics and nuclear structure studies with rare isotope beams

    International Nuclear Information System (INIS)

    Roeder, B.T.; McCleskey, M.; Trache, L.; Alharbi, A.A.; Banu, A.; Cherubini, S.; Davinson, T.; Goldberg, V.Z.; Gulino, M.; Pizzone, R.G.; Simmons, E.; Sparta, R.; Spiridon, A.; Spitaleri, C.; Wallace, J.P.; Tribble, R.E.; Woods, P.J.

    2011-01-01

    We present the details of the construction and commissioning of the Texas-Edinburgh-Catania Silicon Array (TECSA). TECSA is composed of up to 16 Micron Semiconductor Ltd. type-YY1 silicon strip detectors and associated electronics, which is designed for use in studies of nuclear astrophysics and nuclear structure with rare isotope beams. TECSA was assembled at the Texas A and M University Cyclotron Institute and will be housed there for the next few years. The array was commissioned in a recent experiment where the d( 14 C,p) 15 C reaction at 11.7 MeV/u was measured in inverse kinematics. The results of the measurement and a discussion of the future use of this array are presented.

  17. SAQC: SNP Array Quality Control

    Directory of Open Access Journals (Sweden)

    Li Ling-Hui

    2011-04-01

    Full Text Available Abstract Background Genome-wide single-nucleotide polymorphism (SNP arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed. Results We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples. Conclusions This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC. SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm.

  18. Coupling in reflector arrays

    DEFF Research Database (Denmark)

    Appel-Hansen, Jørgen

    1968-01-01

    In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present communic......In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present...

  19. Studying the Formation and Development of Molecular Clouds: With the CCAT Heterodyne Array Instrument (CHAI)

    Science.gov (United States)

    Goldsmith, Paul F.

    2012-01-01

    Surveys of all different types provide basic data using different tracers. Molecular clouds have structure over a very wide range of scales. Thus, "high resolution" surveys and studies of selected nearby clouds add critical information. The combination of large-area and high resolution allows Increased spatial dynamic range, which in turn enables detection of new and perhaps critical morphology (e.g. filaments). Theoretical modeling has made major progress, and suggests that multiple forces are at work. Galactic-scale modeling also progressing - indicates that stellar feedback is required. Models must strive to reproduce observed cloud structure at all scales. Astrochemical observations are not unrelated to questions of cloud evolution and star formation but we are still learning how to use this capability.

  20. Study of Transitions between Wetting States on Microcavity Arrays by Optical Transmission Microscopy

    DEFF Research Database (Denmark)

    Søgaard, Emil; Andersen, Nis Korsgaard; Smistrup, Kristian

    2014-01-01

    In this article, we present a simple and fast optical method based on transmission microscopy to study the stochastic wetting transitions on micro- and nanostructured polymer surfaces immersed in water. We analyze the influence of immersion time and the liquid pressure on the degree of water......-Laplace equation for the water menisci in the cavities and the diffusion of dissolved gas molecules in the water. In addition, the wetting transitions had a stochastic nature, which resulted from the short diffusion distance for dissolved gas molecules in the water between neighboring cavities. Furthermore, we...... compared the contact angle properties of two polymeric materials (COC and PP) with moderate hydrophobicity. We attributed the difference in the water repellency of the two materials to a difference in the wetting of their nanostructures. Our experimental observations thus indicate that both the diffusion...

  1. Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat.

    Science.gov (United States)

    Nazari-Ghadikolaei, Anahit; Mehrabani-Yeganeh, Hassan; Miarei-Aashtiani, Seyed R; Staiger, Elizabeth A; Rashidi, Amir; Huson, Heather J

    2018-01-01

    The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY , and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and

  2. Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat

    Directory of Open Access Journals (Sweden)

    Anahit Nazari-Ghadikolaei

    2018-04-01

    Full Text Available The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS. This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic

  3. Microfluidic Trap Arrays: Passive Sensors for Studying Aquatic Protozoan Ecology and Biogeography

    Science.gov (United States)

    Chau, J. F.; Bouchillon, G.; Shor, L. M.

    2012-12-01

    Microscopic organisms such as bacteria and protozoa are the engine that drives global biogeochemical processes: microbes fix carbon, produce oxygen, mediate nutrient cycling, and break down anthropogenic contaminants. In many habitats, the bacterial community structure and its net production is controlled in a top-down fashion by predation by protozoa. Despite their importance, many researchers have noted a significant gap in our understanding of their diversity, biogeography, and ecosystem function. We developed a microfluidic field sampling and analysis tool to study the biogeography and function of microbial eukaryotes. Microfluidic samplers were created to systematically target the morphology, function, and habitat of different microbial eukaryotes. Features such as channel dimensions, branching angles and radii of curvature were varied to allow organisms to be selected and captured based on cell size, shape, plasticity, and swimming or crawling modalities. We also developed genetic analysis protocols to extract and amplify DNA from a single trapped cell, allowing for molecular identification of trapped species. Results from freshwater sediment and water column deployments confirmed design efficiencies in trapping and concentrating protozoa based on biomass density, allowed for analysis of body plasticity and cell size, and also confirmed the viability of this technology for future real time monitoring of protozoa in aquatic ecosystems. This research offers a radical departure from existing approaches to study microbial eukaryotic communities in the field. Our novel methodology involving trapping, observation and recording of physical characteristics and genetic analysis of single cells allows comparison with bulk samples to place trapped microbes within a function- and habitat-specific context.

  4. Birth of the Program for Array Seismic Studies of the Continental Lithosphere (PASSCAL)

    Science.gov (United States)

    James, D. E.; Sacks, I. S.

    2002-05-01

    As recently as 1984 institutions doing portable seismology depended upon their own complement of instruments, almost all designed and built in-house, and all of limited recording capability and flexibility. No data standards existed. Around 1980 the National Research Council (NRC) of the National Academy of Sciences (NAS), with National Science Foundation (NSF) support, empanelled a committee to study a major new initiative in Seismic Studies of the Continental Lithosphere (SSCL). The SSCL report in 1983 recommended that substantial numbers (1000 or more) of new generation digital seismographs be acquired for 3-D high resolution imaging of the continental lithosphere. Recommendations of the SSCL committee dovetailed with other NRC/NAS and NSF reports that highlighted imaging of the continental lithosphere as an area of highest priority. For the first time in the history of portable seismology the question asked was "What do seismologists need to do the job right?" A grassroots effort was undertaken to define instrumentation and data standards for a powerful new set of modern seismic research tools to serve the national seismological community. In the spring and fall of 1983 NSF and IASPEI sponsored workshops were convened to develop specifications for the design of a new generation of portable instrumentation. PASSCAL was the outgrowth of these seminal studies and workshops. The first step toward the formal formation of PASSCAL began with an ad-hoc organizing committee, comprised largely of the members of the NAS lithospheric seismology panel, convened by the authors at Carnegie Institution in Washington in November 1983. From that meeting emerged plans and promises of NSF support for an open organizational meeting to be held in January 1984, in Madison, Wisconsin. By the end of the two-day Madison meeting PASSCAL and an official consortium of seismological institutions for portable seismology were realities. Shortly after, PASSCAL merged with the complementary

  5. Studies on the resonant properties in the asymmetric dipole-array terahertz metamaterials

    Science.gov (United States)

    Chen, Wei; Zhou, Qingli; Li, Chenyu; Shi, Lan; Liu, Changxiang; Zhang, Cunlin

    2018-01-01

    Artificial metamaterials with appropriate design can exhibit unique electromagnetic phenomena which do not exist in natural materials. Some studies have shown that the method of breaking the geometric symmetry is capable to modify the electromagnetic response, such as the metamaterial induced transparency in the Fano resonators. In this work, by using the finite-difference time-domain method, we firstly simulate the process that terahertz wave interacts with double-bar structures, in which one bar length is fixed at 36 μm and the other bar length is set to be 12, 24, 36, 48, and 56 μm, respectively. The incident terahertz polarization is along the bar direction. Simulated results show when the variable bar length is less than 36 μm, there is only one obvious resonant dip in transmission spectrum. Meanwhile, with the decreased bar length, this dip frequency presents a slight blueshift. Additionally, by tuning the spacing vertical to bar direction between these two bars, it still exhibits one dip. This result indicates the short bar less than 36 μm does not play important role and the coupling between vertical bars is weak. However, when the variable bar length is larger than 36 μm there are two obvious Fano-shaped resonant dips. With the increased bar length, the low-frequency dip shows a remarkable redshift, while the high-frequency one is almost unchanged. By further tuning the bar spacing vertical to the bar direction, two dips always exist. This phenomenon implies that the coupling between horizontal bars is dominated in this process. Moreover, the metamaterial induced transparency window is found between two resonant dips. The appearance of the resonances is attributed to the excitation of trapped mode. Our obtained results indicate that such metamaterials with very simple configuration could also provide the potential application in the field of terahertz slow-light devices, amplitude and phase modulators.

  6. Charge-partitioning study of a wide-pitch silicon micro-strip detector with a 64-channel CMOS preamplifier array

    International Nuclear Information System (INIS)

    Ikeda, H.; Tsuboyama, T.; Okuno, S.; Saitoh, Y.; Akamine, T.; Satoh, K.; Inoue, M.; Yamanaka, J.; Mandai, M.; Takeuchi, H.; Kitta, T.; Miyahara, S.; Kamiya, M.

    1996-01-01

    The wider pitch readout operation of a 50 μm-pitch double-sided silicon micro-strip detector has been studied specifically concerning its ohmic side. Every second readout and ganged configuration was examined by employing a newly developed 64-channel preamplifier array. The observed charge responses for collimated IR light were compared with a numerical model. (orig.)

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

    Science.gov (United States)

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

    2011-06-01

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

  8. ArraySolver: An Algorithm for Colour-Coded Graphical Display and Wilcoxon Signed-Rank Statistics for Comparing Microarray Gene Expression Data

    OpenAIRE

    Khan, Haseeb Ahmad

    2004-01-01

    The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two-groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for tra...

  9. The Mouse Solitary Odorant Receptor Gene Promoters as Models for the Study of Odorant Receptor Gene Choice.

    Directory of Open Access Journals (Sweden)

    Andrea Degl'Innocenti

    Full Text Available In vertebrates, several anatomical regions located within the nasal cavity mediate olfaction. Among these, the main olfactory epithelium detects most conventional odorants. Olfactory sensory neurons, provided with cilia exposed to the air, detect volatile chemicals via an extremely large family of seven-transmembrane chemoreceptors named odorant receptors. Their genes are expressed in a monogenic and monoallelic fashion: a single allele of a single odorant receptor gene is transcribed in a given mature neuron, through a still uncharacterized molecular mechanism known as odorant receptor gene choice.Odorant receptor genes are typically arranged in genomic clusters, but a few are isolated (we call them solitary from the others within a region broader than 1 Mb upstream and downstream with respect to their transcript's coordinates. The study of clustered genes is problematic, because of redundancy and ambiguities in their regulatory elements: we propose to use the solitary genes as simplified models to understand odorant receptor gene choice.Here we define number and identity of the solitary genes in the mouse genome (C57BL/6J, and assess the conservation of the solitary status in some mammalian orthologs. Furthermore, we locate their putative promoters, predict their homeodomain binding sites (commonly present in the promoters of odorant receptor genes and compare candidate promoter sequences with those of wild-caught mice. We also provide expression data from histological sections.In the mouse genome there are eight intact solitary genes: Olfr19 (M12, Olfr49, Olfr266, Olfr267, Olfr370, Olfr371, Olfr466, Olfr1402; five are conserved as solitary in rat. These genes are all expressed in the main olfactory epithelium of three-day-old mice. The C57BL/6J candidate promoter of Olfr370 has considerably varied compared to its wild-type counterpart. Within the putative promoter for Olfr266 a homeodomain binding site is predicted. As a whole, our findings

  10. 1-D Metal Nanobead Arrays within Encapsulated Nanowires via a Red-Ox-Induced Dewetting: Mechanism Study by Atom-Probe Tomography.

    Science.gov (United States)

    Sun, Zhiyuan; Tzaguy, Avra; Hazut, Ori; Lauhon, Lincoln J; Yerushalmi, Roie; Seidman, David N

    2017-12-13

    Metal nanoparticle arrays are excellent candidates for a variety of applications due to the versatility of their morphology and structure at the nanoscale. Bottom-up self-assembly of metal nanoparticles provides an important complementary alternative to the traditional top-down lithography method and makes it possible to assemble structures with higher-order complexity, for example, nanospheres, nanocubes, and core-shell nanostructures. Here we present a mechanism study of the self-assembly process of 1-D noble metal nanoparticles arrays, composed of Au, Ag, and AuAg alloy nanoparticles. These are prepared within an encapsulated germanium nanowire, obtained by the oxidation of a metal-germanium nanowire hybrid structure. The resulting structure is a 1-D array of equidistant metal nanoparticles with the same diameter, the so-called nanobead (NB) array structure. Atom-probe tomography and transmission electron microscopy were utilized to investigate the details of the morphological and chemical evolution during the oxidation of the encapsulated metal-germanium nanowire hybrid-structures. The self-assembly of nanoparticles relies on the formation of a metal-germanium liquid alloy and the migration of the liquid alloy into the nanowire, followed by dewetting of the liquid during shape-confined oxidation where the liquid column breaks-up into nanoparticles due to the Plateau-Rayleigh instability. Our results demonstrate that the encapsulating oxide layer serves as a structural scaffold, retaining the overall shape during the eutectic liquid formation and demonstrates the relationship between the oxide mechanical properties and the final structural characteristics of the 1-D arrays. The mechanistic details revealed here provide a versatile tool-box for the bottom-up fabrication of 1-D arrays nanopatterning that can be modified for multiple applications according to the RedOx properties of the material system components.

  11. Protocol: using virus-induced gene silencing to study the arbuscular mycorrhizal symbiosis in Pisum sativum

    DEFF Research Database (Denmark)

    Grønlund, Mette; Olsen, Anne; Johansen, Elisabeth

    2010-01-01

    , the available PEBV-VIGS protocols are inadequate for studying genes involved in the symbiosis with arbuscular mycorrhizal fungi (AMF). Here we describe a PEBV-VIGS protocol suitable for reverse genetics studies in pea of genes involved in the symbiosis with AMF and show its effectiveness in silencing genes...... involved in the early and late stages of AMF symbiosis....

  12. Dynamics of nucleus nucleus collisions below 100 MeV/u a study with a 4π detection array

    International Nuclear Information System (INIS)

    Peter, J.

    1990-06-01

    Charged particles and fragments emitted in reactions between 40 Ar, at energies ranging from 25 to 85 MeV/u, and an 27 Al target have been detected in a geometry close to 4π in the center of mass with the multidetector array MUR + TONNEAU. A new global variable, the average parallel velocity, has been used to sort the events as a function of the impact parameter value. The multiplicity of pre-equilibrium charged particles emitted from the interaction region (participants) increases strongly when the impact parameter value decreases, and reaches 7 in head-on reactions. The flow of these particles is attributed to scattering at negative angles. When the energy increases, compression gradually opposes this negative scattering, until the flow falls to zero. This is obtained at a beam energy in the range 70-80 MeV/u for impact parameters below 2 fm and increases with the impact parameter. This study as a function of the impact parameter and the energy should allow information both on the nucleon-nucleon cross section in medium and the equation of state of nuclear matter to be obtained

  13. A novel multiplex-protein array for serum diagnostics of colon cancer: a case–control study

    International Nuclear Information System (INIS)

    Bünger, Stefanie; Gemoll, Timo; Laubert, Tilman; Büning, Jürgen; Fellermann, Klaus; Bruch, Hans-Peter; Roblick, Uwe J; Brenner, Hermann; Eggeling, Ferdinand von; Habermann, Jens K; Haug, Ulrike; Kelly, Maria; Posorski, Nicole; Klempt-Giessing, Katja; Cartwright, Andrew; Fitzgerald, Stephen P; Toner, Vicki; McAleer, Damien

    2012-01-01

    More than 1.2 million new cases of colorectal cancer are reported each year worldwide. Despite actual screening programs, about 50% of the patients are diagnosed at advanced tumor stages presenting poor prognosis. Innovative screening tools could aid the detection at early stages and allow curative treatment interventions. A nine target multiplex serum protein biochip was generated and evaluated using a training- and validation-set of 317 highly standardized, liquid nitrogen preserved serum samples comprising controls, adenomas, and colon cancers. Serum levels of CEA, IL-8, VEGF, S100A11, MCSF, C3adesArg, CD26, and CRP showed significant differences between cases and controls. The largest areas under the receiver operating characteristics curve were observed for CEA, IL-8, and CRP. At threshold levels yielding 90% specificity, sensitivities for CEA, IL-8 and CRP were 26%, 22%, and 17%, respectively. The most promising marker combinations were CEA + IL-8 reaching 37% sensitivity at 83% specificity and CEA + CRP with 35% sensitivity at 81% specificity. In an independent validation set CEA + IL-8 reached 47% sensitivity at 86% specificity while CEA + CRP obtained 39% sensitivity at 86% specificity. Early carcinomas were detected with 33% sensitivity for CEA + IL-8 and 28% for CEA + CRP. Apart from CEA, IL-8, and CRP, the screening value of additional blood markers and the potential advantage of combining serum biochip testing with fecal occult blood testing needs to be studied. Multiplex biochip array technology utilizing serum samples offers an innovative approach to colorectal cancer screening

  14. Research and Development of solar cell frame. Study on solar cell array solid with building material-business building

    Energy Technology Data Exchange (ETDEWEB)

    1986-08-01

    This is a NEDO annual report for 1985. A feasibility study was carried out from the viewpoints demanded both from the building material side and the solar cell. Evaluation from the technical, institutional, and economical viewpoints indicated the possibility of using a roof material solid with carbon-fiber-reinforced concrete and a curtain wall. The solar cell module was verified as a building material to be resistant against the external force, water, and heat. A problem left is how to enlarge the module. Integrated use of CFRC (Carbon Fiber Reinforced Concrete) and a cell of maximum size (1,240 x 700 mm), which is industrially available, can be expected. Present solar cell array can be utilized as a building material as it is for a curtain wall. Cost calculation of the CFRC solid roofing material indicates 276 yen/KWH for 15 years depreciation, 10 % residual value, and 8% annual interest, which is a little expensive, but this cost may be applicable to the use as a curtain wall.

  15. Reference genes for normalization: A study of rat brain tissue

    DEFF Research Database (Denmark)

    Bonefeld, Birgit; Elfving, Betina; Wegener, Gregers

    2008-01-01

    are warranted. With the overall aim to inspect the gene expression of three target genes, NMDAR1, SORT, and CREB, in rat hippocampus, we tested a panel of eight HKGs, 18s rRNA, ActB, CycA, Gapd, Hmbs, Hprt1, Rpl13A, and Ywhaz in order to select the most stably expressed gene, using the NormFinder and ge...

  16. Gene expression studies on human keratinocytes transduced with human growth hormone gene for a possible utilization in gene therapy

    International Nuclear Information System (INIS)

    Mathor, Monica Beatriz.

    1994-01-01

    Taking advantage of the recent progress in the DNA-recombinant techniques and of the potentiality of normal human keratinocytes primary culture to reconstitute the epidermis, it was decided to genetically transform these keratinocytes to produce human growth hormone under controllable conditions that would be used in gene therapy at this hormone deficient patients. The first step to achieve this goal was to standardize infection of keratinocytes with retrovirus producer cells containing a construct which included the gene of bacterial b-galactosidase. The best result was obtained cultivating the keratinocytes for 3 days in a 2:1 mixture of retrovirus producer cells and 3T3-J2 fibroblasts irradiated with 60 Gy, and splitting these infected keratinocytes on 3T3-J2 fibroblasts feeder layer. Another preliminary experiment was to infect normal human keratinocytes with interleukin-6 gene (hIL-6) that, in pathologic conditions, could be reproduced by keratinocytes and secreted to the blood stream. Thus, we verify that infected keratinocytes secrete an average amount of 500 ng/10 6 cell/day of cytokin during the in vitro life time, that certify the stable character of the injection. These keratinocytes, when grafted in mice, secrete hIL-6 to the blood stream reaching levels of 40 pg/ml of serum. After these preliminary experiments, we construct a retroviral vector with the human growth hormone gene (h GH) driven by human metallothionein promoter (h PMT), designated DChPMTGH. Normal human keratinocytes were infected with DChPMTGH producer cells, following previously standardized protocol, obtaining infected keratinocytes secreting to the culture media 340 ng h GH/10 6 cell/day without promoter activation. This is the highest level of h GH secreted in human keratinocytes primary culture described in literature. The h GH value increases approximately 10 times after activation with 100 μM Zn +2 for 8-12 hours. (author). 158 refs., 42 figs., 6 tabs

  17. Identification of Reference Genes for Quantitative Gene Expression Studies in a Non-Model Tree Pistachio (Pistacia vera L..

    Directory of Open Access Journals (Sweden)

    Maryam Moazzam Jazi

    Full Text Available The tree species, Pistacia vera (P. vera is an important commercial product that is salt-tolerant and long-lived, with a possible lifespan of over one thousand years. Gene expression analysis is an efficient method to explore the possible regulatory mechanisms underlying these characteristics. Therefore, having the most suitable set of reference genes is required for transcript level normalization under different conditions in P. vera. In the present study, we selected eight widely used reference genes, ACT, EF1α, α-TUB, β-TUB, GAPDH, CYP2, UBQ10, and 18S rRNA. Using qRT-PCR their expression was assessed in 54 different samples of three cultivars of P. vera. The samples were collected from different organs under various abiotic treatments (cold, drought, and salt across three time points. Several statistical programs (geNorm, NormFinder, and BestKeeper were applied to estimate the expression stability of candidate reference genes. Results obtained from the statistical analysis were then exposed to Rank aggregation package to generate a consensus gene rank. Based on our results, EF1α was found to be the superior reference gene in all samples under all abiotic treatments. In addition to EF1α, ACT and β-TUB were the second best reference genes for gene expression analysis in leaf and root. We recommended β-TUB as the second most stable gene for samples under the cold and drought treatments, while ACT holds the same position in samples analyzed under salt treatment. This report will benefit future research on the expression profiling of P. vera and other members of the Anacardiaceae family.

  18. Identification of Reference Genes for Quantitative Gene Expression Studies in a Non-Model Tree Pistachio (Pistacia vera L.).

    Science.gov (United States)

    Moazzam Jazi, Maryam; Ghadirzadeh Khorzoghi, Effat; Botanga, Christopher; Seyedi, Seyed Mahdi

    2016-01-01

    The tree species, Pistacia vera (P. vera) is an important commercial product that is salt-tolerant and long-lived, with a possible lifespan of over one thousand years. Gene expression analysis is an efficient method to explore the possible regulatory mechanisms underlying these characteristics. Therefore, having the most suitable set of reference genes is required for transcript level normalization under different conditions in P. vera. In the present study, we selected eight widely used reference genes, ACT, EF1α, α-TUB, β-TUB, GAPDH, CYP2, UBQ10, and 18S rRNA. Using qRT-PCR their expression was assessed in 54 different samples of three cultivars of P. vera. The samples were collected from different organs under various abiotic treatments (cold, drought, and salt) across three time points. Several statistical programs (geNorm, NormFinder, and BestKeeper) were applied to estimate the expression stability of candidate reference genes. Results obtained from the statistical analysis were then exposed to Rank aggregation package to generate a consensus gene rank. Based on our results, EF1α was found to be the superior reference gene in all samples under all abiotic treatments. In addition to EF1α, ACT and β-TUB were the second best reference genes for gene expression analysis in leaf and root. We recommended β-TUB as the second most stable gene for samples under the cold and drought treatments, while ACT holds the same position in samples analyzed under salt treatment. This report will benefit future research on the expression profiling of P. vera and other members of the Anacardiaceae family.

  19. Simple method for assembly of CRISPR synergistic activation mediator gRNA expression array.

    Science.gov (United States)

    Vad-Nielsen, Johan; Nielsen, Anders Lade; Luo, Yonglun

    2018-05-20

    When studying complex interconnected regulatory networks, effective methods for simultaneously manipulating multiple genes expression are paramount. Previously, we have developed a simple method for generation of an all-in-one CRISPR gRNA expression array. We here present a Golden Gate Assembly-based system of synergistic activation mediator (SAM) compatible CRISPR/dCas9 gRNA expression array for the simultaneous activation of multiple genes. Using this system, we demonstrated the simultaneous activation of the transcription factors, TWIST, SNAIL, SLUG, and ZEB1 a human breast cancer cell line. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Feasibility study of using a Zener diode as the selection device for bipolar RRAM and WORM memory arrays

    International Nuclear Information System (INIS)

    Li, Yingtao; Fu, Liping; Tao, Chunlan; Jiang, Xinyu; Sun, Pengxiao

    2014-01-01

    Cross-bar arrays are usually used for the high density application of resistive random access memory (RRAM) devices. However, cross-talk interference limits an increase in the integration density. In this paper, the Zener diode is proposed as a selection device to suppress the sneak current in bipolar RRAM arrays. Measurement results show that the Zener diode can act as a good selection device, and the sneak current can be effectively suppressed. The readout margin is sufficiently improved compared to that obtained without the selection device. Due to the improvement for the reading disturbance, the size of the cross-bar array can be enhanced to more than 10 3  × 10 3 . Furthermore, the possibility of using a write-once-read-many-times (WORM) cross-bar array is also demonstrated by connecting the Zener diode and the bipolar RRAM in series. These results strongly suggest that using a Zener diode as a selection device opens up great opportunities to realize high density bipolar RRAM arrays. (paper)

  1. Comparison of Wenner and dipole–dipole arrays in the study of an underground three-dimensional cavity

    International Nuclear Information System (INIS)

    Neyamadpour, Ahmad; Wan Abdullah, W A T; Taib, Samsudin; Neyamadpour, Behrang

    2010-01-01

    The objective of this paper was to compare Wenner and dipole–dipole configurations in delineating an underground cavity at a site near the University of Malaya, Malaysia. A three-dimensional electrical resistivity imaging survey was carried out along seven parallel lines using Wenner and dipole–dipole arrays. A three-dimensional least-squares algorithm, based on the robust inversion method, was used in the inversion of the apparent resistivity data. In the inverted model, both the horizontal and vertical extents of the anomalous zones were displayed. Results indicate the superiority of the Wenner array over the dipole–dipole array for determining the vertical distribution of the subsurface resistivity, although the dipole–dipole array produced a better lateral extent of the subsurface features. The results show that the three-dimensional electrical resistivity imaging survey using both the Wenner and dipole–dipole arrays, in combination with an appropriate three-dimensional inversion method and synthetic model analysis, can be highly useful for engineering and environmental applications, especially for underground three-dimensional cavity detection

  2. Leakage analysis of crossbar memristor arrays

    KAUST Repository

    Zidan, Mohammed A.

    2014-07-01

    Crossbar memristor arrays provide a promising high density alternative for the current memory and storage technologies. These arrays suffer from parasitic current components that significantly increase the power consumption, and could ruin the readout operation. In this work we study the trade-off between the crossbar array density and the power consumption required for its readout. Our analysis is based on simulating full memristor arrays on a SPICE platform.

  3. Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors

    Directory of Open Access Journals (Sweden)

    Frank Emmert-Streib

    2013-02-01

    Full Text Available The inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC3NET, CLR, C3NET and MRNET, and compare the results for three different conditions: (I observational gene expression data: normal environmental condition, (II interventional gene expression data: growth in rich media, (III interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks.

  4. Study of differential gene expression in human hepatocyte exposed to 50 cGy γ ray

    International Nuclear Information System (INIS)

    Wen Jianhua; Li Jianguo; Tian Huancheng; Li Yanling; Wang Xiaoli; Zuo Yanhui

    2008-01-01

    The study analyzed the differential transcriptional profile of the normal human hepatic cell and the human hepatic cell radiated with 50 cGy γ ray by gene chip technique. The results showed that there were 614 differentially expressed genes among 14 112 human genes analyzed, in which 521 genes were up-regulated and 93 genes down-regulated. These genes are associated with mitochondrial regulation, homo sapiens hepatitis A virus cellular receptor, tumor necrosis factor, cell cycle regulation, kinase and zinc finger protein etc. RT-PCR results indicated that up-regulated expression of gene HAVcr-1, HAVcr-2, MFTC, MOAP1 and down-regulated expression of gene TRIP12, DCN were consistent with gene chip data. (authors)

  5. Study on the optimization of the water Cherenkov detector array of the LHAASO project for surveying VHE gamma ray sources

    Science.gov (United States)

    Li, Hui-Cai; Chen, Ming-Jun; Jia, Huan-Yu; Gao, Bo; Wu, Han-Rong; Yao, Zhi-Guo; Yuo, Xiao-Hao; Zhou, Bin; Zhu, Feng-Rong

    2014-01-01

    It is prpopsed that a water Cherenkov detector array, LHAASO-WCDA, is to be built at Shangri-la, Yunnan Province, China. As one of the major components of the LHAASO project, the main purpose of it is to survey the northern sky for gamma ray sources in the energy range of 100 GeV-30 TeV. In order to design the water Cherenkov array efficiently to economize the budget, a Monte Carlo simulation is carried out. With the help of the simulation, the cost performance of different configurations of the array are obtained and compared with each other, serving as a guide for the more detailed design of the experiment in the next step.

  6. Study on the optimization of the water Cherenkov detector array of the LHAASO project for surveying VHE gamma ray sources

    International Nuclear Information System (INIS)

    Li Huicai; Chen Mingjun; Gao Bo; Wu Hanrong; Yao Zhiguo; Zhou Bin; Jia Huanyu; Zhu Fengrong; You Xiaohao

    2014-01-01

    It is proposed that a water Cherenkov detector array, LHAASO-WCDA, is to be built at Shangri-la, Yunnan Province, China. As one of the major components of the LHAASO project, the main purpose of it is to survey the northern sky for gamma ray sources in the energy range of 100 GeV-30 TeV. In order to design the water Cherenkov array efficiently to economize the budget, a Monte Carlo simulation is carried out. With the help of the simulation, the cost performance of different configurations of the array are obtained and compared with each other, serving as a guide for the more detailed design of the experiment in the next step. (authors)

  7. Spectroscopic studies of resonant coupling of silver optical antenna arrays to a near-surface quantum well

    International Nuclear Information System (INIS)

    Gehl, Michael; Zandbergen, Sander; Gibson, Ricky; Nader, Nima; Sears, Jasmine; Keiffer, Patrick; Khitrova, Galina; Béchu, Muriel; Wegener, Martin; Hendrickson, Joshua

    2014-01-01

    The coupling of radiation emitted on semiconductor inter-band transitions to resonant optical-antenna arrays allows for enhanced light–matter interaction via the Purcell effect. Semiconductor optical gain also potentially allows for loss reduction in metamaterials. Here we extend our previous work on optically pumped individual near-surface InGaAs quantum wells coupled to silver split-ring-resonator arrays to wire and square-antenna arrays. By comparing the transient pump-probe experimental results with the predictions of a simple model, we find that the effective coupling is strongest for the split rings, even though the split rings have the weakest dipole moment. The effect of the latter must thus be overcompensated by a smaller effective mode volume of the split rings. Furthermore, we also present a systematic variation of the pump-pulse energy, which was fixed in our previous experiments. (paper)

  8. Photovoltaic array: Power conditioner interface characteristics

    Science.gov (United States)

    Gonzalez, C. C.; Hill, G. M.; Ross, R. G., Jr.

    1982-01-01

    The electrical output (power, current, and voltage) of flat plate solar arrays changes constantly, due primarily to changes in cell temperature and irradiance level. As a result, array loads such as dc-to-ac power conditioners must be capable of accommodating widely varying input levels while maintaining operation at or near the maximum power point of the array. The array operating characteristics and extreme output limits necessary for the systematic design of array load interfaces under a wide variety of climatic conditions are studied. A number of interface parameters are examined, including optimum operating voltage, voltage energy, maximum power and current limits, and maximum open circuit voltage. The effect of array degradation and I-V curve fill factor or the array power conditioner interface is also discussed. Results are presented as normalized ratios of power conditioner parameters to array parameters, making the results universally applicable to a wide variety of system sizes, sites, and operating modes.

  9. RNA preparation and characterization for gene expression studies

    DEFF Research Database (Denmark)

    Stangegaard, Michael

    2009-01-01

    Much information can be obtained from knowledge of the relative expression level of each gene in the transcriptome. With the current advances in technology as little as a single cell is required as starting material for gene expression experiments. The mRNA from a single cell may be linearly...

  10. NovoTTF™-100A System (Tumor Treating Fields) transducer array layout planning for glioblastoma: a NovoTAL™ system user study.

    Science.gov (United States)

    Chaudhry, Aafia; Benson, Laura; Varshaver, Michael; Farber, Ori; Weinberg, Uri; Kirson, Eilon; Palti, Yoram

    2015-11-11

    Optune™, previously known as the NovoTTF-100A System™, generates Tumor Treating Fields (TTFields), an effective anti-mitotic therapy for glioblastoma. The system delivers intermediate frequency, alternating electric fields to the supratentorial brain. Patient therapy is personalized by configuring transducer array layout placement on the scalp to the tumor site using MRI measurements and the NovoTAL System. Transducer array layout mapping optimizes therapy by maximizing electric field intensity to the tumor site. This study evaluated physician performance in conducting transducer array layout mapping using the NovoTAL System compared with mapping performed by the Novocure in-house clinical team. Fourteen physicians (7 neuro-oncologists, 4 medical oncologists, and 3 neurosurgeons) evaluated five blinded cases of recurrent glioblastoma and performed head size and tumor location measurements using a standard Digital Imaging and Communications in Medicine reader. Concordance with Novocure measurement and intra- and inter-rater reliability were assessed using relevant correlation coefficients. The study criterion for success was a concordance correlation coefficient (CCC) >0.80. CCC for each physician versus Novocure on 20 MRI measurements was 0.96 (standard deviation, SD ± 0.03, range 0.90-1.00), indicating very high agreement between the two groups. Intra- and inter-rater reliability correlation coefficients were similarly high: 0.83 (SD ±0.15, range 0.54-1.00) and 0.80 (SD ±0.18, range 0.48-1.00), respectively. This user study demonstrated an excellent level of concordance between prescribing physicians and Novocure in-house clinical teams in performing transducer array layout planning. Intra-rater reliability was very high, indicating reproducible performance. Physicians prescribing TTFields, when trained on the NovoTAL System, can independently perform transducer array layout mapping required for the initiation and maintenance of patients on TTFields

  11. Methodological issues in detecting gene-gene interactions in breast cancer susceptibility: a population-based study in Ontario

    Directory of Open Access Journals (Sweden)

    Onay Venus

    2007-08-01

    Full Text Available Abstract Background There is growing evidence that gene-gene interactions are ubiquitous in determining the susceptibility to common human diseases. The investigation of such gene-gene interactions presents new statistical challenges for studies with relatively small sample sizes as the number of potential interactions in the genome can be large. Breast cancer provides a useful paradigm to study genetically complex diseases because commonly occurring single nucleotide polymorphisms (SNPs may additively or synergistically disturb the system-wide communication of the cellular processes leading to cancer development. Methods In this study, we systematically studied SNP-SNP interactions among 19 SNPs from 18 key genes involved in major cancer pathways in a sample of 398 breast cancer cases and 372 controls from Ontario. We discuss the methodological issues associated with the detection of SNP-SNP interactions in this dataset by applying and comparing three commonly used methods: the logistic regression model, classification and regression trees (CART, and the multifactor dimensionality reduction (MDR method. Results Our analyses show evidence for several simple (two-way and complex (multi-way SNP-SNP interactions associated with breast cancer. For example, all three methods identified XPD-[Lys751Gln]*IL10-[G(-1082A] as the most significant two-way interaction. CART and MDR identified the same critical SNPs participating in complex interactions. Our results suggest that the use of multiple statistical approaches (or an integrated approach rather than a single methodology could be the best strategy to elucidate complex gene interactions that have generally very different patterns. Conclusion The strategy used here has the potential to identify complex biological relationships among breast cancer genes and processes. This will lead to the discovery of novel biological information, which will improve breast cancer risk management.

  12. A Combinatory Approach for Selecting Prognostic Genes in Microarray Studies of Tumour Survivals

    Directory of Open Access Journals (Sweden)

    Qihua Tan

    2009-01-01

    Full Text Available Different from significant gene expression analysis which looks for genes that are differentially regulated, feature selection in the microarray-based prognostic gene expression analysis aims at finding a subset of marker genes that are not only differentially expressed but also informative for prediction. Unfortunately feature selection in literature of microarray study is predominated by the simple heuristic univariate gene filter paradigm that selects differentially expressed genes according to their statistical significances. We introduce a combinatory feature selection strategy that integrates differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival outcomes. Empirical application to leukemia and ovarian cancer survival data through-within- and cross-study validations shows that the feature space can be largely reduced while achieving improved testing performances.

  13. GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies.

    Science.gov (United States)

    Yung, Ling Sing; Yang, Can; Wan, Xiang; Yu, Weichuan

    2011-05-01

    Collecting millions of genetic variations is feasible with the advanced genotyping technology. With a huge amount of genetic variations data in hand, developing efficient algorithms to carry out the gene-gene interaction analysis in a timely manner has become one of the key problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST), a recent work in GWAS, completes gene-gene interaction analysis in 2.5 days on a desktop computer. Compared with central processing units (CPUs), graphic processing units (GPUs) are highly parallel hardware and provide massive computing resources. We are, therefore, motivated to use GPUs to further speed up the analysis of gene-gene interactions. We implement the BOOST method based on a GPU framework and name it GBOOST. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34 h on a desktop computer equipped with Nvidia GeForce GTX 285 display card. GBOOST code is available at http://bioinformatics.ust.hk/BOOST.html#GBOOST.

  14. Gas Sensing Studies of an n-n Hetero-Junction Array Based on SnO2 and ZnO Composites

    Directory of Open Access Journals (Sweden)

    Anupriya Naik

    2016-02-01

    Full Text Available A composite metal oxide semiconductor (MOS sensor array based on tin dioxide (SNO2 and zinc oxide (ZnO has been fabricated using a straight forward mechanical mixing method. The array was characterized using X-ray photoelectron spectroscopy, scanning electron microscopy, Raman spectroscopy and X-ray diffraction. The array was evaluated against a number of environmentally important reducing and oxidizing gases across a range of operating temperatures (300–500 °C. The highest response achieved was against 100 ppm ethanol by the 50 wt% ZnO–50 wt% SnO2 device, which exhibited a response of 109.1, a 4.5-fold increase with respect to the pure SnO2 counterpart (which displayed a response of 24.4 and a 12.3-fold enhancement with respect to the pure ZnO counterpart (which was associated with a response of 8.9, towards the same concentration of the analyte. Cross sensitivity studies were also carried out against a variety of reducing gases at an operating temperature of 300 °C. The sensors array showed selectivity towards ethanol. The enhanced behaviour of the mixed oxide materials was influenced by junction effects, composition, the packing structure and the device microstructure. The results show that it is possible to tune the sensitivity and selectivity of a composite sensor, through a simple change in the composition of the composite.

  15. Comparative study of single-nucleotide polymorphism array and next generation sequencing based strategies on triploid identification in preimplantation genetic diagnosis and screen.

    Science.gov (United States)

    Xu, Jiawei; Niu, Wenbin; Peng, Zhaofeng; Bao, Xiao; Zhang, Meixiang; Wang, Linlin; Du, Linqing; Zhang, Nan; Sun, Yingpu

    2016-12-06

    Triploidy occurred about 2-3% in human pregnancies and contributed to approximately 15% of chromosomally caused human early miscarriage. It is essential for preimplantation genetic diagnosis and screen to distinct triploidy sensitively. Here, we performed comparative investigations between MALBAC-NGS and MDA-SNP array sensitivity on triploidy detection. Self-correction and reference-correction algorism were used to analyze the NGS data. We identified 5 triploid embryos in 1198 embryos of 218 PGD and PGS cycles using MDA-SNP array, the rate of tripoidy was 4.17‰ in PGS and PGD patients. Our results indicated that the MDA-SNP array was sensitive to digyny and diandry triploidy, MALBAC-NGS combined with self and reference genome correction strategies analyze were not sensitive to detect triploidy. Our study demonstrated that triploidy occurred at 4.17‰ in PGD and PGS, MDA-SNP array could successfully identify triploidy in PGD and PGS and genomic DNA. MALBAC-NGS combined with self and reference genome correction strategies were not sensitive to triploidy.

  16. Gene study within the 5' flanking regions of growth hormone gene of ...

    African Journals Online (AJOL)

    user

    2011-01-17

    Jan 17, 2011 ... Expression of more than one gene for GH has been reported, indicating ..... hormone levels of palsmáticos IGF-1 and carcass traits in beef cattle. Dissertation ... Structure-function relation of somatotropin with reference to ...

  17. Study of oral clefts: Indication of gene-environment interaction

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, S.J.; Beaty, T.H.; Panny, S. [Johns Hopkins Univ., Baltimore, MD (United States)] [and others

    1994-09-01

    In this study of infants with isolated birth defects, 69 cleft palate-only (CPO) cases, 114 cleft lip with or without palate (CL/P), and 284 controls with non-cleft birth defects (all born in Maryland during 1984-1992) were examined to test for associations among genetic markers and different oral clefts. Modest associations were found between transforming growth factor {alpha} (TGF{alpha}) marker and CPO, as well as that between D17S579 (Mfd188) and CL/P in this study. The association between TGF{alpha} marker and CPO reflects a statistical interaction between mother`s smoking and child`s TGF{alpha} genotype. A significantly higher risk of CPO was found among those reporting maternal smoking during pregnancy and carrying less common TGF{alpha} TaqI allele (odds ratio=7.02 with 95% confidence interval 1.8-27.6). This gene-environment interaction was also found among those who reported no family history of any type of birth defect (odds ratio=5.60 with 95% confidence interval 1.4-22.9). Similar associations were seen for CL/P, but these were not statistically significant.

  18. Impact study of the Argo array definition in the Mediterranean Sea based on satellite altimetry gridded data

    Science.gov (United States)

    Sanchez-Roman, Antonio; Ruiz, Simón; Pascual, Ananda; Guinehut, Stéphanie; Mourre, Baptiste

    2016-04-01

    the Mediterranean as the "true" field. The choice of the reference depth of Argo profiles impacts the number of valid profiles used to compute DHA and therefore the spatial coverage by the network. Results show that the impact of the reference level in the computation of Argo DH is statistically significant since the standard deviation of the differences between DH computed from Altimetry and Argo data referred to reference depth of 400 dbar and 900 dbar are quite different (4.85 and 5.11 cm, respectively). Therefore, 400 dbar should be taken as reference depth to compute DHA from Argo data in the Mediterranean. On the contrary, similar scores are obtained when shallow floats are not included in the computation (4.85 cm against 4.87 cm). In any case, we must highlight that all the studies show significant correlations (95 %) higher than 0.70 between Altimetry and Argo data with a STD for the differences between both datasets of around 4.90 cm. Furthermore, the sub-basin study shows improved statistics for the eastern sub-basin for DHA referred to 400 dbar while minimum values are obtained for the western sub-basin when computing DHA referred to 900 dbar. On the other hand, results about the OSSEs suggest that maintaining an array of Argo floats of 100×100 km, the variance of the large-scale signal and most of the mesoscale features of SLA fields are recovered. Therefore, the network coverage should be enlarged in the Mediterranean in order to achieve at least this spatial resolution.

  19. The Association Study between Twenty One Polymorphisms in Seven Candidate Genes and Coronary Heart Diseases in Chinese Han Population.

    Directory of Open Access Journals (Sweden)

    Barrak F Alobeidy

    Full Text Available Previous genome-wide association studies (GWAS in multiple populations identified several genetic loci for coronary heart diseases (CHD. Here we utilized a 2-stage candidate gene association strategy in Chinese Han population to shed light on the putative association between several metabolic-related candidate genes and CHD. At the 1(st stage, 190 patients with CHD and 190 controls were genotyped through the MassARRAY platform. At the 2(nd stage, a larger sample including 400 patients and 392 controls was genotyped by the High Resolution Melt (HRM method to confirm or rule out the associations with CHD. MLXIP expression level was quantified by the real time PCR in 65 peripheral blood samples. From the 21 studied single nucleotide polymorphisms (SNPs of seven candidate genes: MLXIPL, MLXIP, MLX, ADIPOR1, VDR, SREBF1 and NR1H3, only one tag SNP rs4758685 (T→C was found to be statistically associated with CHD (P-value = 0.02, Odds ratio (OR of 0.83. After adjustment for the age, sex, lipid levels and diabetes, the association remained significant (P-value = 0.03. After adjustment for the hypertension, P-value became 0.20 although there was a significant difference in the allele distribution between the CHD patients with hypertension and the controls (P-value = 0.04, 406 vs 582. In conclusion, among the 21 tested SNPs, we identified a novel association between rs4758685 of MLXIP gene and CHD. The C allele of common variant rs4758685 interacted with hypertension, and was found to be protective against CHD in both allelic and genotypic models in Chinese Han population.

  20. Transcranial passive acoustic mapping with hemispherical sparse arrays using CT-based skull-specific aberration corrections: a simulation study

    International Nuclear Information System (INIS)

    Jones, Ryan M; O’Reilly, Meaghan A; Hynynen, Kullervo

    2013-01-01

    The feasibility of transcranial passive acoustic mapping with hemispherical sparse arrays (30 cm diameter, 16 to 1372 elements, 2.48 mm receiver diameter) using CT-based aberration corrections was investigated via numerical simulations. A multi-layered ray acoustic transcranial ultrasound propagation model based on CT-derived skull morphology was developed. By incorporating skull-specific aberration corrections into a conventional passive beamforming algorithm (Norton and Won 2000 IEEE Trans. Geosci. Remote Sens. 38 1337–43), simulated acoustic source fields representing the emissions from acoustically-stimulated microbubbles were spatially mapped through three digitized human skulls, with the transskull reconstructions closely matching the water-path control images. Image quality was quantified based on main lobe beamwidths, peak sidelobe ratio, and image signal-to-noise ratio. The effects on the resulting image quality of the source’s emission frequency and location within the skull cavity, the array sparsity and element configuration, the receiver element sensitivity, and the specific skull morphology were all investigated. The system’s resolution capabilities were also estimated for various degrees of array sparsity. Passive imaging of acoustic sources through an intact skull was shown possible with sparse hemispherical imaging arrays. This technique may be useful for the monitoring and control of transcranial focused ultrasound (FUS) treatments, particularly non-thermal, cavitation-mediated applications such as FUS-induced blood–brain barrier disruption or sonothrombolysis, for which no real-time monitoring techniques currently exist. (paper)

  1. Transcranial passive acoustic mapping with hemispherical sparse arrays using CT-based skull-specific aberration corrections: a simulation study

    Science.gov (United States)

    Jones, Ryan M.; O’Reilly, Meaghan A.; Hynynen, Kullervo

    2013-01-01

    The feasibility of transcranial passive acoustic mapping with hemispherical sparse arrays (30 cm diameter, 16 to 1372 elements, 2.48 mm receiver diameter) using CT-based aberration corrections was investigated via numerical simulations. A multi-layered ray acoustic transcranial ultrasound propagation model based on CT-derived skull morphology was developed. By incorporating skull-specific aberration corrections into a conventional passive beamforming algorithm (Norton and Won 2000 IEEE Trans. Geosci. Remote Sens. 38 1337–43), simulated acoustic source fields representing the emissions from acoustically-stimulated microbubbles were spatially mapped through three digitized human skulls, with the transskull reconstructions closely matching the water-path control images. Image quality was quantified based on main lobe beamwidths, peak sidelobe ratio, and image signal-to-noise ratio. The effects on the resulting image quality of the source’s emission frequency and location within the skull cavity, the array sparsity and element configuration, the receiver element sensitivity, and the specific skull morphology were all investigated. The system’s resolution capabilities were also estimated for various degrees of array sparsity. Passive imaging of acoustic sources through an intact skull was shown possible with sparse hemispherical imaging arrays. This technique may be useful for the monitoring and control of transcranial focused ultrasound (FUS) treatments, particularly non-thermal, cavitation-mediated applications such as FUS-induced blood-brain barrier disruption or sonothrombolysis, for which no real-time monitoring technique currently exists. PMID:23807573

  2. Studying local earthquakes in the area Baltic-Bothnia Megashear using the data of the POLENET/LAPNET temporary array

    Science.gov (United States)

    Usoltseva, Olga; Kozlovskaya, Elena

    2016-07-01

    Earthquakes in areas within continental plates are still not completely understood, and progress on understanding intraplate seismicity is slow due to a short history of instrumental seismology and sparse regional seismic networks in seismically non-active areas. However, knowledge about position and depth of seismogenic structures in such areas is necessary in order to estimate seismic hazard for such critical facilities such as nuclear power plants and nuclear waste deposits. In the present paper we address the problem of seismicity in the intraplate area of northern Fennoscandia using the information on local events recorded by the POLENET/LAPNET (Polar Earth Observing Network) temporary seismic array during the International Polar Year 2007-2009. We relocate the seismic events using the program HYPOELLIPS (a computer program for determining local earthquake hypocentral parameters) and grid search method. We use the first arrivals of P waves of local events in order to calculate a 3-D tomographic P wave velocity model of the uppermost crust (down to 20 km) for a selected region inside the study area and show that the velocity heterogeneities in the upper crust correlate well with known tectonic units. We compare the position of the velocity heterogeneities with the seismogenic structures delineated by epicentres of relocated events and demonstrate that these structures generally do not correlate with the crustal units formed as a result of crustal evolution in the Archaean and Palaeoproterozoic. On the contrary, they correlate well with the postglacial faults located in the area of the Baltic-Bothnia Megash