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Sample records for microarray experiments electronic

  1. Normalization for triple-target microarray experiments

    Directory of Open Access Journals (Sweden)

    Magniette Frederic

    2008-04-01

    Full Text Available Abstract Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

  2. Dynamic, electronically switchable surfaces for membrane protein microarrays.

    Science.gov (United States)

    Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

    2006-02-01

    Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

  3. SNP typing on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez Sanchez, Juan Jose; Morling, Niels

    2005-01-01

    We describe a single nucleotide polymorphism (SNP) typing protocol developed for the NanoChip electronic microarray. The NanoChip array consists of 100 electrodes covered by a thin hydrogel layer containing streptavidin. An electric currency can be applied to one, several, or all electrodes...

  4. Universal Reference RNA as a standard for microarray experiments

    Directory of Open Access Journals (Sweden)

    Fero Michael

    2004-03-01

    Full Text Available Abstract Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR, developed with the goal of providing hybridization signal at each microarray probe location (spot. Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment. Results Human, mouse and rat URR (UHRR, UMRR and URRR, respectively were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage. Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97. Conclusion Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and

  5. Advanced spot quality analysis in two-colour microarray experiments

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    Vetter Guillaume

    2008-09-01

    Full Text Available Abstract Background Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. Findings We evaluated the performance of two image analysis packages MAIA and GenePix (GP using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5% than GP with default spot filtering conditions. Conclusion Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.

  6. Development and application of a microarray meter tool to optimize microarray experiments

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    Rouse Richard JD

    2008-07-01

    Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

  7. Systematic interpretation of microarray data using experiment annotations

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    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  8. Design issues in toxicogenomics using DNA microarray experiment

    International Nuclear Information System (INIS)

    Lee, Kyoung-Mu; Kim, Ju-Han; Kang, Daehee

    2005-01-01

    The methods of toxicogenomics might be classified into omics study (e.g., genomics, proteomics, and metabolomics) and population study focusing on risk assessment and gene-environment interaction. In omics study, microarray is the most popular approach. Genes falling into several categories (e.g., xenobiotics metabolism, cell cycle control, DNA repair etc.) can be selected up to 20,000 according to a priori hypothesis. The appropriate type of samples and species should be selected in advance. Multiple doses and varied exposure durations are suggested to identify those genes clearly linked to toxic response. Microarray experiments can be affected by numerous nuisance variables including experimental designs, sample extraction, type of scanners, etc. The number of slides might be determined from the magnitude and variance of expression change, false-positive rate, and desired power. Instead, pooling samples is an alternative. Online databases on chemicals with known exposure-disease outcomes and genetic information can aid the interpretation of the normalized results. Gene function can be inferred from microarray data analyzed by bioinformatics methods such as cluster analysis. The population study often adopts hospital-based or nested case-control design. Biases in subject selection and exposure assessment should be minimized, and confounding bias should also be controlled for in stratified or multiple regression analysis. Optimal sample sizes are dependent on the statistical test for gene-to-environment or gene-to-gene interaction. The design issues addressed in this mini-review are crucial in conducting toxicogenomics study. In addition, integrative approach of exposure assessment, epidemiology, and clinical trial is required

  9. Fast gene ontology based clustering for microarray experiments.

    Science.gov (United States)

    Ovaska, Kristian; Laakso, Marko; Hautaniemi, Sampsa

    2008-11-21

    Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map. These methods facilitate advanced annotation of genes resulting from data analysis.

  10. Fast Gene Ontology based clustering for microarray experiments

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    Ovaska Kristian

    2008-11-01

    Full Text Available Abstract Background Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. Results We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Conclusion Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map. These methods facilitate advanced annotation of genes resulting from data analysis.

  11. Electronics for LHC Experiments

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2004-07-01

    This document gathers the abstracts of most presentations made at this workshop on electronics for the large hadron collider (LHC) experiments. The presentations were arranged into 6 sessions: 1) electronics for tracker, 2) trigger electronics, 3) detector control systems, 4) data acquisition, 5) electronics for calorimeters and electronics for muons, and 6) links, power systems, grounding and shielding, testing and quality assurance.

  12. Electronics for LHC Experiments

    International Nuclear Information System (INIS)

    2004-01-01

    This document gathers the abstracts of most presentations made at this workshop on electronics for the large hadron collider (LHC) experiments. The presentations were arranged into 6 sessions: 1) electronics for tracker, 2) trigger electronics, 3) detector control systems, 4) data acquisition, 5) electronics for calorimeters and electronics for muons, and 6) links, power systems, grounding and shielding, testing and quality assurance

  13. Identification of potential biomarkers from microarray experiments using multiple criteria optimization

    International Nuclear Information System (INIS)

    Sánchez-Peña, Matilde L; Isaza, Clara E; Pérez-Morales, Jaileene; Rodríguez-Padilla, Cristina; Castro, José M; Cabrera-Ríos, Mauricio

    2013-01-01

    Microarray experiments are capable of determining the relative expression of tens of thousands of genes simultaneously, thus resulting in very large databases. The analysis of these databases and the extraction of biologically relevant knowledge from them are challenging tasks. The identification of potential cancer biomarker genes is one of the most important aims for microarray analysis and, as such, has been widely targeted in the literature. However, identifying a set of these genes consistently across different experiments, researches, microarray platforms, or cancer types is still an elusive endeavor. Besides the inherent difficulty of the large and nonconstant variability in these experiments and the incommensurability between different microarray technologies, there is the issue of the users having to adjust a series of parameters that significantly affect the outcome of the analyses and that do not have a biological or medical meaning. In this study, the identification of potential cancer biomarkers from microarray data is casted as a multiple criteria optimization (MCO) problem. The efficient solutions to this problem, found here through data envelopment analysis (DEA), are associated to genes that are proposed as potential cancer biomarkers. The method does not require any parameter adjustment by the user, and thus fosters repeatability. The approach also allows the analysis of different microarray experiments, microarray platforms, and cancer types simultaneously. The results include the analysis of three publicly available microarray databases related to cervix cancer. This study points to the feasibility of modeling the selection of potential cancer biomarkers from microarray data as an MCO problem and solve it using DEA. Using MCO entails a new optic to the identification of potential cancer biomarkers as it does not require the definition of a threshold value to establish significance for a particular gene and the selection of a normalization

  14. Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray

    DEFF Research Database (Denmark)

    Børsting, Claus; Sanchez, Juan J; Morling, Niels

    2004-01-01

    We tested the SNP typing protocol developed for the NanoChip electronic microarray by analyzing the four Y chromosome loci SRY1532, SRY8299, TAT, and 92R7. Amplicons of different lengths containing the same locus were purified and addressed to the NanoChip array and fluorescently labelled reporte...

  15. The MGED Ontology: a resource for semantics-based description of microarray experiments.

    Science.gov (United States)

    Whetzel, Patricia L; Parkinson, Helen; Causton, Helen C; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Game, Laurence; Heiskanen, Mervi; Morrison, Norman; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; White, Joseph; Stoeckert, Christian J

    2006-04-01

    The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). Stoeckrt@pcbi.upenn.edu Supplementary data are available at Bioinformatics online.

  16. A Reliable and Distributed LIMS for Efficient Management of the Microarray Experiment Environment

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    Jin Hee-Jeong

    2007-03-01

    Full Text Available A microarray is a principal technology in molecular biology. It generates thousands of expressions of genotypes at once. Typically, a microarray experiment contains many kinds of information, such as gene names, sequences, expression profiles, scanned images, and annotation. So, the organization and analysis of vast amounts of data are required. Microarray LIMS (Laboratory Information Management System provides data management, search, and basic analysis. Recently, microarray joint researches, such as the skeletal system disease and anti-cancer medicine have been widely conducted. This research requires data sharing among laboratories within the joint research group. In this paper, we introduce a web based microarray LIMS, SMILE (Small and solid MIcroarray Lims for Experimenters, especially for shared data management. The data sharing function of SMILE is based on Friend-to-Friend (F2F, which is based on anonymous P2P (Peer-to-Peer, in which people connect directly with their “friends”. It only allows its friends to exchange data directly using IP addresses or digital signatures you trust. In SMILE, there are two types of friends: “service provider”, which provides data, and “client”, which is provided with data. So, the service provider provides shared data only to its clients. SMILE provides useful functions for microarray experiments, such as variant data management, image analysis, normalization, system management, project schedule management, and shared data management. Moreover, it connections with two systems: ArrayMall for analyzing microarray images and GENAW for constructing a genetic network. SMILE is available on http://neobio.cs.pusan.ac.kr:8080/smile.

  17. Electronics for LHC experiments

    International Nuclear Information System (INIS)

    Bourgeois, Francois

    1995-01-01

    Full text: A major effort is being mounted to prepare the way handling the high interaction rates expected from CERN's new LHC proton-proton collider (see, for example, November, page 6). September saw the First Workshop on Electronics for LHC Experiments, organized by Lisbon's Particle Physics Instrumentation Laboratory (LIP) on behalf of CERN's LHC Electronics Review Board (LERB - March, page 2). Its purpose was not only for the LERB to have a thorough review of ongoing activities, but also to promote cross fertilization in the engineering community involved in electronics design for LHC experiments. The Workshop gathered 187 physicists and engineers from 20 countries including USA and Japan. The meeting comprised six sessions and 82 talks, with special focus on radiation-hard microelectronic processes, electronics for tracking, calorimetry and muon detectors, optoelectronics, trigger and data acquisition systems. Each topic was introduced by an invited speaker who reviewed the requirements set by the particular detector technology at LHC. At the end of each session, panel discussions were chaired by each invited speaker. Representatives from four major integrated circuit manufacturers covered advanced radiation hard processes. Two talks highlighted the importance of obsolescence and quality systems in the long-lived and demanding environment of LHC. The Workshop identified areas and encouraged efforts for rationalization and common developments within and between the different detector groups. As a result, it will also help ensure the reliability and the long term maintainability of installed equipment. The proceedings of the Workshop are available from LIP Lisbon*. The LERB Workshop on Electronics for LHC Experiments will become a regular event, with the second taking place in Hungary, by Lake Balaton, from 23-27 September 1996. The Hungarian institutes KFKIRMKI have taken up the challenge of being as successful as LIP Lisbon in the organization

  18. Position dependent mismatch discrimination on DNA microarraysexperiments and model

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    Michel Wolfgang

    2008-12-01

    Full Text Available Abstract Background The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study. Results We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results. Conclusion Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.

  19. Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

    DEFF Research Database (Denmark)

    Hedegaard, Jakob; Arce, Christina; Bicciato, Silvio

    2009-01-01

    The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microa...... a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria...

  20. Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

    Directory of Open Access Journals (Sweden)

    Hedegaard Jakob

    2009-07-01

    Full Text Available Abstract Background The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experiment.

  1. A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine.

    Science.gov (United States)

    Erickson, A; Fisher, M; Furukawa-Stoffer, T; Ambagala, A; Hodko, D; Pasick, J; King, D P; Nfon, C; Ortega Polo, R; Lung, O

    2018-04-01

    Microarray technology can be useful for pathogen detection as it allows simultaneous interrogation of the presence or absence of a large number of genetic signatures. However, most microarray assays are labour-intensive and time-consuming to perform. This study describes the development and initial evaluation of a multiplex reverse transcription (RT)-PCR and novel accompanying automated electronic microarray assay for simultaneous detection and differentiation of seven important viruses that affect swine (foot-and-mouth disease virus [FMDV], swine vesicular disease virus [SVDV], vesicular exanthema of swine virus [VESV], African swine fever virus [ASFV], classical swine fever virus [CSFV], porcine respiratory and reproductive syndrome virus [PRRSV] and porcine circovirus type 2 [PCV2]). The novel electronic microarray assay utilizes a single, user-friendly instrument that integrates and automates capture probe printing, hybridization, washing and reporting on a disposable electronic microarray cartridge with 400 features. This assay accurately detected and identified a total of 68 isolates of the seven targeted virus species including 23 samples of FMDV, representing all seven serotypes, and 10 CSFV strains, representing all three genotypes. The assay successfully detected viruses in clinical samples from the field, experimentally infected animals (as early as 1 day post-infection (dpi) for FMDV and SVDV, 4 dpi for ASFV, 5 dpi for CSFV), as well as in biological material that were spiked with target viruses. The limit of detection was 10 copies/μl for ASFV, PCV2 and PRRSV, 100 copies/μl for SVDV, CSFV, VESV and 1,000 copies/μl for FMDV. The electronic microarray component had reduced analytical sensitivity for several of the target viruses when compared with the multiplex RT-PCR. The integration of capture probe printing allows custom onsite array printing as needed, while electrophoretically driven hybridization generates results faster than conventional

  2. A permutation-based multiple testing method for time-course microarray experiments

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    George Stephen L

    2009-10-01

    Full Text Available Abstract Background Time-course microarray experiments are widely used to study the temporal profiles of gene expression. Storey et al. (2005 developed a method for analyzing time-course microarray studies that can be applied to discovering genes whose expression trajectories change over time within a single biological group, or those that follow different time trajectories among multiple groups. They estimated the expression trajectories of each gene using natural cubic splines under the null (no time-course and alternative (time-course hypotheses, and used a goodness of fit test statistic to quantify the discrepancy. The null distribution of the statistic was approximated through a bootstrap method. Gene expression levels in microarray data are often complicatedly correlated. An accurate type I error control adjusting for multiple testing requires the joint null distribution of test statistics for a large number of genes. For this purpose, permutation methods have been widely used because of computational ease and their intuitive interpretation. Results In this paper, we propose a permutation-based multiple testing procedure based on the test statistic used by Storey et al. (2005. We also propose an efficient computation algorithm. Extensive simulations are conducted to investigate the performance of the permutation-based multiple testing procedure. The application of the proposed method is illustrated using the Caenorhabditis elegans dauer developmental data. Conclusion Our method is computationally efficient and applicable for identifying genes whose expression levels are time-dependent in a single biological group and for identifying the genes for which the time-profile depends on the group in a multi-group setting.

  3. GeneRank: Using search engine technology for the analysis of microarray experiments

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    Breitling Rainer

    2005-09-01

    Full Text Available Abstract Background Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method – based on the PageRank algorithm employed by the popular search engine Google – that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. Results GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.

  4. GeneRank: using search engine technology for the analysis of microarray experiments.

    Science.gov (United States)

    Morrison, Julie L; Breitling, Rainer; Higham, Desmond J; Gilbert, David R

    2005-09-21

    Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method--based on the PageRank algorithm employed by the popular search engine Google--that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings. Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.

  5. A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments.

    Science.gov (United States)

    Gómez-Villegas, Miguel A; Salazar, Isabel; Sanz, Luis

    2014-02-01

    DNA microarray experiments require the use of multiple hypothesis testing procedures because thousands of hypotheses are simultaneously tested. We deal with this problem from a Bayesian decision theory perspective. We propose a decision criterion based on an estimation of the number of false null hypotheses (FNH), taking as an error measure the proportion of the posterior expected number of false positives with respect to the estimated number of true null hypotheses. The methodology is applied to a Gaussian model when testing bilateral hypotheses. The procedure is illustrated with both simulated and real data examples and the results are compared to those obtained by the Bayes rule when an additive loss function is considered for each joint action and the generalized loss 0-1 function for each individual action. Our procedure significantly reduced the percentage of false negatives whereas the percentage of false positives remains at an acceptable level.

  6. Gene Expression Browser: Large-Scale and Cross-Experiment Microarray Data Management, Search & Visualization

    Science.gov (United States)

    The amount of microarray gene expression data in public repositories has been increasing exponentially for the last couple of decades. High-throughput microarray data integration and analysis has become a critical step in exploring the large amount of expression data for biological discovery. Howeve...

  7. Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

    Science.gov (United States)

    Severgnini, Marco; Bicciato, Silvio; Mangano, Eleonora; Scarlatti, Francesca; Mezzelani, Alessandra; Mattioli, Michela; Ghidoni, Riccardo; Peano, Clelia; Bonnal, Raoul; Viti, Federica; Milanesi, Luciano; De Bellis, Gianluca; Battaglia, Cristina

    2006-06-01

    Meta-analysis of microarray data is increasingly important, considering both the availability of multiple platforms using disparate technologies and the accumulation in public repositories of data sets from different laboratories. We addressed the issue of comparing gene expression profiles from two microarray platforms by devising a standardized investigative strategy. We tested this procedure by studying MDA-MB-231 cells, which undergo apoptosis on treatment with resveratrol. Gene expression profiles were obtained using high-density, short-oligonucleotide, single-color microarray platforms: GeneChip (Affymetrix) and CodeLink (Amersham). Interplatform analyses were carried out on 8414 common transcripts represented on both platforms, as identified by LocusLink ID, representing 70.8% and 88.6% of annotated GeneChip and CodeLink features, respectively. We identified 105 differentially expressed genes (DEGs) on CodeLink and 42 DEGs on GeneChip. Among them, only 9 DEGs were commonly identified by both platforms. Multiple analyses (BLAST alignment of probes with target sequences, gene ontology, literature mining, and quantitative real-time PCR) permitted us to investigate the factors contributing to the generation of platform-dependent results in single-color microarray experiments. An effective approach to cross-platform comparison involves microarrays of similar technologies, samples prepared by identical methods, and a standardized battery of bioinformatic and statistical analyses.

  8. Data analysis for electronic experiments

    International Nuclear Information System (INIS)

    Grote, H.

    1981-01-01

    In this lecture I schell attempt to cover the principal off-line software aspects in electronic experiments. Of course, this is too ambitious an undertaking for two reasons: Firstly the field is vast, and some important aspect will certainly have escaped my attention. Secondly, the choice of methods, features, algorithms, and packages presented will be biased through my personal opinion and experience, although to some extent it is influenced as well by the opinion and experience of my colleagues, who, like myself, are working in this field at CERN. Therefore, beware. Whenever I shall claim something to be evident, a matter of experience -- a fact --it ain't necessarily so. On the other hand, it will not be entirely wrong, since our experience is based on something like 30 experiments in high-energy physics using electronic for other people, and although these people are of course misled, one has to admit their existence. (orig.)

  9. Carbohydrate microarrays

    DEFF Research Database (Denmark)

    Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

    2012-01-01

    In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research....

  10. Preliminary experiments of electronic duplication

    International Nuclear Information System (INIS)

    Fay, Bernard

    1974-01-01

    Systems of electron sputtering (at the unit scale) use as master mask a photocathode with localized emitting zones. Emitted electrons are accelerated and focussed on a silicon substrate covered with an electrosensitive resin. The very high definition associated with electron masking is obtained whatever the complexity of the master mask is, for a printing duration of the order of the minute. This is a duplication method without any contact that prevents the master mask from any mechanical erosion. Alignment of the successive masks is obtained from an electric signal directly usable through an automatic alignment system. Experiments using the apparatus for reproducing masks through an electronic image or ''electronic duplicator'' developed in Thomson-CSF Laboratory at Corbeville, are presented [fr

  11. Holey carbon micro-arrays for transmission electron microscopy: A microcontact printing approach

    International Nuclear Information System (INIS)

    Chester, David W.; Klemic, James F.; Stern, Eric; Sigworth, Fred J.; Klemic, Kathryn G.

    2007-01-01

    We have used a microcontact printing approach to produce high quality and inexpensive holey carbon micro-arrays. Fabrication involves: (1) micromolding a poly(dimethylsiloxane) (PDMS) elastomer stamp from a microfabricated master that contains the desired array pattern; (2) using the PDMS stamp for microcontact printing a thin sacrificial plastic film that contains an array of holes; (3) floating the plastic film onto TEM grids; (4) evaporating carbon onto the plastic film and (5) removing the sacrificial plastic film. The final holey carbon micro-arrays are ready for use as support films in TEM applications with the fidelity of the original microfabricated pattern. This approach is cost effective as both the master and the stamps have long-term reusability. Arbitrary array patterns can be made with microfabricated masters made through a single-step photolithographic process

  12. Towards the integration, annotation and association of historical microarray experiments with RNA-seq.

    Science.gov (United States)

    Chavan, Shweta S; Bauer, Michael A; Peterson, Erich A; Heuck, Christoph J; Johann, Donald J

    2013-01-01

    Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via cluster assignment, and a 70 gene risk score. Both enabled an improved molecular understanding of MM, and have provided prognostic information for the purposes of clinical management. Many researchers are now transitioning to Next Generation Sequencing (NGS) approaches and RNA-seq in particular, due to its discovery-based nature, improved sensitivity, and dynamic range. Additionally, RNA-seq allows for the analysis of gene isoforms, splice variants, and novel gene fusions. Given the voluminous amounts of historical microarray data, there is now a need to associate and integrate microarray and RNA-seq data via advanced bioinformatic approaches. Custom software was developed following a model-view-controller (MVC) approach to integrate Affymetrix probe set-IDs, and gene annotation information from a variety of sources. The tool/approach employs an assortment of strategies to integrate, cross reference, and associate microarray and RNA-seq datasets. Output from a variety of transcriptome reconstruction and quantitation tools (e.g., Cufflinks) can be directly integrated, and/or associated with Affymetrix probe set data, as well as necessary gene identifiers and/or symbols from a diversity of sources. Strategies are employed to maximize the annotation and cross referencing process. Custom gene sets (e.g., MM 70 risk score (GEP-70)) can be specified, and the tool can be directly assimilated into an RNA-seq pipeline. A novel bioinformatic approach to aid in the facilitation of both annotation and association of historic microarray data, in conjunction with richer RNA-seq data, is now assisting with the study of MM cancer biology.

  13. Facility for electron cooling experiments

    International Nuclear Information System (INIS)

    Budker, G.I.; Dikanskij, N.S.; Kudelajnen, V.I.

    1982-01-01

    The NAP-M proton storage ring intended for electron cooling experiments is described. The NAP-M magnetic system comprises four bending magnets and eight correction elements. located at the ends of rectilinear gaps. An electron beam facility is located in one of the rectilinear gaps. An 1.5 MeV electrostatic accelerator is used as a proton injector. The NAP-M accelerating system includes a driving generator, a power amplifier and a resonator. The proton beam lifetime (at the RF-system switched-off) up to 7 s has been obtained at the NAP-N at the injection energy, and up to 600 s at 65 MeV and the proton current of 120 μA

  14. Close-To-Practice Assessment Of Meat Freshness With Metal Oxide Sensor Microarray Electronic Nose

    International Nuclear Information System (INIS)

    Musatov, V. Yu.; Sysoev, V. V.; Sommer, M.; Kiselev, I.

    2009-01-01

    In this report we estimate the ability of KAMINA e-nose, based on a metal oxide sensor (MOS) microarray and Linear Discriminant Analysis (LDA) pattern recognition, to evaluate meat freshness. The received results show that, 1) one or two exposures of standard meat samples to the e-nose are enough for the instrument to recognize the fresh meat prepared by the same supplier with 100% probability; 2) the meat samples of two kinds, stored at 4 deg. C and 25 deg. C, are mutually recognized at early stages of decay with the help of the LDA model built independently under the e-nose training to each kind of meat; 3) the 3-4 training cycles of exposure to meat from different suppliers are necessary for the e-nose to build a reliable LDA model accounting for the supplier factor. This study approves that the MOS e-nose is ready to be currently utilised in food industry for evaluation of product freshness. The e-nose performance is characterized by low training cost, a confident recognition power of various product decay conditions and easy adjustment to changing conditions.

  15. The tissue micro-array data exchange specification: a web based experience browsing imported data

    Science.gov (United States)

    Nohle, David G; Hackman, Barbara A; Ayers, Leona W

    2005-01-01

    Background The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11

  16. Automated detection of regions of interest for tissue microarray experiments: an image texture analysis

    International Nuclear Information System (INIS)

    Karaçali, Bilge; Tözeren, Aydin

    2007-01-01

    Recent research with tissue microarrays led to a rapid progress toward quantifying the expressions of large sets of biomarkers in normal and diseased tissue. However, standard procedures for sampling tissue for molecular profiling have not yet been established. This study presents a high throughput analysis of texture heterogeneity on breast tissue images for the purpose of identifying regions of interest in the tissue for molecular profiling via tissue microarray technology. Image texture of breast histology slides was described in terms of three parameters: the percentage of area occupied in an image block by chromatin (B), percentage occupied by stroma-like regions (P), and a statistical heterogeneity index H commonly used in image analysis. Texture parameters were defined and computed for each of the thousands of image blocks in our dataset using both the gray scale and color segmentation. The image blocks were then classified into three categories using the texture feature parameters in a novel statistical learning algorithm. These categories are as follows: image blocks specific to normal breast tissue, blocks specific to cancerous tissue, and those image blocks that are non-specific to normal and disease states. Gray scale and color segmentation techniques led to identification of same regions in histology slides as cancer-specific. Moreover the image blocks identified as cancer-specific belonged to those cell crowded regions in whole section image slides that were marked by two pathologists as regions of interest for further histological studies. These results indicate the high efficiency of our automated method for identifying pathologic regions of interest on histology slides. Automation of critical region identification will help minimize the inter-rater variability among different raters (pathologists) as hundreds of tumors that are used to develop an array have typically been evaluated (graded) by different pathologists. The region of interest

  17. Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments

    Science.gov (United States)

    Jourdren, Laurent; Duclos, Aurélie; Brion, Christian; Portnoy, Thomas; Mathis, Hugues; Margeot, Antoine; Le Crom, Stéphane

    2010-01-01

    Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/. PMID:20176570

  18. OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments

    Directory of Open Access Journals (Sweden)

    Arkin Adam P

    2006-01-01

    Full Text Available Abstract Background Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Conclusion Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

  19. DNA Microarray Technology; TOPICAL

    International Nuclear Information System (INIS)

    WERNER-WASHBURNE, MARGARET; DAVIDSON, GEORGE S.

    2002-01-01

    Collaboration between Sandia National Laboratories and the University of New Mexico Biology Department resulted in the capability to train students in microarray techniques and the interpretation of data from microarray experiments. These studies provide for a better understanding of the role of stationary phase and the gene regulation involved in exit from stationary phase, which may eventually have important clinical implications. Importantly, this research trained numerous students and is the basis for three new Ph.D. projects

  20. Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments

    Directory of Open Access Journals (Sweden)

    Kitchen Robert R

    2011-12-01

    Full Text Available Abstract Background Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR and individual or pooled breast-tumour RNA. Results A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependant upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content. Conclusions The magnitude of systematic

  1. Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments.

    Science.gov (United States)

    Kitchen, Robert R; Sabine, Vicky S; Simen, Arthur A; Dixon, J Michael; Bartlett, John M S; Sims, Andrew H

    2011-12-01

    Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR) and individual or pooled breast-tumour RNA. A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependent upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement) and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content. The magnitude of systematic processing noise in a microarray experiment is variable

  2. Mann-Whitney Type Tests for Microarray Experiments: The R Package gMWT

    Directory of Open Access Journals (Sweden)

    Daniel Fischer

    2015-06-01

    Full Text Available We present the R package gMWT which is designed for the comparison of several treatments (or groups for a large number of variables. The comparisons are made using certain probabilistic indices (PI. The PIs computed here tell how often pairs or triples of observations coming from different groups appear in a specific order of magnitude. Classical two and several sample rank test statistics such as the Mann-Whitney-Wilcoxon, Kruskal-Wallis, or Jonckheere-Terpstra test statistics are simple functions of these PI. Also new test statistics for directional alternatives are provided. The package gMWT can be used to calculate the variable-wise PI estimates, to illustrate their multivariate distribution and mutual dependence with joint scatterplot matrices, and to construct several classical and new rank tests based on the PIs. The aim of the paper is first to briefly explain the theory that is necessary to understand the behavior of the estimated PIs and the rank tests based on them. Second, the use of the package is described and illustrated with simulated and real data examples. It is stressed that the package provides a new flexible toolbox to analyze large gene or microRNA expression data sets, collected on microarrays or by other high-throughput technologies. The testing procedures can be used in an eQTL analysis, for example, as implemented in the package GeneticTools.

  3. A random variance model for detection of differential gene expression in small microarray experiments.

    Science.gov (United States)

    Wright, George W; Simon, Richard M

    2003-12-12

    Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true. We propose a model by which the within gene variances are drawn from an inverse gamma distribution, whose parameters are estimated across all genes. This results in a test statistic that is a minor variation of those used in standard linear models. We demonstrate that the model assumptions are valid on experimental data, and that the model has more power than standard tests to pick up large changes in expression, while not increasing the rate of false positives. This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf

  4. miRNAs in lung cancer - Studying complex fingerprints in patient's blood cells by microarray experiments

    Directory of Open Access Journals (Sweden)

    Huwer Hanno

    2009-10-01

    Full Text Available Abstract Background Deregulated miRNAs are found in cancer cells and recently in blood cells of cancer patients. Due to their inherent stability miRNAs may offer themselves for blood based tumor diagnosis. Here we addressed the question whether there is a sufficient number of miRNAs deregulated in blood cells of cancer patients to be able to distinguish between cancer patients and controls. Methods We synthesized 866 human miRNAs and miRNA star sequences as annotated in the Sanger miRBase onto a microarray designed by febit biomed gmbh. Using the fully automated Geniom Real Time Analyzer platform, we analyzed the miRNA expression in 17 blood cell samples of patients with non-small cell lung carcinomas (NSCLC and in 19 blood samples of healthy controls. Results Using t-test, we detected 27 miRNAs significantly deregulated in blood cells of lung cancer patients as compared to the controls. Some of these miRNAs were validated using qRT-PCR. To estimate the value of each deregulated miRNA, we grouped all miRNAs according to their diagnostic information that was measured by Mutual Information. Using a subset of 24 miRNAs, a radial basis function Support Vector Machine allowed for discriminating between blood cellsamples of tumor patients and controls with an accuracy of 95.4% [94.9%-95.9%], a specificity of 98.1% [97.3%-98.8%], and a sensitivity of 92.5% [91.8%-92.5%]. Conclusion Our findings support the idea that neoplasia may lead to a deregulation of miRNA expression in blood cells of cancer patients compared to blood cells of healthy individuals. Furthermore, we provide evidence that miRNA patterns can be used to detect human cancers from blood cells.

  5. Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments

    Directory of Open Access Journals (Sweden)

    Pistoia Vito

    2008-10-01

    Full Text Available Abstract Background Most microarray experiments are carried out with the purpose of identifying genes whose expression varies in relation with specific conditions or in response to environmental stimuli. In such studies, genes showing similar mean expression values between two or more groups are considered as not differentially expressed, even if hidden subclasses with different expression values may exist. In this paper we propose a new method for identifying differentially expressed genes, based on the area between the ROC curve and the rising diagonal (ABCR. ABCR represents a more general approach than the standard area under the ROC curve (AUC, because it can identify both proper (i.e., concave and not proper ROC curves (NPRC. In particular, NPRC may correspond to those genes that tend to escape standard selection methods. Results We assessed the performance of our method using data from a publicly available database of 4026 genes, including 14 normal B cell samples (NBC and 20 heterogeneous lymphomas (namely: 9 follicular lymphomas and 11 chronic lymphocytic leukemias. Moreover, NBC also included two sub-classes, i.e., 6 heavily stimulated and 8 slightly or not stimulated samples. We identified 1607 differentially expressed genes with an estimated False Discovery Rate of 15%. Among them, 16 corresponded to NPRC and all escaped standard selection procedures based on AUC and t statistics. Moreover, a simple inspection to the shape of such plots allowed to identify the two subclasses in either one class in 13 cases (81%. Conclusion NPRC represent a new useful tool for the analysis of microarray data.

  6. A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment

    NARCIS (Netherlands)

    Aguirre von Wobeser, E.; Huisman, J.; Ibelings, B.; Matthijs, H.C.P.; Matthijs, H.C.P.

    2005-01-01

    A newly designed 45 to 60 mer oligonucleotide Agilent platform microarray for global gene expression studies of Synechocystis PCC6803: example salt stress experiment Eneas Aguirre-von-Wobeser 1, Jef Huisman1, Bas Ibelings2 and Hans C.P. Matthijs1 1 Universiteit van Amsterdam, Amsterdam, The

  7. Experiences with remote electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    O' Keefe, Michael A.; Parvin, Bahram

    2002-02-22

    With the advent of a rapidly proliferating international computer network, it became feasible to consider remote operation of instrumentation normally operated locally. For modern electron microscopes, the growing automation and computer control of many instrumental operations facilitated the task of providing remote operation. In order to provide use of NCEM TEMs by distant users, a project was instituted in 1995 to place a unique instrument, a Kratos EM-1500 operating at 1.5MeV, on-line for remote use. In 1996, the Materials Microcharacterization Collaboratory (MMC) was created as a pilot project within the US Department of Energy's DOE2000 program to establish national collaboratories to provide access via the Internet to unique or expensive DOE research facilities as well as to expertise for remote collaboration, experimentation, production, software development, modeling, and measurement. A major LBNL contribution to the MMC was construction of DeepView, a microscope-independent computer-control system that could be ported to other MMC members to provide a common graphical user-interface (GUI) for control of any MMC instrument over the wide area network.

  8. Optimising electron microscopy experiment through electron optics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kubo, Y. [CEMES-CNRS, 29 Rue Jeanne Marvig, 31055 Toulouse France (France); Hitachi High-Technologies Corporation, 882, Ichige, Hitachinaka, Ibaraki 312-8504 (Japan); Gatel, C.; Snoeck, E. [CEMES-CNRS, 29 Rue Jeanne Marvig, 31055 Toulouse France (France); Houdellier, F., E-mail: florent.houdellier@cemes.fr [CEMES-CNRS, 29 Rue Jeanne Marvig, 31055 Toulouse France (France)

    2017-04-15

    We developed a new type of electron trajectories simulation inside a complete model of a modern transmission electron microscope (TEM). Our model incorporates the precise and real design of each element constituting a TEM, i.e. the field emission (FE) cathode, the extraction optic and acceleration stages of a 300 kV cold field emission gun, the illumination lenses, the objective lens, the intermediate and projection lenses. Full trajectories can be computed using magnetically saturated or non-saturated round lenses, magnetic deflectors and even non-cylindrical symmetry elements like electrostatic biprism. This multi-scale model gathers nanometer size components (FE tip) with parts of meter length (illumination and projection systems). We demonstrate that non-trivial TEM experiments requiring specific and complex optical configurations can be simulated and optimized prior to any experiment using such model. We show that all the currents set in all optical elements of the simulated column can be implemented in the real column (I2TEM in CEMES) and used as starting alignment for the requested experiment. We argue that the combination of such complete electron trajectory simulations in the whole TEM column with automatic optimization of the microscope parameters for optimal experimental data (images, diffraction, spectra) allows drastically simplifying the implementation of complex experiments in TEM and will facilitate the development of advanced use of the electron microscope in the near future. - Highlights: • Using dedicated electron optics software, we calculate full electrons trajectories inside a modern transmission electron microscope. • We have determined how to deal with multi-scale electron optics elements like high voltage cold field emission source. • W • e have succeed to model both weak and strong magnetic lenses whether in saturated or unsaturated conditions as well as electrostatic biprism and magnetic deflectors. • We have applied this model

  9. Optimising electron microscopy experiment through electron optics simulation

    International Nuclear Information System (INIS)

    Kubo, Y.; Gatel, C.; Snoeck, E.; Houdellier, F.

    2017-01-01

    We developed a new type of electron trajectories simulation inside a complete model of a modern transmission electron microscope (TEM). Our model incorporates the precise and real design of each element constituting a TEM, i.e. the field emission (FE) cathode, the extraction optic and acceleration stages of a 300 kV cold field emission gun, the illumination lenses, the objective lens, the intermediate and projection lenses. Full trajectories can be computed using magnetically saturated or non-saturated round lenses, magnetic deflectors and even non-cylindrical symmetry elements like electrostatic biprism. This multi-scale model gathers nanometer size components (FE tip) with parts of meter length (illumination and projection systems). We demonstrate that non-trivial TEM experiments requiring specific and complex optical configurations can be simulated and optimized prior to any experiment using such model. We show that all the currents set in all optical elements of the simulated column can be implemented in the real column (I2TEM in CEMES) and used as starting alignment for the requested experiment. We argue that the combination of such complete electron trajectory simulations in the whole TEM column with automatic optimization of the microscope parameters for optimal experimental data (images, diffraction, spectra) allows drastically simplifying the implementation of complex experiments in TEM and will facilitate the development of advanced use of the electron microscope in the near future. - Highlights: • Using dedicated electron optics software, we calculate full electrons trajectories inside a modern transmission electron microscope. • We have determined how to deal with multi-scale electron optics elements like high voltage cold field emission source. • W • e have succeed to model both weak and strong magnetic lenses whether in saturated or unsaturated conditions as well as electrostatic biprism and magnetic deflectors. • We have applied this model

  10. Operational experience with SLAC's beam containment electronics

    International Nuclear Information System (INIS)

    Constant, T.N.; Crook, K.; Heggie, D.

    1977-03-01

    Considerable operating experience was accumulated at SLAC with an extensive electronic system for the containment of high power accelerated beams. Average beam power at SLAC can approach 900 kilowatts with the potential for burning through beam stoppers, protection collimators, and other power absorbers within a few seconds. Fast, reliable, and redundant electronic monitoring circuits have been employed to provide some of the safeguards necessary for minimizing the risk to personnel. The electronic systems are described, and the design philosophy and operating experience are discussed

  11. Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening

    Directory of Open Access Journals (Sweden)

    Vitulli Federico

    2008-04-01

    Full Text Available Abstract Background Since its discovery more than 100 years ago, potato (Solanum tuberosum tuber cold-induced sweetening (CIS has been extensively investigated. Several carbohydrate-associated genes would seem to be involved in the process. However, many uncertainties still exist, as the relative contribution of each gene to the process is often unclear, possibly as the consequence of the heterogeneity of experimental systems. Some enzymes associated with CIS, such as β-amylases and invertases, have still to be identified at a sequence level. In addition, little is known about the early events that trigger CIS and on the involvement/association with CIS of genes different from carbohydrate-associated genes. Many of these uncertainties could be resolved by profiling experiments, but no GeneChip is available for the potato, and the production of the potato cDNA spotted array (TIGR has recently been discontinued. In order to obtain an overall picture of early transcriptional events associated with CIS, we investigated whether the commercially-available tomato Affymetrix GeneChip could be used to identify which potato cold-responsive gene family members should be further studied in detail by Real-Time (RT-PCR (qPCR. Results A tomato-potato Global Match File was generated for the interpretation of various aspects of the heterologous dataset, including the retrieval of best matching potato counterparts and annotation, and the establishment of a core set of highly homologous genes. Several cold-responsive genes were identified, and their expression pattern was studied in detail by qPCR over 26 days. We detected biphasic behaviour of mRNA accumulation for carbohydrate-associated genes and our combined GeneChip-qPCR data identified, at a sequence level, enzymatic activities such as β-amylases and invertases previously reported as being involved in CIS. The GeneChip data also unveiled important processes accompanying CIS, such as the induction of redox

  12. Direct calibration of PICKY-designed microarrays

    Directory of Open Access Journals (Sweden)

    Ronald Pamela C

    2009-10-01

    Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

  13. The intraclass correlation coefficient applied for evaluation of data correction, labeling methods and rectal biopsy sampling in DNA microarray experiments

    NARCIS (Netherlands)

    Pellis, E.P.M.; Franssen-Hal, van N.L.W.; Burema, J.; Keijer, J.

    2003-01-01

    We show that the intraclass correlation coefficient (ICC) can be used as a relatively simple statistical measure to assess methodological and biological variation in DNA microarray analysis. The ICC is a measure that determines the reproducibility of a variable, which can easily be calculated from

  14. Electron beam optics for the FEL experiment and IFEL experiment

    International Nuclear Information System (INIS)

    van Steenbergen, A.

    1990-01-01

    Electron beam transport system parameters for the FEL experiment and for the FEL experiment are given. The perturbation of the ''interaction region'' optics due to wiggler focussing is taken into account and a range of solutions are provided for relevant Twiss parameters in the FEL or IFEL region. Modifications of the transport optics in specific sections of the overall beam transport lines, for reasons of enhanced diagnostic capability or enhanced beam momentum analysis resolution, is also presented

  15. Modeling the Nab Experiment Electronics in SPICE

    Science.gov (United States)

    Blose, Alexander; Crawford, Christopher; Sprow, Aaron; Nab Collaboration

    2017-09-01

    The goal of the Nab experiment is to measure the neutron decay coefficients a, the electron-neutrino correlation, as well as b, the Fierz interference term to precisely test the Standard Model, as well as probe for Beyond the Standard Model physics. In this experiment, protons from the beta decay of the neutron are guided through a magnetic field into a Silicon detector. Event reconstruction will be achieved via time-of-flight measurement for the proton and direct measurement of the coincident electron energy in highly segmented silicon detectors, so the amplification circuitry needs to preserve fast timing, provide good amplitude resolution, and be packaged in a high-density format. We have designed a SPICE simulation to model the full electronics chain for the Nab experiment in order to understand the contributions of each stage and optimize them for performance. Additionally, analytic solutions to each of the components have been determined where available. We will present a comparison of the output from the SPICE model, analytic solution, and empirically determined data.

  16. Free-electron laser experiments in the microwave tokamak experiment

    International Nuclear Information System (INIS)

    Allen, S.L.; Brown, M.D.; Byers, J.A.; Casper, T.A.; Cohen, B.I.; Cohen, R.H.; Cummings, J.C.; Fenstermacher, M.E.; Foote, J.H.; Hooper, E.B.; Jong, R.A.; Langdon, A.B.; Lasinski, B.F.; Lasnier, C.J.; Matsuda, Y.; Meyer, W.H.; Moller, J.M.; Nexsen, W.E.; Rice, B.W.; Rognlien, T.D.; Smith, G.R.; Stallard, B.W.; Thomassen, K.I.; Throop, A.L.; Turner, W.C.; Wood, R.D.; Cook, D.R.; Makowski, M.A.; Oasa, K.; Ogawa, T.

    1990-08-01

    Microwave pulses have been injected from a free electron-laser (FEL) into the Microwave Tokamak Experiment (MTX) at up to 0.2 GW at 140 GHz in short pulses (10-ns duration) with O-mode polarization. The power transmitted through the plasma was measured in a first experimental study of high power pulse propagation in the plasma; no nonlinear effects were found at this power level. Calculations indicate that nonlinear effects may be found at the higher power densities expected in future experiments. 9 refs., 2 figs

  17. A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments

    Directory of Open Access Journals (Sweden)

    Vassal Aurélien

    2008-01-01

    Full Text Available Abstract Background The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types for class prediction of limited sample populations. Affymetrix® technology provides both a quantitative fluorescence signal and a decision (detection call: absent or present based on signed-rank algorithms applied to several hybridization repeats of each gene, with a per-chip normalization. We developed a new prediction method for class belonging based on the detection call only from recent Affymetrix chip type. Biological data were obtained by hybridization on U133A, U133B and U133Plus 2.0 microarrays of purified normal B cells and cells from three independent groups of multiple myeloma (MM patients. Results After a call-based data reduction step to filter out non class-discriminative probe sets, the gene list obtained was reduced to a predictor with correction for multiple testing by iterative deletion of probe sets that sequentially improve inter-class comparisons and their significance. The error rate of the method was determined using leave-one-out and 5-fold cross-validation. It was successfully applied to (i determine a sex predictor with the normal donor group classifying gender with no error in all patient groups except for male MM samples with a Y chromosome deletion, (ii predict the immunoglobulin light and heavy chains expressed by the malignant myeloma clones of the validation group and (iii predict sex, light and heavy chain nature for every new patient. Finally, this method was shown powerful when compared to the popular classification method Prediction Analysis of Microarray (PAM. Conclusion This normalization-free method is routinely used for quality control and correction of collection errors in patient reports to clinicians. It can be easily extended to multiple class prediction suitable with

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

    Science.gov (United States)

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

    2016-11-01

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

  19. Electronic trigger for the ASP experiment

    International Nuclear Information System (INIS)

    Wilson, R.J.

    1985-11-01

    The Anomalous Single Photon (ASP) electronic trigger is described. The experiments is based on an electromagnetic calorimeter composed of arrays of lead glass blocks, read out with photo-multiplier tubes, surrounding the interaction point at the PEP storage ring. The primary requirement of the trigger system is to be sensitive to low energy (approx. =0.5 GeV and above) photons whilst discriminating against high backgrounds at PEP. Analogue summing of the PMT signals and a sequence of programmable digital look-up tables produces a ''dead-timeless'' trigger for the beam collision rate of 408 kHz. 6 refs., 6 figs

  20. Identification of Differentially Expressed IGFBP5-Related Genes in Breast Cancer Tumor Tissues Using cDNA Microarray Experiments.

    Science.gov (United States)

    Akkiprik, Mustafa; Peker, İrem; Özmen, Tolga; Amuran, Gökçe Güllü; Güllüoğlu, Bahadır M; Kaya, Handan; Özer, Ayşe

    2015-11-10

    IGFBP5 is an important regulatory protein in breast cancer progression. We tried to identify differentially expressed genes (DEGs) between breast tumor tissues with IGFBP5 overexpression and their adjacent normal tissues. In this study, thirty-eight breast cancer and adjacent normal breast tissue samples were used to determine IGFBP5 expression by qPCR. cDNA microarrays were applied to the highest IGFBP5 overexpressed tumor samples compared to their adjacent normal breast tissue. Microarray analysis revealed that a total of 186 genes were differentially expressed in breast cancer compared with normal breast tissues. Of the 186 genes, 169 genes were downregulated and 17 genes were upregulated in the tumor samples. KEGG pathway analyses showed that protein digestion and absorption, focal adhesion, salivary secretion, drug metabolism-cytochrome P450, and phenylalanine metabolism pathways are involved. Among these DEGs, the prominent top two genes (MMP11 and COL1A1) which potentially correlated with IGFBP5 were selected for validation using real time RT-qPCR. Only COL1A1 expression showed a consistent upregulation with IGFBP5 expression and COL1A1 and MMP11 were significantly positively correlated. We concluded that the discovery of coordinately expressed genes related with IGFBP5 might contribute to understanding of the molecular mechanism of the function of IGFBP5 in breast cancer. Further functional studies on DEGs and association with IGFBP5 may identify novel biomarkers for clinical applications in breast cancer.

  1. Electron cooling experiments at the ESR

    International Nuclear Information System (INIS)

    Steck, M.; Beller, P.; Beckert, K.; Franzke, B.; Nolden, F.

    2004-01-01

    The properties of electron cooled beams of highly charged ions have been studied at the ESR. New experiments using a beam scraper to determine the transverse beam size provide the beam parameters in the intrabeam scattering dominated intensity regime, but also at very low intensity when the ion beam enters into an ultra-cold state. Extremely low values of longitudinal and transverse beam temperature on the order of meV were achieved for less than 1000 stored ions. An experiment with bunched ultra-cold beam showed a limit of the line density which agrees with the one observed for coasting beams. Cooling of decelerated ions at a minimum energy of 3 MeV/u has been demonstrated recently

  2. Electron collisions—experiment, theory, and applications

    Science.gov (United States)

    Bartschat, Klaus

    2018-07-01

    Electron collisions with atoms, ions, and molecules have represented an important area of ‘applied quantum mechanics’ for more than a century. This Topical Review is the write-up of the Allis Prize Lecture given by the author at the 2016 meeting of the Division of Atomic, Molecular, and Optical Physics of the American Physical Society and the 2017 Gaseous Electronics Conference. In light of the enormous size of the field, the examples presented were selected in order to tell the story of how experimental and theoretical/numerical methods have developed over time, how fruitful collaborations between data producers (experimentalists and theorists) and data users have led to significant progress, and how the results of these studies, which were often designed for fundamental research in order to push both experiment and theory to new frontiers, continue to be highly sought after for modeling applications in a variety of fields. The impact of electron collision studies on other fields, such as photoinduced processes and quantum information, is also discussed.

  3. Complete experiments in electron-atom collisions

    International Nuclear Information System (INIS)

    Anderson, N.; Bartschat, K.

    1996-01-01

    This paper addresses the advances up to the present in complete electron-atom collision experiments. The aim is to present a series of key examples for fundamental scattering processes, together with the experimental techniques that have been used. The purpose is not a full presentation of all processes studied, nor of all data that have been accumulated; rather, it is to select examples of the most recent theoretical and experimental results that will enable the reader to assess the present level of achievement. We hope that the power of this approach will become evident along the way, in the sense that it provides an efficient framework for a systematic, and complete test of the current theoretical understanding. In addition, it may produce specific recipes for ways to select experimental geometries that most efficiently test theoretical predictions, and it may reveal connections between apparently unrelated observables from often very different and highly sophisticated experiments, thus providing valuable consistency checks. The presentation is structured in the following way. To begin with, a general analysis of scattering amplitude properties concludes in a recipe for determination of the number of independent parameters necessary to define a complete experiment for a given process. We then proceed to analyze in a systematic way a string of specific cases of elastic and inelastic collisions, with gradually increasing levels of sophistication. Finally, we comment on directions in which future studies could fruitfully be pursued. 77 refs., 53 figs

  4. The ALTA cosmic ray experiment electronics system

    International Nuclear Information System (INIS)

    Brouwer, W.; Burris, W.J.; Caron, B.; Hewlett, J.; Holm, L.; Hamilton, A.; McDonald, W.J.; Pinfold, J.L.; Price, P.; Schaapman, J.R.; Sibley, L.; Soluk, R.A.; Wampler, L.J.

    2005-01-01

    Understanding the origin and propagation of high-energy cosmic rays is a fundamental area of astroparticle physics with major unanswered questions. The study of cosmic rays with energy more than 10 14 eV, probed only by ground-based experiments, has been restricted by the low particle flux. The Alberta Large-area Time-coincidence Array (ALTA) uses a sparse array of cosmic ray detection stations located in high schools across a large geographical area to search for non-random high-energy cosmic ray phenomena. Custom-built ALTA electronics is based on a modular board design. Its function is to control the detectors at each ALTA site allowing precise measurements of event timing and energy in the local detectors as well as time synchronization of all of the sites in the array using the global positioning system

  5. miRNAs in lung cancer - Studying complex fingerprints in patient's blood cells by microarray experiments

    International Nuclear Information System (INIS)

    Keller, Andreas; Leidinger, Petra; Borries, Anne; Wendschlag, Anke; Wucherpfennig, Frank; Scheffler, Matthias; Huwer, Hanno; Lenhof, Hans-Peter; Meese, Eckart

    2009-01-01

    Deregulated miRNAs are found in cancer cells and recently in blood cells of cancer patients. Due to their inherent stability miRNAs may offer themselves for blood based tumor diagnosis. Here we addressed the question whether there is a sufficient number of miRNAs deregulated in blood cells of cancer patients to be able to distinguish between cancer patients and controls. We synthesized 866 human miRNAs and miRNA star sequences as annotated in the Sanger miRBase onto a microarray designed by febit biomed gmbh. Using the fully automated Geniom Real Time Analyzer platform, we analyzed the miRNA expression in 17 blood cell samples of patients with non-small cell lung carcinomas (NSCLC) and in 19 blood samples of healthy controls. Using t-test, we detected 27 miRNAs significantly deregulated in blood cells of lung cancer patients as compared to the controls. Some of these miRNAs were validated using qRT-PCR. To estimate the value of each deregulated miRNA, we grouped all miRNAs according to their diagnostic information that was measured by Mutual Information. Using a subset of 24 miRNAs, a radial basis function Support Vector Machine allowed for discriminating between blood cellsamples of tumor patients and controls with an accuracy of 95.4% [94.9%-95.9%], a specificity of 98.1% [97.3%-98.8%], and a sensitivity of 92.5% [91.8%-92.5%]. Our findings support the idea that neoplasia may lead to a deregulation of miRNA expression in blood cells of cancer patients compared to blood cells of healthy individuals. Furthermore, we provide evidence that miRNA patterns can be used to detect human cancers from blood cells

  6. Microstrip resonators for electron paramagnetic resonance experiments

    Science.gov (United States)

    Torrezan, A. C.; Mayer Alegre, T. P.; Medeiros-Ribeiro, G.

    2009-07-01

    In this article we evaluate the performance of an electron paramagnetic resonance (EPR) setup using a microstrip resonator (MR). The design and characterization of the resonator are described and parameters of importance to EPR and spin manipulation are examined, including cavity quality factor, filling factor, and microwave magnetic field in the sample region. Simulated microwave electric and magnetic field distributions in the resonator are also presented and compared with qualitative measurements of the field distribution obtained by a perturbation technique. Based on EPR experiments carried out with a standard marker at room temperature and a MR resonating at 8.17 GHz, the minimum detectable number of spins was found to be 5×1010 spins/GHz1/2 despite the low MR unloaded quality factor Q0=60. The functionality of the EPR setup was further evaluated at low temperature, where the spin resonance of Cr dopants present in a GaAs wafer was detected at 2.3 K. The design and characterization of a more versatile MR targeting an improved EPR sensitivity and featuring an integrated biasing circuit for the study of samples that require an electrical contact are also discussed.

  7. Microstrip resonators for electron paramagnetic resonance experiments.

    Science.gov (United States)

    Torrezan, A C; Mayer Alegre, T P; Medeiros-Ribeiro, G

    2009-07-01

    In this article we evaluate the performance of an electron paramagnetic resonance (EPR) setup using a microstrip resonator (MR). The design and characterization of the resonator are described and parameters of importance to EPR and spin manipulation are examined, including cavity quality factor, filling factor, and microwave magnetic field in the sample region. Simulated microwave electric and magnetic field distributions in the resonator are also presented and compared with qualitative measurements of the field distribution obtained by a perturbation technique. Based on EPR experiments carried out with a standard marker at room temperature and a MR resonating at 8.17 GHz, the minimum detectable number of spins was found to be 5 x 10(10) spins/GHz(1/2) despite the low MR unloaded quality factor Q0=60. The functionality of the EPR setup was further evaluated at low temperature, where the spin resonance of Cr dopants present in a GaAs wafer was detected at 2.3 K. The design and characterization of a more versatile MR targeting an improved EPR sensitivity and featuring an integrated biasing circuit for the study of samples that require an electrical contact are also discussed.

  8. An inverse free electron laser accelerator experiment

    International Nuclear Information System (INIS)

    Wernick, I.; Marshall, T.C.

    1992-01-01

    A free electron laser was configured as an autoaccelerator to test the principle of accelerating electrons by stimulated absorption of radiation (λ = 1.65mm) by an electron beam (750kV) traversing an undulator. Radiation is produced in the first section of a constant period undulator (1 w1 = 1.43cm) and then absorbed (∼ 40%) in a second undulator, having a tapered period (1 w2 = 1.8 - 2.25cm), which results in the acceleration of a subgroup (∼ 9%) of electrons to ∼ 1MeV

  9. Experience with spice teaching power electronics

    DEFF Research Database (Denmark)

    Munk-Nielsen, Stig

    2009-01-01

    A free Spice version allowing general circuit simulation is used teaching power electronics. There is no lock on the circuit size, stabile and user friendly operation is experienced. A collection of transformer, converter and drive system models are implemented to investigate the usability...... of the programme in high power electronics....

  10. The EADGENE Microarray Data Analysis Workshop

    DEFF Research Database (Denmark)

    de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

    2007-01-01

    Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

  11. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-01-01

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

  12. Experiments with polarized electron beams at SLAC

    International Nuclear Information System (INIS)

    Cooper, P.

    1977-01-01

    Elastic and deep inelastic scattering of electrons on protons are studied. Cross sections for elastic scattering are plotted, and the parity nonconservation and neutral currents are diagramed for the deep inelastic scattering

  13. 6. workshop on electronics for LHC experiments. Proceedings

    International Nuclear Information System (INIS)

    2000-01-01

    The purpose of the workshop was to review the electronics for LHC experiments and to identify areas and encourage common efforts for the development of electronics within and between the different LHC experiments and to promote collaboration in the engineering and physics communities involved in the LHC activities. (orig.)

  14. 6. workshop on electronics for LHC experiments. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-10-25

    The purpose of the workshop was to review the electronics for LHC experiments and to identify areas and encourage common efforts for the development of electronics within and between the different LHC experiments and to promote collaboration in the engineering and physics communities involved in the LHC activities. (orig.)

  15. Electron characterization in OPERA Experiment; Caracterisation des electrons dans l'experience OPERA

    Energy Technology Data Exchange (ETDEWEB)

    Caffari, Yvan [Institut de Physique Nucleaire de Lyon, 4, Rue Enrico Fermi, 69622 Villeurbanne Cedex (France); Universite Claude Bernard Lyon-I, 43 boulevard du 11 Novembre 1918, 69622 Villeurbanne cedex (France)

    2006-09-15

    In 1998 by making use of a water Cherenkov detector the Super-Kamiokande Experiment in Japan has measured a deficit of {nu}{sub {tau}} atmospheric neutrinos without observing a corresponding rise in the {nu}{sub e} flux. This phenomenon is understood as neutrino oscillations, a mechanism implying a non vanishing neutrino mass. In 1999 the CHOOZ Experiment has definitely excluded the oscillations {nu}{sub {mu}} {yields} {nu}{sub e} within atmosphere. The OPERA Experiment aims at evidencing the {nu}{sub {mu}} {yields} {nu}{sub {tau}}oscillations through occurrence of {nu}{sub {tau}} and of {nu}{sub {mu}} {yields} {nu}{sub e} oscillations by occurrence of {nu}{sub e} starting from a muon neutrino beam almost totally clean. Such a beam is actually produced at CERN (CNGS beam) in Switzerland and then directed upon the OPERA detector located 732 km southward under Gran Sasso mountains in Italy. The detector consists of more than 200,000 bricks (what amounts to a total mass of 1,800 tons made up of a nuclear emulsion foils / lead foils sandwich. This module structure allows reconstructing with a high spatial resolution ({delta}{sub {theta}} {approx_equal} 1 mrad and {delta}{sub r} {approx_equal} 1 {mu}m) the kink topology created by the {tau} lepton (issued from charged current interaction of a {nu}{sub {tau}} lepton with a lead nucleus) and its decay products. The work reported in this thesis consists in characterization of the electrons needed in the study of {nu}{sub {mu}} {yields} {nu}{sub {tau}}oscillations, with {tau} {yields} e, and the {nu}{sub {mu}} {yields} {nu}{sub e} oscillations, the {nu}{sub e} interacting through charged currents with a lead nucleus and producing an electron. A reconstruction algorithm of the electromagnetic cascades in nuclear emulsion was developed. This algorithm allows reproducing the longitudinal and transverse profiles used in evaluating the electron energies and their identification as well ({pi}/e separation by mean of a neuron

  16. Electron beam facility for divertor target experiments

    International Nuclear Information System (INIS)

    Anisimov, A.; Gagen-Torn, V.; Giniyatulin, R.N.

    1994-01-01

    To test different concepts of divertor targets and bumpers an electron beam facility was assembled in Efremov Institute. It consists of a vacuum chamber (3m 3 ), vacuum pump, electron beam gun, manipulator to place and remove the samples, water loop and liquid metal loop. The following diagnostics of mock-ups is stipulated: (1) temperature distribution on the mock-up working surface (scanning pyrometer and infra-red imager); (2) temperature distribution over mocked-up thickness in 3 typical cross-sections (thermo-couples); (3) cracking dynamics during thermal cycling (acoustic-emission method), (4) defects in the mock-up before and after tests (ultra-sonic diagnostics, electron and optical microscopes). Carbon-based and beryllium mock-ups are made for experimental feasibility study of water and liquid-metal-cooled divertor/bumper concepts

  17. Low noise electronics for experiments at LHC

    International Nuclear Information System (INIS)

    Manfredi, P.F.

    1984-01-01

    The need of reducing the collection times of solid state detectors will lead to thin layers, 150 to 200 μm thickness. Consequently, the charge made available by minimum ionizing particles will be rather small, between 1.2 x 10 4 and 1.6 x 10 4 electrons for unity muliplicity. Front-end electronics with adequately low noise must be designed to detect such small amounts of charge and the problem looks to be harder if the short times available to process the signals are accounted for. (orig.)

  18. The learning experience with electronic museum guides

    NARCIS (Netherlands)

    Bartneck, C.; Masuoka, A.; Takahashi, T.; Fukaya, T.

    2006-01-01

    Within the contextual model of learning framework, the authors conducted a study with electronic handheld guides at the Van Abbemuseum (Eindhoven, the Netherlands). This study investigated the influence that limiting users' freedom of choice and control by facilitated mediation of others has on

  19. Plasma wave observations during electron and ion gun experiments

    International Nuclear Information System (INIS)

    Olsen, R.C.; Lowery, D.R.; Weddle, L.E.

    1988-01-01

    Plasma wave instruments with high temporal and frequency resolution in the 0-6 kHz frequency range have been used to monitor electron gun-employing charge control experiments with the USAF/NASA p78-2 satellite, in order to determine whether plasma wave signatures consistent with the previous inference of electron heating were present. Strong plasma waves were noted near the electron gyrofrequency; these waves can heat ambient low energy electrons, as previously inferred. Attention is given to the two distinct classes of behavior revealed by the ion gun experiments. 16 references

  20. Coulomb Interactions in Hanbury Brown-Twiss Experiments with Electrons

    Science.gov (United States)

    Shen, Kan

    2009-01-01

    This dissertation examines the effect of Coulomb interactions in Hanbury Brown-Twiss (HBT) type experiments with electrons. HBT experiments deal with intensity interference, which is related to the second-order correlation function of the particle field. This is an extension of the usual amplitude interference experiment, such as Young's…

  1. Fibre optic microarrays.

    Science.gov (United States)

    Walt, David R

    2010-01-01

    This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical fibres and arrays, the different microarray architectures, and describes a multitude of applications. Such arrays enable multiplexed sensing for a variety of analytes including nucleic acids, vapours, and biomolecules. Polymer-coated fibre arrays can be used for measuring microscopic chemical phenomena, such as corrosion and localized release of biochemicals from cells. In addition, these microarrays can serve as a substrate for fundamental studies of single molecules and single cells. The review covers topics of interest to chemists, biologists, materials scientists, and engineers.

  2. The electron accelerator for the AWAKE experiment at CERN

    Energy Technology Data Exchange (ETDEWEB)

    Pepitone, K., E-mail: kevin.pepitone@cern.ch [CERN, Geneva (Switzerland); Doebert, S., E-mail: steffen.doebert@cern.ch [CERN, Geneva (Switzerland); Burt, G. [The University of Lancaster, Lancaster (United Kingdom); Chevallay, E.; Chritin, N.; Delory, C.; Fedosseev, V.; Hessler, Ch.; McMonagle, G. [CERN, Geneva (Switzerland); Mete, O. [The University of Manchester, Manchester (United Kingdom); Verzilov, V. [Triumf, Vancouver (Canada); Apsimon, R. [The University of Lancaster, Lancaster (United Kingdom)

    2016-09-01

    The AWAKE collaboration prepares a proton driven plasma wakefield acceleration experiment using the SPS beam at CERN. A long proton bunch extracted from the SPS interacts with a high power laser and a 10 m long rubidium vapour plasma cell to create strong wakefields allowing sustained electron acceleration. The electron bunch to probe these wakefields is supplied by a 20 MeV electron accelerator. The electron accelerator consists of an RF-gun and a short booster structure. This electron source should provide beams with intensities between 0.1 and 1 nC, bunch lengths between 0.3 and 3 ps and an emittance of the order of 2 mm mrad. The wide range of parameters should cope with the uncertainties and future prospects of the planned experiments. The layout of the electron accelerator, its instrumentation and beam dynamics simulations are presented.

  3. A control system for a free electron laser experiment

    International Nuclear Information System (INIS)

    Giove, D.

    1992-01-01

    The general layout of a control and data acquisition system for a Free Electron Laser experiment will be discussed. Some general considerations about the requirements and the architecture of the whole system will be developed. (author)

  4. Strategy for the procurement of electronics for the LHC experiments

    CERN Document Server

    2002-01-01

    At its meeting on 14 March 2001 the Finance Committee requested the preparation of a document outlining the strategy for future procurement of electronics for the LHC experiments. The bulk of the electronics for the LHC experiments is based on custom-developed designs, the manufacturing of which will be contracted out to industry using the CERN purchasing procedures to ensure competitive prices. Analysis of on-going procurement activities for the electronics for the LHC experiments shows that in almost all cases the application of the CERN purchasing procedures has resulted in bids from a sufficient number of qualified companies to ensure competitive prices and a reasonable distribution of returns between CERN Member States. There is no reason to expect that this pattern will change significantly for the electronics that still remains to be purchased to complete the construction of the LHC experiments.

  5. High-efficiency free-electron-laser experiments

    International Nuclear Information System (INIS)

    Boyer, K.; Brau, C.A.; Goldstein, J.C.; Hohla, K.L.; Newnam, B.E.; Stein, W.E.; Warren, R.W.; Winston, J.G.

    1983-01-01

    Experiments with a tapered-wiggler free-electron laser have demonstrated extraction of about 3% of the energy from the electron beam and measured the corresponding optical emission. These results are in excellent agreement with theory and represent an order-of-magnitude improvement over all previous results

  6. The Heisenberg Uncertainty Principle Demonstrated with An Electron Diffraction Experiment

    Science.gov (United States)

    Matteucci, Giorgio; Ferrari, Loris; Migliori, Andrea

    2010-01-01

    An experiment analogous to the classical diffraction of light from a circular aperture has been realized with electrons. The results are used to introduce undergraduate students to the wave behaviour of electrons. The diffraction fringes produced by the circular aperture are compared to those predicted by quantum mechanics and are exploited to…

  7. Quantum Hall Effect: proposed multi-electron tunneling experiment

    International Nuclear Information System (INIS)

    Kostadinov, I.Z.

    1985-11-01

    Here we propose a tunneling experiment for the fractional and Integral Quantum Hall Effect. It may demonstrate multi-electron tunneling and may provide information about the nature of the macroscopic quantum states of 2D electronic liquid or solid. (author)

  8. DNA Microarray Technology

    Science.gov (United States)

    Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...

  9. Electron identification capabilities of the CBM experiment at FAIR

    Energy Technology Data Exchange (ETDEWEB)

    Hoehne, Claudia; Kisel, Ivan [GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); Lebedev, Semen [GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna (Russian Federation); Ososkov, Gennady [Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna (Russian Federation)

    2010-07-01

    The Compressed Baryonic Matter (CBM) experiment at the future FAIR facility at Darmstadt will measure dileptons emitted from the hot and dense phase in heavy-ion collisions. In case of an electron measurement, a high purity of identified electrons is required in order to suppress the background. Electron identification in CBM will be performed by a RICH and TRD detectors. In this contribution, methods which have been developed for the electron identification in CBM are presented. A fast and efficient RICH ring recognition algorithm based on the Hough Transform has been implemented. An ellipse fitting algorithm has been elaborated because most of the CBM RICH rings have elliptic shapes. An Artificial Neural Network can be used in order to suppress fake rings. The electron identification in RICH is substantially improved by the use of TRD detectors for which several different algorithms for electron identification are implemented. Results of electron identification and pion suppression are presented.

  10. Electron Neutrino Appearance in the MINOS Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Holin, Anna Maria [Univ. College London, Bloomsbury (United Kingdom)

    2010-02-01

    The MINOS experiment is a long-baseline neutrino oscillation experiment which sends a high intensity muon neutrino beam through two functionally identical detectors, a Near detector at the Fermi National Accelerator Laboratory in Illinois, 1km from the beam source, and a Far detector, 734km away, in the Soudan Mine in Minnesota. MINOS may be able to measure the neutrino mixing angle parameter sin213 for the rst time. Detector granularity, however, makes it very hard to distinguish any e appearance signal events characteristic of a non-zero value of θ 13 from background neutral current (NC) and short-track vμ charged current (CC) events. Also, uncertainties in the hadronic shower modeling in the kinematic region characteristic of this analysis are relatively large. A new data-driven background decomposition method designed to address those issues is developed and its results presented. By removing the long muon tracks from vμ-CC events, the Muon Removed Charge Current (MRCC) method creates independent pseudo-NC samples that can be used to correct the MINOS Monte Carlo to agree with the high-statistics Near detector data and to decompose the latter into components so as to predict the expected Far detector background. The MRCC method also provides an important cross-check in the Far detector to test the background in the signal selected region. MINOS finds a 1.0-1.5 σ ve-CC excess above background in the Far detector data, depending on method used, for a total exposure of 3.14 x 1020 protons-on-target. Interpreting this excess as signal, MINOS can set limits on sin213. Using the MRCC method, MINOS sets a limit of sin2 2 θ 13 < 0.265 at the 90% confidence limit for a CP-violating phase δ = 0.

  11. Electron Neutrino Appearance in the MINOS Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Orchanian, Mhair-armen Hagop [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2012-01-01

    This thesis describes a search for ve appearance in the two-detector long-baseline MINOS neutrino experiment at Fermilab, based on a data set representing an exposure of 8.2×1020 protons on the NuMI target. The analysis detailed herein represents an increase in sensitivity to the θ13 mixing angle of approximately 25% over previous analyses, due to improvements in the event discriminant and fitting technique. Based on our observation, we constrain the value of θ13 further, finding 2 sin2θ 23 sin2θ 13< 0.12(0.20) at the 90% confidence level for δCP = 0 and the normal (inverted) neutrino mass hierarchy. The best-fit value is 2 sin2θ 23 sin2θ 13 = 0.041+0.047 -0.031(0.079+0.071 -0.053) under the same assumptions. We exclude the θ 13 = 0 hypothesis at the 89% confidence level.

  12. Pixel electronics for the ATLAS experiment

    International Nuclear Information System (INIS)

    Fischer, P.

    2001-01-01

    The ATLAS experiment at LHC will use 3 barrel layers and 2x5 disks of silicon pixel detectors as the innermost elements of the semiconductor tracker. The basic building blocks are pixel modules with an active area of 16.4 mmx60.8 mm which include an n + on n-type silicon sensor and 16 VLSI front-end (FE) chips. Every FE chip contains a low power, high speed charge sensitive preamplifier, a fast discriminator, and a readout system which operates at the 40 MHz rate of LHC. The addresses of hit pixels (as well as a low resolution pulse height information) are stored on the FE chips until arrival of a level 1 trigger signal. Hits are then transferred to a module controller chip (MCC) which collects the data of all 16 FE chips, builds complete events and sends the data through two optical links to the data acquisition system. The MCC receives clock and data through an additional optical link and provides timing and configuration information for the FE chips. Two additional chips are used to amplify and decode the pin diode signal and to drive the VCSEL laser diodes of the optical links

  13. Stern-Gerlach experiment, electron spin and intermediate quantum mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Mackintosh, A.R. (Copenhagen Univ. (Denmark). H.C. Oersted Inst.)

    1983-01-01

    The paper deals with the theory of electron spin. The Stern-Gerlach experiment, the anticommutation relations and the properties of spin operators are discussed. The Pauli theory, Dirac transformation theory, the double Stern-Gerlach experiment, the EPR paradox and Bell's inequality are also covered.

  14. RADLAC II high current electron beam propagation experiment

    International Nuclear Information System (INIS)

    Frost, C.A.; Shope, S.L.; Mazarakis, M.G.; Poukey, J.W.; Wagner, J.S.; Turman, B.N.; Crist, C.E.; Welch, D.R.; Struve, K.W.

    1993-01-01

    The resistive hose instability of an electron beam was observed to be convective in recent RADLAC II experiments for higher current shots. The effects of air scattering for these shots were minimal. These experiments and theory suggest low-frequency hose motion which does not appear convective may be due to rapid expansion and subsequent drifting of the beam nose

  15. Staged electron laser accelerator (STELLA) experiment at brookhaven ATF

    Energy Technology Data Exchange (ETDEWEB)

    Pogorelsky, I V; Steenbergen, A van; Gallardo, J C [Brookhaven National Lab., Upton, NY (United States); and others

    1998-03-01

    The STELLA experiment is being prepared at the BNL Accelerator Test Facility (STF). The goal of the experiment is to demonstrate quasi-monochromatic inverse Cherenkov acceleration (ICA) of electrons bunched to the laser wavelength period. Microbunches on the order of 2 {mu}m in length separated by 10.6 {mu}m will be produced using an inverse free electron laser (IFEL) accelerator driven by a CO{sub 2} laser. The design and simulations for two phases of this experiment including demonstration of 10 MeV and 100 MeV acceleration are presented. (author)

  16. On the scalar electron mass limit from single photon experiments

    International Nuclear Information System (INIS)

    Grivaz, J.F.

    1987-03-01

    We discuss how the 90% C.L. lower limit on the mass of the scalar electron, as extracted from the single photon experiments, is affected by the way the background from radiative neutrino pair production is handled. We argue that some of the results presented at the Berkeley conference are overoptimistic, and that the mass lower limit is 65 GeV rather than the advertized value of 84 GeV, for the case of degenerate scalar electrons with massless photinos

  17. Electron beam injection during active experiments. I - Electromagnetic wave emissions

    Science.gov (United States)

    Winglee, R. M.; Kellogg, P. J.

    1990-01-01

    The wave emissions produced in Echo 7 experiment by active injections of electron beams were investigated to determine the properties of the electromagnetic and electrostatic fields for both the field-aligned and cross-field injection in such experiments and to evaluate the sources of free energy and relative efficiencies for the generation of the VLF and HF emissions. It is shown that, for typical beam energies in active experiments, electromagnetic effects do not substantially change the bulk properties of the beam, spacecraft charging, and plasma particle acceleration. Through simulations, beam-generated whistlers; fundamental z-mode and harmonic x-mode radiation; and electrostatic electron-cyclotron, upper-hybrid, Langmuir, and lower-hybrid waves were identified. The characteristics of the observed wave spectra were found to be sensitive to both the ratio of the electron plasma frequency to the cyclotron frequency and the angle of injection relative to the magnetic field.

  18. Electron-ion recombination rates for merged-beams experiments

    International Nuclear Information System (INIS)

    Pajek, M.

    1994-01-01

    Energy dependence of the electron-ion recombination rates are studied for different recombination processes (radiative recombination, three-body recombination, dissociative recombination) for Maxwellian relative velocity distribution of arbitrary asymmetry. The results are discussed in context of the electron-ion merged beams experiments in cooling ion storage rings. The question of indication of a possible contribution of the three-body recombination to the measured recombination rates versus relative energy is particularly addressed. Its influence on the electron beam temperature derived from the energy dependence of recombination rate is discussed

  19. Analytic model of electron pulse propagation in ultrafast electron diffraction experiments

    International Nuclear Information System (INIS)

    Michalik, A.M.; Sipe, J.E.

    2006-01-01

    We present a mean-field analytic model to study the propagation of electron pulses used in ultrafast electron diffraction experiments (UED). We assume a Gaussian form to characterize the electron pulse, and derive a system of ordinary differential equations that are solved quickly and easily to give the pulse dynamics. We compare our model to an N-body numerical simulation and are able to show excellent agreement between the two result sets. This model is a convenient alternative to time consuming and computationally intense N-body simulations in exploring the dynamics of UED electron pulses, and as a tool for refining UED experimental designs

  20. Longitudinal electron cooling experiments at HIRFL-CSRe

    International Nuclear Information System (INIS)

    Mao, L.J.; Zhao, H.; Yang, X.D.; Li, J.; Yang, J.C.; Yuan, Y.J.; Parkhomchuk, V.V.; Reva, V.B.; Ma, X.M.; Yan, T.L.; Tang, M.T.; Xia, J.W.

    2016-01-01

    At the heavy ion storage ring HIRFL-CSRe an electron cooler is operated to improve the beam conditions for experiments. The properties of cooled beams have been studied. The longitudinal beam dynamics during the cooling process was measured by a resonant Schottky detector. The dependencies of the parameters electron beam density and profile on cooling times were investigated. The friction force was measured directly with the aid of the high voltage system of the cooler and with the application of the beam bunching system as well. An experiment with bunched cold beam showed a dependence of the bunch length on the beam density.

  1. Longitudinal electron cooling experiments at HIRFL-CSRe

    Energy Technology Data Exchange (ETDEWEB)

    Mao, L.J., E-mail: maolijun@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Zhao, H. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Yang, X.D.; Li, J.; Yang, J.C.; Yuan, Y.J. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Parkhomchuk, V.V.; Reva, V.B. [Budker Institute of Nuclear Physics, Novosibirsk 630090 (Russian Federation); Ma, X.M.; Yan, T.L. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Tang, M.T. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Xia, J.W. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2016-02-01

    At the heavy ion storage ring HIRFL-CSRe an electron cooler is operated to improve the beam conditions for experiments. The properties of cooled beams have been studied. The longitudinal beam dynamics during the cooling process was measured by a resonant Schottky detector. The dependencies of the parameters electron beam density and profile on cooling times were investigated. The friction force was measured directly with the aid of the high voltage system of the cooler and with the application of the beam bunching system as well. An experiment with bunched cold beam showed a dependence of the bunch length on the beam density.

  2. A ferroelectric electron gun in a free-electron maser experiment

    CERN Document Server

    Einat, M; Rosenman, G

    2002-01-01

    An electron-gun based on a ferroelectric cathode is studied in a free-electron maser (FEM) experiment. In this gun, the electrons are separated from the cathode surface plasma, and are accelerated in two stages. The electron energy-spread is reduced sufficiently for an FEM operation in the microwave regime. A 14 keV, 1-2 A e-beam is obtained in a 0.1-2.1 mu s pulse width. The pulse repetition frequency attains 3.1 MHz in approx 50% duty-cycle. This gun is implemented in an FEM oscillator experiment operating around 3 GHz. The paper presents experimental results and discusses the applicability of ferroelectric guns in free-electron laser devices.

  3. A ferroelectric electron gun in a free-electron maser experiment

    International Nuclear Information System (INIS)

    Einat, M.; Jerby, E.; Rosenman, G.

    2002-01-01

    An electron-gun based on a ferroelectric cathode is studied in a free-electron maser (FEM) experiment. In this gun, the electrons are separated from the cathode surface plasma, and are accelerated in two stages. The electron energy-spread is reduced sufficiently for an FEM operation in the microwave regime. A 14 keV, 1-2 A e-beam is obtained in a 0.1-2.1 μs pulse width. The pulse repetition frequency attains 3.1 MHz in ∼50% duty-cycle. This gun is implemented in an FEM oscillator experiment operating around 3 GHz. The paper presents experimental results and discusses the applicability of ferroelectric guns in free-electron laser devices

  4. Ion-electron recombination in merged-beams experiments

    International Nuclear Information System (INIS)

    Schmidt, H.T.

    1994-01-01

    In the present thesis, studies of recombination processes applying the technique of merged beams of fast ions and electrons are described. The main advantage of this technique is that the low relative velocity of ions and electrons necessary for these investigations can be achieved, at the same time as the velocity of the ions relative to the molecules of the residual gas is high. The high ion velocity leads to a very low reaction cross section for the leading contribution to the background signal, the capture of electrons in collisions with residual gas molecules. The experimental technique is described, emphasizing the electron beam velocity distribution and its relation to the energy resolution of the experiments. The presentation of the process of electron cooling is aimed at introducing this process as a tool for merged-beams experiments in storage rings rather than investigating the process itself. The non-resonant process of radiative recombination for non-fully stripped ions, showing evidence of incomplete screening is presented. Experimental investigation of dielectronic recombination is presented. Results of measurements of this process for He-like ions form the Aarhus single-pass experiment and the Heidelberg storage ring experiment are compared. Recombination is reduced from being the aim of the investigation to being a tool for high-precision measurements of the lifetimes of the 1s2s 3 S metastable states of HE-like ions of boron, carbon, and nitrogen, performed at the Heidelberg storage ring. The experiment is concerned with the process of dissociative recombination of molecular hydrogen ions. The discussion of this experiment emphasizes the distribution of population on the different vibrational levels of the ions in the initial state. In particular, a laser photo-dissociation technique was introduced to reduce the number of initial levels in the experiment. (EG) 24 refs

  5. A 20 keV electron gun system for the electron irradiation experiments

    International Nuclear Information System (INIS)

    Mahapatra, S.K.; Dhole, S.D.; Bhoraskar, V.N.

    2005-01-01

    An electron gun consisting of cathode, focusing electrode, control electrode and anode has been designed and fabricated for the electron irradiation experiments. This electron gun can provide electrons of any energy over the range 1-20 keV, with current upto 50 μA. This electron gun and a Faraday cup are mounted in the cylindrical chamber. The samples are fixed on the Faraday cup and irradiated with electrons at a pressure ∼10 -7 mbar. The special features of this electron gun system are that, at any electron energy above 1 keV, the electron beam diameter can be varied from 5 to 120 mm on the Faraday cup mounted at a distance of 200 mm from the anode in the chamber. The variation in the electron current over the beam spot of 120 mm diameter is less than 15% and the beam current stability is better than 5%. This system is being used for studying the irradiation effects of 1-20 keV energy electrons on the space quality materials in which the irradiation time may vary from a few tens of seconds to hours

  6. A 20 keV electron gun system for the electron irradiation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Mahapatra, S.K. [Department of Physics, University of Pune, Pune 411007 (India); Dhole, S.D. [Department of Physics, University of Pune, Pune 411007 (India); Bhoraskar, V.N. [Department of Physics, University of Pune, Pune 411007 (India)]. E-mail: vnb@physics.unipune.ernet.in

    2005-01-01

    An electron gun consisting of cathode, focusing electrode, control electrode and anode has been designed and fabricated for the electron irradiation experiments. This electron gun can provide electrons of any energy over the range 1-20 keV, with current upto 50 {mu}A. This electron gun and a Faraday cup are mounted in the cylindrical chamber. The samples are fixed on the Faraday cup and irradiated with electrons at a pressure {approx}10{sup -7} mbar. The special features of this electron gun system are that, at any electron energy above 1 keV, the electron beam diameter can be varied from 5 to 120 mm on the Faraday cup mounted at a distance of 200 mm from the anode in the chamber. The variation in the electron current over the beam spot of 120 mm diameter is less than 15% and the beam current stability is better than 5%. This system is being used for studying the irradiation effects of 1-20 keV energy electrons on the space quality materials in which the irradiation time may vary from a few tens of seconds to hours.

  7. Advancing Small Satellite Electronics Heritage for Microfluidic Biological Experiments

    Science.gov (United States)

    White, Bruce; Mazmanian, Edward; Tapio, Eric

    2016-01-01

    DLR's Eu:CROPIS (Euglena and Combined Regenerative Organic-Food Production in Space) mission, launching in 2017, will carry multiple biological payloads into a sun-synchronous orbit, including NASA Ames' PowerCell experiment. PowerCell will attempt to characterize the viability of synthetic biology at micro-g, Lunar, and Martian gravity levels. PowerCell experiment requirements demand an electronic system similar to previous microfluidic biology payloads, but with an expanded feature set. As such, the system was based on PharmaSat (Diaz-Aguado et al. 2009), a previous successful biology payload from NASA Ames, and improved upon. Newer, more miniaturized electronics allow for greater capability with a lower part count and smaller size. Two identical PowerCell enclosures will fly. Each enclosure contains two separate and identical experiments with a 48-segment optical density measurement system, grow light system, microfluidic system for nutrient delivery and waste flushing, plus thermal control and environmental sensing/housekeeping including temperature, pressure, humidity, and acceleration. Electronics consist of a single Master PCB that interfaces to the spacecraft bus and regulates power and communication, plus LED, Detector, and Valve Manifold PCBs for each experiment. To facilitate ease of reuse on future missions, experiment electronics were designed to be compatible with a standard 3U small sat form factor and power bus, or to interface with a Master power/comm PCB for use in a larger satellite as in the case of PowerCell's flight on Eu:CROPIS.

  8. Electron microbeam specifications for use in cell irradiation experiments

    International Nuclear Information System (INIS)

    Kim, E.-H.; Choi, M.-C.; Lee, D.-H.; Chang, M.; Kang, C.-S.

    2003-01-01

    The microbeam irradiation system was devised originally to identify the hit and unhit cells by confining the beam within the target cell. The major achievement through the microbeam experiment studies has turned out to be the discovery of the 'bystander effect'. Microbeam experiments have been performed with alpha and proton beams in major and with soft x-rays in minor. The study with electron microbeam has been deferred mainly due to the difficulty in confining the electron tracks within a single target cell. In this paper, the electron microbeam irradiation system under development in Korea is introduced in terms of the beam specifications. The KIRAMS electron microbeam irradiation system consists of an electron gun, a vacuum chamber for beam collimation into 5 μm in diameter and a biology stage. The beam characteristics in terms of current and energy spectrum of the electrons entering a target cell and its neighbor cells were investigated by Monte Carlo simulation for the electron source energies of 25, 50, 75 and 100 keV. Energy depositions in the target cell and the neighbor cells were also calculated. The beam attenuation in current and energy occurs while electrons pass through the 2 μm-thick Mylar vacuum window, 100 μm-thick air gap and the 2 μm-thick Mylar bottom of cell dish. With 25 keV electron source, 80 % of decrease in current and 30 % of decrease in average energy were estimated before entering the target cell. With 75 keV electron source, on the other hand, 55 % of decrease in current and less than 1 % of decrease in average energy were estimated. Average dose per single collimated electron emission was 0.067 cGy to the target cell nucleus of 5 μm in diameter and 0.030 cGy to the cytoplasm of 2.5 μm in thickness with 25 keV electron source while they were 0.15 cGy and 0.019 cGy, respectively, with 75 keV electron source. The multiple scattering of electrons resulted in energy deposition in the neighbor cells as well. Dose to the first

  9. The industrial policy experience of the electronics industry in Malaysia

    OpenAIRE

    Rasiah, Rajah

    2015-01-01

    Despite the use of industrial policies to stimulate economic growth by several successful developers, latecomers have faced mixed experiences. Hence, this paper analyses the industrial policy experience of the electronics industry in Malaysia. A blend of institutions have guided technological upgrading in the industry, especially in the state of Penang. Smooth co-ordination between the state government, multinational corporations, national firms, and the federal government helped stimulate te...

  10. Electron-cyclotron heating in the Constance 2 mirror experiment

    Energy Technology Data Exchange (ETDEWEB)

    Mauel, Michael E.

    1982-09-01

    Electron cyclotron heating of a highly-ionized plasma in mirror geometry is investigated. The experimental diagnosis of the electron energy distribution and the comparison of the results of this diagnosis with a two dimensional, time-dependent Fokker-Planck simulation are accomplished in four steps. (1) First, the power balance of the heated and unheated Constance 2 plasma is analyzed experimentally. It is concluded that the heated electrons escape the mirror at a rate dominated by a combination of the influx of cool electrons from outside the mirror and the increased loss rate of the ions. (2) The microwave parameters at the resonance zones are then calculated by cold-plasma ray tracing. High N/sub parallel/ waves are launched and for these waves, strong first-pass absorption is predicted. The absorption strength is qualitatively checked in the experiment by surrounding the plasma with non-reflecting liners. (3) A simplified quasilinear theory including the effect of N/sub parallel/ is developed to model the electrons. An analytic expression is derived for the RF-induced pump-out of the magnetically-confined warm electrons. Results of the Fokker-Planck simulations show the development of the electron energy distribution for several plasma conditions and verify the scaling of the analytic expression for RF-induced diffusion into the loss cone. (4) Sample x-ray and endloss data are presented, and the overall comparison between the simulation and experiment is discussed. The x-ray signals indicate that, for greater RF power, the hot electrondensity increases more rapidly than its temperature. The time history of the endloss data, illustrating RF-enhancement, suggests the predicted scaling for warm-electron pump-out. Finally, a comparison between the measured and predicted energy distribution shows that the bulk, warm and hot components of the heated Constance 2 electrons are indeed reproduced by the simulation.

  11. Electron-cyclotron heating in the Constance 2 mirror experiment

    International Nuclear Information System (INIS)

    Mauel, M.E.

    1982-09-01

    Electron cyclotron heating of a highly-ionized plasma in mirror geometry is investigated. The experimental diagnosis of the electron energy distribution and the comparison of the results of this diagnosis with a two dimensional, time-dependent Fokker-Planck simulation are accomplished in four steps. (1) First, the power balance of the heated and unheated Constance 2 plasma is analyzed experimentally. It is concluded that the heated electrons escape the mirror at a rate dominated by a combination of the influx of cool electrons from outside the mirror and the increased loss rate of the ions. (2) The microwave parameters at the resonance zones are then calculated by cold-plasma ray tracing. High N/sub parallel/ waves are launched and for these waves, strong first-pass absorption is predicted. The absorption strength is qualitatively checked in the experiment by surrounding the plasma with non-reflecting liners. (3) A simplified quasilinear theory including the effect of N/sub parallel/ is developed to model the electrons. An analytic expression is derived for the RF-induced pump-out of the magnetically-confined warm electrons. Results of the Fokker-Planck simulations show the development of the electron energy distribution for several plasma conditions and verify the scaling of the analytic expression for RF-induced diffusion into the loss cone. (4) Sample x-ray and endloss data are presented, and the overall comparison between the simulation and experiment is discussed. The x-ray signals indicate that, for greater RF power, the hot electrondensity increases more rapidly than its temperature. The time history of the endloss data, illustrating RF-enhancement, suggests the predicted scaling for warm-electron pump-out. Finally, a comparison between the measured and predicted energy distribution shows that the bulk, warm and hot components of the heated Constance 2 electrons are indeed reproduced by the simulation

  12. Experiments on hot-electron ECRH in the Tandem Mirror Experiment-Upgrade

    International Nuclear Information System (INIS)

    Stallard, B.W.

    1983-01-01

    Experiments have begun on the Tandem Mirror Experiment Upgrade (TMX-U) using electron-cyclotron resonant heating (ECRH) to generate the hot electron populations required for thermal barrier operation (Energy E/sub eh/ approx. 50 keV, density n/sub eh/ 12 , and hot-to-cold fraction n/sub eh/n approx. 0.9). For this operation, rf power produced by 28-GHz gyrotrons is injected with extraordinary mode polarization at both fundamental and second harmonic locations. Our initial experiments, which concentrated on startup of the hot electrons, were carried out at low density ( 12 cm - 3 ) where Fokker-Planck calculations predict high heating efficiency when the electron temperature (T/sub e/) is low. Under these conditions, we produced substantial hot electron populations (diamagnetic energy > 400 J, E/sub eh/ in the range of 15 to 50 keV, and n/sub eh//n > 0.5)

  13. Nanotechnology: moving from microarrays toward nanoarrays.

    Science.gov (United States)

    Chen, Hua; Li, Jun

    2007-01-01

    Microarrays are important tools for high-throughput analysis of biomolecules. The use of microarrays for parallel screening of nucleic acid and protein profiles has become an industry standard. A few limitations of microarrays are the requirement for relatively large sample volumes and elongated incubation time, as well as the limit of detection. In addition, traditional microarrays make use of bulky instrumentation for the detection, and sample amplification and labeling are quite laborious, which increase analysis cost and delays the time for obtaining results. These problems limit microarray techniques from point-of-care and field applications. One strategy for overcoming these problems is to develop nanoarrays, particularly electronics-based nanoarrays. With further miniaturization, higher sensitivity, and simplified sample preparation, nanoarrays could potentially be employed for biomolecular analysis in personal healthcare and monitoring of trace pathogens. In this chapter, it is intended to introduce the concept and advantage of nanotechnology and then describe current methods and protocols for novel nanoarrays in three aspects: (1) label-free nucleic acids analysis using nanoarrays, (2) nanoarrays for protein detection by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy, and (3) nanoarray for enzymatic-based assay. These nanoarrays will have significant applications in drug discovery, medical diagnosis, genetic testing, environmental monitoring, and food safety inspection.

  14. Electron cooling and recombination experiments with an adiabatically expanded electron beam

    International Nuclear Information System (INIS)

    Pastuszka, S.; Heidelberg Univ.; Schramm, U.; Heidelberg Univ.; Grieser, M.; Heidelberg Univ.; Broude, C.; Heidelberg Univ.; Grimm, R.; Heidelberg Univ.; Habs, D.; Heidelberg Univ.; Kenntner, J.; Heidelberg Univ.; Miesner, H.J.; Heidelberg Univ.; Schuessler, T.; Heidelberg Univ.; Schwalm, D.; Heidelberg Univ.; Wolf, A.; Heidelberg Univ.

    1996-01-01

    Magnetically guided electron beams with transverse temperatures reduced with respect to the cathode temperature by a factor of more than 7 were realized in the electron cooling device of the heavy-ion storage ring TSR and the effect of the reduced transverse temperature in recombination and electron cooling experiments was studied. Measured dielectronic recombination resonances at low relative energy and spectra of laser-stimulated recombination indicate that transverse electron temperatures of about 17 meV have been obtained at cathode temperatures of about 110 meV. The temperature dependence of the spontaneous electron-ion recombination rate during electron cooling was investigated and found to follow the inverse square-root law expected from the theory of radiative recombination, although the measured absolute rates are higher than predicted. A new method based on analyzing the intensity of the fluorescence light emitted during simultaneous laser and electron cooling is used to measure the longitudinal electron cooling force in a range of relative velocities extending over two orders of magnitude (10 5 -10 7 cm/s). The results confirm the occurrence of 'magnetized electron cooling' also at the reduced transverse temperature and show that, compared to earlier measurements at the high transverse temperature, the cooling force increases by about a factor of 2; a considerably larger increase by a factor of ∼5 would be expected if 'magnetized electron cooling' would not exist. (orig.)

  15. Source theory analysis of electron--positron annihilation experiments

    International Nuclear Information System (INIS)

    Schwinger, J.

    1975-01-01

    The phenomenological viewpoint already applied to deep inelastic scattering is extended to the discussion of electron-positron annihilation experiments. Some heuristic arguments lead to simple forms for the pion differential cross section that are in reasonable accord with the published experimental data in the energy interval 3 to 4.8 GeV

  16. Experiments on neutron-proton and neutron-electron interaction

    International Nuclear Information System (INIS)

    Koester, L.

    1975-01-01

    The paper reports on zero-energy experiments with neutrons, protons and electrons with a wavelength that is considerably longer than the particle expansion. Scattering amplitudes are measured for the reactions n + p and n + e. A neutron gravity refractometer is used. (WL/AK) [de

  17. TeV electron measurement with CREST experiment

    Science.gov (United States)

    Park, Nahee; Anderson, T.; Bower, C.; Coutu, S.; Gennaro, J.; Geske, M.; Muller, D.; Musser, J.; Nutter, S.

    CREST, the Cosmic Ray Electron Synchrotron Telescope is a balloon-borne experiment de-signed to measure the spectrum of multi-TeV electrons by the detection of the x-ray synchrotron photons generated in the magnetic field of the Earth. Electrons in the TeV range are expected to reflect the properties of local sources because fluxes from remote locations are suppressed by radiative losses during propagation. Since CREST needs to intersect only a portion of the kilometers-long trail of photons generated by the high-energy electron, the method yields a larger effective area than the physical size of the detector, boosting detection areas. The in-strument is composed of an array of 1024 BaF2 crystals and a set of scintillating veto counters. A long duration balloon flight in Antarctica is currently planned for the 2010-11 season.

  18. Modelling hot electron generation in short pulse target heating experiments

    Directory of Open Access Journals (Sweden)

    Sircombe N.J.

    2013-11-01

    Full Text Available Target heating experiments planned for the Orion laser facility, and electron beam driven fast ignition schemes, rely on the interaction of a short pulse high intensity laser with dense material to generate a flux of energetic electrons. It is essential that the characteristics of this electron source are well known in order to inform transport models in radiation hydrodynamics codes and allow effective evaluation of experimental results and forward modelling of future campaigns. We present results obtained with the particle in cell (PIC code EPOCH for realistic target and laser parameters, including first and second harmonic light. The hot electron distributions are characterised and their implications for onward transport and target heating are considered with the aid of the Monte-Carlo transport code THOR.

  19. Neutrino Signals in Electron-Capture Storage-Ring Experiments

    Directory of Open Access Journals (Sweden)

    Avraham Gal

    2016-06-01

    Full Text Available Neutrino signals in electron-capture decays of hydrogen-like parent ions P in storage-ring experiments at GSI are reconsidered, with special emphasis placed on the storage-ring quasi-circular motion of the daughter ions D in two-body decays P → D + ν e . It is argued that, to the extent that daughter ions are detected, these detection rates might exhibit modulations with periods of order seconds, similar to those reported in the GSI storage-ring experiments for two-body decay rates. New dedicated experiments in storage rings, or using traps, could explore these modulations.

  20. An angular selective electron gun for the KATRIN experiment

    Energy Technology Data Exchange (ETDEWEB)

    Zacher, Michael; Ortjohann, Hans-Werner; Steinbrink, Nicholas; Josten, Lorenz; Hannen, Volker; Weinheimer, Christian; Winzen, Daniel [Westfaelische Wilhelms-Universitaet, Muenster (Germany); Collaboration: KATRIN-Collaboration

    2013-07-01

    The KArlsruhe TRItium Neutrino experiment aims for a measurement of the electron anti-neutrino mass with a sensitivity of 200 meV/c{sup 2} (95% C.L.) by analysing the endpoint region of the tritium β-decay. The main spectrometer (MAC-E filter type, 23m length) is one of the central parts of the experiment, featuring an energy resolution of Δ E<1 eV. For commissioning of the spectrometer a well defined electron source is needed that allows to determine the transmission characteristics and compare the electromagnetic properties to simulations. For this purpose an angular selective electron gun was developed. A pulsed UV-Laser produces electrons via the photo-electric effect, which are then accelerated electrostatically in a magnetic field. It features a small energy spread, a sharp selectable emission angle and covers the whole magnetic flux tube of KATRIN. By that, the characteristics of the spectrometer can be investigated with high precision. The time structure of the electron pulses allows time of flight measurements, offering enhanced sensitivity. The talk gives an overview about the e-gun design and its properties.

  1. Integrative missing value estimation for microarray data.

    Science.gov (United States)

    Hu, Jianjun; Li, Haifeng; Waterman, Michael S; Zhou, Xianghong Jasmine

    2006-10-12

    Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  2. Integrative missing value estimation for microarray data

    Directory of Open Access Journals (Sweden)

    Zhou Xianghong

    2006-10-01

    Full Text Available Abstract Background Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. Results We present the integrative Missing Value Estimation method (iMISS by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS imputation algorithm by up to 15% improvement in our benchmark tests. Conclusion We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  3. Theory and Simulation of an Inverse Free Electron Laser Experiment

    Science.gov (United States)

    Guo, S. K.; Bhattacharjee, A.; Fang, J. M.; Marshall, T. C.

    1996-11-01

    An experimental demonstration of the acceleration of electrons using a high power CO2 laser in an inverse free electron laser (IFEL) is underway at the Brookhaven National Laboratory. This experiment has generated data, which we are attempting to simulate. Included in our studies are such effects as: a low-loss metallic waveguide with a dielectric coating on the walls; multi-mode coupling due to self-consistent interaction between the electrons and the optical wave; space charge (which is significant at lower laser power); energy-spread of the electrons; arbitrary wiggler field profile; and slippage. Two types of wiggler profile have been considered: a linear taper of the period, and a step-taper of the period (the period is ~ 3cm, the field is ~ 1T, and the wiggler length is 47cm). The energy increment of the electrons ( ~ 1-2%) is analyzed in detail as a function of laser power, wiggler parameters, and the initial beam energy (40MeV). For laser power ~ 0.5GW, the predictions of the simulations are in good accord with experimental results. A matter currently under study is the discrepancy between theory and observations for the electron energy distribution observed at the end of the IFEL. This work is supported by the Department of Energy.

  4. An inverse free electron laser accelerator: Experiment and theoretical interpretation

    International Nuclear Information System (INIS)

    Fang, Jyan-Min.

    1997-01-01

    Experimental and numerical studies of the Inverse Free Electron Laser using a GW-level 10.6 μm CO 2 laser have been carried out at Brookhaven's Accelerator Test Facility. An energy gain of 2.5 % (ΔE/E) on a 40 MeV electron beam has been observed E which compares well with theory. The effects on IFEL acceleration with respect to the variation of the laser electric field, the input electron beam energy, and the wiggler magnetic field strength were studied, and show the importance of matching the resonance condition in the IFEL. The numerical simulations were performed under various conditions and the importance of the electron bunching in the IFEL is shown. The numerical interpretation of our IFEL experimental results was examined. Although good numerical agreement with the experimental results was obtained, there is a discrepancy between the level of the laser power measured in the experiment and used in the simulation, possibly due to the non-Gaussian profile of the input high power laser beam. The electron energy distribution was studied numerically and a smoothing of the energy spectrum by the space charge effect at the location of the spectrometer was found, compared with the spectrum at the exit of the wiggler. The electron bunching by the IFEL and the possibility of using the IFEL as an electron prebuncher for another laser-driven accelerator were studied numerically. We found that bunching of the electrons at 1 meter downstream from the wiggler can be achieved using the existing facility. The simulation shows that there is a fundamental difference between the operating conditions for using the IFEL as a high gradient accelerator, and as a prebuncher for another accelerator

  5. Stabilization of electron-scale turbulence by electron density gradient in national spherical torus experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz Ruiz, J.; White, A. E. [MIT-Plasma Science and Fusion Center, Cambridge, Massachusetts 02139 (United States); Ren, Y.; Guttenfelder, W.; Kaye, S. M.; Leblanc, B. P.; Mazzucato, E. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States); Lee, K. C. [National Fusion Research Institute, Daejeon (Korea, Republic of); Domier, C. W. [University of California at Davis, Davis, California 95616 (United States); Smith, D. R. [University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Yuh, H. [Nova Photonics, Inc., Princeton, New Jersey 08540 (United States)

    2015-12-15

    Theory and experiments have shown that electron temperature gradient (ETG) turbulence on the electron gyro-scale, k{sub ⊥}ρ{sub e} ≲ 1, can be responsible for anomalous electron thermal transport in NSTX. Electron scale (high-k) turbulence is diagnosed in NSTX with a high-k microwave scattering system [D. R. Smith et al., Rev. Sci. Instrum. 79, 123501 (2008)]. Here we report on stabilization effects of the electron density gradient on electron-scale density fluctuations in a set of neutral beam injection heated H-mode plasmas. We found that the absence of high-k density fluctuations from measurements is correlated with large equilibrium density gradient, which is shown to be consistent with linear stabilization of ETG modes due to the density gradient using the analytical ETG linear threshold in F. Jenko et al. [Phys. Plasmas 8, 4096 (2001)] and linear gyrokinetic simulations with GS2 [M. Kotschenreuther et al., Comput. Phys. Commun. 88, 128 (1995)]. We also found that the observed power of electron-scale turbulence (when it exists) is anti-correlated with the equilibrium density gradient, suggesting density gradient as a nonlinear stabilizing mechanism. Higher density gradients give rise to lower values of the plasma frame frequency, calculated based on the Doppler shift of the measured density fluctuations. Linear gyrokinetic simulations show that higher values of the electron density gradient reduce the value of the real frequency, in agreement with experimental observation. Nonlinear electron-scale gyrokinetic simulations show that high electron density gradient reduces electron heat flux and stiffness, and increases the ETG nonlinear threshold, consistent with experimental observations.

  6. "Harshlighting" small blemishes on microarrays

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M

    2005-03-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs. Results We present a method that harnesses the statistical power provided by having several HDONAs available, which are obtained under similar conditions except for the experimental factor. This method "harshlights" blemishes and renders them evident. We find empirically that about 25% of our chips are blemished, and we analyze the impact of masking them on screening for differentially expressed genes. Conclusion Experiments attempting to assess subtle expression changes should be carefully screened for blemishes on the chips. The proposed method provides investigators with a novel robust approach to improve the sensitivity of microarray analyses. By utilizing topological information to identify and mask blemishes prior to model based analyses, the method prevents artefacts from confounding the process of background correction, normalization, and summarization.

  7. The electron capture in 163Ho experiment - ECHo

    Science.gov (United States)

    Gastaldo, L.; Blaum, K.; Chrysalidis, K.; Day Goodacre, T.; Domula, A.; Door, M.; Dorrer, H.; Düllmann, Ch. E.; Eberhardt, K.; Eliseev, S.; Enss, C.; Faessler, A.; Filianin, P.; Fleischmann, A.; Fonnesu, D.; Gamer, L.; Haas, R.; Hassel, C.; Hengstler, D.; Jochum, J.; Johnston, K.; Kebschull, U.; Kempf, S.; Kieck, T.; Köster, U.; Lahiri, S.; Maiti, M.; Mantegazzini, F.; Marsh, B.; Neroutsos, P.; Novikov, Yu. N.; Ranitzsch, P. C. O.; Rothe, S.; Rischka, A.; Saenz, A.; Sander, O.; Schneider, F.; Scholl, S.; Schüssler, R. X.; Schweiger, Ch.; Simkovic, F.; Stora, T.; Szücs, Z.; Türler, A.; Veinhard, M.; Weber, M.; Wegner, M.; Wendt, K.; Zuber, K.

    2017-06-01

    Neutrinos, and in particular their tiny but non-vanishing masses, can be considered one of the doors towards physics beyond the Standard Model. Precision measurements of the kinematics of weak interactions, in particular of the 3H β-decay and the 163Ho electron capture (EC), represent the only model independent approach to determine the absolute scale of neutrino masses. The electron capture in 163Ho experiment, ECHo, is designed to reach sub-eV sensitivity on the electron neutrino mass by means of the analysis of the calorimetrically measured electron capture spectrum of the nuclide 163Ho. The maximum energy available for this decay, about 2.8 keV, constrains the type of detectors that can be used. Arrays of low temperature metallic magnetic calorimeters (MMCs) are being developed to measure the 163Ho EC spectrum with energy resolution below 3 eV FWHM and with a time resolution below 1 μs. To achieve the sub-eV sensitivity on the electron neutrino mass, together with the detector optimization, the availability of large ultra-pure 163Ho samples, the identification and suppression of background sources as well as the precise parametrization of the 163Ho EC spectrum are of utmost importance. The high-energy resolution 163Ho spectra measured with the first MMC prototypes with ion-implanted 163Ho set the basis for the ECHo experiment. We describe the conceptual design of ECHo and motivate the strategies we have adopted to carry on the present medium scale experiment, ECHo-1K. In this experiment, the use of 1 kBq 163Ho will allow to reach a neutrino mass sensitivity below 10 eV/ c 2. We then discuss how the results being achieved in ECHo-1k will guide the design of the next stage of the ECHo experiment, ECHo-1M, where a source of the order of 1 MBq 163Ho embedded in large MMCs arrays will allow to reach sub-eV sensitivity on the electron neutrino mass.

  8. Recent single ARM electron scattering experiments at Saclay

    International Nuclear Information System (INIS)

    Frois, B.

    1981-07-01

    Some recent electron scattering experiments at intermediate energies performed at the Saclay linear accelerator (ALS) are presented. First the definitive results of the measurements of the size of valence orbits by magnetic elastic electron scattering are discussed and followed by an overview of the study of charge distributions in closed shell nuclei. These results are among the most stringent experimental tests of nuclear theory because they probe without ambiguity the shape of nuclei. Then, it is shown how the details of the transition densities of the first excited states of 152 Sm have been brought out by very high momentum transfer experiments. Finally, the results of the investigation of mesonic degrees of freedom in deuterium and helium-3 are presented

  9. Hot-electron-plasma accumulation in the CIRCE mirror experiment

    International Nuclear Information System (INIS)

    Bardet, R.; Briand, P.; Dupas, L.; Gormezano, C.; Melin, G.

    1975-01-01

    In the CIRCE experiment, the plasma is obtained by the trapping of a plasma injected into a magnetic bottle by electron heating at cyclotron resonance. The plasma density lies between 5x10 11 cm -3 and 10 12 cm -3 , the electron temperature is about 100 keV and the ion temperature is in the range of few hundred electronvolts. Gross instabilities are not observed. The ratio of the plasma density to the neutral-gas density inside the plasma is higher than 100. A few kilowatts of r.f. power at 8 GHz are sufficient to obtain these results, a fact which looks encouraging as far as the creation of a more effective fast-neutral-target plasma using the CIRCE-experiment concept is concerned. (author)

  10. Electron effects in the Neutralized Transport Experiment (NTX)

    Energy Technology Data Exchange (ETDEWEB)

    Eylon, S. [Lawrence Berkeley National Laboratory (LBNL), MS47R 0112, 1 Cyclotron Road, Berkeley, CA 94720 (United States) and Heavy Ion Fusion Virtual National Laboratory, Cyclotron Road, CA 94720 (United States)]. E-mail: S_Eylon@lbl.gov; Henestroza, E. [Lawrence Berkeley National Laboratory (LBNL), MS47R 0112, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Heavy Ion Fusion Virtual National Laboratory, Cyclotron Road, CA 94720 (United States); Roy, P.K. [Lawrence Berkeley National Laboratory (LBNL), MS47R 0112, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Heavy Ion Fusion Virtual National Laboratory, Cyclotron Road, CA 94720 (United States); Yu, S.S. [Lawrence Berkeley National Laboratory (LBNL), MS47R 0112, 1 Cyclotron Road, Berkeley, CA 94720 (United States); Heavy Ion Fusion Virtual National Laboratory, Cyclotron Road, CA 94720 (United States)

    2005-05-21

    The Neutralized Transport Experiment (NTX) at the Heavy Ion Fusion Virtual National Laboratory is exploring the performance of neutralized final focus systems for high-perveance heavy ion beams. To focus a high-intensity beam to a small spot requires a high-brightness beam. In the NTX experiment, a potassium ion beam of up to 400 keV and 80 mA is generated in a Pierce-type diode. At the diode exit, an aperture with variable opening provides the capability to vary the beam perveance. The beam is transported through four quadrupole magnets to a distance of 2.5 m. The beam can be neutralized and focused using a MEVVA plasma plug and a RF plasma source. We shall report on the measurement of the electron effects and the ways to mitigate the effects. Furthermore, we shall present the results of EGUN calculations consistent with the measurements effects of the electrons.

  11. Electron effects in the Neutralized Transport Experiment (NTX)

    International Nuclear Information System (INIS)

    Eylon, S.; Henestroza, E.; Roy, P.K.; Yu, S.S.

    2005-01-01

    The Neutralized Transport Experiment (NTX) at the Heavy Ion Fusion Virtual National Laboratory is exploring the performance of neutralized final focus systems for high-perveance heavy ion beams. To focus a high-intensity beam to a small spot requires a high-brightness beam. In the NTX experiment, a potassium ion beam of up to 400 keV and 80 mA is generated in a Pierce-type diode. At the diode exit, an aperture with variable opening provides the capability to vary the beam perveance. The beam is transported through four quadrupole magnets to a distance of 2.5 m. The beam can be neutralized and focused using a MEVVA plasma plug and a RF plasma source. We shall report on the measurement of the electron effects and the ways to mitigate the effects. Furthermore, we shall present the results of EGUN calculations consistent with the measurements effects of the electrons

  12. Electron effects in the Neutralized Transport Experiment (NTX)

    Science.gov (United States)

    Eylon, S.; Henestroza, E.; Roy, P. K.; Yu, S. S.

    2005-05-01

    The Neutralized Transport Experiment (NTX) at the Heavy Ion Fusion Virtual National Laboratory is exploring the performance of neutralized final focus systems for high-perveance heavy ion beams. To focus a high-intensity beam to a small spot requires a high-brightness beam. In the NTX experiment, a potassium ion beam of up to 400 keV and 80 mA is generated in a Pierce-type diode. At the diode exit, an aperture with variable opening provides the capability to vary the beam perveance. The beam is transported through four quadrupole magnets to a distance of 2.5 m. The beam can be neutralized and focused using a MEVVA plasma plug and a RF plasma source. We shall report on the measurement of the electron effects and the ways to mitigate the effects. Furthermore, we shall present the results of EGUN calculations consistent with the measurements effects of the electrons.

  13. Comparison of electron cloud simulation and experiments in the high-current experiment

    International Nuclear Information System (INIS)

    Cohen, R.H.; Friedman, A.; Covo, M. Kireeff; Lund, S.M.; Molvik, A.W.; Bieniosek, F.M.; Seidl, P.A.; Vay, J.-L.; Verboncoeur, J.; Stoltz, P.; Veitzer, S.

    2004-01-01

    A set of experiments has been performed on the High-Current Experiment (HCX) facility at LBNL, in which the ion beam is allowed to collide with an end plate and thereby induce a copious supply of desorbed electrons. Through the use of combinations of biased and grounded electrodes positioned in between and downstream of the quadrupole magnets, the flow of electrons upstream into the magnets can be turned on or off. Properties of the resultant ion beam are measured under each condition. The experiment is modeled via a full three-dimensional, two species (electron and ion) particle simulation, as well as via reduced simulations (ions with appropriately chosen model electron cloud distributions, and a high-resolution simulation of the region adjacent to the end plate). The three-dimensional simulations are the first of their kind and the first to make use of a timestep-acceleration scheme that allows the electrons to be advanced with a timestep that is not small compared to the highest electron cyclotron period. The simulations reproduce qualitative aspects of the experiments, illustrate some unanticipated physical effects, and serve as an important demonstration of a developing simulation capability

  14. The {nu}MSM and muon to electron conversion experiments

    Energy Technology Data Exchange (ETDEWEB)

    Canetti, Laurent, E-mail: laurent.canetti@epfl.ch; Shaposhnikov, Mikhail, E-mail: mikhail.shaposhnikov@epfl.ch [EPFL, ITP (Switzerland)

    2013-03-15

    We review briefly the different constraints on the three right-handed neutrinos of the {nu}MSM, an extension of the Standard Model that can explain baryon asymmetry, dark matter and neutrino masses. We include in the discussion the proposed experiments on muon to electron conversion Mu2e (Carey et al., Mu2e Collaboration, 2012), COMET and PRISM (Hungerford, COMET Collaboration, AIP Conf Proc 1182:694, 2009; Cui et al., COMET Collaboration, 2012). We find that the expected sensitivity of these experiments is weaker by about two orders of magnitude than the constraints coming from successful baryogenesis.

  15. Experiments on the Nuclear Interactions of Pions and Electrons

    International Nuclear Information System (INIS)

    Ralph C. Minehart

    2005-01-01

    This is the final technical report. Yearly Progress Reports were submitted throughout the duration of the project. Along with our publications, these reports provide a detailed record of our accomplishments. This report largely consists of a summary of the technical activities carried out during last 2-1/2 years of the project, along with a list of papers published in the period from 2002-2005. Our work during this period involved the following: 1. Electro-production of excited states of the nucleon through the analysis of exclusive single pion production reactions induced by polarized electrons incident on both polarized and unpolarized nucleon targets. (JLab) 2. Measurement of proton and deuteron spin structure functions in and above the nucleon resonance region at low and moderate Q 2 , using inclusive electron-proton and electron deuteron scattering (JLAB). 3. Contributions to the PRIMEX experiment (JLab). 4. A precise measurement of the branching ratio for pion beta decay was carried out along with other members of the PIBETA collaboration (PSI). The first three, labeled JLab, were experiments made with the CLAS detector at the Thomas Jefferson Laboratory in Newport News, VA. The PIBETA experiment was carried out using a low energy pion beam at the Paul Scherrer Institute in Villigen, Switzerland

  16. Preliminary experiments on a planar electron beam for an intense free electron maser

    International Nuclear Information System (INIS)

    Kato, Katsumasa; Iwata, Kazuma; Kitamura, Taro; Yamada, Naohisa; Soga, Yukihiro; Kamada, Keiichi; Yoshida, Mitsuhiro; Ginzburg, Naum S.

    2013-01-01

    A planar wiggler magnetic field was used to increase the output power of an intense free electron maser. As a preliminary experiment, a cylindrical electron beam was injected into a planar wiggler field with an axial magnetic field. Without the axial magnetic field, the cylindrical beam could not propagate through the wiggler field with length of 1 m. The microwave with frequency of 40 GHz was observed only when the beam propagates through the wiggler field. The frequency was nearly equal to the expected frequency of the free electron maser interaction. Though a sheet electron beam with nearly the same energy propagated through the planar wiggler field with deformation of its cross section, the microwave with frequency of 40 GHz was not observed. (author)

  17. Computational biology of genome expression and regulation--a review of microarray bioinformatics.

    Science.gov (United States)

    Wang, Junbai

    2008-01-01

    Microarray technology is being used widely in various biomedical research areas; the corresponding microarray data analysis is an essential step toward the best utilizing of array technologies. Here we review two components of the microarray data analysis: a low level of microarray data analysis that emphasizes the designing, the quality control, and the preprocessing of microarray experiments, then a high level of microarray data analysis that focuses on the domain-specific microarray applications such as tumor classification, biomarker prediction, analyzing array CGH experiments, and reverse engineering of gene expression networks. Additionally, we will review the recent development of building a predictive model in genome expression and regulation studies. This review may help biologists grasp a basic knowledge of microarray bioinformatics as well as its potential impact on the future evolvement of biomedical research fields.

  18. Development of an electron gun for high power CW electron linac (1). Beam experiment for basic performance of electron gun

    International Nuclear Information System (INIS)

    Yamazaki, Yoshio; Nomura, Masahiro; Komata, Tomoki

    1999-05-01

    Presently, the Beam Group of Oarai Engineering Center in Japan Nuclear Cycle Development Institute (JNC) completed the high power CW electron linac. Then we started full-scale beam experiments after the government permission for a radiation equipment had given last January. Measurements of basic performance for the mesh-grid type electron gun have been done to launch stable beam at 300 mA peak current downstream of the accelerator. These experiments disclosed to increase beam loss in the electron gun in some cases of voltage supplied the mesh-grid in spite of same beam current from gun. Consequently, we could find the best condition for mesh-grid voltage and heater current to supply stable beam at 300 mA peak current for accelerator study. (author)

  19. Ion and electron heating in ICRF heating experiments on LHD

    Energy Technology Data Exchange (ETDEWEB)

    Saito, K. [Nagoya Univ. (Japan). Faculty of Engineering; Kumazawa, R.; Mutoh, T. [National Inst. for Fusion Science, Toki, Gifu (Japan)] [and others

    2001-02-01

    This paper reports on the Ion Cyclotron Range of Frequency (ICRF) heating conducted in 1999 in the 3rd experimental campaign on the Large Helical Device (LHD) with an emphasis on the optimization of the heating regime. Specifically, an exhaustive study of seven different heating regimes was carried out by changing the RF frequency relative to the magnetic field intensity, and the dependence of the heating efficiency on H-minority concentration was investigated. It was found in the experiment that both ion and electron heating are attainable with the same experimental setup by properly choosing the frequency relative to the magnetic field intensity. In the cases of both electron heating and ion heating, the power absorption efficiency depends on the minority ion concentration. An optimum minority concentration exists in the ion heating case while, in the electron heating case, the efficiency increases with concentration monotonically. A simple model calculation is introduced to provide a heuristic understanding of these experimental results. Among the heating regimes examined in this experiment, one of the ion heating regimes was finally chosen as the optimized heating regime and various high performance discharges were realized with it. (author)

  20. Experiments on the nuclear interactions of pions and electrons

    International Nuclear Information System (INIS)

    Minehart, R.C.; Ziock, K.O.H.

    1989-07-01

    We have completed the analysis of the 3 He(π + ,pp)n reaction, and are working on the analysis of data for the 3 He(π - ,pn)p reaction. An experiment to study the π + d → 2p reaction at LAMPF was successful in studying incident pion energies as low as 6 MeV. Preliminary results have been reported, and work is continuing to improve the accuracy in the calculation of the fraction of pions in the incident beam. A proposal has been accepted by LAMPF for a new experiment, scheduled to run in the summer of 1990, to study pion absorption in 3 He and 4 He using an extensive scintillator time-of-flight system capable of detecting neutrons as well as charged particles. We are continuing to analyze data obtained in PSI in the search for the admixture of massive neutrinos in pion decay and have continued the search for fractionally charged particles. We are also fully involved in some major collaborations: the search for the decay μ + → e + + γ, and the study of anti-proton absorption in heavy nuclei. We are taking part in a U.Va.-PSI collaboration to measure pion beta decay to an accuracy of about 1%, using a large acceptance CsI detector to measure the π 0 following decay of stopped π + mesons. We have also been working on experiments to study electron scattering, using the SLAC-NPAS facility for nuclear physics and the electron accelerator at SACLAY in France. Data from experiment NE-9 at SLAC are being analyzed. This experiment, which was run near the end of 1987, is intended to separate the transverse and longitudinal cross sections for inclusive electron scattering in the QFS region. Experiment NE-8 measured the cross section for photo-disintegration of the deuteron in the GeV range. Some design work was carried out this year on Experiment NE-16 at SLAC, a study of the (e,e'p) reaction in 4 He, expected to run late in 1990

  1. Electron-cyclotron current drive in the tokamak physics experiment

    International Nuclear Information System (INIS)

    Smith, G.R.; Kritz, A.H.; Radin, S.H.

    1992-01-01

    Ray-tracking calculations provide estimates of the electron-cyclotron heating (ECH) power required to suppress tearing modes near the q=2 surface in the Tokamak Physics Experiment. Effects of finite beam width and divergence are included, as are the effects of scattering of the ECH power by drift-wave turbulence. A frequency of about 120 GHz allows current drive on the small-R (high-B) portion of q=2, while 80 GHz drives current on the large-R (low-B) portion. The higher frequency has the advantages of less sensitivity to wave and plasma parameters and of no trapped-electron degradation of current-drive efficiency. Less than 1 MW suffices to suppress tearing modes even with high turbulence levels

  2. Radiation load experiments with electronic components of the SYMPHONIE satellite

    International Nuclear Information System (INIS)

    Spencker, A.; Wagemann, H.G.; Braeunig, D.

    1975-09-01

    This report surveys fundamentals, realization and results of irradiation experiments which applied to 36 different electronic components of the Symphonie satellite and which were completed at the HMI Berlin and the C.N.E.T. Lannion in the years 1972/73. In a general section the evaluation of equivalent fluencies concerning 1 MeV electrons as radiation simulating the extraterrestric particle spectra with regard to the well-known semiconductor damage mechanisms is discussed. Then the realization of irradiation testing for the Symphonie satellite is described. Three selected examples demonstrate typical failure modes of semiconductor devices under radiation stress: Finally the main experimental results are shown in a standardized manner; a survey in English is given on p. 44. (orig.) [de

  3. New experiments on few-electron very heavy atoms

    International Nuclear Information System (INIS)

    Gould, H.

    1985-07-01

    New experiments, to test quantum electrodynamics (QED) in strong Coulomb fields and to study atomic collisions at ultrarelativistic energies, are proposed. A 0.1% measurement of the 2 2 P/sub 1/2/-2 2 S/sub 1/2/ splitting in lithium like uranium (Z=92) and the 2 3 P 0 - 2 3 S 1 splitting in heliumlike uranium is proposed as a sub 1% test of the Lamb shift in a strong Coulomb field. Measurements of the hyperfine splitting of hydrogenlike thallium (Z=81) and the g/sub j/ factor of the ground state of hydrogenlike uranium are propsed as a test of the QED contribution to the magnetic moment of an electron bound in a strong Coulomb field. Measurements of capture cross sections for ultra relativistic very heavy nuclei are proposed to look for the capture of electrons from pair production. 40 refs., 7 figs., 2 tabs

  4. Electron cyclotron current drive experiments on DIII-D

    International Nuclear Information System (INIS)

    James, R.A.; Giruzzi, G.; Gentile, B. de; Rodriguez, L.; Fyaretdinov, A.; Gorelov, Yu.; Trukhin, V.; Harvey, R.; Lohr, J.; Luce, T.C.; Matsuda, K.; Politzer, P.; Prater, R.; Snider, R.; Janz, S.

    1990-05-01

    Electron Cyclotron Current Drive (ECCD) experiments on the DIII-D tokamak have been performed using 60 GHz waves launched from the high field side of the torus. Preliminary analysis indicates rf driven currents between 50 and 100 kA in discharges with total plasma currents between 200 and 500 kA. These are the first ECCD experiments with strong first pass absorption, localized deposition of the rf power, and τ E much longer than the slowing-down time of the rf generated current carriers. The experimentally measured profiles for T e , η e and Z eff are used as input for a 1D transport code and a multiply-ray, 3D ray tracing code. Comparisons with theory and assessment of the influence of the residual electric field, using a Fokker-Planck code, are in progress. The ECH power levels were between 1 and 1.5 MW with pulse lengths of about 500 msec. ECCD experiments worldwide are motivated by issues relating to the physics and technical advantages of the use of high frequency rf waves to drive localized currents. ECCD is accomplished by preferentially heating electrons moving in one toroidal direction, reducing their collisionality and thereby producing a non-inductively driven toroidal current. 6 refs., 4 figs

  5. Electron cyclotron current drive experiments on DIII-D

    Energy Technology Data Exchange (ETDEWEB)

    James, R.A. (Lawrence Livermore National Lab., CA (USA)); Giruzzi, G.; Gentile, B. de; Rodriguez, L. (Association Euratom-CEA, Centre d' Etudes Nucleaires de Cadarache, 13 - Saint-Paul-les-Durance (France)); Fyaretdinov, A.; Gorelov, Yu.; Trukhin, V. (Kurchatov Inst. of Atomic Energy, Moscow (USSR)); Harvey, R.; Lohr, J.; Luce, T.C.; Matsuda, K.; Politzer, P.; Prater, R.; Snider, R. (General Atomics, San Di

    1990-05-01

    Electron Cyclotron Current Drive (ECCD) experiments on the DIII-D tokamak have been performed using 60 GHz waves launched from the high field side of the torus. Preliminary analysis indicates rf driven currents between 50 and 100 kA in discharges with total plasma currents between 200 and 500 kA. These are the first ECCD experiments with strong first pass absorption, localized deposition of the rf power, and {tau}{sub E} much longer than the slowing-down time of the rf generated current carriers. The experimentally measured profiles for T{sub e}, {eta}{sub e} and Z{sub eff} are used as input for a 1D transport code and a multiply-ray, 3D ray tracing code. Comparisons with theory and assessment of the influence of the residual electric field, using a Fokker-Planck code, are in progress. The ECH power levels were between 1 and 1.5 MW with pulse lengths of about 500 msec. ECCD experiments worldwide are motivated by issues relating to the physics and technical advantages of the use of high frequency rf waves to drive localized currents. ECCD is accomplished by preferentially heating electrons moving in one toroidal direction, reducing their collisionality and thereby producing a non-inductively driven toroidal current. 6 refs., 4 figs.

  6. Free electron laser experiments using a long pulse induction linac

    International Nuclear Information System (INIS)

    Pasour, J.A.; Lucey, R.

    1983-01-01

    The NRL Long Pulse Induction Linac is being employed in a Free Electron Laser (FEL) experiment. The authors present results of beam transport and focusing experiments as well as measurements of the output radiation generated by various magnetic wigglers. The electron gun of the accelerator presently has a 17-cmdiam. cold cathode which is located in a nearly zero magnetic field (B /SUB z/ less than or equal to 5 G). The gun voltage is flat to within approx. = + or - 5% for 1.5 μsec with this graphite brush cathode. The beam is focused by a series of solenoidal coils as it propagates through the 4-m-long accelerator. 2 A solenoidal field which can be varied from 1-10 kG confines the beam in the FEL interaction region. Previous experiments were limited by poor beam transport, focusing, and matching into the relatively large solenoidal field in the FEL region. By smoothing the axial magnetic field profile in the accelerator and making a more adiabatic transition from the low field in the accelerator to the high field in the FEL, beam transport into the wiggler has been substantially improved. Currently, a 700 kV beam with I > 500 A and r /SUB b/ < 0.75 cm is transported through the FEL region. Beam transport is in qualitative agreement with envelope code calculations

  7. Scaled electron experiments at the University of Maryland

    International Nuclear Information System (INIS)

    Haber, I.; Bai, G.; Bernal, S.; Beaudoin, B.; Feldman, D.; Fiorito, R.B.; Godlove, T.F.; Kishek, R.A.; O'Shea, P.G.; Quinn, B.; Papadopoulos, C.; Reiser, M.; Rodgers, J.; Stratakis, D.; Sutter, D.; Thangaraj, J.C.T.; Tian, K.; Walter, M.; Wu, C.

    2007-01-01

    The University of Maryland Electron Ring (UMER) and the Long Solenoid Experiment (LSE) are two electron machines that were designed explicitly to study the physics of space-charge-dominated beams. The operating parameters of these machines can be varied by choice of apertures and gun operating conditions to access a wide range of parameters that reproduce, on a scaled basis, the full nonlinear time-dependent physics that is expected in much costlier ion systems. Early operation of these machines has demonstrated the importance of the details of beam initial conditions in determining the downstream evolution. These machines have also been a convenient tested for benchmarking simulation codes such as WARP, and for development of several novel diagnostic techniques. We present our recent experience with multi-turn operation as well as recent longitudinal and transverse physics experiments and comparisons to simulation results. Development of novel diagnostic techniques such as time-dependent imaging using optical transition radiation and tomographic beam reconstruction are also described

  8. The electron accelerator for FELIX [Free Electron Laser for Infrared eXperiments

    International Nuclear Information System (INIS)

    Amersfoort, P.W. van; Geer, C.A.J. van der; Meer, A.F.G. van der; Bruinsma, P.J.T.; Hoekstra, R.; Kroes, F.B.; Luyckx, G.; Noomen, J.G.; Poole, M.W.; Saxon, G.

    1989-01-01

    The authors discuss the design of the electron accelerator for the Free Electron Laser for Infrared eXperiments (FELIX), which is meant to provide the Dutch science community with a rapidly tunable source of infrared radiation. The first stage of the project will (at least) cover the wavelength range between 8 and 80 μm. The accelerator consists of a triode with a grid modulated at 1 GHz, a 3.8-MeV buncher, and two travelling-wave S-band linac structures, with which 70-A, 3-ps bunches are accelerated to an energy between 15 and 4-5 MeV. The system has been designed to minimize the energy spread in the electron beam. 8 refs., 2 figs., 1 tab

  9. 'TRISTAN'; a database for electron colliding beam experiments

    International Nuclear Information System (INIS)

    Shimizu, Y.; Igarashi, M.; Nakazawa, N.; Oyanagi, Y.

    1982-01-01

    In this data base, the reference papers on the experiments of positron-electron colliding beam were collected for the purpose to utilize them for the TRISTAN project. The on-line retrieval of the references is possible. The number of the references is 289 during the period from January, 1974, to September, 1981. The collection of data will be continued hereafter. The terms retrievable are accelerator, incident beam, code, and radiation correction formula. The SC (name of the first author, year), incident energy, detector, luminocity, integrated luminosity, reaction, purpose and comments are also included as the data. The system is written in FORTRAN 77, and is portable. (Kato, T.)

  10. Future photomultiplier assemblies and associated electrons in large experiments

    International Nuclear Information System (INIS)

    Duteil, P.; Hammarstroem, R.; Innocenti, P.G.; Michelini, A.; Smith, B.; Soso, F.

    1977-01-01

    The results are presented of a working group study on reducing costs of proposed counter experiments in high-energy physics where several thousand photomultipliers are involved. Photomultiplier design is briefly discussed and new designs are presented for tube housings and high-voltage supplies. An outline presentation is given of a simplified electronics system, based on the Eurocard, for fast logic, data handling, and associated power supplies, suitable for photomultipliers or wire counters. Substantial savings in cost are shown to be possible without affecting performance but with some loss in convenience. (Auth.)

  11. Modification Of The Electron Energy Distribution Function During Lithium Experiments On The National Spherical Torus Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Jaworski, M A; Gray, T K; Kaita, R; Kallman, J; Kugel, H; LeBlanc, B; McLean, A; Sabbagh, S A; Soukanovskii, V; Stotler, D P

    2011-06-03

    The National Spherical Torus Experiment (NSTX) has recently studied the use of a liquid lithium divertor (LLD). Divertor Langmuir probes have also been installed for making measurements of the local plasma conditions. A non-local probe interpretation method is used to supplement the classical probe interpretation and obtain measurements of the electron energy distribution function (EEDF) which show the occurrence of a hot-electron component. Analysis is made of two discharges within a sequence that exhibited changes in plasma fueling efficiency. It is found that the local electron temperature increases and that this increase is most strongly correlated with the energy contained within the hot-electron population. Preliminary interpretative modeling indicates that kinetic effects are likely in the NSTX.

  12. Determination of the Electron Neutrino Mass from Experiments on Electron-Capture Beta-Decay (EC)

    CERN Multimedia

    2002-01-01

    The aim of the programme is to measure the electron-neutrino mass, for which at present an upper limit of 500~eV is known. \\\\ \\\\ The experiment studies the shape of the internal bremsstrahlung spectrum in electron-capture near its upper end-point and deduces a mass from small shape changes completely analogous to those in the well-known determination of the electron antineutrino mass in the tritium beta-minus decay. \\\\ \\\\ In a low-energy bremsstrahlung process, the capture takes place from a virtual S state associated with a radiative P~@A~S electromagnetic transition, and the resonant nature of the process leads to important enhancements of the photon intensities at low energy, in particular near the resonance energies co (X-rays). This effect gives this type of experiment a chance to compete with experiments on continuous beta spectra. \\\\ \\\\ The programme concentrates on two long-lived isotopes: \\\\ \\\\ 1)~~|1|6|3Ho. The Q value for this isotope has been found to be 2.6-2.7 keV. A detector specially construct...

  13. Development of an electron momentum spectrometer for time-resolved experiments employing nanosecond pulsed electron beam

    Science.gov (United States)

    Tang, Yaguo; Shan, Xu; Liu, Zhaohui; Niu, Shanshan; Wang, Enliang; Chen, Xiangjun

    2018-03-01

    The low count rate of (e, 2e) electron momentum spectroscopy (EMS) has long been a major limitation of its application to the investigation of molecular dynamics. Here we report a new EMS apparatus developed for time-resolved experiments in the nanosecond time scale, in which a double toroidal energy analyzer is utilized to improve the sensitivity of the spectrometer and a nanosecond pulsed electron gun with a repetition rate of 10 kHz is used to obtain an average beam current up to nA. Meanwhile, a picosecond ultraviolet laser with a repetition rate of 5 kHz is introduced to pump the sample target. The time zero is determined by photoionizing the target using a pump laser and monitoring the change of the electron beam current with time delay between the laser pulse and electron pulse, which is influenced by the plasma induced by the photoionization. The performance of the spectrometer is demonstrated by the EMS measurement on argon using a pulsed electron beam, illustrating the potential abilities of the apparatus for investigating the molecular dynamics in excited states when employing the pump-probe scheme.

  14. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    2010-09-01

    Full Text Available International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  15. Experiments in electron microscopy: from metals to nerves

    International Nuclear Information System (INIS)

    Unwin, Nigel

    2015-01-01

    Electron microscopy has advanced remarkably as a tool for biological structure research since the development of methods to examine radiation-sensitive unstained specimens and the introduction of cryo-techniques. Structures of biological molecules at near-atomic resolution can now be obtained from images of single particles as well as crystalline arrays. It has also become possible to analyze structures of molecules in their functional context, i.e. in their natural membrane or cellular setting, and in an ionic environment like that in living tissue. Electron microscopy is thus opening ways to answer definitively questions about physiological mechanisms. Here I recall a number of experiments contributing to, and benefiting from the technical advances that have taken place. I begin—in the spirit of this crystallography series—with some biographical background, and then sketch the path to an analysis by time-resolved microscopy of the opening mechanism of an ion channel (nicotinic acetylcholine receptor). This analysis illustrates how electron imaging can be combined with freeze-trapping to illuminate a transient biological event: in our case, chemical-to-electrical transduction at the nerve-muscle synapse. (invited comment)

  16. Millimeter wave free electron laser amplifiers: Experiments and designs

    International Nuclear Information System (INIS)

    Bidwell, S.W.; Zhang, Z.X.; Antonsen, T.M. Jr.; Bensen, D.M.; Destler, W.W.; Granatstein, V.L.; Lantham, P.E.; Levush, B.; Rodgers, J.

    1991-01-01

    Free electron laser amplifies are investigated as sources of high- average-power (1 MW) millimeter to submillimeter wave radiation (200 GHz - 600 GHz) for application to electron cyclotron resonance heating of magnetically confined fusion plasmas. As a stepping-stone to higher frequencies and cw operation a pulsed amplifier (τ pulse ≅ 80 ns) at 98 GHz is being developed. Status is reported on this experiment which investigates linear gain amplification with use of sheet electron beam (transverse cross section = 0.1 cm x 2.0 cm, V beam = 440 keV, I beam ≅ 10 A) and short-period wiggler (ell w = 0.96 cm) and with expected output of 140 W. Predictions of gain and efficiency from a 1-D universal formulation are presented. Beam propagation results, with wiggler focusing as a means of sheet beam confinement in both transverse dimensions, through the 54 cm (56 period) pulsed electromagnet wiggler are discussed. Peak wiggler fields of 5.1 kG on-axis have been achieved

  17. Monte Carlo simulation of Tabata's electron backscattering experiments

    International Nuclear Information System (INIS)

    Kirihara, Y.; Namito, Y.; Iwase, H.; Hirayama, H.

    2010-01-01

    Electron backscattering coefficients, η, obtained from several targets in the MeV range were calculated by using electron-photon Monte Carlo transport calculation codes, i.e., EGS5 and ITS 3.0. These calculated values were compared with those obtained from the electron backscattering experiment performed by Tabata using an ionization chamber . We found that Tabata's estimation of the multiplication factor of the ionization chamber, f, had a non-negligible error. Then, we calculated the ionization chamber output, I, which is a product of η and f. The ratios of I between the experimental and the calculated values were within 1.5 and 1.3 for the EGS5 code and the ITS 3.0 code, respectively. The ratios of η between the experimental and the calculated values were within 2.4 and 1.5 for the EGS5 code and the ITS 3.0 code, respectively. The differences between the experimental and the calculated values of I and η are large for low-Z targets (Be and C). Here, the ratios obtained by using the ITS 3.0 code are closer to unity than those obtained by using the EGS5 code. The reason of this is the fact that the calculated value obtained by using the ITS 3.0 code is underestimated for low-Z targets; this underestimation can, in turn, be attributed to the use of the default value of the number of steps in the electron transport algorithm in the ITS 3.0 code.

  18. Mining meiosis and gametogenesis with DNA microarrays.

    Science.gov (United States)

    Schlecht, Ulrich; Primig, Michael

    2003-04-01

    Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

  19. Progress on Electron Cyclotron Heating Experiments in LHD

    International Nuclear Information System (INIS)

    Shimozuma, T.; Kubo, S.; Yoshimura, Y.; Igami, H.; Nagasaki, K.; Notake, T.; Inagaki, S.; Ito, S.; Kobayashi, S.; Mizuno, Y.; Takita, Y.; Ohkubo, K.; Saito, K.; Seki, T.; Kumazawa, R.; Watari, T.; Mutoh, T.

    2005-01-01

    Electron cyclotron resonance heating (ECH) is a powerful heating method because of its well-controlled local heating and high deposition power density. Together with the development of high power long pulse gyrotrons, ECH becomes one of the major heating scenarios to control electron temperature and current profiles for the improved plasma confinement and suppression of some magneto-hydro-dainamic (MHD) instabilities in both tokamaks and stellarators [1]. In the Large Helical Device (LHD), ECH has been worked as a method of plasma initiation and electron heating. The ECH system has been improved with respect to each experimental campaign. In the recent campaign, nine gyrotrons were operated reliably and steadily. As a diagnostic objective, a modulated ECH (MECH) was injected together with main ECH power. A Fourier analysis of the induced heat wave gave useful information of not only the heat transport in the plasmas but also precise power deposition layer [2]. Several kinds of ECH experiment were performed by using this flexible ECH system. In LHD, electron ITB formation have been observed by using strongly focused ECH in the plasma core [3].Two different kinds of improved confinement were realized depending on the direction of tangentially injected NBI. NBI beam driven currents modify the profiles of the rotational transform 2 ro and the existence low order rational surfaces, 2 = 0.5 in special, affects the difference of appearance of the improved confinement states. The MECH method was used to investigate the internal structure of the thermal diffusion in such plasmas [4]. Another important role of the MECH is the precise determination of the ECH power deposition. Shift of the deposition location by changing an injection polarization in the electron Bernstein wave (EBW) heating was clearly demonstrated by the MECH method. Electron cyclotron current drive (ECCD) experiments were proceeded by using a flexible antenna system, which had wide scanning range in both

  20. Immobilization Techniques for Microarray: Challenges and Applications

    Directory of Open Access Journals (Sweden)

    Satish Balasaheb Nimse

    2014-11-01

    Full Text Available The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

  1. Electron Spin Resonance Experiments on a Single Electron in Silicon Implanted with Phosphorous

    Science.gov (United States)

    Luhman, Dwight R.; Nguyen, K.; Tracy, L. A.; Carr, S.; Borchardt, J.; Bishop, N.; Ten Eyck, G.; Pluym, T.; Wendt, J.; Lilly, M. P.; Carroll, M. S.

    2015-03-01

    In this talk we will discuss the results of our ongoing experiments involving electron spin resonance (ESR) on a single electron in a natural silicon sample. The sample consists of an SET, defined by lithographic polysilicon gates, coupled to nearby phosphorous donors. The SET is used to detect charge transitions and readout the spin of the electron being investigated with ESR. The measurements were done with the sample at dilution refrigerator temperatures in the presence of a 1.3 T magnetic field. We will present data demonstrating Rabi oscillations of a single electron in this system as well as measurements of the coherence time, T2. We will also discuss our results using these and various other pulsing schemes in the context of a donor-SET system. This work was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. DOE Office of Basic Energy Sciences user facility. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the U. S. Department of Energy under Contract No. DE-AC04-94AL85000.

  2. Free electron laser amplifier experiments on SG-1

    International Nuclear Information System (INIS)

    Hui Zhongxi; Zhou Chuanming; Wu Ruian

    1994-01-01

    The SG-1 FEL facility is composed of a linear induction accelerator (LIA), an electron beam transport system, a wiggler, a microwave source and a diagnostic system. SG-1 LIA provides a 2 kA, 3.0 MeV beam with a normalized emittance of 0.4∼0.6 (π rad·cm), an energy spread (FWHM) of 4%, resulting in a beam brightness of nearly 10 8 A/πm·rad) 2[1] . The beam current through the wiggler is about 600 A. The first ASE experiments began in September 1991. A 2.6-m long wiggler with a peak magnetic field of 0.3 T was used. At 35.8∼36.5 GHz an ASE output of 0.5 W was obtained for a beam current of nearly 50 A. After a shutdown of about 8 months, the second series of ASE experiments began in October 1992. The second series of ASE experiments were performed with a wiggler magnetic field between 0.25∼0.27 T. The maximum output power is about 100 kw for B w = 0.24 T, I = 600 A, At ν = 35.2 GHz. Based on the ASE experiments the amplifier experiments was carried out on SG-1. Using an 300 W input signal (TE 01 ), a beam current of about 600 A and wiggler magnetic fields of 0.24∼0.28 T, the authors measured the FEL output power as a function of the wiggler magnetic field. The resonant magnetic field was about 0.25 T. Meanwhile, in order to study the amplifier gain, the authors measured the FEL output power as a function of the wiggler length at a peak wiggler magnetic field of 0.26 T. The exponential gain is approximately 19 dB/m and the maximum output power is about 10 MW

  3. Pleasurable and Intersubjectively Embodied Experiences of Electronic Dance Music

    Directory of Open Access Journals (Sweden)

    Ragnhild Torvanger Solberg

    2017-04-01

    Full Text Available How do dancers engage with electronic dance music (EDM when dancing? This paper reports on an empirical study of dancers' pleasurable engagement with three structural properties of EDM: (1 breakdown, (2 build-up, and (3 drop. Sixteen participants danced to a DJ mix in a club-like environment, and the group’s bodily activity was recorded with an infrared, marker-based motion capture system. After they danced, the subjects filled out questionnaires about the pleasure they experienced and their relative desire to move while dancing. Subsequent analyses revealed associations between the group’s quantity of motion and self-reported experiences of pleasure. Associations were also found between certain sonic features and dynamic changes in the dancers' movements. Pronounced changes occurred in the group's quantity of motion during the breakdown, build-up, and drop sections, suggesting a high level of synchronization between the group and the structural properties of the music. The questionnaire confirmed this intersubjective agreement: participants perceived the musical passages consistently and marked the build-up and drop as particularly pleasurable and motivational in terms of dancing. Self-reports demonstrated that the presence and activity of other participants were also important in the shaping of one's own experience, thus supporting the idea of clubbing as an intersubjectively embodied experience.

  4. Clinical experience with routine diode dosimetry for electron beam radiotherapy

    International Nuclear Information System (INIS)

    Yaparpalvi, Ravindra; Fontenla, Doracy P.; Vikram, Bhadrasain

    2000-01-01

    Purpose: Electron beam radiotherapy is frequently administered based on clinical setups without formal treatment planning. We felt, therefore, that it was important to monitor electron beam treatments by in vivo dosimetry to prevent errors in treatment delivery. In this study, we present our clinical experience with patient dose verification using electron diodes and quantitatively assess the dose perturbations caused by the diodes during electron beam radiotherapy. Methods and Materials: A commercial diode dosimeter was used for the in vivo dose measurements. During patient dosimetry, the patients were set up as usual by the therapists. Before treatment, a diode was placed on the patient's skin surface and secured with hypoallergenic tape. The patient was then treated and the diode response registered and stored in the patient radiotherapy system database via our in-house software. A customized patient in vivo dosimetry report showing patient details, expected and measured dose, and percent difference was then generated and printed for analysis and record keeping. We studied the perturbation of electron beams by diodes using film dosimetry. Beam profiles at the 90% prescription isodose depths were obtained with and without the diode on the beam central axis, for 6-20 MeV electron beams and applicator/insert sizes ranging from a 3-cm diameter circular field to a 25 x 25 cm open field. Results: In vivo dose measurements on 360 patients resulted in the following ranges of deviations from the expected dose at the various anatomic sites: Breast (222 patients) -20.3 to +23.5% (median deviation 0%); Head and Neck (63 patients) -21.5 to +14.8% (median -0.7%); Other sites (75 patients) -17.6 to +18.8% (median +0.5%). Routine diode dosimetry during the first treatment on 360 patients (460 treatment sites) resulted in 11.5% of the measurements outside our acceptable ±6% dose deviation window. Only 3.7% of the total measurements were outside ±10% dose deviation. Detailed

  5. Structure and Electronic Properties of Cerium Orthophosphate: Theory and Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Adelstein, Nicole; Mun, B. Simon; Ray, Hannah; Ross Jr, Phillip; Neaton, Jeffrey; De Jonghe, Lutgard

    2010-07-27

    Structural and electronic properties of cerium orthophosphate (CePO{sub 4}) are calculated using density functional theory (DFT) with the local spin-density approximation (LSDA+U), with and without gradient corrections (GGA-(PBE)+U), and compared to X-ray diffraction and photoemission spectroscopy measurements. The density of states is found to change significantly as the Hubbard parameter U, which is applied to the Ce 4f states, is varied from 0 to 5 eV. The calculated structural properties are in good agreement with experiment and do not change significantly with U. Choosing U = 3 eV for LDSA provides the best agreement between the calculated density of states and the experimental photoemission spectra.

  6. Terrestrial effects on dark matter-electron scattering experiments

    DEFF Research Database (Denmark)

    Emken, Timon; Kouvaris, Chris; Shoemaker, Ian M.

    2017-01-01

    A well-studied possibility is that dark matter may reside in a sector secluded from the Standard Model, except for the so-called photon portal: kinetic mixing between the ordinary and dark photons. Such interactions can be probed in dark matter direct detection experiments, and new experimental...... techniques involving detection of dark matter-electron scattering offer new sensitivity to sub-GeV dark matter. Typically however it is implicitly assumed that the dark matter is not altered as it traverses the Earth to arrive at the detector. In this paper we study in detail the effects of terrestrial...... stopping on dark photon models of dark matter, and find that they significantly reduce the sensitivity of XENON10 and DAMIC. In particular we find that XENON10 only excludes masses in the range (5-3000) MeV while DAMIC only probes (20-50) MeV. Their corresponding cross section sensitivity is reduced...

  7. Broadband electron spin resonance experiments using superconducting coplanar waveguides

    Energy Technology Data Exchange (ETDEWEB)

    Clauss, Conrad; Bogani, Lapo; Scheffler, Marc; Dressel, Martin [1. Physikalisches Institut, Universitaet Stuttgart (Germany); Bothner, Daniel; Koelle, Dieter; Kleiner, Reinhold [Physikalisches Institut - Experimentalphysik II and Center for Collective Quantum Phenomena in LISA+, Universitaet Tuebingen (Germany)

    2012-07-01

    In recent years superconducting coplanar devices operating at microwave/GHz frequencies are employed in more and more experimental studies. Here, we present electron spin resonance (ESR) experiments using a superconducting coplanar waveguide to provide the RF field to drive the spin flips. In contrast to conventional ESR studies this allows broadband frequency as well as magnetic field swept observation of the spin resonance. We show experimental data of the spin resonance of the organic radical NitPhoMe (2-(4'-methoxyphenyl)-4,4,5,5-tetra-methylimidazoline-1-oxyl-3-oxide) for frequencies in the range of 1 GHz to 40 GHz and corresponding magnetic fields up to 1.4 T (for g=2). In addition we show the temperature dependence of the ESR signals for temperatures up to 30 K, which is well above the critical temperature of the niobium superconductor.

  8. DNA microarrays : a molecular cloning manual

    National Research Council Canada - National Science Library

    Sambrook, Joseph; Bowtell, David

    2002-01-01

    .... DNA Microarrays provides authoritative, detailed instruction on the design, construction, and applications of microarrays, as well as comprehensive descriptions of the software tools and strategies...

  9. Electronic medical record in cardiology: a 10-year Italian experience.

    Science.gov (United States)

    Carpeggiani, Clara; Macerata, Alberto; Morales, Maria Aurora

    2015-08-01

    the aim of this study was to report a ten years experience in the electronic medical record (EMR) use. An estimated 80% of healthcare transactions are still paper-based. an EMR system was built at the end of 1998 in an Italian tertiary care center to achieve total integration among different human and instrumental sources, eliminating paper-based medical records. Physicians and nurses who used EMR system reported their opinions. In particular the hospital activity supported electronically, regarding 4,911 adult patients hospitalized in the 2004- 2008 period, was examined. the final EMR product integrated multimedia document (text, images, signals). EMR presented for the most part advantages and was well adopted by the personnel. Appropriateness evaluation was also possible for some procedures. Some disadvantages were encountered, such as start-up costs, long time required to learn how to use the tool, little to no standardization between systems and the EMR technology. the EMR is a strategic goal for clinical system integration to allow a better health care quality. The advantages of the EMR overcome the disadvantages, yielding a positive return on investment to health care organization.

  10. Electronic medical record in cardiology: a 10-year Italian experience

    Directory of Open Access Journals (Sweden)

    Clara Carpeggiani

    2015-08-01

    Full Text Available SummaryObjectives:the aim of this study was to report a ten years experience in the electronic medical record (EMR use. An estimated 80% of healthcare transactions are still paper-based.Methods:an EMR system was built at the end of 1998 in an Italian tertiary care center to achieve total integration among different human and instrumental sources, eliminating paper-based medical records. Physicians and nurses who used EMR system reported their opinions. In particular the hospital activity supported electronically, regarding 4,911 adult patients hospitalized in the 2004- 2008 period, was examined.Results:the final EMR product integrated multimedia document (text, images, signals. EMR presented for the most part advantages and was well adopted by the personnel. Appropriateness evaluation was also possible for some procedures. Some disadvantages were encountered, such as start-up costs, long time required to learn how to use the tool, little to no standardization between systems and the EMR technology.Conclusion:the EMR is a strategic goal for clinical system integration to allow a better health care quality. The advantages of the EMR overcome the disadvantages, yielding a positive return on investment to health care organization.

  11. Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

    Directory of Open Access Journals (Sweden)

    Nobumasa Hitoshi

    2007-04-01

    Full Text Available Abstract Background Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. Results Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. Conclusion Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross

  12. How people with cognitive disabilities experience electronic planning devices.

    Science.gov (United States)

    Adolfsson, Päivi; Lindstedt, Helena; Janeslätt, Gunnel

    2015-01-01

    People with cognitive disabilities have difficulties in accomplishing everyday tasks. Electronic planning devices (EPDs) may compensate for the gap between a person's capacity and everyday challenges. However, the devices are not always used as intended. Despite that, cognitive assistive technology has been investigated in several studies, knowledge regarding when and what makes adults decide to use EPDs is incomplete. The aim was to explore the subjective experiences of people with cognitive disabilities in relation to the use of EPDs. A qualitative approach was applied with a qualitative content analysis. Twelve respondents were interviewed with support from a study specific guide. A model representing the respondents' experiences in the use of EPDs, comprising one theme, Possibility to master my daily life, four categories, Degree of fit to my needs, I am aware of my cognitive disability, I get help to structure my everyday life and The EPD improves my volition and ten subcategories, was developed. EPDs allow people with cognitive disabilities the possibility to deal with daily challenges; those who find EPDs beneficial tend to use them. EPDs can help people with cognitive disabilities in organisation, managing time and improve volition.

  13. Electron beam injection during active experiments. 1. Electromagnetic wave emissions

    International Nuclear Information System (INIS)

    Winglee, R.M.; Kellogg, P.J.

    1990-01-01

    During the active injection of an electron beam, a broad spectrum of waves is generated. In this paper examples of spectra from the recent Echo 7 experiment are presented. These results show that the characteristics of the emissions can change substantially with altitude. Two-dimensional (three velocity) relativistic electromagnetic particle simulations are used to investigate the changes in the plasma conditions required to account for the observed spectral variations. It is shown that many of these variations can be accounted for by assuming that the ratio of the electron plasma frequency ω pe to cyclotron frequency Ω e is less than unity at the lower altitudes of about 200 km and near or above unity at apogee of about 300 km. In the former case, whistlers with a cutoff at ω pe , lower hybrid and plasma waves are driven by the parallel beam energy while electromagnetic fundamental z mode and second harmonic x mode and electrostatic upper hybrid waves are driven by the perpendicular beam energy through the master instability. E x B drifts driven by perpendicular electric fields associated with the beam-plasma interaction can also be important in generating maser emission, particularly for field-aligned injection where there is no intrinsic perpendicular beam energy. The power in the electrostatic waves is a few percent of the beam energy and that in the electromagnetic waves a few tenths of a percent. In the latter case, where ω pe /Ω e increases above unity, emission in the fundamental z mode and second harmonic x mode become suppressed

  14. Laboratory Experiments Enabling Electron Beam use in Tenuous Space Plasmas

    Science.gov (United States)

    Miars, G.; Leon, O.; Gilchrist, B. E.; Delzanno, G. L.; Castello, F. L.; Borovsky, J.

    2017-12-01

    A mission concept is under development which involves firing a spacecraft-mounted electron beam from Earth's magnetosphere to connect distant magnetic field lines in real time. To prevent excessive spacecraft charging and consequent beam return, the spacecraft must be neutralized in the tenuous plasma environment of the magnetosphere. Particle-In-Cell (PIC) simulations suggest neutralization can be accomplished by emitting a neutral plasma with the electron beam. Interpretation of these simulations also led to an ion emission model in which ion current is emitted from a quasi-neutral plasma as defined by the space charge limit [1,2]. Experiments were performed at the University of Michigan's Plasmadynamics and Electric Propulsion Laboratory (PEPL) to help validate the ion emission model. A hollow cathode plasma contactor was used as a representative spacecraft and charged with respect to the chamber walls to examine the effect of spacecraft charging on ion emission. Retarding Potential Analyzer (RPA) measurements were performed to understand ion flow velocity as this parameter relates directly to the expected space charge limit. Planar probe measurements were also made to identify where ion emission primarily occurred and to determine emission current density levels. Evidence of collisions within the plasma (particularly charge exchange collisions) and a simple model predicting emitted ion velocities are presented. While a detailed validation of the ion emission model and of the simulation tools used in [1,2] is ongoing, these measurements add to the physical understanding of ion emission as it may occur in the magnetosphere. 1. G.L. Delzanno, J.E. Borovsky, M.F. Thomsen, J.D. Moulton, and E.A. MacDonald, J. Geophys. Res. Space Physics 120, 3647, 2015. 2. G.L. Delzanno, J.E. Borovsky, M.F. Thomsen, and J.D. Moulton, J. Geophys. Res. Space Physics 120, 3588, 2015. ________________________________ * This work is supported by Los Alamos National Laboratory.

  15. Experiments on the nuclear interactions of pions and electrons

    International Nuclear Information System (INIS)

    Minehart, R.C.; Ziock, K.O.H.

    1992-08-01

    The analysis of the deuterium content in the CD target used in an experiment to study the π + d → 2p reaction at incident pion energies from 4 to 20 MeV was completed. The final paper describing this experiment will be submitted for publication this summer. Analysis of LAMPF Exp. on pion absorption in 4 He is continuing. In 1991, we collaborated with D. Pocanic from the Univ. of Virginia on a measurement at LAMPF of the π 0 production in π + p interactions. This run proved the validity of the method and additional data were obtained in a second run during the summer of 1992, using a new target. Current collaborations at LAMPF include the search for the decay μ + → e + + γ(MEGA) and a measurement of the Michel ρ parameter in the decay μ → e + v + v. A U.Va.--PSI collaboration is measuring pion beta decay to an accuracy of less than 1%, using a large acceptance CsI detector to measure the π 0 following decay of stopped π + mesons. Most of the U.Va. effort is devoted to the CEBAF Large Acceptance Spectrometer (CLAS) program to the construction of the CLAS forward calorimeter. An apparatus to measure the properties of the scintillators with light from a N 2 laser was built in the spring of 1992. The electronic circuitry for the energy signal from the EGN detector and the circuitry needed to route the signals from the all the photomultipliers to the TDC and ADC circuits are being developed. Experimental proposals for the study of electroproduction of nucleon resonances at CEBAF, including measurements with polarized beam and targets, are being developed

  16. Electron and photon identification in the D0 experiment

    Energy Technology Data Exchange (ETDEWEB)

    Abazov, V. M.; Abbott, B.; Acharya, B. S.; Adams, M.; Adams, T.; Agnew, J. P.; Alexeev, G. D.; Alkhazov, G.; Alton, A.; Askew, A.; Atkins, S.; Augsten, K.; Avila, C.; Badaud, F.; Bagby, L.; Baldin, B.; Bandurin, D. V.; Banerjee, S.; Barberis, E.; Baringer, P.; Bartlett, J. F.; Bassler, U.; Bazterra, V.; Bean, A.; Begalli, M.; Bellantoni, L.; Beri, S. B.; Bernardi, G.; Bernhard, R.; Bertram, I.; Besançon, M.; Beuselinck, R.; Bhat, P. C.; Bhatia, S.; Bhatnagar, V.; Blazey, G.; Blessing, S.; Bloom, K.; Boehnlein, A.; Boline, D.; Boos, E. E.; Borissov, G.; Borysova, M.; Brandt, A.; Brandt, O.; Brock, R.; Bross, A.; Brown, D.; Bu, X. B.; Buehler, M.; Buescher, V.; Bunichev, V.; Burdin, S.; Buszello, C. P.; Camacho-Pérez, E.; Casey, B. C. K.; Castilla-Valdez, H.; Caughron, S.; Chakrabarti, S.; Chan, K. M.; Chandra, A.; Chapon, E.; Chen, G.; Cho, S. W.; Choi, S.; Choudhary, B.; Cihangir, S.; Claes, D.; Clutter, J.; Cooke, M.; Cooper, W. E.; Corcoran, M.; Couderc, F.; Cousinou, M. -C.; Cutts, D.; Das, A.; Davies, G.; de Jong, S. J.; De La Cruz-Burelo, E.; Déliot, F.; Demina, R.; Denisov, D.; Denisov, S. P.; Desai, S.; Deterre, C.; DeVaughan, K.; Diehl, H. T.; Diesburg, M.; Ding, P. F.; Dominguez, A.; Dubey, A.; Dudko, L. V.; Duperrina, A.; Dutt, S.; Eads, M.; Edmunds, D.; Ellison, J.; Elvira, V. D.; Enari, Y.; Evans, H.; Evdokimov, V. N.; Feng, L.; Ferbel, T.; Fiedler, F.; Filthaut, F.; Fisher, W.; Fisk, H. E.; Fortner, M.; Fox, H.; Fuess, S.; Garbincius, P. H.; Garcia-Bellido, A.; García-González, J. A.; Gavrilov, V.; Geng, W.; Gerber, C. E.; Gershtein, Y.; Ginther, G.; Golovanov, G.; Grannis, P. D.; Greder, S.; Greenlee, H.; Grenier, G.; Gris, Ph.; Grivaz, J. -F.; Grohsjean, A.; Grünendahl, S.; Grünewald, M. W.; Guillemin, T.; Gutierrez, G.; Gutierrez, P.; Haley, J.; Han, L.; Harder, K.; Harel, A.; Hauptman, J. M.; Hays, J.; Head, T.; Hebbeker, T.; Hedin, D.; Hegab, H.; Heinson, A. P.; Heintz, U.; Hensel, C.; Heredia-De La Cruz, I.; Herner, K.; Hesketh, G.; Hildreth, M. D.; Hirosky, R.; Hoang, T.; Hobbs, J. D.; Hoeneisen, B.; Hogan, J.; Hohlfeld, M.; Holzbauer, J. L.; Howley, I.; Hubacek, Z.; Hynek, V.; Iashvili, I.; Ilchenko, Y.; Illingworth, R.; Ito, A. S.; Jabeen, S.; Jaffré, M.; Jayasinghe, A.; Jeong, M. S.; Jesik, R.; Jiang, P.; Johns, K.; Johnson, E.; Johnson, M.; Jonckheere, A.; Jonsson, P.; Joshi, J.; Jung, A. W.; Juste, A.; Kajfasz, E.; Karmanov, D.; Katsanos, I.; Kehoe, R.; Kermiche, S.; Khalatyan, N.; Khanov, A.; Kharchilava, A.; Kharzheev, Y. N.; Kiselevich, I.; Kohli, J. M.; Kozelov, A. V.; Kraus, J.; Kumar, A.; Kupco, A.; Kurča, T.; Kuzmin, V. A.; Lammers, S.; Lebrun, P.; Lee, H. S.; Lee, S. W.; Lee, W. M.; Lei, X.; Lellouch, J.; Li, D.; Li, H.; Li, L.; Li, Q. Z.; Lim, J. K.; Lincoln, D.; Linnemann, J.; Lipaev, V. V.; Lipton, R.; Liu, H.; Liu, Y.; Lobodenko, A.; Lokajicek, M.; Lopes de Sa, R.; Luna-Garcia, R.; Lyon, A. L.; Maciel, A. K. A.; Madar, R.; Magaña-Villalba, R.; Malik, S.; Malyshev, V. L.; Mansour, J.; Martínez-Ortega, J.; McCarthy, R.; McGivern, C. L.; Meijer, M. M.; Melnitchouk, A.; Menezes, D.; Mercadante, P. G.; Merkin, M.; Meyer, A.; Meyer, J.; Miconi, F.; Mondal, N. K.; Mulhearn, M.; Nagy, E.; Narain, M.; Nayyar, R.; Neal, H. A.; Negret, J. P.; Neustroev, P.; Nguyen, H. T.; Nunnemann, T.; Orduna, J.; Osman, N.; Osta, J.; Pal, A.; Parashar, N.; Parihar, V.; Park, S. K.; Partridge, R.; Parua, N.; Patwa, A.; Penning, B.; Perfilov, M.; Peters, Y.; Petridis, K.; Petrillo, G.; Pétroff, P.; Pleier, M. -A.; Podstavkov, V. M.; Popov, A. V.; Prewitt, M.; Price, D.; Prokopenko, N.; Qian, J.; Quadt, A.; Quinn, B.; Raja, R.; Ratoff, P. N.; Razumov, I.; Ripp-Baudot, I.; Rizatdinova, F.; Rominsky, M.; Ross, A.; Royon, C.; Rubinov, P.; Ruchti, R.; Sajot, G.; Sánchez-Hernández, A.; Sanders, M. P.; Santos, A. S.; Savage, G.; Sawyer, L.; Scanlon, T.; Schamberger, R. D.; Scheglov, Y.; Schellman, H.; Schwanenberger, C.; Schwienhorst, R.; Sekaric, J.; Severini, H.; Shabalina, E.; Shary, V.; Shaw, S.; Shchukin, A. A.; Simak, V.; Skubic, P.; Slattery, P.; Smirnov, D.; Snow, G. R.; Snow, J.; Snyder, S.; Söldner-Rembold, S.; Sonnenschein, L.; Soustruznik, K.; Stark, J.; Stoyanova, D. A.; Strauss, M.; Suter, L.; Svoisky, P.; Titov, M.; Tokmenin, V. V.; Tsai, Y. -T.; Tsybychev, D.; Tuchming, B.; Tully, C.; Uvarov, L.; Uvarov, S.; Uzunyan, S.; Van Kooten, R.; van Leeuwen, W. M.; Varelas, N.; Varnes, E. W.; Vasilyev, I. A.; Verkheev, A. Y.; Vertogradov, L. S.; Verzocchi, M.; Vesterinen, M.; Vilanova, D.; Vokac, P.; Wahl, H. D.; Wang, M. H. L. S.; Warchol, J.; Watts, G.; Wayne, M.; Weichert, J.; Welty-Rieger, L.; Williams, M. R. J.; Wilson, G. W.; Wobisch, M.; Wood, D. R.; Wyatt, T. R.; Xie, Y.; Yamada, R.; Yang, S.; Yasuda, T.; Yatsunenko, Y. A.; Ye, W.; Ye, Z.; Yin, H.; Yip, K.; Youn, S. W.; Yu, J. M.; Zennamo, J.; Zhao, T. G.; Zhou, B.; Zhu, J.; Zielinski, M.; Zieminska, D.; Zivkovic, L.

    2014-06-01

    The electron and photon reconstruction and identification algorithms used by the D0 Collaboration at the Fermilab Tevatron collider are described. The determination of the electron energy scale and resolution is presented. Studies of the performance of the electron and photon reconstruction and identification are summarized.

  17. Electron Bernstein Wave Research on the National Spherical Torus Experiment

    International Nuclear Information System (INIS)

    Taylor, G.; Bers, A.; Bigelow, T.S.; Carter, M.D.; Caughman, J.B.; Decker, J.; Diem, S.; Efthimion, P.C.; Ershov, N.M.; Fredd, E.; Harvey, R.W.; Hosea, J.; Jaeger, F.; Preinhaelter, J.; Ram, A.K.; Rasmussen, D.A.; Smirnov, A.P.; Wilgen, J.B.; Wilson, J.R.

    2005-01-01

    Off-axis electron Bernstein wave current drive (EBWCD) may be critical for sustaining noninductive high-beta National Spherical Torus Experiment (NSTX) plasmas. Numerical modeling results predict that the ∼100 kA of off-axis current needed to stabilize a solenoid-free high-beta NSTX plasma could be generated via Ohkawa current drive with 3 MW of 28 GHz EBW power. In addition, synergy between EBWCD and bootstrap current may result in a 10% enhancement in current-drive efficiency with 4 MW of EBW power. Recent dual-polarization EBW radiometry measurements on NSTX confirm that efficient coupling to EBWs can be readily accomplished by launching elliptically polarized electromagnetic waves oblique to the confining magnetic field, in agreement with numerical modeling. Plans are being developed for implementing a 1 MW, 28 GHz proof-of-principle EBWCD system on NSTX to test the EBW coupling, heating and current-drive physics at high radio-frequency power densities

  18. From hadronic parity violation to electron parity-violating experiments

    International Nuclear Information System (INIS)

    Oers, Willem T.H. van

    2010-01-01

    The weak interaction is manifested in parity-violating observables. With the weak interaction extremely well known parity-violating measurements in hadronic systems can be used to deduce strong interaction effects in those systems. Parity-violating analyzing powers in electron-proton scattering have led to determining the strange quark contributions to the charge and magnetization distributions of the nucleon. Parity-violating electron-proton and electron-electron scattering can also be performed to test the predictions of the Standard Model in the 'running' of the electroweak mixing angle or sin 2 θ W .

  19. Emerging use of gene expression microarrays in plant physiology.

    Science.gov (United States)

    Wullschleger, Stan D; Difazio, Stephen P

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  20. Emerging Use of Gene Expression Microarrays in Plant Physiology

    Directory of Open Access Journals (Sweden)

    Stephen P. Difazio

    2006-04-01

    Full Text Available Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

  1. Plant-pathogen interactions: what microarray tells about it?

    Science.gov (United States)

    Lodha, T D; Basak, J

    2012-01-01

    Plant defense responses are mediated by elementary regulatory proteins that affect expression of thousands of genes. Over the last decade, microarray technology has played a key role in deciphering the underlying networks of gene regulation in plants that lead to a wide variety of defence responses. Microarray is an important tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides. Till date, microarray technology has been used in the identification of regulatory genes, end-point defence genes, to understand the signal transduction processes underlying disease resistance and its intimate links to other physiological pathways. Microarray technology can be used for in-depth, simultaneous profiling of host/pathogen genes as the disease progresses from infection to resistance/susceptibility at different developmental stages of the host, which can be done in different environments, for clearer understanding of the processes involved. A thorough knowledge of plant disease resistance using successful combination of microarray and other high throughput techniques, as well as biochemical, genetic, and cell biological experiments is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to microarray technology, followed by the basics of plant-pathogen interaction, the use of DNA microarrays over the last decade to unravel the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

  2. Polyadenylation state microarray (PASTA) analysis.

    Science.gov (United States)

    Beilharz, Traude H; Preiss, Thomas

    2011-01-01

    Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.

  3. Linking probe thermodynamics to microarray quantification

    International Nuclear Information System (INIS)

    Li, Shuzhao; Pozhitkov, Alexander; Brouwer, Marius

    2010-01-01

    Understanding the difference in probe properties holds the key to absolute quantification of DNA microarrays. So far, Langmuir-like models have failed to link sequence-specific properties to hybridization signals in the presence of a complex hybridization background. Data from washing experiments indicate that the post-hybridization washing has no major effect on the specifically bound targets, which give the final signals. Thus, the amount of specific targets bound to probes is likely determined before washing, by the competition against nonspecific binding. Our competitive hybridization model is a viable alternative to Langmuir-like models. (comment)

  4. Solid electron sources for the energy scale monitoring in the KATRIN experiment

    CERN Document Server

    Zbořil, Miroslav; Vénos, D

    The KArlsruhe TRItium Neutrino (KATRIN) experiment represents a next-generation tritium $\\beta$-decay experiment designed to perform a high precision direct measurement of the electron anti-neutrino mass m($\

  5. Monitoring electronics during the experiments with the OSIRIS (HMI Berlin)

    International Nuclear Information System (INIS)

    Grebosz, J.

    1992-01-01

    This report presents the software to perform the constant monitoring of the electronics dedicated to control the multidetector system. It supervises the correct status of the gamma spectroscopy measurements. (author). 3 figs

  6. Electronics for the LAMPF neutrino experiment's veto counter system

    International Nuclear Information System (INIS)

    Dalton, C.

    1981-09-01

    A cosmic-ray veto detector has been constructed in the neutrino cave at Los Alamos National Laboratory. This report describes the electronic readout system designed to buffer and compact the data from the detector

  7. Operating experience with the polarized electron gun at SLAC

    International Nuclear Information System (INIS)

    Alguard, M.J.; Baum, G.; Clendenin, J.E.; Hughes, V.W.; Lubell, M.S.; Miller, R.H.; Raith, W.; Schuler, K.P.; Sodja, J.

    1977-03-01

    During the two years of operation of the SLAC Polarized Electron Gun (PEGGY), the electron intensity delivered to the target has increased from 7 x 10 7 e - /pulse to 1 x 10 9 e - /pulse. The polarization is 0.85 with no measurable degradation caused by acceleration through the linear accelerator. The predominant cause of downtime is replenishment of lithium, which now averages 43 hours. The lifetime of a lithium load is about 175 hours

  8. An Introduction to MAMA (Meta-Analysis of MicroArray data) System.

    Science.gov (United States)

    Zhang, Zhe; Fenstermacher, David

    2005-01-01

    Analyzing microarray data across multiple experiments has been proven advantageous. To support this kind of analysis, we are developing a software system called MAMA (Meta-Analysis of MicroArray data). MAMA utilizes a client-server architecture with a relational database on the server-side for the storage of microarray datasets collected from various resources. The client-side is an application running on the end user's computer that allows the user to manipulate microarray data and analytical results locally. MAMA implementation will integrate several analytical methods, including meta-analysis within an open-source framework offering other developers the flexibility to plug in additional statistical algorithms.

  9. Auger electron emitters: Insights gained from in vitro experiments

    International Nuclear Information System (INIS)

    Makrigiorgos, G.; Adelstein, S.J.; Kassis, A.I.

    1990-01-01

    This paper outlines the evolution of the current rationale for research into the biological effects of tissue-incorporated Auger electron emitters. The first section is a brief review of the research conducted by several groups in the last fifteen years. The second section describes the in vitro model used in our studies, dosimetric calculations, experimental techniques and recent findings. The third section focuses on the use of Auger electron emitters as in vitro microprobes for the investigation of the radiosensitivity of distinct subcellular components. Examination of the biological effects of the Auger electron emitter 125 I located in different cellular compartments of a single cell line (V 79 hamster lung fibroblast) verifies that DNA is the critical cell structure for radiation damage and that the sensitive sites are of nanometer dimensions. The data from incorporation of several Auger electron emitters at the same location within DNA suggest that there are no saturation effects from the decay of these isotopes (i.e. all the emitted energy is biologically effective) and provide some insight into which of the numerous physical mechanisms accompanying the Auger decay are most important in causing cell damage. Finally the implications of Auger electron emission for radiotherapy and radiation protection in diagnostic nuclear medicine are detailed and further research possibilities are suggested. (orig.)

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

    Science.gov (United States)

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

    2006-10-13

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

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

    Directory of Open Access Journals (Sweden)

    Munson Ethan V

    2006-10-01

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

  12. Time resolved electron microscopy for in situ experiments

    International Nuclear Information System (INIS)

    Campbell, Geoffrey H.; McKeown, Joseph T.; Santala, Melissa K.

    2014-01-01

    Transmission electron microscopy has functioned for decades as a platform for in situ observation of materials and processes with high spatial resolution. Yet, the dynamics often remain elusive, as they unfold too fast to discern at these small spatial scales under traditional imaging conditions. Simply shortening the exposure time in hopes of capturing the action has limitations, as the number of electrons will eventually be reduced to the point where noise overtakes the signal in the image. Pulsed electron sources with high instantaneous current have successfully shortened exposure times (thus increasing the temporal resolution) by about six orders of magnitude over conventional sources while providing the necessary signal-to-noise ratio for dynamic imaging. We describe here the development of this new class of microscope and the principles of its operation, with examples of its application to problems in materials science

  13. Time resolved electron microscopy for in situ experiments

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, Geoffrey H., E-mail: ghcampbell@llnl.gov; McKeown, Joseph T.; Santala, Melissa K. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

    2014-12-15

    Transmission electron microscopy has functioned for decades as a platform for in situ observation of materials and processes with high spatial resolution. Yet, the dynamics often remain elusive, as they unfold too fast to discern at these small spatial scales under traditional imaging conditions. Simply shortening the exposure time in hopes of capturing the action has limitations, as the number of electrons will eventually be reduced to the point where noise overtakes the signal in the image. Pulsed electron sources with high instantaneous current have successfully shortened exposure times (thus increasing the temporal resolution) by about six orders of magnitude over conventional sources while providing the necessary signal-to-noise ratio for dynamic imaging. We describe here the development of this new class of microscope and the principles of its operation, with examples of its application to problems in materials science.

  14. Data acquisition electronics for NESTOR experiment: project and tests

    International Nuclear Information System (INIS)

    Ameli, Fabrizio; Bonori, Maurizio; Bottai, Sergio; Capone, Antonio; Curti, Franco; Desiati, Paolo; De Marchis, Giancarlo; Massa, Fabrizio; Masullo, Rocco; Piccari, Luigi; Vannucci, Italo

    1999-01-01

    The NESTOR detector, at present under construction, is a telescope for high-energy neutrino astronomy. The apparatus, based on Cherenkov light detection, will be deployed in deep sea (about 4000 m) near the S.W. Greek coast. We briefly describe the NESTOR detector, then we describe with more details the electronics for NESTOR data acquisition and transmission. The detector signals are sampled at 200 MHz and all the resulting information are transmitted to the laboratory on 30 km long electro-optical cable. The estimated Mean Time Between Failure of the full electronics system is greater than 20 years. Tests performed on the first prototypes confirm the main characteristics of these electronics: the dynamic range allowed for the signals is bigger than 1000, the pulse shape is reconstructed with an 8 bit ADC accuracy and the resolution in the measurement of the signal 'threshold crossing time' is better than 200 ps

  15. Electron temperature diagnostics in the RFX reversed field pinch experiment

    International Nuclear Information System (INIS)

    Bartiromo, R.; Carraro, L.; Marrelli, L.; Murari, A.; Pasqualotto, R.; Puiatti, M.E.; Scarin, P.; Valisa, M.; Franz, P.; Martin, P.; Zabeo, L.

    2000-01-01

    The paper presents an integrated approach to the problem of electron temperature diagnostics of the plasma in a reversed field pinch. Three different methods, sampling different portions of the electron distribution function, are adopted, namely Thomson scattering, soft X-ray spectroscopy by pulse-height analysis and filtered soft X-ray intensity ratio. A careful analysis of the different sources of systematic errors is performed and a novel statistical approach is adopted to mutually validate the three independent measurements. A satisfactory agreement is obtained over a large range of experimental conditions, indicating that in the plasma core the energy distribution function is well represented by a maxwellian. (author)

  16. The GaAs electron source: simulations and experiments

    International Nuclear Information System (INIS)

    Aleksandrov, A.V.; Ciullo, G.; Guidi, V.; Kudelainen, V.I.; Lamanna, G.; Lenisa, P.; Logachov, P.V.; Maciga, B.; Novokhatsky, A.; Tecchio, L.; Yang, B.

    1994-01-01

    In this paper we calculate electron emission from GaAs photocathodes using the Monte Carlo technique. Typical data of energy spread of the electron beam are presented. For photoenergy ranging from 1.6 to 2.1 eV, the calculated longitudinal and transverse energy spreads are 14.4-78 and 4-14.7 meV respectively. Temporal measurement of GaAs photocathodes has been performed. The preliminary results show that the temporal response is faster than 200 ps. (orig.)

  17. Direct measurement of macroscopic electric fields produced by collective effects in electron-impact experiments

    International Nuclear Information System (INIS)

    Velotta, R.; Avaldi, L.; Camilloni, R.; Giammanco, F.; Spinelli, N.; Stefani, G.

    1996-01-01

    The macroscopic electric field resulting from the space charge produced in electron-impact experiments has been characterized by using secondary electrons of well-defined energy (e.g., Auger or autoionizing electrons) as a probe. It is shown that the measurement of the kinetic-energy shifts suffered by secondary electrons is a suitable tool for the analysis of the self-generated electric field in a low-density plasma. copyright 1996 The American Physical Society

  18. Electron density and plasma dynamics of a colliding plasma experiment

    Energy Technology Data Exchange (ETDEWEB)

    Wiechula, J., E-mail: wiechula@physik.uni-frankfurt.de; Schönlein, A.; Iberler, M.; Hock, C.; Manegold, T.; Bohlender, B.; Jacoby, J. [Plasma Physics Group, Institute of Applied Physics, Goethe University, 60438 Frankfurt am Main (Germany)

    2016-07-15

    We present experimental results of two head-on colliding plasma sheaths accelerated by pulsed-power-driven coaxial plasma accelerators. The measurements have been performed in a small vacuum chamber with a neutral-gas prefill of ArH{sub 2} at gas pressures between 17 Pa and 400 Pa and load voltages between 4 kV and 9 kV. As the plasma sheaths collide, the electron density is significantly increased. The electron density reaches maximum values of ≈8 ⋅ 10{sup 15} cm{sup −3} for a single accelerated plasma and a maximum value of ≈2.6 ⋅ 10{sup 16} cm{sup −3} for the plasma collision. Overall a raise of the plasma density by a factor of 1.3 to 3.8 has been achieved. A scaling behavior has been derived from the values of the electron density which shows a disproportionately high increase of the electron density of the collisional case for higher applied voltages in comparison to a single accelerated plasma. Sequences of the plasma collision have been taken, using a fast framing camera to study the plasma dynamics. These sequences indicate a maximum collision velocity of 34 km/s.

  19. Issues and Experiments in Electronic Publishing and Dissemination.

    Science.gov (United States)

    Hunter, Karen

    1994-01-01

    Examines three topics related to electronic publishing and distribution: the national context, including NREN (National Education and Research Network); issues of market readiness, funding, delivery standards, access software, intellectual property concerns, and pricing and licensing models that must be resolved; and descriptions of seven services…

  20. Current Knowledge on Microarray Technology - An Overview

    African Journals Online (AJOL)

    Erah

    This paper reviews basics and updates of each microarray technology and serves to .... through protein microarrays. Protein microarrays also known as protein chips are nothing but grids that ... conditioned media, patient sera, plasma and urine. Clontech ... based antibody arrays) is similar to membrane-based antibody ...

  1. Diagnostic and analytical applications of protein microarrays

    DEFF Research Database (Denmark)

    Dufva, Hans Martin; Christensen, C.B.V.

    2005-01-01

    DNA microarrays have changed the field of biomedical sciences over the past 10 years. For several reasons, antibody and other protein microarrays have not developed at the same rate. However, protein and antibody arrays have emerged as a powerful tool to complement DNA microarrays during the post...

  2. Electronic licensing filing system development and implementation experience

    International Nuclear Information System (INIS)

    Walderhaug, J.

    1993-01-01

    The Electronic Licensing Filing System (ELFS) is a microcomputer-based integrated document search and retrieval system for the Nuclear Regulatory Affairs Division of Southern California Edison (SCE). ELFS allows the user access to the current licensing basis of a subject by providing an easily searchable electronic information data base consisting of regulatory correspondence, design-bases documentation, licensing documents [updated final safety and analysis report (UFSAR) and technical specifications], and regulatory guidance or directives [10CFR, generic letters, bulletins, notices, circulars, regulatory guides, policy statements, and selected US Nuclear Regulatory Commission (NRC) regulations]. It is used in the preparation of correspondence and submittals to the NRC, 50.59 safety evaluations, design-bases reconstitution, and commitment tracking and management

  3. Spot detection and image segmentation in DNA microarray data.

    Science.gov (United States)

    Qin, Li; Rueda, Luis; Ali, Adnan; Ngom, Alioune

    2005-01-01

    Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

  4. GenePublisher: automated analysis of DNA microarray data

    DEFF Research Database (Denmark)

    Knudsen, Steen; Workman, Christopher; Sicheritz-Ponten, T.

    2003-01-01

    GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with aspecification of the data. The server performs normalization...

  5. Development of DNA Microarrays for Metabolic Pathway and Bioprocess Monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Gregory Stephanopoulos

    2004-07-31

    Transcriptional profiling experiments utilizing DNA microarrays to study the intracellular accumulation of PHB in Synechocystis has proved difficult in large part because strains that show significant differences in PHB which would justify global analysis of gene expression have not been isolated.

  6. DNA microarray data and contextual analysis of correlation graphs

    Directory of Open Access Journals (Sweden)

    Hingamp Pascal

    2003-04-01

    Full Text Available Abstract Background DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. Results We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved. Conclusions We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from http://tagc.univ-mrs.fr/bioinformatics/trixy.html.

  7. A Java-based tool for the design of classification microarrays.

    Science.gov (United States)

    Meng, Da; Broschat, Shira L; Call, Douglas R

    2008-08-04

    Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for

  8. ELECTRON SCATTERING EXPERIMENTS ON THE NEUTRON AND PROTON

    Energy Technology Data Exchange (ETDEWEB)

    Berkelman, Karl

    1963-06-15

    The electric and magnetic helicity form factors of the proton are measured at 4-momentum transfers (squared) of 25 to 45 f/sup -2/, by means of electron scattering by protons at high energies. The results are combined with other e/sup -/--p and e/sup -/--d experimental findings in order to show the proton form fuctors from 0 to 45 f/sup -2/ and the neutron form factors from 0 to 25 f/sup -2/. (T.F.H.)

  9. First experiments with the Greifswald electron-beam ion trap

    Science.gov (United States)

    Schabinger, B.; Biedermann, C.; Gierke, S.; Marx, G.; Radtke, R.; Schweikhard, L.

    2013-09-01

    The former Berlin electron-beam ion trap (EBIT) was moved to Greifswald. In addition to x-ray studies the setup will be used for the investigation of interaction processes between highly charged ions and atomic clusters such as charge exchange and fragmentation. The EBIT setup has now been reassembled and highly charged ions have been produced from Xe-Ar gas mixtures to study the ‘sawtooth effect’. In addition, the layout of the extraction beamline, the interaction region and product analysis for interaction studies with highly charged ions are presented.

  10. Low-energy electron transmission and secondary-electron emission experiments on crystalline and molten long-chain alkanes

    International Nuclear Information System (INIS)

    Ueno, N.; Sugita, K.; Seki, K.; Inokuchi, H.

    1986-01-01

    This paper describes the results of low-energy electron transmission and secondary-electron emission experiments on thin films of long-chain alkanes deposited on metal substrates. The spectral changes due to crystal-melt phase transition were measured in situ in both experiments. The ground-state energy V 0 of the quasifree electron in crystalline state was determined to be 0.5 +- 0.1 eV. The value of V 0 for the molten state was found to be negative. Further, in the crystalline state evidence is found for a direct correspondence between the transmission maxima and the high value of the density of states in the conduction bands

  11. High Average Power UV Free Electron Laser Experiments At JLAB

    International Nuclear Information System (INIS)

    Douglas, David; Benson, Stephen; Evtushenko, Pavel; Gubeli, Joseph; Hernandez-Garcia, Carlos; Legg, Robert; Neil, George; Powers, Thomas; Shinn, Michelle; Tennant, Christopher; Williams, Gwyn

    2012-01-01

    Having produced 14 kW of average power at ∼2 microns, JLAB has shifted its focus to the ultraviolet portion of the spectrum. This presentation will describe the JLab UV Demo FEL, present specifics of its driver ERL, and discuss the latest experimental results from FEL experiments and machine operations.

  12. AMDA: an R package for the automated microarray data analysis

    Directory of Open Access Journals (Sweden)

    Foti Maria

    2006-07-01

    Full Text Available Abstract Background Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being performed. In spite of this fact, few and limited tools exist for quickly and easily analyzing the results. Microarray analysis can be challenging for researchers without the necessary training and it can be time-consuming for service providers with many users. Results To address these problems we have developed an automated microarray data analysis (AMDA software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image analysis, quality controls, normalization, selection of differentially expressed genes, clustering, correspondence analysis and functional evaluation. Finally a LaTEX document is dynamically generated depending on the performed analysis steps. The generated report contains comments and analysis results as well as the references to several files for a deeper investigation. Conclusion AMDA is freely available as an R package under the GPL license. The package as well as an example analysis report can be downloaded in the Services/Bioinformatics section of the Genopolis http://www.genopolis.it/

  13. Comparing transformation methods for DNA microarray data

    Directory of Open Access Journals (Sweden)

    Zwinderman Aeilko H

    2004-06-01

    Full Text Available Abstract Background When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include subtraction of an estimated background signal, subtracting the reference signal, smoothing (to account for nonlinear measurement effects, and more. Different authors use different approaches, and it is generally not clear to users which method they should prefer. Results We used the ratio between biological variance and measurement variance (which is an F-like statistic as a quality measure for transformation methods, and we demonstrate a method for maximizing that variance ratio on real data. We explore a number of transformations issues, including Box-Cox transformation, baseline shift, partial subtraction of the log-reference signal and smoothing. It appears that the optimal choice of parameters for the transformation methods depends on the data. Further, the behavior of the variance ratio, under the null hypothesis of zero biological variance, appears to depend on the choice of parameters. Conclusions The use of replicates in microarray experiments is important. Adjustment for the null-hypothesis behavior of the variance ratio is critical to the selection of transformation method.

  14. Integrated olfactory receptor and microarray gene expression databases

    Directory of Open Access Journals (Sweden)

    Crasto Chiquito J

    2007-06-01

    Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

  15. NIKEL-AMC: readout electronics for the NIKA2 experiment

    International Nuclear Information System (INIS)

    Bourrion, O.; Bouly, J.L.; Bouvier, J.; Bosson, G.; Catalano, A.; Li, C.; Macías-Pérez, J.F.; Tourres, D.; Ponchant, N.; Vescovi, C.; Benoit, A.; Calvo, M.; Goupy, J.; Monfardini, A.

    2016-01-01

    The New Iram Kid Arrays-2 (NIKA2) instrument has recently been installed at the IRAM 30 m telescope. NIKA2 is a state-of-art instrument dedicated to mm-wave astronomy using microwave kinetic inductance detectors (KID) as sensors. The three arrays installed in the camera, two at 1.25 mm and one at 2.05 mm, feature a total of 3300 KIDs. To instrument these large array of detectors, a specifically designed electronics, composed of 20 readout boards and hosted in three microTCA crates, has been developed. The implemented solution and the achieved performances are presented in this paper. We find that multiplexing factors of up to 400 detectors per board can be achieved with homogeneous performance across boards in real observing conditions, and a factor of more than 3 decrease in volume with respect to previous generations.

  16. The G3 Experience with Electronic Publishing: An Editor's Perspective

    Science.gov (United States)

    White, W. M.

    2003-12-01

    G3 (Geochemistry, Geophysics, Geosystems) is an all-electronic journal published jointly by the AGU, the Geochemical Society, and the European Association of Geochemistry. G3 publishes original scientific contributions pertaining to understanding the Earth as a system, including relevant observational, experimental, and theoretical investigations of the solid Earth, hydrosphere, atmosphere, and biosphere. The journal was initiated as a result of a grass roots effort with the following goals in mind: a copyright policy designed to enhance, rather than inhibit, the dissemination of scientific information (for example, allowing authors to post electronic reprints on their web sites), provide a means of publishing, in immediately useable formats, large data sets, provide a means for ready dissemination of computer modeling and analysis tools, and provide a forum where authors could use novel ways of illustrating both data and models (e.g., formats such as movies, virtual reality images, sound, mathematical models, etc.), and finally to reduce costs and speed publication. In most respects, G3 has been enormously successful and has met most of its goals. G3 began publishing in December of 1999; in the subsequent 3 1/2 years 625 papers have been submitted to it and 325 have been published. It currently has over 600 institutional and personal subscribers. Papers are submitted through the web (a variety of formats are accepted, however, Microsoft Word is most common) and are converted to Adobe pdf format for peer review. Except that it is fully electronic using the web and e-mail, the peer review process is traditional, which insures the quality of the papers published. Accepted papers are copyedited and converted to SGML for archival purposes. HTML and Acrobat pdf versions are then generated from the SGML and published as they are ready on the G3 web site (www.g-cubed.org). Large data sets are routinely published in digital formats that can be readily downloaded by readers

  17. Electron beam irradiation experiments of monoblock divertor mock-up

    International Nuclear Information System (INIS)

    Satoh, Kazuyoshi; Akiba, Masato; Araki, Masanori; Suzuki, Satoshi; Yokoyama, Kenji; Smid, I.; Cardella, A.; Duwe, R.; Di Pietro, E.

    1993-03-01

    It is one of the key issues for ITER to develop the divertor plate. Electron beam irradiation tests were carried out on a NET divertor mock-up using JEBIS at JAERI under a collaboration between The NET team, JAERI and KFA Juelich. Screening tests (maximum heat flux of 23 MW/m 2 ) and thermal cycling tests (18 MW/m 2 , 30s, 1000cycle) were carried out. As a result of the screening tests, the erosion caused by sublimation of C/C was observed on the surface of armor tile. No serious damage such as cracks or detachments, however, were found. As a result of the thermal cycling tests, no major damage was detected on the C/C surface. However cooling time constant of the divertor mock-up increased over 600cycle. Therefore it implies that some defects would occur at the brazing interface of the divertor mock-up. (author)

  18. NINO ASIC electronics used in MRPC/TOF experiment

    International Nuclear Information System (INIS)

    Sun Yongjie; Li Cheng

    2008-01-01

    In order to meet the excellent properties of MRPC, an front-end amplifier/discriminator chip-NINO ASIC, was developed in ALICE TOF group at CERN. This ASIC was fabricated with the 0.25 μm CMOS technology. It is highly integrated and can deal with 8 channels per chip. It has differential input and is differential signal shaping and throughout transition. The peaking time of the amplifier is less than 1 ns. It has LVDS outputs and the width of the output signal depended on the charge of input. This allows the TOT measurement of HPTDC system. A position sensitive MRPC was tested with beam facility using the front-end electronics based on NINO and good results were obtained. (authors)

  19. Electronic laboratory books in fusion experiments and engineering

    Energy Technology Data Exchange (ETDEWEB)

    Landgraf, B., E-mail: b.landgraf@fz-juelich.d [Institut fuer Energieforschung - Plasmaphysik, Forschungszentrum Juelich GmbH, EURATOM Association, D-52425 Juelich (Germany); Kraemer-Flecken, A. [Institut fuer Energieforschung - Plasmaphysik, Forschungszentrum Juelich GmbH, EURATOM Association, D-52425 Juelich (Germany)

    2010-07-15

    In this work we introduce eLaBo-an electronic laboratory book system. ELaBo is a tool that enables collaboration of distributed teams by using standard internet browsers. It provides several functions: Users can create books for specific purposes, e.g. an experimental session or for recording on diagnostics. A book contains pages and resources (e.g. binary files), which are created and manipulated by users of the book. A simple WIKI syntax is used to edit the contents of pages including formatted text, images, and LaTeX for expressing mathematical equations. ELaBo provides for different types of links, a full-text search for the WIKI pages and a version history. Access control is implemented using a key methaphor. Recently (since the last login) modified or created pages or books can be displayed on demand.

  20. Electronic laboratory books in fusion experiments and engineering

    International Nuclear Information System (INIS)

    Landgraf, B.; Kraemer-Flecken, A.

    2010-01-01

    In this work we introduce eLaBo-an electronic laboratory book system. ELaBo is a tool that enables collaboration of distributed teams by using standard internet browsers. It provides several functions: Users can create books for specific purposes, e.g. an experimental session or for recording on diagnostics. A book contains pages and resources (e.g. binary files), which are created and manipulated by users of the book. A simple WIKI syntax is used to edit the contents of pages including formatted text, images, and LaTeX for expressing mathematical equations. ELaBo provides for different types of links, a full-text search for the WIKI pages and a version history. Access control is implemented using a key methaphor. Recently (since the last login) modified or created pages or books can be displayed on demand.

  1. Observation of fluxes of electrons scattered by the atmosphere in the second Araks experiment

    International Nuclear Information System (INIS)

    Lyachov, S.B.; Managadze, G.G.

    1980-01-01

    This paper describes the results of the USHBA spectrometer measurements of the fluxes of atmospheric scattered electrons in the second Araks experiment. The experimental data are presented for heights from 100 to 140 km. The spectral distributions of the scattered electron fluxes are given and the altitude variation of their intensity is compared with the atmosphere models. The conclusion is made about the possible effect of rocket gassing on the electron scattering processes for definite angles of injection

  2. Design and performance of TPC readout electronics for the NA49 experiment

    Energy Technology Data Exchange (ETDEWEB)

    Bieser, F. [Lawrence Berkeley Lab., CA (United States); Cooper, G. [Lawrence Berkeley Lab., CA (United States); Cwienk, W. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Eckardt, V. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Fessler, H. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Fischer, H.G. [European Lab. for Particle Physics (CERN), Geneva (Switzerland); Gabler, F. [Frankfurt Univ. (Germany). Fachbereich 13 - Physik; Gornicki, E. [Institute of Nuclear Physics, Cracow (Poland); Hearn, W.E. [Lawrence Berkeley Lab., CA (United States); Heupke, W. [Frankfurt Univ. (Germany). Fachbereich 13 - Physik; Irmscher, D. [Lawrence Berkeley Lab., CA (United States); Jacobs, P. [Lawrence Berkeley Lab., CA (United States); Kleinfelder, S. [Lawrence Berkeley Lab., CA (United States); Lindenstruth, V. [Lawrence Berkeley Lab., CA (United States); Machowski, B. [Institute of Nuclear Physics, Cracow (Poland); Marks, K. [Lawrence Berkeley Lab., CA (United States); Milgrome, O. [Lawrence Berkeley Lab., CA (United States); Mock, A. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Noggle, T. [Lawrence Berkeley Lab., CA (United States); Pimpl, W. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Poskanzer, A.M. [Lawrence Berkeley Lab., CA (United States); Rauch, W. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Renfordt, R. [European Lab. for Particle Physics (CERN), Geneva (Switzerland)]|[Frankfurt Univ. (Germany). Fachbereich 13 -Physik; Ritter, H.G. [Lawrence Berkeley Lab., CA (United States)]|[European Lab. for Particle Physics (CERN), Geneva (Switzerland); Roehrich, D. [Frankfurt Univ. (Germany). Fachbereich 13 - Physik; Rudolph, H. [Lawrence Berkeley Lab., CA (United States); Rueschmann, G.W. [Frankfurt Univ. (Germany). Fachbereich 13 - Physik; Schaefer, E. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Seyboth, P. [Max-Planck-Institut fuer Physik, Muenchen (Germany); Seyerlein, J.

    1997-02-01

    Highly integrated readout electronics were developed and produced for the 182000 channels of the four TPCs of the NA49 heavy-ion fixed target experiment at the CERN SPS. The large number of channels, the high packing density and required cost minimization led to the choice of a custom electronics system. The requirements, the design and the performance of the electronics components are described. (orig.).

  3. Theory of electron cyclotron heating in the Constance II experiment

    International Nuclear Information System (INIS)

    Mauel, M.E.

    1981-03-01

    The bounce-averaged quasi-linear equation for a non-relativistic mirror-confined plasma interacting with electromagnetic waves is derived for use in the study of ECRH of the Constance II mirror experiment. The derivations follows the more formal examples given by Berk for electrostatic waves and Bernstein and Baxter for relativistic plasmas. The validity of the theory is discussed by examining individual particle orbits in an EM field. The local dispersion relation is found while deriving a self-consistent WKB theory which can be used to estimate the power transferred from the launching horn to the plasma

  4. Internal interface for RFC muon trigger electronics at CMS experiment

    CERN Document Server

    Pozniak, Krzysztof T; Pietrusinski, Michall

    2004-01-01

    The paper describes design and practical realization of an internal communication layer referred to as the Internal Interface (II). The system was realized for the RFC Muon Trigger of the CMS experiment. Fully automatic implementation of the communication layer is realized in the FPGA chips and in the control software. The methodology of implementation was presented in the description form of the interface structure from the sides of hardware and software. The examples of the communication layer realizations were given for the RFC Muon Trigger.

  5. Ultrafast electron field emission from gold resonant antennas studied by two terahertz pulse experiments

    DEFF Research Database (Denmark)

    Iwaszczuk, Krzysztof; Zalkovskij, Maksim; Strikwerda, Andrew C.

    2015-01-01

    Summary form only given. Ultrafast electron field emission from gold resonant antennas induced by strong terahertz (THz) transient is investigated using two THz pulse experiments. It is shown that UV emission from nitrogen plasma generated by liberated electrons is a good indication of the local...

  6. Electron distributions in the plasmas of the earth's magnetosphere - an experiment for AMPTE-UKS

    International Nuclear Information System (INIS)

    Hall, D.S.; Chaloner, C.P.; Shah, H.

    1982-06-01

    The objectives, measurement techniques and technical requirements of the electron experiment to be included in the UK-Satellite of the Active Magnetospheric Particle Explorer (AMPTE) mission are described under sections entitled; experiment objectives, experiment technique, mechanical, electrical, command and data handling requirements, ground support equipment interfaces, test procedures, and special requirements. In appendices the experiment controller and the measurement sequence are shown. (U.K.)

  7. Electron irradiation experiments in support of fusion materials development

    International Nuclear Information System (INIS)

    Gelles, D.S.; Ohnuki, S.; Takahashi, H.; Matsui, H.; Kohno, Y.

    1991-11-01

    Microstructural evolution in response to 1 MeV irradiation has been investigated for three simple ferritic alloys, pure beryllium, pure vanadium, and two simple vanadium alloys over a range of temperatures and doses. Microstructural evolution in Fe-3, -9, and -18Cr ferritic alloys is found to consist of crenulated, faulted a loops and circular, unfaulted a/2 loops at low temperatures, but with only unfaulted loops at high temperatures. The complex dislocation evolution is attributed to sigma phase precipifaults arising from chromium segregation to point defect sinks. Beryllium is found to be resistant to electron damage; the only effect observed was enhanced dislocation mobility. Pure vanadium, V-5Fe, and V-1Ni microstructural response was complicated by precipitation on heating to 400 degrees C and above, but dislocation evolution was investigated in the range of room temperature to 300 degrees C and at 600 degrees C. The three materials behaved similarly, except that pure vanadium showed more rapid dislocation evolution. This difference does not explain the enhanced swelling observed in vanadium alloys

  8. Precise measurement in elastic electron scattering: HAPPEX and E-158 experiments

    International Nuclear Information System (INIS)

    Vacheret, A.

    2004-12-01

    Parity Violation asymmetry measurements in elastic electron scattering are in one hand an interesting way of retrieving new informations about the sea quarks of the nucleon and in the other hand a powerful test of the Standard Model electroweak sector at low energy. This thesis describes the HAPPEX experiment at JLab and the E-158 experiment at SLAC (USA) which measure de parity violation asymmetries in elastic scattering of polarized electron on nuclei like Hydrogen or Helium and on atomic electrons. With the measurements on hadronic targets one can extract the strange quarks contribution to the charge and current density of the nucleon. With the electron-electron scattering one can test the standard model at the loop level and far from the Z pole by extracting sin 2 θ W . In this thesis we describe the formalism associated with the electroweak probe. We present in detail the experimental methods used to make such precise measurements of parity violation asymmetry. Then, we describe the experimental set-up of each experiment and in particular the electron detector and the feedback loop on the beam current for the HAPPEX experiment and the analysis of E-158 run III with a dedicated systematic study on the beam sub-pulse fluctuations. We present the preliminary results for each experiment with a comparison with the other existing results and the future experiments. (author)

  9. Discovering the puzzling behaviour of electrons with the Grimaldi-Young experiment

    International Nuclear Information System (INIS)

    Matteucci, Giorgio; Castaneda, Roman; Serna, Samuel; Garcia-Sucerquia, Jorge; Medina, Francisco

    2010-01-01

    An experiment analogous to that devised by Grimaldi and subsequently repeated by Young to study the nature of light has been realized with electrons. Following the Grimaldi and Young line of thought, an original approach is presented to introduce undergraduate physics students to the wave behaviour of electrons. An electron microscope equipped with a low coherent source of electrons and a thin platinum wire, acting as an opaque obstacle, is used to reproduce the experimental conditions adopted by Grimaldi and Young with light. Electron interference fringes produced in the geometrical shadow of the obstacle are interpreted by assuming that electrons behave like a sound or a light wave. This hypothesis is confirmed by the modelling of the experimental electron interference patterns.

  10. Optically isolated electronic trigger system for experiments on a subnanosecond time scale with a pulsed Van de Graaff electron accelerator

    International Nuclear Information System (INIS)

    Luthjens, L.H.; Vermeulen, M.J.W.; Hom, M.L.

    1980-01-01

    An optically isolated electronic trigger system for a pulsed Van de Graaff electron accelerator, producing an external pretrigger pulse 75 ns before arrival of the electron pulse at the target, is described. The total time jitter between trigger signal and electron pulse is 50 ps. The measurement of optical and electrical transients on a subnanosecond time scale with a sequential sampling oscilloscope is demonstrated. The contribution of various parts of the equipment to the total jitter is discussed. Those contributions to the jitter due to the electron transit time fluctuations in the accelerator assuming a constant acceleration voltage gradient and to the shot noise in the photomultiplier detector of the trigger system are calculated to be 5 ps and 12 to 21 ps respectively. Comparison with the experimental results leads to the conclusion that a considerable part of the total jitter may be attributed to acceleration voltage gradient fluctuations, to accelerator vibrations and possibly to density fluctuations in the insulation gas. Possible improvements of the trigger system are discussed. The apparatus is used for pulse radiolysis experiments with subnanosecond time resolution down to 100 ps in combination with subnanosecond time duration electron pulses

  11. Measurement of electron neutrino appearance with the MINOS experiment

    International Nuclear Information System (INIS)

    Boehm, Joshua Adam Alpern

    2009-01-01

    MINOS is a long-baseline two-detector neutrino oscillation experiment that uses a high intensity muon neutrino beam to investigate the phenomena of neutrino oscillations. By measuring the neutrino interactions in a detector near the neutrino source and again 735 km away from the production site, it is possible to probe the parameters governing neutrino oscillation. The majority of the ν μ oscillate to ν τ but a small fraction may oscillate instead to ν e . This thesis presents a measurement of the ν e appearance rate in the MINOS far detector using the first two years of exposure. Methods for constraining the far detector backgrounds using the near detector measurements is discussed and a technique for estimating the uncertainty on the background and signal selection are developed. A 1.6σ excess over the expected background rate is found providing a hint of ν e appearance.

  12. On the presentation of wave phenomena of electrons with the Young-Feynman experiment

    International Nuclear Information System (INIS)

    Matteucci, Giorgio

    2011-01-01

    The Young-Feynman two-hole interferometer is widely used to present electron wave-particle duality and, in particular, the buildup of interference fringes with single electrons. The teaching approach consists of two steps: (i) electrons come through only one hole but diffraction effects are disregarded and (ii) electrons come through both holes and interference fringes are described. Therefore, a student might believe that wave phenomena are not revealed in case (i), but they arise only by the combined effect of electrons from the two holes. To avoid misunderstanding regarding the distribution of electrons passing through one hole, Fresnel and Fraunhofer diffraction patterns are discussed. In particular, an original experiment, realized with a standard electron microscope and a sample with round holes, is presented to introduce the wave nature of electrons. The experimental results clearly show that a careful discussion of electron diffraction phenomena from one hole provides students with the evidence that the interference experiment from both holes is not strictly required to show the superposition of electron waves.

  13. Observation of suprathermal electron fluxes during ionospheric modification experiments

    International Nuclear Information System (INIS)

    Fejer, J.A.; Sulzer, M.P.

    1987-01-01

    The temporal behavior of backscatter by ionospheric Langmuir waves was observed with the 430-MHz radar at Arecibo while a powerful HF wave was cycled 2 s on, 3 s off. The time resolution was 0.1 s. Late at night, in the absence of photoelectrons, using an HF equivalent radiated power of 80 MW at 3.175 MHz, the initial enhancement of about 6% above system noise of the backscattered power with Doppler shifts between -3.75 and -3.85 MHz was reached about 0.25 s after switching on the HF transmitter. In the following second the enhancement gradually decreased to about 3% and remained there until switching off. During the late afternoon, in the presence of photoelectrons, using the same HF power at 5.1 MHz, an initial enhancement by 25% of the backscattered power with Doppler shifts between -5.25 and -5.35 MHz appeared within less than 0.1 s after switching on the HF transmitter. The incoherent backscatter by Langmuir waves enhanced by photoelectrons was already above system noise by a factor greatly in excess of 10 before switching on the HF transmitter; the 25% enhancement thus corresponds to an enhancement greatly in excess of 250% above system noise. The enhancement drops to less than one tenth of its original value in less than a second. The nighttime effect is attributed to multiple acceleration of electrons from the high-energy tail of the Maxwellian distribution. The daytime effect is believed to be due to a modification in the distribution function of photoelectrons

  14. Electron beam injection during active experiments. 2. Collisional effects

    International Nuclear Information System (INIS)

    Winglee, R.M.

    1990-01-01

    During active beam experiments the presence of high neutral densities at low altitudes and/or during thruster firings has been observed to modify the spacecraft charging and the properties of the beam. Two-dimensional (three velocity) electromagnetic particle simulations with ionizing collisions incorporated are used to investigate the modification of the beam-plasma interaction as the neutral density is increased. It is shown that when the spacecraft is uniformly immersed in a neutral cloud, most of the ionization is produced by direct ionization by the beam and its secondaries, rather than via vehicle-induced or wave-ineuced ionization for the neutral densities considered. This ionization enhances the return current into the spacecraft with the spacecraft potential being reduced well below the beam energy whent he collison period is shorter than the spacecraft charging time. Neutral densities of about 10 11 -10 12 cm -3 are required to produce this reduction in the spacecraft potential for typical ionospheric and beam parameters. At these densities, the beam is able to propagate away from the spacecraft with little distortion except in the case of thruster firings where the beam can be subject to large space-charge oscillations near the boundaries of the neutral cloud. The ionization of neutrals in the beam region also modifies the wave emissions and spatial profile of return currents into the spacecraft, both of which tend to become localized to the beam region in high neutral densities

  15. Measurement of electron neutrino appearance with the MINOS experiment

    Energy Technology Data Exchange (ETDEWEB)

    Boehm, Joshua Adam Alpern [Harvard Univ., Cambridge, MA (United States)

    2009-05-01

    MINOS is a long-baseline two-detector neutrino oscillation experiment that uses a high intensity muon neutrino beam to investigate the phenomena of neutrino oscillations. By measuring the neutrino interactions in a detector near the neutrino source and again 735 km away from the production site, it is possible to probe the parameters governing neutrino oscillation. The majority of the vμ oscillate to vτ but a small fraction may oscillate instead to ve. This thesis presents a measurement of the ve appearance rate in the MINOS far detector using the first two years of exposure. Methods for constraining the far detector backgrounds using the near detector measurements is discussed and a technique for estimating the uncertainty on the background and signal selection are developed. A 1.6σ excess over the expected background rate is found providing a hint of ve appearance.

  16. Design and Development of a CPCI-Based Electronics Package for Space Station Experiments

    Science.gov (United States)

    Kolacz, John S.; Clapper, Randy S.; Wade, Raymond P.

    2006-01-01

    The NASA John H. Glenn Research Center is developing a Compact-PCI (CPCI) based electronics package for controlling space experiment hardware on the International Space Station. Goals of this effort include an easily modified, modular design that allows for changes in experiment requirements. Unique aspects of the experiment package include a flexible circuit used for internal interconnections and a separate enclosure (box in a box) for controlling 1 kW of power for experiment fuel heating requirements. This electronics package was developed as part of the FEANICS (Flow Enclosure Accommodating Novel Investigations in Combustion of Solids) mini-facility which is part of the Fluids and Combustion Facility s Combustion Integrated Rack (CIR). The CIR will be the platform for future microgravity combustion experiments and will reside on the Destiny Module of the International Space Station (ISS). The FEANICS mini-facility will be the primary means for conducting solid fuel combustion experiments in the CIR on ISS. The main focus of many of these solid combustion experiments will be to conduct applied scientific investigations in fire-safety to support NASA s future space missions. A description of the electronics package and the results of functional testing are the subjects of this report. The report concludes that the use of innovative packaging methods combined with readily available COTS hardware can provide a modular electronics package which is easily modified for changing experiment requirements.

  17. The Stern-Gerlach experiment, electron spin and intermediate quantum mechanics

    International Nuclear Information System (INIS)

    Mackintosh, A.R.

    1983-01-01

    The paper deals with the theory of electron spin. The Stern-Gerlach experiment, the anticommutation relations and the properties of spin operators are discussed. The Pauli theory, Dirac transformation theory, the double Stern-Gerlach experiment, the EPR paradox and Bell's inequality are also covered. (U.K.)

  18. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Science.gov (United States)

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  19. Design of a Flexible Hardware Interface for Multiple Remote Electronic practical Experiments of Virtual Laboratory

    Directory of Open Access Journals (Sweden)

    Farah Said

    2012-03-01

    Full Text Available The objective of this work is to present a new design of a Flexible Hardware Interface (FHI based on PID control techniques to use in a virtual laboratory. This flexible hardware interface allows the easy implementation of different and multiple remote electronic practical experiments for undergraduate engineering classes. This interface can be viewed as opened hardware architecture to easily develop simple or complex remote experiments in the electronic domain. The philosophy of the use of this interface can also be expanded to many other domains as optic experiments for instance. It is also demonstrated that software can be developed to enable remote measurements of electronic circuits or systems using only Web site Interface. Using standard browsers (such as Internet explorer, Firefox, Chrome or Safari, different students can have a remote access to different practical experiments at a time.

  20. Triggering, front-end electronics, and data acquisition for high-rate beauty experiments

    International Nuclear Information System (INIS)

    Johnson, M.; Lankford, A.J.

    1988-04-01

    The working group explored the feasibility of building a trigger and an electronics data acquisition system for both collider and fixed target experiments. There appears to be no fundamental technical limitation arising from either the rate or the amount of data for a collider experiment. The fixed target experiments will likely require a much higher rate because of the smaller cross section. Rates up to one event per RF bucket (50 MHz) appear to be feasible. Higher rates depend on the details of the particular experiment and trigger. Several ideas were presented on multiplicity jump and impact parameter triggers for fixed target experiments. 14 refs., 3 figs

  1. Washing scaling of GeneChip microarray expression

    Directory of Open Access Journals (Sweden)

    Krohn Knut

    2010-05-01

    Full Text Available Abstract Background Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities. Results We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of the number of washing cycles. For calibration and analysis of the intensity data we make use of the 'hook' method which allows intensity contributions due to non-specific and specific hybridization of perfect match (PM and mismatch (MM probes to be disentangled in a sequence specific manner. On average, washing according to the standard protocol removes about 90% of the non-specific background and about 30-50% and less than 10% of the specific targets from the MM and PM, respectively. Analysis of the washing kinetics shows that the signal-to-noise ratio doubles roughly every ten stringent washing cycles. Washing can be characterized by time-dependent rate constants which reflect the heterogeneous character of target binding to microarray probes. We propose an empirical washing function which estimates the survival of probe bound targets. It depends on the intensity contribution due to specific and non-specific hybridization per probe which can be estimated for each probe using existing methods. The washing function allows probe intensities to be calibrated for the effect of washing. On a relative scale, proper calibration for washing markedly increases expression measures, especially in the limit of small and large values. Conclusions Washing is among the factors which potentially distort expression measures. The proposed first-order correction method allows direct implementation in existing calibration algorithms for microarray data. We provide an experimental

  2. Integrating Biological Perspectives:. a Quantum Leap for Microarray Expression Analysis

    Science.gov (United States)

    Wanke, Dierk; Kilian, Joachim; Bloss, Ulrich; Mangelsen, Elke; Supper, Jochen; Harter, Klaus; Berendzen, Kenneth W.

    2009-02-01

    Biologists and bioinformatic scientists cope with the analysis of transcript abundance and the extraction of meaningful information from microarray expression data. By exploiting biological information accessible in public databases, we try to extend our current knowledge over the plant model organism Arabidopsis thaliana. Here, we give two examples of increasing the quality of information gained from large scale expression experiments by the integration of microarray-unrelated biological information: First, we utilize Arabidopsis microarray data to demonstrate that expression profiles are usually conserved between orthologous genes of different organisms. In an initial step of the analysis, orthology has to be inferred unambiguously, which then allows comparison of expression profiles between orthologs. We make use of the publicly available microarray expression data of Arabidopsis and barley, Hordeum vulgare. We found a generally positive correlation in expression trajectories between true orthologs although both organisms are only distantly related in evolutionary time scale. Second, extracting clusters of co-regulated genes implies similarities in transcriptional regulation via similar cis-regulatory elements (CREs). Vice versa approaches, where co-regulated gene clusters are found by investigating on CREs were not successful in general. Nonetheless, in some cases the presence of CREs in a defined position, orientation or CRE-combinations is positively correlated with co-regulated gene clusters. Here, we make use of genes involved in the phenylpropanoid biosynthetic pathway, to give one positive example for this approach.

  3. Kernel Based Nonlinear Dimensionality Reduction and Classification for Genomic Microarray

    Directory of Open Access Journals (Sweden)

    Lan Shu

    2008-07-01

    Full Text Available Genomic microarrays are powerful research tools in bioinformatics and modern medicinal research because they enable massively-parallel assays and simultaneous monitoring of thousands of gene expression of biological samples. However, a simple microarray experiment often leads to very high-dimensional data and a huge amount of information, the vast amount of data challenges researchers into extracting the important features and reducing the high dimensionality. In this paper, a nonlinear dimensionality reduction kernel method based locally linear embedding(LLE is proposed, and fuzzy K-nearest neighbors algorithm which denoises datasets will be introduced as a replacement to the classical LLE’s KNN algorithm. In addition, kernel method based support vector machine (SVM will be used to classify genomic microarray data sets in this paper. We demonstrate the application of the techniques to two published DNA microarray data sets. The experimental results confirm the superiority and high success rates of the presented method.

  4. Microarray expression profiling of human dental pulp from single subject.

    Science.gov (United States)

    Tete, Stefano; Mastrangelo, Filiberto; Scioletti, Anna Paola; Tranasi, Michelangelo; Raicu, Florina; Paolantonio, Michele; Stuppia, Liborio; Vinci, Raffaele; Gherlone, Enrico; Ciampoli, Cristian; Sberna, Maria Teresa; Conti, Pio

    2008-01-01

    Microarray is a recently developed simultaneous analysis of expression patterns of thousand of genes. The aim of this research was to evaluate the expression profile of human healthy dental pulp in order to find the presence of genes activated and encoding for proteins involved in the physiological process of human dental pulp. We report data obtained by analyzing expression profiles of human tooth pulp from single subjects, using an approach based on the amplification of the total RNA. Experiments were performed on a high-density array able to analyse about 21,000 oligonucleotide sequences of about 70 bases in duplicate, using an approach based on the amplification of the total RNA from the pulp of a single tooth. Obtained data were analyzed using the S.A.M. system (Significance Analysis of Microarray) and genes were merged according to their molecular functions and biological process by the Onto-Express software. The microarray analysis revealed 362 genes with specific pulp expression. Genes showing significant high expression were classified in genes involved in tooth development, protoncogenes, genes of collagen, DNAse, Metallopeptidases and Growth factors. We report a microarray analysis, carried out by extraction of total RNA from specimens of healthy human dental pulp tissue. This approach represents a powerful tool in the study of human normal and pathological pulp, allowing minimization of the genetic variability due to the pooling of samples from different individuals.

  5. Coherent operation of detector systems and their readout electronics in a complex experiment control environment

    Energy Technology Data Exchange (ETDEWEB)

    Koestner, Stefan [CERN (Switzerland)], E-mail: koestner@mpi-halle.mpg.de

    2009-09-11

    With the increasing size and degree of complexity of today's experiments in high energy physics the required amount of work and complexity to integrate a complete subdetector into an experiment control system is often underestimated. We report here on the layered software structure and protocols used by the LHCb experiment to control its detectors and readout boards. The experiment control system of LHCb is based on the commercial SCADA system PVSS II. Readout boards which are outside the radiation area are accessed via embedded credit card sized PCs which are connected to a large local area network. The SPECS protocol is used for control of the front end electronics. Finite state machines are introduced to facilitate the control of a large number of electronic devices and to model the whole experiment at the level of an expert system.

  6. Retrocausation acting in the single-electron double-slit interference experiment

    Science.gov (United States)

    Hokkyo, Noboru

    The single electron double-slit interference experiment is given a time-symmetric interpretation and visualization in terms of the intermediate amplitude of transition between the particle source and the detection point. It is seen that the retarded (causal) amplitude of the electron wave expanding from the source shows an advanced (retrocausal) bifurcation and merging in passing through the double-slit and converges towards the detection point as if guided by the advanced (retrocausal) wave from the detected electron. An experiment is proposed to confirm the causation-retrocausation symmetry of the electron behavior by observing the insensitivity of the interference pattern to non-magnetic obstacles placed in the shadows of the retarded and advanced waves appearing on the rear and front sides of the double-slit.

  7. Measurements of Plasma Expansion due to Background Gas in the Electron Diffusion Gauge Experiment

    International Nuclear Information System (INIS)

    Morrison, Kyle A.; Paul, Stephen F.; Davidson, Ronald C.

    2003-01-01

    The expansion of pure electron plasmas due to collisions with background neutral gas atoms in the Electron Diffusion Gauge (EDG) experiment device is observed. Measurements of plasma expansion with the new, phosphor-screen density diagnostic suggest that the expansion rates measured previously were observed during the plasma's relaxation to quasi-thermal-equilibrium, making it even more remarkable that they scale classically with pressure. Measurements of the on-axis, parallel plasma temperature evolution support the conclusion

  8. Hot-electron plasma formation and confinement in the Tandem Mirror Experiment-Upgrade

    International Nuclear Information System (INIS)

    Ress, D.B.

    1988-01-01

    Electron-cyclotron range-of-frequency heating (ECRH) at 28 GHz is used to create a population of mirror-confined hot electrons in the Tandem Mirror Experiment-Upgrade (TMX-U). Generation of a large fraction of such electrons within each end-cell of TMX-U is essential to the formation of the desired electrostatic potential profile of the thermal-barrier tandem mirror. The formation and confinement of the ECRH-generated hot-electron plasma was investigated with a variety of diagnostic instruments, including a novel instrumented limiter probe. The author characterized the spatial structure of the hot-electron plasma. Details of the heating process cause the plasma to separate into two regions: a halo, consisting entirely of energetic electrons, and a core, which is dominated by cooler electrons. The plasma structure forms rapidly under the action of second-harmonic ECRH. Fundamental ECRH, which is typically applied simultaneously, is only weakly absorbed and generally does not create energetic electrons. The ECRH-generated plasma displays several loss mechanisms. Hot electrons in the halo region, with T e ∼ 30 keV, are formed by localized ECRH near the plasma boundary, and are lost through a radial process involving open magnetic-curvature-drift surfaces

  9. Advanced microarray technologies for clinical diagnostics

    NARCIS (Netherlands)

    Pierik, Anke

    2011-01-01

    DNA microarrays become increasingly important in the field of clinical diagnostics. These microarrays, also called DNA chips, are small solid substrates, typically having a maximum surface area of a few cm2, onto which many spots are arrayed in a pre-determined pattern. Each of these spots contains

  10. Searching for TeV cosmic electrons with the CREST experiment

    International Nuclear Information System (INIS)

    Coutu, S.; Anderson, T.; Bower, C.; Gennaro, J.; Geske, M.; Mueller, D.; Musser, J.; Nutter, S.; Park, N.H.; Schubnell, M.; Tarle, G.; Wakely, S.; Yagi, A.

    2011-01-01

    The Cosmic Ray Electron Synchrotron Telescope (CREST) high-altitude balloon experiment is a pathfinding effort to detect for the first time multi-TeV cosmic-ray electrons. Such would be the markers of nearby cosmic accelerators, as energetic electrons from distant Galactic sources are expected to be depleted by radiative losses during interstellar transport. Electrons will be detected indirectly by the characteristic signature of their geomagnetic synchrotron losses, in the form of a burst of coaligned x-ray photons intersecting the plane of the instrument. Since the primary electron itself need not traverse the payload, an effective detection area is achieved that is several times the nominal 6.4 m 2 instrument. The payload is composed of an array of 1024 BaF2 crystals surrounded by a set of veto scintillator detectors. A long-duration balloon flight in Antarctica is planned for the 2011-12 season.

  11. Searching for TeV cosmic electrons with the CREST experiment

    Energy Technology Data Exchange (ETDEWEB)

    Coutu, S., E-mail: coutu@phys.psu.edu [Department of Physics, Pennsylvania State University, 104 Davey Laboratory, University Park, PA 16802 (United States); Anderson, T. [Department of Physics, Pennsylvania State University, 104 Davey Laboratory, University Park, PA 16802 (United States); Bower, C. [Physics Department, Indiana University, 117 Swain Hall West, Bloomington, IN 47405 (United States); Gennaro, J. [Department of Physics, University of Michigan, Randall Physics Laboratory, 500 E. University Ave, Ann Arbor, MI 48109 (United States); Geske, M. [Department of Physics, Pennsylvania State University, 104 Davey Laboratory, University Park, PA 16802 (United States); Mueller, D. [Enrico Fermi Institute and Department of Physics, University of Chicago, 933 E. 56th St., Chicago, IL 60637 (United States); Musser, J. [Physics Department, Indiana University, 117 Swain Hall West, Bloomington, IN 47405 (United States); Nutter, S. [Department of Physics and Geology, Northern Kentucky University, Highland Heights, KY 41099 (United States); Park, N.H. [Enrico Fermi Institute and Department of Physics, University of Chicago, 933 E. 56th St., Chicago, IL 60637 (United States); Schubnell, M.; Tarle, G. [Department of Physics, University of Michigan, Randall Physics Laboratory, 500 E. University Ave, Ann Arbor, MI 48109 (United States); Wakely, S. [Enrico Fermi Institute and Department of Physics, University of Chicago, 933 E. 56th St., Chicago, IL 60637 (United States); Yagi, A. [Department of Physics, University of Michigan, Randall Physics Laboratory, 500 E. University Ave, Ann Arbor, MI 48109 (United States)

    2011-06-15

    The Cosmic Ray Electron Synchrotron Telescope (CREST) high-altitude balloon experiment is a pathfinding effort to detect for the first time multi-TeV cosmic-ray electrons. Such would be the markers of nearby cosmic accelerators, as energetic electrons from distant Galactic sources are expected to be depleted by radiative losses during interstellar transport. Electrons will be detected indirectly by the characteristic signature of their geomagnetic synchrotron losses, in the form of a burst of coaligned x-ray photons intersecting the plane of the instrument. Since the primary electron itself need not traverse the payload, an effective detection area is achieved that is several times the nominal 6.4 m{sup 2} instrument. The payload is composed of an array of 1024 BaF2 crystals surrounded by a set of veto scintillator detectors. A long-duration balloon flight in Antarctica is planned for the 2011-12 season.

  12. Electron beam effects on the spectroscopy of multiply charged ions in plasma focus experiments

    International Nuclear Information System (INIS)

    Abdallah, J.; Clark, R.E.H.; Faenov, A.Y.; Karpinski, L.; Pikuz, S.A.; Romanova, V.M.; Sadowski, M.; Scholz, M.; Szydlowski, A.

    1999-01-01

    Argon-hydrogen mixture plasma focus experiments performed at the Warsaw Institute of Plasma Physics and Laser Microfusion show detailed space resolved spectra for Ar K-shell satellite lines up to F-like Ar and K-alpha of Ar. These transitions originating from autoionizing levels are caused by collisions of ions with the energetic electron beams which are created by the constrictions of the plasma column due to the development of magnetohydrodynamic instabilities. A collisional-radiative model was constructed using a non-Maxwellian electron energy distribution consisting of a thermal Maxwellian part plus a Gaussian part to represent the high-energy electron beam. The shapes of the observed satellite structures are consistent with the calculated spectrum for electron temperatures between 20 and 230 eV, and beam densities of about 10 -3 times the plasma electron density. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  13. Electron beam effects on the spectroscopy of multiply charged ions in plasma focus experiments

    Energy Technology Data Exchange (ETDEWEB)

    Abdallah, J. [UCLA Plasma Physics Laboratory, Los Angeles, CA (United States); Clark, R.E.H. [Los Alamos National Laboratory, Los Alamos, NM (United States); Faenov, A.Y. [MISDC, NPO ' VNIIFTRI' , Mendeleevo, Moscow region, 141570 (Russian Federation); Karpinski, L. [Institute of Plasma Physics and Laser Microfusion, Warsaw (Poland); Pikuz, S.A.; Romanova, V.M. [P. N. Lebedev Physical Institute, Moscow (Russian Federation); Sadowski, M. [Soltan Institute for Nuclear Studies, Swierk (Poland); Scholz, M.; Szydlowski, A. [Institute of Plasma Physics and Laser Microfusion, Warsaw (Poland)

    1999-05-01

    Argon-hydrogen mixture plasma focus experiments performed at the Warsaw Institute of Plasma Physics and Laser Microfusion show detailed space resolved spectra for Ar K-shell satellite lines up to F-like Ar and K-alpha of Ar. These transitions originating from autoionizing levels are caused by collisions of ions with the energetic electron beams which are created by the constrictions of the plasma column due to the development of magnetohydrodynamic instabilities. A collisional-radiative model wasconstructed using a non-Maxwellian electron energy distribution consisting of a thermal Maxwellian part plus a Gaussian part to represent the high-energy electron beam. The shapes of the observed satellite structures are consistent with the calculated spectrum for electron temperatures between 20 and 230 eV, and beam densities of about 10{sup -3} times the plasma electron density. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  14. Carbohydrate Microarrays in Plant Science

    DEFF Research Database (Denmark)

    Fangel, Jonatan Ulrik; Pedersen, H.L.; Vidal-Melgosa, S.

    2012-01-01

    Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important...... industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high...... for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities....

  15. Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs.

    Science.gov (United States)

    Pancoska, Petr; Moravek, Zdenek; Moll, Ute M

    2004-01-01

    Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of 'DNA processing elements' that can be readily manufactured. To achieve the desired functionality, polynucleotide sequences are currently designed by a process that involves tedious and laborious filtering of potential candidates against a series of requirements and parameters. Here, we present a complete novel methodology for the rapid rational design of large sets of DNA sequences. This method allows for the direct implementation of very complex and detailed requirements for the generated sequences, thus avoiding 'brute force' filtering. At the same time, these sequences have narrow distributions of melting temperatures. The molecular part of the design process can be done without computer assistance, using an efficient 'human engineering' approach by drawing a single blueprint graph that represents all generated sequences. Moreover, the method eliminates the necessity for extensive thermodynamic calculations. Melting temperature can be calculated only once (or not at all). In addition, the isostability of the sequences is independent of the selection of a particular set of thermodynamic parameters. Applications are presented for DNA sequence designs for microarrays, universal microarray zip sequences and electron transfer experiments.

  16. Preparation for electron ring - plasma ring merging experiments in RECE-MERGE

    International Nuclear Information System (INIS)

    Taggart, D.; Sekiguchi, A.; Fleischmann, H.H.

    1986-01-01

    The formation of a mixed-CT using relativistic electron rings and gun-produced plasma rings by MERGE-ing them axially is simulated. This process is similar to the axial stacking of relativistic electron rings in RECE-Christa. The results of their first plasm production experiment are reported here. After study of the gun-produced plasma's properties is completed, the gun will be mounted at the downstream end of the vacuum tank and the source of relativistic electron rings will be at the upstream end. The two rings, formed at opposite ends of the tank, will be translated axially and merged

  17. Test of New Readout Electronics for the BONuS12 Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ehrhart, Mathieu [Inst. de Physique Nucleaire (IPN), Orsay (France)

    2017-07-01

    For decades, electron-proton scattering experiments have been providing a large amount of data on the proton structure function. However, because of the instability of free neutrons, fewer experiments have been able to study the neutron structure function. The BONuS collaboration at Jefferson Laboratory addresses this challenge by scattering electrons off a deuterium target, using a RTPC capable of detecting the low-momentum spectator protons near the target. Events of electrons scattering on almost free neutrons are selected by constraining the spectator protons to very low momenta and very backward scattering angles. In 2005, BONuS successfully measured the neutron structure with scattering electrons of up to 5.3 GeV energy. An extension of this measurement has been approved using the newly upgraded 12 GeV electron beam and CLAS12 (CEBAF Large Acceptance Spectrometer). For this new set of measurements, a new RTPC detector using GEM trackers is being developed to allow measurements of spectator protons with momenta as low as 70 MeV/c. The new RTPC will use a new readout electronic system, which is also used by other trackers in CLAS12. This thesis will present the first tests of this electronics using a previously built RTPC of similar design.

  18. ELECTRON CYCLOTRON CURRENT DRIVE IN DIII-D: EXPERIMENT AND THEORY

    International Nuclear Information System (INIS)

    PRATER, R; PETTY, CC; LUCE, TC; HARVEY, RW; CHOI, M; LAHAYE, RJ; LIN-LIU, Y-R; LOHR, J; MURAKAMI, M; WADE, MR; WONG, K-L

    2003-01-01

    A271 ELECTRON CYCLOTRON CURRENT DRIVE IN DIII-D: EXPERIMENT AND THEORY. Experiments on the DIII-D tokamak in which the measured off-axis electron cyclotron current drive has been compared systematically to theory over a broad range of parameters have shown that the Fokker-Planck code CQL3D provides an excellent model of the relevant current drive physics. This physics understanding has been critical in optimizing the application of ECCD to high performance discharges, supporting such applications as suppression of neoclassical tearing modes and control and sustainment of the current profile

  19. Mikheyev-Smirnov-Wolfenstein effect in electron-neutrino scattering experiments

    International Nuclear Information System (INIS)

    Bahcall, J.N.; Gelb, J.M.; Rosen, S.P.

    1987-01-01

    We calculate the influence of resonant neutrino scattering [the Mikheyev-Smirnov-Wolfenstein (MSW) effect] in the Sun and in the Earth on measurable quantities in solar-neutrino--electron scattering experiments. The MSW effect reduces the expected rate for 8 B-neutrino--electron scattering by a factor that ranges from --0.8 to --0.2 if resonant scattering is the correct explanation for the discrepancy between observation and calculation in the /sup 37/Cl experiment. The Earth can produce a significant diurnal effect for certain values of the neutrino mixing angle and mass difference

  20. Translating microarray data for diagnostic testing in childhood leukaemia

    International Nuclear Information System (INIS)

    Hoffmann, Katrin; Firth, Martin J; Beesley, Alex H; Klerk, Nicholas H de; Kees, Ursula R

    2006-01-01

    and with microarray experiments being performed by a different research team

  1. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

    Full Text Available Abstract Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data and therefore are close to

  2. Workflows for microarray data processing in the Kepler environment.

    Science.gov (United States)

    Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

    2012-05-17

    Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R

  3. Workflows for microarray data processing in the Kepler environment

    Science.gov (United States)

    2012-01-01

    Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or

  4. An analysis of the SCEX 3 ionospheric electron beam injection experiment

    International Nuclear Information System (INIS)

    Goerke, R.T.

    1992-01-01

    The SCEX 3 experiment (Several Compatible EXperiments using a rocket-borne accelerator) was carried to ionospheric altitudes (375 km) by a Black Brant 11 rocket on February 1, 1990. The experiment was launched from Poker Flat Research Range (65.1 degree N, 147.5 degree W) at 1207 UT. The payload split into two parts (hereafter forward and aft payloads) 116 seconds after launch. The aft payload carried two electron accelerators as well as several diagnostic instruments. The forward payload was ejected at an angle of 6 degree with the magnetic field in a northwesterly direction. This payload carried a multiband plasma wave receiver and various particle detectors to make in situ measurements of the Beam Plasma Interaction (BPI) region. Two Throw Away Detectors (TAD's 1 and 2) were also ejected from the aft payload in the east and west directions respectively. TAD 1 also carried a multiband plasma wave receiver. Preceding the launch an auroral arch along the southern boundary of a diffuse auroral patch suddenly brightened, split into two separate arcs and moved to a position north of the rocket's trajectory. SCEX 3 was launched into an active breakup aurora consisting of tall rays and diffuse patches. The purpose of this experiment were (1) to observe injected electrons reflected from the naturally occurring parallel electric field structures which are thought to accelerate the auroral electron, (2) to observe a variety of plasma effects caused by the artificial electron beam and the associated spacecraft charging, and (3) study the natural phenomena associated with auroral activity. This work is a summary of the interesting observations made by the SCEX 3 experiment. These observations include VHF emissions produced by the electron beam via the Beam Plasma Discharge (BPD), Diffuse resonance emissions by the hot plasma region surrounding the electron beam and auroral Z-mode emissions

  5. Electron Neutrino Charged-Current Quasielastic Scattering in the MINERvA Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Wolcott, Jeremy [Rochester U.

    2015-10-28

    The electron-neutrino charged-current quasielastic (CCQE) cross section on nuclei is an important input parameter to appearance-type neutrino oscillation experiments. Current experiments typically work from the muon neutrino cross section and apply corrections from theoretical arguments to obtain a prediction for the electron neutrino cross section, but to date there has been no experimental verification of the estimates for this channel at an energy scale appropriate to such experiments. We present the first measurement of an exclusive reaction in few-GeV electron neutrino interactions, namely, the cross section for a CCQE-like process, made using the MINERvA detector. The result is given as differential cross-sections vs. the electron energy, electron angle, and square of the four-momentum transferred to the nucleus, $Q^2$. We also compute the ratio to a muon neutrino cross-section in $Q^2$ from MINERvA. We find satisfactory agreement between this measurement and the predictions of the GENIE generator.

  6. Electron collector and ion species experiments on the LION extractor ion diode

    International Nuclear Information System (INIS)

    Rondeau, G.; Greenly, J.B.; Hammer, D.A.; Horioka, K.; Meyerhofer, D.D.

    1987-01-01

    Studies of the effects of an electron collector on the electron flow in an ion diode and on diode impedance history are being done with an extractor geometry ion diode (B/sub r/ magnetic insulation field) on the LION accelerator (1.5 MV, 4Ω, 40 ns). The collector is a flux-penetrable metal protrusion on the inner radius of the anode that collects electrons. This device increases the diode operating impedance particularly during the later part of the pulse when the diode impedance collapses without the collector. In the present set of experiments, several thin wires are inserted into the anode and allowed to protrude a few millimeters into the A-K gap. These wires are damaged by the electron flow during the pulse and by measuring the length of the remaining wire, the distance of the electron layer from the anode can be inferred. The ion current density is also measured in three radial locations across the diode, giving a measure, through the Child-Langmuir law, of the effective gap spacing between the anode and the electron sheath. A simple model is proposed to account for the scaling of ion current density with the diode voltage observed in the experiment

  7. Hierarchical information representation and efficient classification of gene expression microarray data

    OpenAIRE

    Bosio, Mattia

    2014-01-01

    In the field of computational biology, microarryas are used to measure the activity of thousands of genes at once and create a global picture of cellular function. Microarrays allow scientists to analyze expression of many genes in a single experiment quickly and eficiently. Even if microarrays are a consolidated research technology nowadays and the trends in high-throughput data analysis are shifting towards new technologies like Next Generation Sequencing (NGS), an optimum method for sample...

  8. Opportunities for parity violating electron scattering experiments at the planned MESA facility

    Science.gov (United States)

    Aulenbacher, Kurt

    2011-11-01

    We suggest to start an accelerator physics project called the Mainz Energy recovering Superconducting Accelerator (MESA) as an extension to our experimental facilities. MESA may allow to introduce an innovative internal target regime based on the ERL principle. A second mode of operation will be to use an external polarized electron beam for parity violating experiments.

  9. Stakeout electronic total station construction layout boring of the experience and precision

    International Nuclear Information System (INIS)

    Xu Zhiqiang

    2012-01-01

    Electronic total station can simultaneously measure angle and distance, together with the appropriate calculation methods and operating skills, able to efficiently complete the survey work, this paper based on practical experience, theoretical analysis, based on total station introduced in setting out a few boring in the skills and the measurement of total station in the construction layout for accuracy. (authors)

  10. Development of Ultra Low-Temperature Electronics for the AEgIS Experiment

    CERN Document Server

    Kaltenbacher, Thomas; Kellerbauer, Alban; Doser, Michael; Caspers, Friedhelm

    This thesis presents the development of electronics for operation at cryogenic temperatures, with particular emphasis on the cryogenic electronics required for the Antimatter Experiment: Gravity, Interferometry, Spectroscopy (AEgIS) experiment at the European Organisation for Nuclear Research (CERN). The research is focused on a highly sensitive charged particle detection system for a Penning trap, on cryogenic low-pass filters and on a low-loss DC-contact RF switch. The detection system consists of a high quality factor tuned circuit including a superconducting coil, and a low-noise amplifier. Since the experimental setup of the AEgIS experiment requires it, the developed electronics must reliably operate at 4.2 K (~269C) and in high constant magnetic field of more than 1 Tesla. Therefore, the performance of the cryogenic electronic designs were carefully evaluated at low-temperature/high magnetic field, the result of which have important implications for the AEgIS experiment. Moreover, a new possibility of ...

  11. Users' Personal Conceptions of Usability and User Experience of Electronic and Software Products

    NARCIS (Netherlands)

    Haaksma, Tim R.; de Jong, Menno D.T.; Karreman, Joyce

    2018-01-01

    Research problem: Despite the abundance of research into usability and user experience (UX), there is still debate about the relationship between both concepts. The user perspective is underrepresented in all discussions. This study examines the personal conceptions that users of electronic and

  12. Fireworks in noble gas clusters a first experiment with the new "free-electron laser"

    CERN Document Server

    2002-01-01

    An international group of scientists has published first experiments carried out using the new soft X-ray free-electron laser (FEL) at the research center DESY in Hamburg, Germany. Using small clusters of noble gas atoms, for the first time, researchers studied the interaction of matter with intense X-ray radiation from an FEL on extremely short time scales (1 page).

  13. Observation and applications of single-electron charge signals in the XENON100 experiment

    NARCIS (Netherlands)

    Aprile, E.; et al., [Unknown; Alfonsi, M.; Colijn, A.P.; Decowski, M.P.

    2014-01-01

    The XENON100 dark matter experiment uses liquid xenon in a time projection chamber (TPC) to measure xenon nuclear recoils resulting from the scattering of dark matter weakly interacting massive particles (WIMPs). In this paper, we report the observation of single-electron charge signals which are

  14. MARS: Microarray analysis, retrieval, and storage system

    Directory of Open Access Journals (Sweden)

    Scheideler Marcel

    2005-04-01

    Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

  15. Simulation of microarray data with realistic characteristics

    Directory of Open Access Journals (Sweden)

    Lehmussola Antti

    2006-07-01

    Full Text Available Abstract Background Microarray technologies have become common tools in biological research. As a result, a need for effective computational methods for data analysis has emerged. Numerous different algorithms have been proposed for analyzing the data. However, an objective evaluation of the proposed algorithms is not possible due to the lack of biological ground truth information. To overcome this fundamental problem, the use of simulated microarray data for algorithm validation has been proposed. Results We present a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics. The applicability of the proposed model is demonstrated by several examples. Conclusion The proposed microarray simulation model is modular and can be used in different kinds of applications. It includes several error models that have been proposed earlier and it can be used with different types of input data. The model can be used to simulate both spotted two-channel and oligonucleotide based single-channel microarrays. All this makes the model a valuable tool for example in validation of data analysis algorithms.

  16. Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

    Science.gov (United States)

    Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

    2015-01-01

    The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

  17. Implementation of mutual information and bayes theorem for classification microarray data

    Science.gov (United States)

    Dwifebri Purbolaksono, Mahendra; Widiastuti, Kurnia C.; Syahrul Mubarok, Mohamad; Adiwijaya; Aminy Ma’ruf, Firda

    2018-03-01

    Microarray Technology is one of technology which able to read the structure of gen. The analysis is important for this technology. It is for deciding which attribute is more important than the others. Microarray technology is able to get cancer information to diagnose a person’s gen. Preparation of microarray data is a huge problem and takes a long time. That is because microarray data contains high number of insignificant and irrelevant attributes. So, it needs a method to reduce the dimension of microarray data without eliminating important information in every attribute. This research uses Mutual Information to reduce dimension. System is built with Machine Learning approach specifically Bayes Theorem. This theorem uses a statistical and probability approach. By combining both methods, it will be powerful for Microarray Data Classification. The experiment results show that system is good to classify Microarray data with highest F1-score using Bayesian Network by 91.06%, and Naïve Bayes by 88.85%.

  18. Radioactive cDNA microarray in neurospsychiatry

    International Nuclear Information System (INIS)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon

    2003-01-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  19. Radioactive cDNA microarray in neurospsychiatry

    Energy Technology Data Exchange (ETDEWEB)

    Choe, Jae Gol; Shin, Kyung Ho; Lee, Min Soo; Kim, Meyoung Kon [Korea University Medical School, Seoul (Korea, Republic of)

    2003-02-01

    Microarray technology allows the simultaneous analysis of gene expression patterns of thousands of genes, in a systematic fashion, under a similar set of experimental conditions, thus making the data highly comparable. In some cases arrays are used simply as a primary screen leading to downstream molecular characterization of individual gene candidates. In other cases, the goal of expression profiling is to begin to identify complex regulatory networks underlying developmental processes and disease states. Microarrays were originally used with cell lines or other simple model systems. More recently, microarrays have been used in the analysis of more complex biological tissues including neural systems and the brain. The application of cDNA arrays in neuropsychiatry has lagged behind other fields for a number of reasons. These include a requirement for a large amount of input probe RNA in fluorescent-glass based array systems and the cellular complexity introduced by multicellular brain and neural tissues. An additional factor that impacts the general use of microarrays in neuropsychiatry is the lack of availability of sequenced clone sets from model systems. While human cDNA clones have been widely available, high quality rat, mouse, and drosophilae, among others are just becoming widely available. A final factor in the application of cDNA microarrays in neuropsychiatry is cost of commercial arrays. As academic microarray facilitates become more commonplace custom made arrays will become more widely available at a lower cost allowing more widespread applications. In summary, microarray technology is rapidly having an impact on many areas of biomedical research. Radioisotope-nylon based microarrays offer alternatives that may in some cases be more sensitive, flexible, inexpensive, and universal as compared to other array formats, such as fluorescent-glass arrays. In some situations of limited RNA or exotic species, radioactive membrane microarrays may be the most

  20. Search of prompt electrons in the NA14 photoproduction experiment at the CERN

    International Nuclear Information System (INIS)

    de Bouard, G.

    1985-03-01

    The purpose of this thesis is to isolate a prompt electron signal from the data of the NA14 photoproduction experiment at CERN. For that aim, a fast data filtering program has been developed. In order to have a good understanding of the electrons behaviour in the electromagnetic calorimeter, electrons from photon conversion were selected. The observation of events with a reconstructed psi and the sharing between the different psi production mechanism leads to a clear excess of the inelastic process relative to a QCD theoretical expectation. The prompt electrons measurement method, when applied to events obtained from a π - beam, does not give any evidence for a signal. With incident photons, a strong signal is seen which cannot been explained by the Bethe Heitler mechanism and psi production alone. This signal is stronger than the photon-gluon fusion model prediction [fr

  1. Very low frequency valuation of a modulated beam of electrons: an application to the ARAKS experiment

    International Nuclear Information System (INIS)

    Ahmadi, L.

    1982-12-01

    The purpose of the ARAKS experiments was to study the effects due to the injection of energy electrons into the aurora zone. Here we analyse the TBF (2, 4 and 6 kHz) signals observed on the basis of interpretations in a closed or radiated field. We show that these signals are of an electromagnetic nature below fsub(HB) = 5 kHz and electrostatic above that figure, that they are correlated with the functioning of the electron cannon and independent of the electrons' angle of attack. They propagate in the electronic hissing mode. At frequencies below fsub(HB), the main contribution comes from the close field, whereas it comes from the radiated field for f greater than fsub(HB) [fr

  2. Neonatal Nurses Experience Unintended Consequences and Risks to Patient Safety With Electronic Health Records.

    Science.gov (United States)

    Dudding, Katherine M; Gephart, Sheila M; Carrington, Jane M

    2018-04-01

    In this article, we examine the unintended consequences of nurses' use of electronic health records. We define these as unforeseen events, change in workflow, or an unanticipated result of implementation and use of electronic health records. Unintended consequences experienced by nurses while using electronic health records have been well researched. However, few studies have focused on neonatal nurses, and it is unclear to what extent unintended consequences threaten patient safety. A new instrument called the Carrington-Gephart Unintended Consequences of Electronic Health Record Questionnaire has been validated, and secondary analysis using the tool explored the phenomena among neonatal nurses (N = 40). The purposes of this study were to describe unintended consequences of use of electronic health records for neonatal nurses and to explore relationships between the phenomena and characteristics of the nurse and the electronic health record. The most frequent unintended consequences of electronic health record use were due to interruptions, followed by a heavier workload due to the electronic health record, changes to the workflow, and altered communication patterns. Neonatal nurses used workarounds most often with motivation to better assist patients. Teamwork was moderately related to higher unintended consequences including patient safety risks (r = 0.427, P = .007), system design (r = 0.419, P = .009), and technology barriers (r = 0.431, P = .007). Communication about patients was reduced when patient safety risks were high (r = -0.437, P = .003). By determining the frequency with which neonatal nurses experience unintended consequences of electronic health record use, future research can be targeted to improve electronic health record design through customization, integration, and refinement to support patient safety and better outcomes.

  3. Low-cost workbench client / server cores for remote experiments in electronics

    OpenAIRE

    José M. M. Ferreira; Americo Dias; Paulo Sousa; Zorica Nedic; Jan Machotka; Ozdemir Gol; Andrew Nafalski

    2010-01-01

    This paper offers an open-source solution to implement low-cost workbenches serving a wide range of remote experiments in electronics. The proposed solution comprises 1) a small (9,65 x 6,1 cm) Linux server board; 2) a server core supporting two TCP/IP communication channels, and general purpose I/O pin drivers to interface the remote experiment hardware; and 3) a client core based on a multi-tab user interface supporting text file management to exchange experiment scripts / status informatio...

  4. Initial experiment of focusing wiggler of MM wave Free Electron Laser on LAX-1

    International Nuclear Information System (INIS)

    Sakamoto, Keishi; Maebara, Sunao; Watanabe, Akihiko; Kishimoto, Yasuaki; Nagashima, Takashi; Maeda, Hikosuke; Shiho, Makoto; Oda, Hisako; Kawasaki, Sunao.

    1991-03-01

    Initial results of Free Electron laser (FEL) Experiment in the mm wave region are presented. The experiment is carried out using a induction linac system (LAX-1: Large current Accelerator Experiment) of E b = 1 MeV, Ib = 1 ∼ 3 kA. The wiggler of FEL is composed of the curved surface magnets arrays (focusing wiggler), which is found to be effective for a transport of low energy and high current beam through the wiggler. The superradiance of the mm wave region (30 GHz ∼ 40 GHz) is observed. The growth rate of this radiation is 0.42 dB/cm. (author)

  5. Total cross section of furfural by electron impact: Experiment and theory.

    Science.gov (United States)

    Traoré Dubuis, A; Verkhovtsev, A; Ellis-Gibbings, L; Krupa, K; Blanco, F; Jones, D B; Brunger, M J; García, G

    2017-08-07

    We present experimental total cross sections for electron scattering from furfural in the energy range from 10 to 1000 eV, as measured using a double electrostatic analyzer gas cell electron transmission experiment. These results are compared to theoretical data for furfural, as well as to experimental and theoretical values for the structurally similar molecules furan and tetrahydrofuran. The measured total cross section is in agreement with the theoretical results obtained by means of the independent-atom model with screening corrected additivity rule including interference method. In the region of higher electron energies, from 500 eV to 10 keV, the total electron scattering cross section is also estimated using a semi-empirical model based on the number of electrons and dipole polarizabilities of the molecular targets. Together with the recently measured differential and integral cross sections, and the furfural energy-loss spectra, the present total cross section data nearly complete the data set that is required for numerical simulation of low-energy electron processes in furfural, covering the range of projectile energies from a few electron volts up to 10 keV.

  6. Total cross section of furfural by electron impact: Experiment and theory

    Science.gov (United States)

    Traoré Dubuis, A.; Verkhovtsev, A.; Ellis-Gibbings, L.; Krupa, K.; Blanco, F.; Jones, D. B.; Brunger, M. J.; García, G.

    2017-08-01

    We present experimental total cross sections for electron scattering from furfural in the energy range from 10 to 1000 eV, as measured using a double electrostatic analyzer gas cell electron transmission experiment. These results are compared to theoretical data for furfural, as well as to experimental and theoretical values for the structurally similar molecules furan and tetrahydrofuran. The measured total cross section is in agreement with the theoretical results obtained by means of the independent-atom model with screening corrected additivity rule including interference method. In the region of higher electron energies, from 500 eV to 10 keV, the total electron scattering cross section is also estimated using a semi-empirical model based on the number of electrons and dipole polarizabilities of the molecular targets. Together with the recently measured differential and integral cross sections, and the furfural energy-loss spectra, the present total cross section data nearly complete the data set that is required for numerical simulation of low-energy electron processes in furfural, covering the range of projectile energies from a few electron volts up to 10 keV.

  7. Low-energy particle experiments-electron analyzer (LEPe) onboard the Arase spacecraft

    Science.gov (United States)

    Kazama, Yoichi; Wang, Bo-Jhou; Wang, Shiang-Yu; Ho, Paul T. P.; Tam, Sunny W. Y.; Chang, Tzu-Fang; Chiang, Chih-Yu; Asamura, Kazushi

    2017-12-01

    In this report, we describe the low-energy electron instrument LEPe (low-energy particle experiments-electron analyzer) onboard the Arase (ERG) spacecraft. The instrument measures a three-dimensional distribution function of electrons with energies of ˜ 19 eV-19 keV. Electrons in this energy range dominate in the inner magnetosphere, and measurement of such electrons is important in terms of understanding the magnetospheric dynamics and wave-particle interaction. The instrument employs a toroidal tophat electrostatic energy analyzer with a passive 6-mm aluminum shield. To minimize background radiation effects, the analyzer has a background channel, which monitors counts produced by background radiation. Background counts are then subtracted from measured counts. Electronic components are radiation tolerant, and 5-mm-thick shielding of the electronics housing ensures that the total dose is less than 100 kRad for the one-year nominal mission lifetime. The first in-space measurement test was done on February 12, 2017, showing that the instrument functions well. On February 27, the first all-instrument run test was done, and the LEPe instrument measured an energy dispersion event probably related to a substorm injection occurring immediately before the instrument turn-on. These initial results indicate that the instrument works fine in space, and the measurement performance is good for science purposes.[Figure not available: see fulltext.

  8. Hot electron plasma equilibrium and stability in the Constance B mirror experiment

    International Nuclear Information System (INIS)

    Chen, Xing.

    1988-04-01

    An experimental study of the equilibrium and macroscopic stability property of an electron cyclotron resonance heating (ECRH) generated plasma in a minimum-B mirror is presented. The Constance B mirror is a single cell quadrupole magnetic mirror in which high beta (β ≤ 0.3) hot electron plasmas (T/sub e/≅400 keV) are created with up to 4 kW of ECRH power. The plasma equilibrium profile is hollow and resembles the baseball seam geometry of the magnet which provides the confining magnetic field. This configuration coincides with the drift orbit of deeply trapped particles. The on-axis hollowness of the hot electron density profile is 50 /+-/ 10%, and the pressure profile is at least as hollow as, if not more than, the hot electron density profile. The hollow plasma equilibrium is macroscopically stable and generated in all the experimental conditions in which the machine has been operated. Small macroscopic plasma fluctuations in the range of the hot electron curvature drift frequency sometimes occur but their growth rate is small (ω/sub i//ω/sub r/ ≤ 10 -2 ) and saturate at very low level (δB//bar B/ ≤ 10 -3 ). Particle drift reversal is predicted to occur for the model pressure profile which best fits the experimental data under the typical operating conditions. No strong instability is observed when the plasma is near the drift reversal parameter regime, despite a theoretical prediction of instability under such conditions. The experiment shows that the cold electron population has no stabilizing effect to the hot electrons, which disagrees with current hot electron stability theories and results of previous maximum-B experiments. A theoretical analysis using MHD theory shows that the compressibility can stabilize a plasma with a hollowness of 20--30% in the Constance B mirror well. 57 refs

  9. Theory and simulation of an inverse free-electron laser experiment

    Science.gov (United States)

    Gou, S. K.; Bhattacharjee, A.; Fang, J.-M.; Marshall, T. C.

    1997-03-01

    An experimental demonstration of the acceleration of electrons using a high-power CO2 laser interacting with a relativistic electron beam moving along a wiggler has been carried out at the Accelerator Test Facility of the Brookhaven National Laboratory [Phys. Rev. Lett. 77, 2690 (1996)]. The data generated by this inverse free-electron-laser (IFEL) experiment are studied by means of theory and simulation. Included in the simulations are such effects as: a low-loss metallic waveguide with a dielectric coating on the walls; multi-mode coupling due to self-consistent interaction between the electrons and the optical wave; space charge; energy spread of the electrons; and arbitrary wiggler-field profile. Two types of wiggler profile are considered: a linear taper of the period, and a step-taper of the period. (The period of the wiggler is ˜3 cm, its magnetic field is ˜1 T, and the wiggler length is 0.47 m.) The energy increment of the electrons (˜1-2%) is analyzed in detail as a function of laser power, wiggler parameters, and the initial beam energy (˜40 MeV). At a laser power level ˜0.5 Gw, the simulation results on energy gain are in reasonable agreement with the experimental results. Preliminary results on the electron energy distribution at the end of the IFEL are presented. Whereas the experiment produces a near-monotone distribution of electron energies with the peak shifted to higher energy, the simulation shows a more structured and non-monotonic distribution at the end of the wiggler. Effects that may help reconcile these differences are considered.

  10. Metric learning for DNA microarray data analysis

    International Nuclear Information System (INIS)

    Takeuchi, Ichiro; Nakagawa, Masao; Seto, Masao

    2009-01-01

    In many microarray studies, gene set selection is an important preliminary step for subsequent main task such as tumor classification, cancer subtype identification, etc. In this paper, we investigate the possibility of using metric learning as an alternative to gene set selection. We develop a simple metric learning algorithm aiming to use it for microarray data analysis. Exploiting a property of the algorithm, we introduce a novel approach for extending the metric learning to be adaptive. We apply the algorithm to previously studied microarray data on malignant lymphoma subtype identification.

  11. The determination of electron momentum densities by inelastic scattering gamma-ray-electron coincidence measurements: The (γ,eγ)-experiment

    International Nuclear Information System (INIS)

    Rollason, A.J.; Bell, F.; Schneider, J.R.

    1989-09-01

    Measurements have been made of the recoiling electron in 320 keV gamma ray inelastic scattering collisions in thin aluminium targets. The angular correlation of these electrons detected in coincidence with the scattered photon is in agreement with the kinematic requirements of the Compton effect and is correctly predicted by Monte Carlo simulations based on the impulse approximation. Further simulations of ideal-geometry experiments indicate that information about the initial electron momenta is available from an examination of those electron-photon events originating in a surface layer of one electronic mean free path depth and that elastic scattering of the recoil electrons from greater depths produces a nearly flat background to this signal. The results clearly demonstrate the feasibility of the (γ,eγ) experiment for studying electron momentum densities with synchrotron radiation. (orig.) With 23 refs., 17 figs

  12. ESR Experiments on a Single Donor Electron in Isotopically Enriched Silicon

    Science.gov (United States)

    Tracy, Lisa; Luhman, Dwight; Carr, Stephen; Borchardt, John; Bishop, Nathaniel; Ten Eyck, Gregory; Pluym, Tammy; Wendt, Joel; Witzel, Wayne; Blume-Kohout, Robin; Nielsen, Erik; Lilly, Michael; Carroll, Malcolm

    In this talk we will discuss electron spin resonance experiments in single donor silicon qubit devices fabricated at Sandia National Labs. A self-aligned device structure consisting of a polysilicon gate SET located adjacent to the donor is used for donor electron spin readout. Using a cryogenic HEMT amplifier next to the silicon device, we demonstrate spin readout at 100 kHz bandwidth and Rabi oscillations with 0.96 visibility. Electron spin resonance measurements on these devices show a linewidth of 30 kHz and coherence times T2* = 10 us and T2 = 0.3 ms. We also discuss estimates of the fidelity of our donor electron spin qubit measurements using gate set tomography. This work was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. DOE Office of Basic Energy Sciences user facility. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the U. S. Department of Energy under Contract No. DE-AC04-94AL85000. ESR Experiments on a Single Donor Electron in Isotopically Enriched Silicon.

  13. Dosimetry of laser-accelerated electron beams used for in vitro cell irradiation experiments

    International Nuclear Information System (INIS)

    Richter, C.; Kaluza, M.; Karsch, L.; Schlenvoigt, H.-P.; Schürer, M.; Sobiella, M.; Woithe, J.; Pawelke, J.

    2011-01-01

    The dosimetric characterization of laser-accelerated electrons applied for the worldwide first systematic radiobiological in vitro cell irradiation will be presented. The laser-accelerated electron beam at the JeTi laser system has been optimized, monitored and controlled in terms of dose homogeneity, stability and absolute dose delivery. A combination of different dosimetric components were used to provide both an online beam as well as dose monitoring and a precise absolute dosimetry. In detail, the electron beam was controlled and monitored by means of an ionization chamber and an in-house produced Faraday cup for a defined delivery of the prescribed dose. Moreover, the precise absolute dose delivered to each cell sample was determined by an radiochromic EBT film positioned in front of the cell sample. Furthermore, the energy spectrum of the laser-accelerated electron beam was determined. As presented in a previous work of the authors, also for laser-accelerated protons a precise dosimetric characterization was performed that enabled initial radiobiological cell irradiation experiments with laser-accelerated protons. Therefore, a precise dosimetric characterization, optimization and control of laser-accelerated and therefore ultra-short pulsed, intense particle beams for both electrons and protons is possible, allowing radiobiological experiments and meeting all necessary requirements like homogeneity, stability and precise dose delivery. In order to fulfill the much higher dosimetric requirements for clinical application, several improvements concerning, i.e., particle energy and spectral shaping as well as patient safety are necessary.

  14. Studies of improved electron confinement in low density L-mode National Spherical Torus Experiment discharges

    International Nuclear Information System (INIS)

    Stutman, D.; Finkenthal, M.; Tritz, K.; Redi, M. H.; Kaye, S. M.; Bell, M. G.; Bell, R. E.; LeBlanc, B. P.; Hill, K. W.; Medley, S. S.; Menard, J. E.; Rewoldt, G.; Wang, W. X.; Synakowski, E. J.; Levinton, F.; Kubota, S.; Bourdelle, C.; Dorland, W.; The NSTX Team

    2006-01-01

    Electron transport is rapid in most National Spherical Torus Experiment, M. Ono et al., Nucl. Fusion 40, 557 (2000) beam heated plasmas. A regime of improved electron confinement is nevertheless observed in low density L-mode (''low-confinement'') discharges heated by early beam injection. Experiments were performed in this regime to study the role of the current profile on thermal transport. Variations in the magnetic shear profile were produced by changing the current ramp rate and onset of neutral beam heating. An increased electron temperature gradient and local minimum in the electron thermal diffusivity were observed at early times in plasmas with the fastest current ramp and earliest beam injection. In addition, an increased ion temperature gradient associated with a region of reduced ion transport is observed at slightly larger radii. Ultrasoft x-ray measurements of double-tearing magnetohydrodynamic activity, together with current diffusion calculations, point to the existence of negative magnetic shear in the core of these plasmas. Discharges with slower current ramp and delayed beam onset, which are estimated to have more monotonic q-profiles, do not exhibit regions of reduced transport. The results are discussed in the light of the initial linear microstability assessment of these plasmas, which suggests that the growth rate of all instabilities, including microtearing modes, can be reduced by negative or low magnetic shear in the temperature gradient region. Several puzzles arising from the present experiments are also highlighted

  15. Electron cooling application for luminosity preservation in an experiment with internal targets at COSY

    CERN Document Server

    Meshkov, I N; Maier, R; Prasuhn, D; Sidorin, A O; Smirnov, A V; Stein, H J; Stockhorst, H; Trubnikov, G V

    2003-01-01

    This report is an investigation of the beam parameter evolution in the experiments with internal target. In calculations of the proton and deuteron beams we concentrated on cluster, atomic beam, storage cell and pellet targets at ANKE experiment mainly. In these calculations electron and stochastic cooling, intrabeam scattering, scattering on the target and residual gas atoms are taken into account. Beam parameter evolution is investigated in the long-term time scale, up to one hour, at different beam energies in the range from 1.0 to 2.7 GeV for proton beam and from 1 to 2.11 GeV for deuteron beam. The results of numerical simulations of the proton and deuteron beam parameters at different energies obtained using new version of BETACOOL program (elaborated at the first stage of this work [1]) are presented. Optimum parameters of the electron cooling system are estimated. The COSY experiment requirements can be satisfied even when electron cooling time is rather long. That allows to apply an electron cooling ...

  16. Design of simulated nuclear electronics laboratory experiments based on IAEA-TECDOC-530 on pcs

    International Nuclear Information System (INIS)

    Ghousia, S.F.; Nadeem, M.; Khaleeq, M.T.

    2002-05-01

    In this IAEA project, PK-11089 (Design of Simulated Nuclear Electronics Laboratory Experiments based on IAEA-TECDOC-530 on PCs), a software package consisting of Computer-Simulated Laboratory Experiments on Nuclear Electronics compatible with the IAEA-TECDOC-530 (Nuclear Electronics Laboratory Manual) has been developed in OrCAD 9.0 (an electronic circuit simulation software environment) as a self-training aid. The software process model employed in this project is the Feedback Waterfall model with some Rapid Application Model. The project work is completed in the five phases of the SDLC, (all of them have been fully completed) which includes the Requirement Definition, Phase, System and Software Design, Implementation and Unit testing, Integration and System-testing phase and the Operation and Maintenance phase. A total of 125 circuits are designed in 39 experiments from Power Supplies, Analog circuits, Digital circuits and Multi-channel analyzer sections. There is another set of schematic designs present in the package, which contains faulty circuits. This set is designed for the learners to exercise the troubleshooting. The integration and system-testing phase was carried out simultaneously. The Operation and Maintenance phase has been implemented by accomplishing it through some trainees and some undergraduate engineering students by allowing them to play with the software independently. (author)

  17. Rotatable spin-polarized electron source for inverse-photoemission experiments

    International Nuclear Information System (INIS)

    Stolwijk, S. D.; Wortelen, H.; Schmidt, A. B.; Donath, M.

    2014-01-01

    We present a ROtatable Spin-polarized Electron source (ROSE) for the use in spin- and angle-resolved inverse-photoemission (SR-IPE) experiments. A key feature of the ROSE is a variable direction of the transversal electron beam polarization. As a result, the inverse-photoemission experiment becomes sensitive to two orthogonal in-plane polarization directions, and, for nonnormal electron incidence, to the out-of-plane polarization component. We characterize the ROSE and test its performance on the basis of SR-IPE experiments. Measurements on magnetized Ni films on W(110) serve as a reference to demonstrate the variable spin sensitivity. Moreover, investigations of the unoccupied spin-dependent surface electronic structure of Tl/Si(111) highlight the capability to analyze complex phenomena like spin rotations in momentum space. Essentially, the ROSE opens the way to further studies on complex spin-dependent effects in the field of surface magnetism and spin-orbit interaction at surfaces

  18. Gene Expression and Microarray Investigation of Dendrobium ...

    African Journals Online (AJOL)

    blood glucose > 16.7 mmol/L were used as the model group and treated with Dendrobium mixture. (DEN ... Keywords: Diabetes, Gene expression, Dendrobium mixture, Microarray testing ..... homeostasis in airway smooth muscle. Am J.

  19. SLIMarray: Lightweight software for microarray facility management

    Directory of Open Access Journals (Sweden)

    Marzolf Bruz

    2006-10-01

    Full Text Available Abstract Background Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors. Results We present SLIMarray (System for Lab Information Management of Microarrays, an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available. Conclusion SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

  20. Cost effective electronics for proportional and drift chambers of 'EPECUR' experiment

    International Nuclear Information System (INIS)

    Alekseev, I.G.; Andreev, V.A.; Budkovsky, P.E.; Filimonov, E.A.; Golubev, V.V.; Kanavets, V.P.; Kats, M.M.; Koroleva, L.I.; Kovalev, A.I.; Kozlenko, N.G.; Kozlov, V.S.; Krivshich, A.G.; Kulikov, V.V.; Morozov, B.V.; Nesterov, V.M.; Novinsky, D.V.; Ryltsov, V.V.; Sadler, M.E.; Sakharov, V.A.; Soboyede, D.; Sulimov, A.D.; Sumachev, V.V.; Svirida, D.N.; Trautman, V.Yu.; Walker, E.; Watson, S.

    2007-01-01

    The 'EPECUR' experimental setup is under construction at beam line 322 of the ITEP proton synchrotron. The experiment requires several large area drift chambers to provide reasonable acceptance and fine-pitch proportional chambers for beam particle tracking. The total number of electronic channels is about 7000. A new compact and cost effective readout system for these gaseous detectors was designed, prototyped and tested in the last two years. It is based on modern technologies in analog and digital electronics and data transfer protocols. This paper presents the functional description of the whole DAQ system, including test results as an illustration of its performance

  1. Conversion-electron experiment to characterize the decay of the 237Np shape isomer

    International Nuclear Information System (INIS)

    Henry, E.A.; Becker, J.A.; Bauer, R.W.; Gardner, D.G.; Decman, D.J.; Meyer, R.A.; Roy, N.; Sale, K.E.

    1987-01-01

    Conversion electrons from the decay of low-lying levels of 237 Np have been measured to detect the population of these levels by gamma-ray decay of the 237 Np shape isomer. Analysis of the 208-keV transition L conversion-electron peak gives an upper limit of about 17 μb for the population of the 3/2 - 267-keV level in 237 Np from the shape isomer decay. Model calculations are compared with the measured limit. Improvements are suggested for this experiment. 9 refs., 4 figs

  2. Experiments on ion space-charge neutralization with pulsed electron beams

    Energy Technology Data Exchange (ETDEWEB)

    Herleb, U; Riege, H [CERN LHC-Division, Geneva (Switzerland)

    1997-12-31

    The method of space-charge neutralization of heavy ion beams with electron beam pulses generated with electron guns incorporating ferroelectric cathodes was investigated experimentally. Several experiments are described, the results of which prove that the intensity of selected ion beam parts with defined charge states generated in a laser ion source can be increased by an order of magnitude. For elevated charge states the intensity amplification is more significant and may reach a factor of 4 for highly charged ions from an Al target. (author). 7 figs., 3 -refs.

  3. Wave excitation in electron beam experiment on Japanese satellite JIKIKEN (EXOS-B)

    International Nuclear Information System (INIS)

    Kawashima, N.

    1982-01-01

    Beam-plasma interaction experiment has been made in the magnetosphere by emitting an electron beam (100-200 eV, 0.25-1.0 mA) from the satellite JIKIKEN (EXOS-B). Various types of wave emission are detected by LF and HF wave detectors. Waves near at upper-hybrid frequency and at electron cyclotron frequency are detected in a low L-value region, which will be useful diagnostic means for plasma density and magnetic field. Vehicle charging up to the beam energy is also observed outside the plasmapause

  4. Tester of the TRT front-end electronics for the ATLAS-experiment

    CERN Document Server

    Hajduk, Z; Kisielewski, B; Kotarba, A; Malecki, P; Natkaniec, Z; Olszowska, J; Ostrowicz, W; Krupinska, G

    2000-01-01

    The VME based tester for front-end electronics of the TRT (Transition Radiation Tracker) detector of the ATLAS-LHC experiment at CERN, Geneva, is described. The TRT read-out electronics for 424576 proportional tubes grouped on many thousands of cards requires stringent quality control after assembly and during installation. The tester provides all required data, pulses, timing and power supplies for tested cards. The essential part of the tester is its software that allows for device handling as well as facilitates functional and statistical tests. The prototype, present design as well as the new design for mass production tests are discussed. (17 refs).

  5. Electron-nucleon scattering experiments in the GeV range

    International Nuclear Information System (INIS)

    Glawe, U.B.

    1980-01-01

    In the framework of this thesis a computer code systems was developed which describes the inclusive electron scattering on bound nucleons in the impact approximation. It could be shown that the structure functions for the quasi-free scattering can be represented as an incoherent superposition of the structure functions of the free processes. The structure functions of the free processes were determined from experimental cross sections. From the comparison of the calculations with electron scattering experiments on the nuclei 6 Li, 9 Be, 12 C, 27 Al, and 28 Si in the kinematic range 0.0 2 2 and W [de

  6. Experiments on the nuclear interactions of pion and electrons. Final progress report

    International Nuclear Information System (INIS)

    Minehart, R.C.

    1998-05-01

    The work in this report is grouped into four categories. (1) The experiments in pion nucleus physics were primarily studies of pion absorption and scattering in light nuclei, carried out at the Los Alamos Meson Physics Facility (LAMPF). (2) The experiments on fundamental particle properties were carried out at LAMPF and at the Paul Scherrer Institute (PSI) in Switzerland, the pion-beta decay experiment is still under construction and will begin taking data in 1999. (3) The experiments in electro-nuclear physics were performed at the Stanford Linear Electron Accelerator (SLAC), at the Saclay Laboratory in France, at the LEGS facility at the Brookhaven National Laboratory, and at the Continuous Electron Beam Accelerator Facility (CEBAF) at the Jefferson Laboratory. These experiments relate mainly to the question of the role of longitudinal and transverse strength for inelastic scattering from nuclei, measurements of fundamental nuclear properties with tagged polarized photons, and to the quark structure of the nucleon and its excited states. (4) Experiments on absorption of antiprotons in heavy nuclei, were carried out by K. Ziock primarily while on a sabbatical leave in Munich, Germany

  7. Internal electron transport barrier due to neoclassical ambipolarity in the Helically Symmetric Experiment

    International Nuclear Information System (INIS)

    Lore, J.; Briesemeister, A.; Anderson, D. T.; Anderson, F. S. B.; Likin, K. M.; Talmadge, J. N.; Zhai, K.; Guttenfelder, W.; Deng, C. B.; Spong, D. A.

    2010-01-01

    Electron cyclotron heated plasmas in the Helically Symmetric Experiment (HSX) feature strongly peaked electron temperature profiles; central temperatures are 2.5 keV with 100 kW injected power. These measurements, coupled with neoclassical predictions of large 'electron root' radial electric fields with strong radial shear, are evidence of a neoclassically driven thermal transport barrier. Neoclassical transport quantities are calculated using the PENTA code [D. A. Spong, Phys. Plasmas 12, 056114 (2005)], in which momentum is conserved and parallel flow is included. Unlike a conventional stellarator, which exhibits strong flow damping in all directions on a flux surface, quasisymmetric stellarators are free to rotate in the direction of symmetry, and the effect of momentum conservation in neoclassical calculations may therefore be significant. Momentum conservation is shown to modify the neoclassical ion flux and ambipolar ion root radial electric fields in the quasisymmetric configuration. The effect is much smaller in a HSX configuration where the symmetry is spoiled. In addition to neoclassical transport, a model of trapped electron mode turbulence is used to calculate the turbulent-driven electron thermal diffusivity. Turbulent transport quenching due to the neoclassically predicted radial electric field profile is needed in predictive transport simulations to reproduce the peaking of the measured electron temperature profile [Guttenfelder et al., Phys. Rev. Lett. 101, 215002 (2008)].

  8. Intense ion beam transport in magnetic quadrupoles: Experiments on electron and gas effects

    International Nuclear Information System (INIS)

    Seidl, P.A.; Molvik, A.W.; Bieniosek, F.M.; Cohen, R.H.; Faltens, A.; Friedman, A.; Kireef Covo, M.; Lund, S.M.; Prost, L.; Vay, J-L.

    2004-01-01

    Heavy-ion induction linacs for inertial fusion energy and high-energy density physics have an economic incentive to minimize the clearance between the beam edge and the aperture wall. This increases the risk from electron clouds and gas desorbed from walls. We have measured electron and gas emission from 1 MeV K + incident on surfaces near grazing incidence on the High-Current Experiment (HCX) at LBNL. Electron emission coefficients reach values >100, whereas gas desorption coefficients are near 10 4 . Mitigation techniques are being studied: A bead-blasted rough surface reduces electron emission by a factor of 10 and gas desorption by a factor of 2. We also discuss the results of beam transport (of 0.03-0.18 A K + ) through four pulsed room-temperature magnetic quadrupoles in the HCX at LBNL. Diagnostics are installed on HCX, between and within quadrupole magnets, to measure the beam halo loss, net charge and expelled ions, from which we infer gas density, electron trapping, and the effects of mitigation techniques. A coordinated theory and computational effort has made significant progress towards a self-consistent model of positive-ion beam and electron dynamics. We are beginning to compare experimental and theoretical results

  9. Results and analysis of the TMX electron-beam injection experiments

    International Nuclear Information System (INIS)

    Poulsen, P.; Grubb, D.P.

    1980-01-01

    Electron beams (e-beams) were injected into the Tandem Mirror Experiment (TMX) plasma in order to investigate the effect on the ion cyclotron fluctuations of the plasma. The power level of the e-beams was comparable to that of the injected neutral beams. It was found that injection of the e-beams produced no significant effect on the ion cyclotron fluctuations, the measured plasma parameters, or the particle and power flow of the plasma. The increase in bulk electron temperature and the production of mirror-confined electrons found in previous experiments in which e-beams were injected into a mirror-confined plasma were not observed in this experiment. Analysis of the regions and frequencies of wave creation and absorption within the plasma shows that the plasma density and magnetic field profiles through the plasma strongly affect the resonances encountered by the waves. The steep axial density profiles produced by neutral-beam injection in the TMX experiment are not conducive to efficient coupling of the e-beam energy to the plasma

  10. Construction of a cDNA microarray derived from the ascidian Ciona intestinalis.

    Science.gov (United States)

    Azumi, Kaoru; Takahashi, Hiroki; Miki, Yasufumi; Fujie, Manabu; Usami, Takeshi; Ishikawa, Hisayoshi; Kitayama, Atsusi; Satou, Yutaka; Ueno, Naoto; Satoh, Nori

    2003-10-01

    A cDNA microarray was constructed from a basal chordate, the ascidian Ciona intestinalis. The draft genome of Ciona has been read and inferred to contain approximately 16,000 protein-coding genes, and cDNAs for transcripts of 13,464 genes have been characterized and compiled as the "Ciona intestinalis Gene Collection Release I". In the present study, we constructed a cDNA microarray of these 13,464 Ciona genes. A preliminary experiment with Cy3- and Cy5-labeled probes showed extensive differential gene expression between fertilized eggs and larvae. In addition, there was a good correlation between results obtained by the present microarray analysis and those from previous EST analyses. This first microarray of a large collection of Ciona intestinalis cDNA clones should facilitate the analysis of global gene expression and gene networks during the embryogenesis of basal chordates.

  11. Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

    Directory of Open Access Journals (Sweden)

    Tong Weida

    2010-10-01

    Full Text Available Abstract Background The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. In addition, it was not clear whether the two human reference RNA samples established by the MAQC project in 2005 still maintained their transcriptome integrity over a period of four years. Experiments were conducted to answer these questions. Results Microarray data were generated in 2009 in three replicates for each of the two MAQC samples with either expired Affymetrix U133A or unexpired U133Plus2 microarrays. These results were compared with data obtained in 2005 on the U133Plus2 microarray. The percentage of overlap between the lists of differentially expressed genes (DEGs from U133Plus2 microarray data generated in 2009 and in 2005 was 97.44%. While there was some degree of fold change compression in the expired U133A microarrays, the percentage of overlap between the lists of DEGs from the expired and unexpired microarrays was as high as 96.99%. Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005. Conclusions Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the

  12. Scex 3 and Electron Echo 7, a Comparison of Data from Two Rocket Experiments.

    Science.gov (United States)

    Bale, Stuart Douglas

    Results from two separate active sounding rocket experiments are presented and discussed. The SCEX III sounding rocket (NASA 39.002 UE) and Electron Echo 7 (NASA 36.015) were both launched from the Poker Flat Research Range (65.1^circ N, 147.5^circ W) near Fairbanks, Alaska, on 1 February, 1990 and 9 February, 1988, respectively. Each payload was equipped with an electron accelerator to study both natural and beam-related plasma phenomena. Data from the SCEX III retarding potential analyzer (RPA) and 3805 A and 3914 A photometers show evidence of a plasma discharge process occurring concomitant with operation of the electron gun. This appears as an enhanced electron current, nonlinear with gun injection current, in the RPA. The photometers register a sharp increase in luminosity during full current electron injection. This luminosity is an indicator of the ionizing electron-neutral collisions which liberate electrons and lead to the cascade-type discharge process. These observations are used to attempt to infer the mechanism of electron acceleration which leads to the discharge process. Before the electron gun was activated, the SCEX III payload flew through a region of auroral activity as evidenced by ground-based all-sky TV and energetic particle flux in the forward payload RPA. During this time, low frequency (10 Hz) electrostatic waves were observed in the DC receivers and Langmuir probe instrument. This data is analyzed, with a cross-spectral technique, and an approximate wave number is inferred. Comparison with theory suggests that the observed wave is the electrostatic ion cyclotron mode (EIC) operating on a heavy ion species (NO or O _2). The Echo 7 nose payload, carrying a plasma wave receiver, was ejected upfield of the main electron gun -equipped payload. Data from the swept frequency analyzer experiment provide wave amplitudes, at frequencies up to 15 MHz, as a function of separation of the main and nose payloads. These observations, and the wave modes

  13. PATMA: parser of archival tissue microarray

    Directory of Open Access Journals (Sweden)

    Lukasz Roszkowiak

    2016-12-01

    Full Text Available Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images.

  14. Ring recognition and electron identification in the RICH detector of the CBM experiment at FAIR

    International Nuclear Information System (INIS)

    Lebedev, S; Hoehne, C; Ososkov, G

    2010-01-01

    The Compressed Baryonic Matter (CBM) experiment at the future FAIR facility at Darmstadt will measure dileptons emitted from the hot and dense phase in heavy-ion collisions. In case of an electron measurement, a high purity of identified electrons is required in order to suppress the background. Electron identification in CBM will be performed by a Ring Imaging Cherenkov (RICH) detector and Transition Radiation Detectors (TRD). In this contribution we will present algorithms and software which have been developed for electron identification in CBM. Efficient and fast ring recognition in the RICH detector is based on the Hough Transform method which has been accelerated considerably compared to a standard implementation. Ring quality selection is done using an Artificial Neural Network which also has been used for electron identification. Due to optical distortions ellipse fitting and radius corre ction routines are used for improved ring radius resolution. These methods allow for a high purity and efficiency of reconstructed electron rings. For momenta above 2 GeV/c the ring reconstruction efficiency for electrons embedded in central Au+Au collisions at 25 AGeV beam energy is 95% resulting in an electron identification efficiency of 90% at a pion suppression factor of 500. Including information from the TRD a pion suppression of 10 4 is reached at 80% efficiency. The developed algorithm is very robust to a high ring density environment. Current work focusses on detector layout studies in order to optimize the detector setup while keeping a high performance. All developed algorithms were tested on large statistics of simulated events and are included into the CBM software framework for common use.

  15. ``High energy Electron exPeriment (HEP)'' onboard the ERG satellite

    Science.gov (United States)

    Mitani, T.; Takashima, T.; Kasahara, S.; Miyake, W.; Hirahara, M.

    2017-12-01

    The Exploration of energization and Radiation in Geospace (ERG) satellite was successfully launched on December 20, 2016, and now explores how relativistic electrons in the radiation belts are generated during space storms. "High energy Electron exPeriment (HEP)" onboard the ERG satellite observes 70 keV - 2 MeV electrons and provides three-dimensional velocity distribution of electrons every spacecraft spin period. Electrons are observed by two types of camera designs, HEP-L and HEP-H, with regard to geometrical factor and energy range. HEP-L observes 0.1 - 1 MeV electrons and its geometrical factor (G-factor) is 10-3 cm2 str, and HEP-H observes 0.7 - 2 MeV and G-factor is 10-2 cm2 str. HEP-L and HEP-H each consist of three pin-hole type cameras, and each camera consist of mechanical collimator, stacked silicon semiconductor detectors and readout ASICs. HEP-H has larger opening angle of the collimator and more silicon detectors to observe higher energy electrons than HEP-L. The initial checkout in orbit was carried out in February 2017 and it was confirmed that there was no performance degradation by comparing the results of the initial checkout in orbit and the prelaunch function tests. Since late March, HEP has carried out normal observation. HEP observed losses and recovery of the outer radiation belt electrons several times up to now. In this presentation we introduce the HEP instrument design, prelaunch tests results and report the initial results in orbit.

  16. Goober: A fully integrated and user-friendly microarray data management and analysis solution for core labs and bench biologists

    Directory of Open Access Journals (Sweden)

    Luo Wen

    2009-03-01

    Full Text Available Despite the large number of software tools developed to address different areas of microarray data analysis, very few offer an all-in-one solution with little learning curve. For microarray core labs, there are even fewer software packages available to help with their routine but critical tasks, such as data quality control (QC and inventory management. We have developed a simple-to-use web portal to allow bench biologists to analyze and query complicated microarray data and related biological pathways without prior training. Both experiment-based and gene-based analysis can be easily performed, even for the first-time user, through the intuitive multi-layer design and interactive graphic links. While being friendly to inexperienced users, most parameters in Goober can be easily adjusted via drop-down menus to allow advanced users to tailor their needs and perform more complicated analysis. Moreover, we have integrated graphic pathway analysis into the website to help users examine microarray data within the relevant biological content. Goober also contains features that cover most of the common tasks in microarray core labs, such as real time array QC, data loading, array usage and inventory tracking. Overall, Goober is a complete microarray solution to help biologists instantly discover valuable information from a microarray experiment and enhance the quality and productivity of microarray core labs. The whole package is freely available at http://sourceforge.net/projects/goober. A demo web server is available at http://www.goober-array.org.

  17. aCORN: An experiment to measure the electron-antineutrino correlation in neutron decay

    Energy Technology Data Exchange (ETDEWEB)

    Wietfeldt, F.E., E-mail: few@tulane.ed [Department of Physics, Tulane University, New Orleans, LA 70118 (United States); Byrne, J. [University of Sussex (United Kingdom); Collett, B. [Physics Department, Hamilton College, Clinton, NY 13323 (United States); Dewey, M.S. [National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Jones, G.L. [Physics Department, Hamilton College, Clinton, NY 13323 (United States); Komives, A. [Physics Department, DePauw University, Greencastle, IN 46135 (United States); Laptev, A. [Department of Physics, Tulane University, New Orleans, LA 70118 (United States); Nico, J.S. [National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Noid, G.; Stephenson, E.J. [Indiana University Cyclotron Facility, Bloomington, IN 47408 (United States); Stern, I.; Trull, C. [Department of Physics, Tulane University, New Orleans, LA 70118 (United States); Yerozolimsky, B.G. [Physics Department, Harvard University, Cambridge, MA 02139 (United States)

    2009-12-11

    The aCORN experiment is designed to make a precision (<1%) measurement of the electron-antineutrino angular correlation (a-coefficient) in neutron beta decay. It uses a new method proposed in 1996 by Yerozolimsky and Mostovoy. Electrons and recoil protons from neutron decay in a cold beam are detected in coincidence. The momenta of the particles are selected so that the protons form two kinematically distinct time-of-flight groups as a function of electron energy. The count rate asymmetry in these two groups is proportional to the a-coefficient. Precision spectroscopy of the protons is not required. The apparatus is currently under construction. It will be integrated and tested at the Indiana University Cyclotron Facility (IUCF) and then moved to the NIST Center for Neutron Research for the initial physics run.

  18. Recent Operating Experience involving Power Electronics Failure in Korea Nuclear Power Plants

    International Nuclear Information System (INIS)

    Lee, Jaedo

    2015-01-01

    Recently, modern power electronics devices for electrical component were steadily increased in electrical systems which used for main power control and protection. To upgrade the system reliability we recommended the redundancy for electrical equipment trip system. The past several years, Korean Nuclear power plants have changed the electrical control and protection systems (Auto Voltage Regulator, Power Protection Relay) for main generator and main power protection relay systems. In this paper we deal with operating experience involving modern solid state power electronics failure in Korean nuclear power plants. One of the failures we will discuss the degraded phenomenon of power electronics device for CEDMCS(Control Element Drive Mechanism Control System). As the result of the failure we concerned about the modification for trip source of main generator excitation systems and others. We present an interesting issue for modern solid state devices (IGBT, Thyristors). (authors)

  19. Possibility of experiments using radiation counters for test electron stability and Pauli principle violation in atoms

    International Nuclear Information System (INIS)

    Barabash, A.S.

    1989-01-01

    Capabilities of modern radiation detectors for investigation into electron stability and possible violation of Pauli principle in atoms are discussed. For experimental searches of electron instability the following low-background devices are used: scintillation NaI-detectors, semiconducting detectors of enriched germanium, emission chamber, multisection proportional counter and low-temperature detectors. It is ascertained that using modern low-background devices applying the earlier enumerated detectors, it is possible to achieve sensitivity of the order of 10 24 -10 25 years for the electron lifetime relatively to its decay and Pauli principle violation in atoms. Experiments with sensitivity of ∼ 10 26 -10 27 can be realized in massive low-temperature detectors, developed for neutrino physics. 28 refs; 1 fig

  20. Direct determination of exciton wavefunction amplitudes by the momentum-resolved photo-electron emission experiment

    Science.gov (United States)

    Ohnishi, Hiromasa; Tomita, Norikazu; Nasu, Keiichiro

    2018-03-01

    We study conceptional problems of a photo-electron emission (PEE) process from a free exciton in insulating crystals. In this PEE process, only the electron constituting the exciton is suddenly emitted out of the crystal, while the hole constituting the exciton is still left inside and forced to be recoiled back to its original valence band. This recoil on the hole is surely reflected in the spectrum of the PEE with a statistical distribution along the momentum-energy curve of the valence band. This distribution is nothing but the square of the exciton wavefunction amplitude, since it shows how the electron and the hole are originally bound together. Thus, the momentum-resolved PEE can directly determine the exciton wavefunction. These problems are clarified, taking the Γ and the saddle point excitons in GaAs, as typical examples. New PEE experiments are also suggested.

  1. A study of microwave interferometers for electron density measurements in REB-plasma experiments

    International Nuclear Information System (INIS)

    Saxena, A.C.; Paithankar, A.S.; Iyyengar, S.K.; Rohatgi, V.K.

    1981-01-01

    In order to select a suitable microwave interferometer for electron density measurements in Relativistic Electron Beam (REB)-Plasma Experiments, a study has been carried out of four types of interferometers, viz. simple interferometer, standing-wave interferometer, frequency and phase modulated interferometers. Various direct reading interferometers which give a voltage proportional to the phase shift, are also discussed. Systems have been analysed in terms of time resolution, phase sensitivity, system stability, ease of measurement etc. Theoretical and experimental limitations of various systems have been indicated. Summary of the various systems is presented in a table to aid the experimentalist to select the most appropriate system for the prevailina experimental conditions. Finally, an attempt has been made to find out the interferometer system best suited for REB-Plasma Experiments. (author)

  2. Low-cost electron-gun pulser for table-top maser experiments

    Science.gov (United States)

    Grinberg, V.; Jerby, E.; Shahadi, A.

    1995-04-01

    A simple 10 kV electron-gun pulser for small-scale maser experiments is presented. This low-cost pulser has operated successfully in various table-top cyclotron-resonance maser (CRM) and free-electron maser (FEM) experiments. It consists of a low-voltage capacitor bank, an SCR control circuit and a transformer bank (car ignition coils) connected directly to the e-gun. The pulser produces a current of 3 A at 10 kV voltage in a Gaussian like shape of 1 ms pulse width. The voltage sweep during the pulse provides a useful tool to locate resonances of CRM and FEM interactions. Analytical expressions for the pulser design and experimental measurements are presented.

  3. An experiment to measure the electron neutrino mass using a cryogenic tritium source

    International Nuclear Information System (INIS)

    Fackler, O.; Jeziorski, B.; Kolos, W.; Monkhorst, H.; Mugge, M.; Sticker, H.; Szalewicz, K.; White, R.M.; Woerner, R.

    1985-01-01

    An experiment has been performed to determine the electron neutrino mass with the precision of a few eV by measuring the tritium beta decay energy distribution near the endpoint. Key features of the experiment are a 2 eV resolution electrostatic spectrometer and a high-activity frozen tritium source. It is important that the source have electronic wavefunctions which can be accurately calculated. These calculations have been made for tritium and the HeT + daughter ion and allow determination of branching fractions to 0.1% and energy of the excited states to 0.1 eV. The excited final molecular state calculations and the experimental apparatus are discussed. 4 refs., 5 figs

  4. Optical transition radiation measurements for the Los Alamos and Boeing Free-Electron Laser experiments

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A.H.; Feldman, R.B.; Feldman, D.W.; Apgar, S.A.; Calsten, B.E.; Fiorito, R.B.; Rule, D.W.

    1988-01-01

    Optical transition radiation (OTR) measurements of the electron-beam emittance have been performed at a location just before the wiggler in the Los Alamos Free-Electron Laser (FEL) experiment. Beam profiles and beam divergence patterns from a single macropulse were recorded simultaneously using two intensified charge-injection device (CID) television cameras and an optical beamsplitter. Both single-foil OTR and two-foil OTR interference experiments were performed. Preliminary results are compared to a reference variable quadrupole, single screen technique. New aspects of using OTR properties for pointing the e-beam on the FEL oscillator axis, as well as measuring e-beam emittance are addressed. 7 refs., 9 figs.

  5. ELECTRONIC EDUCATION IN UNDERGRADUATE RADIOLOGY: THE EXPERIENCE OF THE UNIVERSITY OF MALAGA

    Directory of Open Access Journals (Sweden)

    Francisco Sendra Portero

    2010-07-01

    Full Text Available Since 1998, radiology teaching and learning electronic resources have been developed at the University of Málaga. Some experiences on undergraduate radiology education are presented in this paper: a self-conducted training on radiology called “A Walk through Radiology”, some projects to create and develop radiology consulting tools, a project about audio-recorded virtual lectures (AMERAM, started on 2005, and a Web portal to collect radiology education Internet resources. Finally, we conclude with some reflections about the experience along these years, which has contributed to improve the student’s radiology learning in our centre and has supplied educative tools to students and postgraduates of this and other cities. We consider that the European Space of Higher Education learning philosophy, student centered and self-learning based, gives a vital role to undergraduate electronic education tools.

  6. Observation of Flat Electron Temperature Profiles in the Lithium Tokamak Experiment

    International Nuclear Information System (INIS)

    Boyle, D. P.; Majeski, R.; Schmitt, J. C.; Auburn University, AL; Hansen, C.

    2017-01-01

    It has been predicted for over a decade that low-recycling plasma-facing components in fusion devices would allow high edge temperatures and flat or nearly flat temperature profiles. In recent experiments with lithium wall coatings in the Lithium Tokamak Experiment (LTX), a hot edge (> 200 eV) and flat electron temperature profiles have been measured following the termination of external fueling. In this work, reduced recycling was demonstrated by retention of ~ 60% of the injected hydrogen in the walls following the discharge. Electron energy confinement followed typical Ohmic confinement scaling during fueling, but did not decrease with density after fueling terminated, ultimately exceeding the scaling by ~ 200% . Lastly, achievement of the low-recycling, hot edge regime has been an important goal of LTX and lithium plasma-facing component research in general, as it has potentially significant implications for the operation, design, and cost of fusion devices.

  7. The relationship between past caries experience and tooth color determined by an opto-electronic method.

    Science.gov (United States)

    Kerosuo, E; Kolehmainen, L

    1982-01-01

    The susceptibility of a tooth to dental caries has been proposed to depend on tooth color. So far there has, however, been no reliable method for tooth color determination. The aims of this study were to evaluate the reliability of an opto-electronic method and to examine the relationship between tooth color and past caries experience. The color of upper right central incisors of 64 school-children was determined using an opto-electronic tri-stimulus color comparator. The intra- and interexaminer reliability of the method was evaluated in vitro and in vivo being 85% and 83%, respectively. To assess the past caries experience the DMFS-index was calculated. Oral hygiene and dietary habits were also assessed. No significant difference in DMFS scores was obtained between the 'white teeth' group and the 'yellow teeth' group. The conclusion is, that the practical importance of possible colorrelated differences in caries resistance is negligible due to the multifaceted nature of dental caries.

  8. Circular waveguide systems for electron-cyclotron-resonant heating of the tandem mirror experiment-upgrade

    International Nuclear Information System (INIS)

    Felker, B.; Calderon, M.O.; Chargin, A.K.

    1983-01-01

    Extensive use of electron cyclotron resonant heating (ECRH) in the Tandem Mirror Experiment-Upgrade (TMX-U) requires continuous development of components to improve efficiency, increase reliability, and deliver power to new locations with respect to the plasma. We have used rectangular waveguide components on the experiment and have developed, tested, and installed circular waveguide components. We replaced the rectangular with the circular components because of the greater transmission efficiency and power-handling capability of the circular ones. Design, fabrication, and testing of all components are complete for all systems. In this paper we describe the design criteria for the system

  9. Electronic ground support equipment for the Cluster Electric Field and Wave Experiment

    International Nuclear Information System (INIS)

    Sten, T.A.

    1992-10-01

    In a collaboration between ESA and NASA, ionosphere plasma structures will be studied by four indentical space probes to be launched in 1995 from French Guiana. The Electric Field and Wave (EFW) experiment will be designed to measure electric field and density fluctations by means of four sensors, each deployed on a 50 meter wire boom. In order to perform comprehensive tests and calibrations of the EFW experiment, computer controlled electronic ground support equipment has been developed. This report describes the hardware of the equipment, produced and assembled at the University of Oslo. 15 figs

  10. Disruption simulation experiment using high-frequency rastering electron beam as the heat source

    International Nuclear Information System (INIS)

    Yamazaki, S.; Seki, M.

    1987-01-01

    The disruption is a serious event which possibly reduces the lifetime of plasm interactive components, so the effects of the resulting high heat flux on the wall materials must be clearly identified. The authors performed disruption simulation experiments to investigate melting, evaporation, and crack initiation behaviors using an electron beam facility as the heat source. The facility was improved with a high-frequency beam rastering system which provided spatially and temporally uniform heat flux on wider test surfaces. Along with the experiments, thermal and mechanical analyses were also performed. A two-dimensional disruption thermal analysis code (DREAM) was developed for the analyses

  11. The source of monoenergetic electrons for the monitoring of spectrometer in the KATRIN neutrino experiment

    CERN Document Server

    Slezák, Martin

    The international project KATRIN (KArlsruhe TRItium Neutrino experiment) is a next-generation tritium $\\beta$-decay experiment. It is designed to measure the electron anti-neutrino mass by means of a unique electron spectrometer with sensitivity of 0.2 eV/c$^2$. This is an improvement of one order of magnitude over the last results. Important part of the measurement will rest in continuous precise monitoring of high voltage of the KATRIN main spectrometer. The monitoring will be done by means of conversion electrons emitted from a solid source based on $^{83}$Rb decay. Properties of several of these sources are studied in this thesis by means of the semiconductor $\\gamma$-ray spectroscopy. Firstly, measurement of precise energy of the 9.4 keV nuclear transition observed in $^{83}$Rb decay, from which the energy of conversion electrons is derived, is reported. Secondly, measurement of activity distribution of the solid sources by means of the Timepix detector is described. Finally, a report on measurement of r...

  12. DNA Microarray Technologies: A Novel Approach to Geonomic Research

    Energy Technology Data Exchange (ETDEWEB)

    Hinman, R.; Thrall, B.; Wong, K,

    2002-01-01

    A cDNA microarray allows biologists to examine the expression of thousands of genes simultaneously. Researchers may analyze the complete transcriptional program of an organism in response to specific physiological or developmental conditions. By design, a cDNA microarray is an experiment with many variables and few controls. One question that inevitably arises when working with a cDNA microarray is data reproducibility. How easy is it to confirm mRNA expression patterns? In this paper, a case study involving the treatment of a murine macrophage RAW 264.7 cell line with tumor necrosis factor alpha (TNF) was used to obtain a rough estimate of data reproducibility. Two trials were examined and a list of genes displaying either a > 2-fold or > 4-fold increase in gene expression was compiled. Variations in signal mean ratios between the two slides were observed. We can assume that erring in reproducibility may be compensated by greater inductive levels of similar genes. Steps taken to obtain results included serum starvation of cells before treatment, tests of mRNA for quality/consistency, and data normalization.

  13. Consumer Electronics Processors for Critical Real-Time Systems: a (Failed) Practical Experience

    OpenAIRE

    Fernandez , Gabriel; Cazorla , Francisco; Abella , Jaume

    2018-01-01

    International audience; The convergence between consumer electronics and critical real-time markets has increased the need for hardware platforms able to deliver high performance as well as high (sustainable) performance guarantees. Using the ARM big.LITTLE architecture as example of those platforms, in this paper we report our experience with one of its implementations (the Qualcomm SnapDragon 810 processor) to derive performance bounds with measurement-based techniques. Our theoretical and ...

  14. Experiments using electronic display information in the NASA terminal configured vehicle

    Science.gov (United States)

    Morello, S. A.

    1980-01-01

    The results of research experiments concerning pilot display information requirements and visualization techniques for electronic display systems are presented. Topics deal with display related piloting tasks in flight controls for approach-to-landing, flight management for the descent from cruise, and flight operational procedures considering the display of surrounding air traffic. Planned research of advanced integrated display formats for primary flight control throughout the various phases of flight is also discussed.

  15. Physics Accomplishments and Future Prospects of the BES Experiments at the Beijing Electron-Positron Collider

    Science.gov (United States)

    Briere, Roy A.; Harris, Frederick A.; Mitchell, Ryan E.

    2016-10-01

    The cornerstone of the Chinese experimental particle physics program is a series of experiments performed in the τ-charm energy region. China began building e+e- colliders at the Institute for High Energy Physics in Beijing more than three decades ago. Beijing Electron Spectrometer (BES) is the common root name for the particle physics detectors operated at these machines. We summarize the development of the BES program and highlight the physics results across several topical areas.

  16. Study of a reconstruction algorithm for electrons in the ATLAS experiment in LHC

    International Nuclear Information System (INIS)

    Kerschen, N.

    2006-09-01

    The ATLAS experiment is a general purpose particle physics experiment mainly aimed at the discovery of the origin of mass through the research of the Higgs boson. In order to achieve this, the Large Hadron Collider at CERN will accelerate two proton beams and make them collide at the centre of the experiment. ATLAS will discover new particles through the measurement of their decay products. Electrons are such decay products: they produce an electromagnetic shower in the calorimeter by which they lose all their energy. The calorimeter is divided into cells and the deposited energy is reconstructed using an algorithm to assemble the cells into clusters. The purpose of this thesis is to study a new kind of algorithm adapting the cluster to the shower topology. In order to reconstruct the energy of the initially created electron, the cluster has to be calibrated by taking into account the energy lost in the dead material in front of the calorimeter. Therefore. a Monte-Carlo simulation of the ATLAS detector has been used to correct for effects of response modulation in position and in energy and to optimise the energy resolution as well as the linearity. An analysis of test beam data has been performed to study the behaviour of the algorithm in a more realistic environment. We show that the requirements of the experiment can be met for the linearity and resolution. The improvement of this new algorithm, compared to a fixed sized cluster. is the better recovery of Bremsstrahlung photons emitted by the electron in the material in front of the calorimeter. A Monte-Carlo analysis of the Higgs boson decay in four electrons confirms this result. (author)

  17. Reliability data bank in electronics: ITALTEL experience over 10 years of operation

    International Nuclear Information System (INIS)

    Turconi, G.

    1986-01-01

    The purpose of this paper is to show the Italtel Reliability Data Bank experience in electronics after ten years from data bank creation. Technological evolution on systems and equipment have originated a reliability data bank evolution in order to maintain and improve its performances. This paper will describe the concepts employed to design the today data bank features enabling it to be an important Company tool for reliability activities. (orig.)

  18. Results from the S-DALINAC: one year of operational experience from a superconducting electron accelerator

    International Nuclear Information System (INIS)

    Graef, H.D.; Horn, J.; Hummel, K.D.; Luettge, C.; Richter, A.; Riedorf, T.; Ruehl, K.; Schardt, P.; Spamer, E.; Stiller, A.; Thomas, F.; Titze, O.; Toepper, J.; Weise, H.; Winkler, T.

    1992-01-01

    Since August 1991 the superconducting cw-electron accelerator S-DALINAC at Darmstadt has produced single and multi pass beam which is used for different experiments. At energies below 10 MeV investigations of channeling radiation production and nuclear resonance fluorescence experiments are performed. Single pass operation yielding beam energies up to 40 MeV has been used for tests of the Free Electron Laser (FEL) beamline and for the investigation of spontaneous emission from the undulator. Two and three pass operation at higher energies produces beam for electron scattering experiments,(e,e') and (e,e'x), as well as for the production of channeling radiation. True cw operation allows for energies up to 84 MeV limited by the capacity of the He refrigerator. At higher energies the duty factor has to be reduced and pulse length is on the order of seconds. The successful operation of the entire accelerator was the result of several developments: six accelerating cavities fabricated from RRR = 280 niobium raised the average field gradient to 6 MV/m; the control systems for gun, rf, cavity tuners, and the beam transport system including beam diagnostics have been integrated into a reliable remote control of the S-DALINAC; and computer controlled path length adjustments for the two recirculating beamlines were installed for optimization of the reinjection phase. (Author) fig., tab., 10 refs

  19. FWCD (fast wave current drive) and ECCD (electron cyclotron current drive) experiments on DIII-D

    International Nuclear Information System (INIS)

    Prater, R.; Austin, M.; Baity, F.W.

    1994-01-01

    Fast wave current drive and electron cyclotron current drive experiments have been performed on the DIII-D tokamak as part of the advanced tokamak program. The goal of this program is to develop techniques for controlling the profile of the current density in order to access regimes of improved confinement and stability. The experiments on fast wave current drive used a four strap antenna with 90deg phasing between straps. A decoupler was used to help maintain the phasing, and feedback control of the plasma position was used to keep the resistive loading constant. RF pickup loops demonstrate that the directivity of the antenna is as expected. Plasma currents up to 0.18 MA were driven by 1.5 MW of fast wave power. Electron cyclotron current drive experiments at 60 GHz have shown 0.1 MA of plasma current driven by 1 MW of power. New fast wave and electron cyclotron heating systems are in development for DIII-D, so that the goals of the advanced tokamak program can be carried out. (author)

  20. FELIX: A proposal for a free electron laser experiment at Daresbury

    International Nuclear Information System (INIS)

    Thompson, D.J.

    1980-01-01

    Although the Stanford Group has clearly demonstrated the feasibility of the free electron laser (of the type working in the low current density regime), and a great deal of theoretical work has been done before and since that time, there is still very little experimental data on such devices and very little practical experience. One of the reasons for this is the cost of suitable electron beam sources. At Daresbury the NINA injector linac is in store and could be recommissioned at much less than the cost of a new machine. It is believed that there is a scientific case for infra-red sources of the FEL type, because of their high power and tunability and that they would complement a synchrotron radiation source which provides intense VUV and X-ray beams. FELIX is a free electron laser experiment using the NINA linac with an output tunable over the range 57-150 μm, proposed as a project to produce experimental data on FEL characteristics and provide practical experience which could lead to a new generation of infra-red sources. The paper will describe a design study which has been carried out and is presently under consideration by the Science Research Council. (orig.)

  1. Status of the proton and electron transfer lines for the AWAKE Experiment at CERN

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, J.S., E-mail: janet.schmidt@cern.ch [CERN, Geneva (Switzerland); Bauche, J. [CERN, Geneva (Switzerland); Biskup, B. [CERN, Geneva (Switzerland); Czech Technical University, Prague (Czech Republic); Bracco, C.; Doebert, S.; Goddard, B.; Gschwendtner, E.; Jensen, L.K.; Jones, O.R.; Mazzoni, S.; Meddahi, M.; Pepitone, K.; Petrenko, A.; Velotti, F.M.; Vorozhtsov, A. [CERN, Geneva (Switzerland)

    2016-09-01

    The AWAKE project at CERN is planned to study proton driven plasma wakefield acceleration with an externally injected electron beam. Therefore two transfer lines are being designed in order to provide the proton beam from the SPS and the electron beam from an RF gun to the plasma cell. The commissioning of the proton line will take place in 2016 for the first phase of the experiment, which is focused on the self-modulation of a 12 cm long proton bunch in the plasma. The electron line will be added for the second phase of AWAKE in 2017, when the wakefield will be probed with an electron beam of 10–20 MeV/c. The challenge for these transfer lines lies in the parallel operation of the proton, electron and laser beam used to ionize the plasma and seed the self-modulation. These beams, of different characteristics, need to be synchronized and positioned for optimized injection conditions into the wakefield. This task requires great flexibility in the transfer line optics. The status of these designs will be presented in this paper.

  2. Fast response of electron-scale turbulence to auxiliary heating cessation in National Spherical Torus Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Y.; Wang, W. X.; LeBlanc, B. P.; Guttenfelder, W.; Kaye, S. M.; Ethier, S.; Mazzucato, E.; Bell, R. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States); Lee, K. C. [National Fusion Research Institute, Daejeon 305-806 (Korea, Republic of); Domier, C. W. [University of California at Davis, Davis, California 95616 (United States); Smith, D. R. [University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Yuh, H. [Nova Photonics, Inc., Princeton, New Jersey 08540 (United States)

    2015-11-15

    In this letter, we report the first observation of the fast response of electron-scale turbulence to auxiliary heating cessation in National Spherical Torus eXperiment [Ono et al., Nucl. Fusion 40, 557 (2000)]. The observation was made in a set of RF-heated L-mode plasmas with toroidal magnetic field of 0.55 T and plasma current of 300 kA. It is observed that electron-scale turbulence spectral power (measured with a high-k collective microwave scattering system) decreases significantly following fast cessation of RF heating that occurs in less than 200 μs. The large drop in the turbulence spectral power has a short time delay of about 1–2 ms relative to the RF cessation and happens on a time scale of 0.5–1 ms, much smaller than the energy confinement time of about 10 ms. Power balance analysis shows a factor of about 2 decrease in electron thermal diffusivity after the sudden drop of turbulence spectral power. Measured small changes in equilibrium profiles across the RF cessation are unlikely able to explain this sudden reduction in the measured turbulence and decrease in electron thermal transport, supported by local linear stability analysis and both local and global nonlinear gyrokinetic simulations. The observations imply that nonlocal flux-driven mechanism may be important for the observed turbulence and electron thermal transport.

  3. Electron beam effects on the spectroscopy of satellite lines in aluminum X-pinch experiments

    International Nuclear Information System (INIS)

    Abdallah, J. Jr.; Csanak, G.; Clark, R.E.H.; Faenov, A.Ya.; Hammer, D.A.; Pikuz, S.A.; Romanova, P.N.; Shelkovenko, T.A.

    1996-01-01

    Aluminum wire X-pinch experiments performed at the Cornell University XP pulsed power generator and at the Lebedev Institute BIN generator show detailed high resolution spectra for satellite lines of Li-like, Be-like, B-like, and C-like ions. These lines, which correspond to transitions originating from autoionizing levels, are observed in the direction of the anode with respect to the bright X-pinch cross point. The intensities of these satellites are much smaller or absent in the direction of the cathode. Such transitions are caused by collisions of ions with energetic electrons (5-15 keV) which are created by the inductive voltage drop between the cross point and the anode. A collisional-radiative model was constructed using a non-Maxwellian electron energy distribution consisting of a thermal Maxwellian part plus a Gaussian part to represent the high energy electron beam. The shapes of the observed satellite structures are consistent with the calculated spectrum for electron temperatures between 30-100 eV, and beam densities of about 10 -7 times the plasma electron density. (author). 3 figs., 7 refs

  4. Electron beam effects on the spectroscopy of satellite lines in aluminum X-pinch experiments

    Energy Technology Data Exchange (ETDEWEB)

    Abdallah, J Jr; Csanak, G; Clark, R E.H. [Los Alamos National Laboratory, NM (United States); Faenov, A Ya [VNIIFTRI, Mendeleevo (Russian Federation); Hammer, D A [Cornell Univ., Ithaca, NY (United States); Pikuz, S A; Romanova, P N; Shelkovenko, T A [P.N. Lebedev Physical Inst., Moscow (Russian Federation)

    1997-12-31

    Aluminum wire X-pinch experiments performed at the Cornell University XP pulsed power generator and at the Lebedev Institute BIN generator show detailed high resolution spectra for satellite lines of Li-like, Be-like, B-like, and C-like ions. These lines, which correspond to transitions originating from autoionizing levels, are observed in the direction of the anode with respect to the bright X-pinch cross point. The intensities of these satellites are much smaller or absent in the direction of the cathode. Such transitions are caused by collisions of ions with energetic electrons (5-15 keV) which are created by the inductive voltage drop between the cross point and the anode. A collisional-radiative model was constructed using a non-Maxwellian electron energy distribution consisting of a thermal Maxwellian part plus a Gaussian part to represent the high energy electron beam. The shapes of the observed satellite structures are consistent with the calculated spectrum for electron temperatures between 30-100 eV, and beam densities of about 10{sup -7} times the plasma electron density. (author). 3 figs., 7 refs.

  5. High-energy electron experiments (HEP) aboard the ERG (Arase) satellite

    Science.gov (United States)

    Mitani, Takefumi; Takashima, Takeshi; Kasahara, Satoshi; Miyake, Wataru; Hirahara, Masafumi

    2018-05-01

    This paper reports the design, calibration, and operation of high-energy electron experiments (HEP) aboard the exploration of energization and radiation in geospace (ERG) satellite. HEP detects 70 keV-2 MeV electrons and generates a three-dimensional velocity distribution for these electrons in every period of the satellite's rotation. Electrons are detected by two instruments, namely HEP-L and HEP-H, which differ in their geometric factor (G-factor) and range of energies they detect. HEP-L detects 70 keV-1 MeV electrons and its G-factor is 9.3 × 10-4 cm2 sr at maximum, while HEP-H observes 0.7-2 MeV electrons and its G-factor is 9.3 × 10-3 cm2 sr at maximum. The instruments utilize silicon strip detectors and application-specific integrated circuits to readout the incident charge signal from each strip. Before the launch, we calibrated the detectors by measuring the energy spectra of all strips using γ-ray sources. To evaluate the overall performance of the HEP instruments, we measured the energy spectra and angular responses with electron beams. After HEP was first put into operation, on February 2, 2017, it was demonstrated that the instruments performed normally. HEP began its exploratory observations with regard to energization and radiation in geospace in late March 2017. The initial results of the in-orbit observations are introduced briefly in this paper.[Figure not available: see fulltext.

  6. Measurements of fast electron beams and soft X-ray emission from plasma-focus experiments

    Directory of Open Access Journals (Sweden)

    Surała Władysław

    2016-06-01

    Full Text Available The paper reports results of the recent experimental studies of pulsed electron beams and soft X-rays in plasma-focus (PF experiments carried out within a modified PF-360U facility at the NCBJ, Poland. Particular attention was focused on time-resolved measurements of the fast electron beams by means of two different magnetic analyzers, which could record electrons of energy ranging from about 41 keV to about 715 keV in several (6 or 8 measuring channels. For discharges performed with the pure deuterium filling, many strong electron signals were recorded in all the measuring channels. Those signals were well correlated with the first hard X-ray pulse detected by an external scintillation neutron-counter. In some of the analyzer channels, electron spikes (lasting about dozens of nanoseconds and appearing in different instants after the current peculiarity (so-called current dip were also recorded. For several discharges, fast ion beams, which were emitted along the z-axis and recorded with nuclear track detectors, were also investigated. Those measurements confirmed a multibeam character of the ion emission. The time-integrated soft X-ray images, which were taken side-on by means of a pinhole camera and sensitive X-ray films, showed the appearance of some filamentary structures and so-called hot spots. The application of small amounts of admixtures of different heavy noble gases, i.e. of argon (4.8% volumetric, krypton (1.6% volumetric, or xenon (0.8% volumetric, decreased intensity of the recorded electron beams, but increased intensity of the soft X-ray emission and showed more distinct and numerous hot spots. The recorded electron spikes have been explained as signals produced by quasi-mono-energetic microbeams emitted from tiny sources (probably plasma diodes, which can be formed near the observed hot spots.

  7. Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

    DEFF Research Database (Denmark)

    Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun

    2006-01-01

    BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have...

  8. BASE - 2nd generation software for microarray data management and analysis

    Directory of Open Access Journals (Sweden)

    Nordborg Nicklas

    2009-10-01

    Full Text Available Abstract Background Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. Results The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE. Conclusion BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.

  9. BASE--2nd generation software for microarray data management and analysis.

    Science.gov (United States)

    Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari

    2009-10-12

    Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2. The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE. BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.

  10. The Electronic Logbook for the Information Storage of ATLAS Experiment at LHC (ELisA)

    CERN Document Server

    Corso-Radu, A; The ATLAS collaboration; Magnoni, L

    2012-01-01

    A large experiment like ATLAS at LHC (CERN), with over three thousand members and a shift crew of 15 people running the experiment 24/7, needs an easy and reliable tool to gather all the information concerning the experiment development, installation, deployment and exploitation over its lifetime. With the increasing number of users and the accumulation of stored information since the experiment start-up, the electronic logbook actually in use, ATLOG, started to show its limitations in terms of speed and usability. Its monolithic architecture makes the maintenance and implementation of new functionality a hard-to-almost-impossible process. A new tool ELisA has been developed to replace the existing ATLOG. It is based on modern web technologies: the Spring framework using a Model-View-Controller architecture was chosen, thus helping building flexible and easy to maintain applications. The new tool implements all features of the old electronic logbook with increased performance and better graphics: it uses the ...

  11. The Electronic Logbook for the Information Storage of ATLAS Experiment at LHC (ELisA)

    International Nuclear Information System (INIS)

    Corso Radu, A; Lehmann Miotto, G; Magnoni, L

    2012-01-01

    A large experiment like ATLAS at LHC (CERN), with over three thousand members and a shift crew of 15 people running the experiment 24/7, needs an easy and reliable tool to gather all the information concerning the experiment development, installation, deployment and exploitation over its lifetime. With the increasing number of users and the accumulation of stored information since the experiment start-up, the electronic logbook actually in use, ATLOG, started to show its limitations in terms of speed and usability. Its monolithic architecture makes the maintenance and implementation of new functionality a hard-to-almost-impossible process. A new tool ELisA has been developed to replace the existing ATLOG. It is based on modern web technologies: the Spring framework using a Model-View-Controller architecture was chosen, thus helping building flexible and easy to maintain applications. The new tool implements all features of the old electronic logbook with increased performance and better graphics: it uses the same database back-end for portability reasons. In addition, several new requirements have been accommodated which could not be implemented in ATLOG. This paper describes the architecture, implementation and performance of ELisA, with particular emphasis on the choices that allowed having a scalable and very fast system and on the aspects that could be re-used in different contexts to build a similar application.

  12. Hot-electron plasma formation and confinement in the tandem mirror experiment-upgrade

    International Nuclear Information System (INIS)

    Ress, D.B.

    1988-06-01

    The tandem mirror experiment-upgrade (TMX-U) at the Lawrence Livermore National Laboratory (LLNL) is the first experiment to investigate the thermal-barrier tandem-mirror concept. One attractive feature of the tandem magnetic mirror as a commercial power reactor is that the fusion reactions occur in an easily accessible center-cell. On the other hand, complicated end-cells are necessary to provide magnetohydrodynamic (MHD) stability and improved particle confinement of the center-cell plasma. In these end-cells, enhanced confinement is achieved with a particular axial potential profile that is formed with electron-cyclotron range-of-frequency heating (ECRF heating, ECRH). By modifying the loss rates of electrons at spatially distinct locations within the end-cells, the ECRH can tailor the plasma potential profile in the desired fashion. Specifically, the thermal-barrier concept requires generation of a population of energetic electrons near the midplane of each end-cell. To be effective, the transverse (to the magnetic field) spatial structure of the hot-electron plasma must be fairly uniform. In this dissertation we characterize the spatial structure of the ECRH-generated plasma, and determine how the structure builds up in time. Furthermore, the plasma should efficiently absorb the ECRF power, and a large fraction of the electrons must be well confined near the end-cell midplane. Therefore, we also examine in detail the ECRH power balance, determining how the ECRF power is absorbed by the plasma, and the processes through which that power is confined and lost. 43 refs., 69 figs., 6 tabs

  13. Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

    Science.gov (United States)

    Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

    2016-09-19

    Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

  14. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  15. ICRF power deposition profile and determination of the electron thermal diffusivity by modulation experiments in JET

    International Nuclear Information System (INIS)

    Gambier, D.J.; Evrard, M.P.; Adam, J.

    1990-01-01

    The power deposition profile in the ion cyclotron range of frequencies (ICRF) has been investigated experimentally in JET by means of a square wave modulated RF perturbation. The study has been conducted in D(H) and D( 3 He) plasmas for two heating scenarios. In D( 3 He) plasmas and for central heating in a scenario where mode conversion to Bernstein waves is accessible, the direct power deposition profile on electrons has been derived. It accounts for 15% of the total coupled power and extends over 25% of the minor radius. Outside the RF power deposition zone, the electron thermal diffusivity χ e inside the inversion radius surface (r i ) can be estimated through observation of the diffusive electronic transport. In discharges without monster sawteeth and for a low central temperature gradient (∇T e (r ≤ r i ) ≤ ∇T e (r ≥ r i ) approx. = 5 keV·m -1 ) the value obtained is small (approx. =0.24 +- 0.05 m 2 · s -1 ), typically ten times lower than χ e values deduced from heat pulse propagation in similar discharges at radii larger than the inversion radius. For the D(H) minority heating scheme, a large fraction of the ICRF modulated power is absorbed by minority ions, and the minority tail is modulated with a characteristic ion-electron (i-e) slowing-down time. In this scheme, electron heating occurs only through collisions with the minority ion tail and no modulation of the electron temperature is observed in sawtoothing discharges. This is interpreted as a consequence of the long i-e equipartition time, acting as an integrator for the modulated ICRF signal. Finally, a correlation between the time of the sawtooth crash and the periodic turn-off of the ICRF power is found and its consequence for modulation experiments is reviewed. (author). 22 refs, 16 figs

  16. A Java-based tool for the design of classification microarrays

    Directory of Open Access Journals (Sweden)

    Broschat Shira L

    2008-08-01

    Full Text Available Abstract Background Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. Results The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. Conclusion In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays–and mixed-plasmid microarrays in particular–it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm, several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text, and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff. Weights

  17. Wave excitation in electron beam experiment on Japanese satellite JIKIKEN (EXOS-B)

    International Nuclear Information System (INIS)

    Kawashima, N.

    1982-01-01

    This chapter reports on a beam-plasma interaction experiment conducted in the magnetosphere by emitting an electron beam (100-200 eV, 0.25-1.0 mA) from the JIKIKEN satellite. Topics considered include instrumentation, wave excitation, and the charging of the satellite. Various types of wave emission are detected by low frequency and high frequency wave detectors. Waves near upper-hybrid frequency and at electron cyclotron frequency are detected in a low L-value region, which will be useful diagnostic means for plasma density and magnetic field. Vehicle charging up to the beam energy is observed outside the plasmapause. The main objectives of the Controlled Beam Experiment (CBE) are to control the satellite potential by an electron beam emission, and to study the wave excitation (linear and non-linear wave phenomena due to the beam-plasma interaction). It is concluded that waves excited in the beamplasma interaction are strongly dependent on plasma and other parameters in the magnetosphere so that it will provide important knowledge of the magnetosphere plasma processes

  18. Physics design of a 28 GHz electron heating system for the National Spherical Torus experiment upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, G.; Bertelli, N.; Ellis, R. A.; Gerhardt, S. P.; Hosea, J. C.; Poli, F. [Princeton Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Harvey, R. W. [CompX, Del Mar, California 92014 (United States); Raman, R. [University of Washington, Seattle, Washington 98195 (United States); Smirnov, A. P. [M.V. Lomonosov Moscow State University, Moscow (Russian Federation)

    2014-02-12

    A megawatt-level, 28 GHz electron heating system is being designed to support non-inductive (NI) plasma current (I{sub p}) start-up and local heating and current drive (CD) in H-mode discharges in the National Spherical Torus Experiment Upgrade (NSTX-U). The development of fully NI I{sub p} start-up and ramp-up is an important goal of the NSTXU research program. 28 GHz electron cyclotron (EC) heating is predicted to rapidly increase the central electron temperature (T{sub e}(0)) of low density NI plasmas generated by Coaxial Helicity Injection (CHI). The increased T{sub e}(0) will significantly reduce the I{sub p} decay rate of CHI plasmas, allowing the coupling of fast wave heating and neutral beam injection. Also 28 GHz electron Bernstein wave (EBW) heating and CD can be used during the I{sub p} flat top in NSTX-U discharges when the plasma is overdense. Ray tracing and Fokker-Planck numerical simulation codes have been used to model EC and EBW heating and CD in NSTX-U. This paper presents a pre-conceptual design for the 28 GHz heating system and some of the results from the numerical simulations.

  19. Comparisons between MCNP, EGS4 and experiment for clinical electron beams.

    Science.gov (United States)

    Jeraj, R; Keall, P J; Ostwald, P M

    1999-03-01

    Understanding the limitations of Monte Carlo codes is essential in order to avoid systematic errors in simulations, and to suggest further improvement of the codes. MCNP and EGS4, Monte Carlo codes commonly used in medical physics, were compared and evaluated against electron depth dose data and experimental backscatter results obtained using clinical radiotherapy beams. Different physical models and algorithms used in the codes give significantly different depth dose curves and electron backscattering factors. The default version of MCNP calculates electron depth dose curves which are too penetrating. The MCNP results agree better with experiment if the ITS-style energy-indexing algorithm is used. EGS4 underpredicts electron backscattering for high-Z materials. The results slightly improve if optimal PRESTA-I parameters are used. MCNP simulates backscattering well even for high-Z materials. To conclude the comparison, a timing study was performed. EGS4 is generally faster than MCNP and use of a large number of scoring voxels dramatically slows down the MCNP calculation. However, use of a large number of geometry voxels in MCNP only slightly affects the speed of the calculation.

  20. Comparisons between MCNP, EGS4 and experiment for clinical electron beams

    International Nuclear Information System (INIS)

    Jeraj, R.; Keall, P.J.; Ostwald, P.M.

    1999-01-01

    Understanding the limitations of Monte Carlo codes is essential in order to avoid systematic errors in simulations, and to suggest further improvement of the codes. MCNP and EGS4, Monte Carlo codes commonly used in medical physics, were compared and evaluated against electron depth dose data and experimental backscatter results obtained using clinical radiotherapy beams. Different physical models and algorithms used in the codes give significantly different depth dose curves and electron backscattering factors. The default version of MCNP calculates electron depth dose curves which are too penetrating. The MCNP results agree better with experiment if the ITS-style energy-indexing algorithm is used. EGS4 underpredicts electron backscattering for high- Z materials. The results slightly improve if optimal PRESTA-I parameters are used. MCNP simulates backscattering well even for high- Z materials. To conclude the comparison, a timing study was performed. EGS4 is generally faster than MCNP and use of a large number of scoring voxels dramatically slows down the MCNP calculation. However, use of a large number of geometry voxels in MCNP only slightly affects the speed of the calculation. (author)

  1. Major results of the electron cyclotron heating experiment in the PDX tokamak

    International Nuclear Information System (INIS)

    Hsuan, H.; Bol, K.; Bowen, N.

    1984-07-01

    Electron Cyclotron Heating (ECH) experiments on PDX have been carried out with two 60 GHz pulsed gyrotrons each yielding up to approximately 100 kW. The ECH system used two waveguide runs each about 30 meters long. One run included 5 bends and the other, 7 bends. Predetermined waveguide modes were transmitted. The electron cyclotron waves were launched in narrow beams from both the high field and the low field sides of the plasma torus. The major new physics results are: (1) efficient central electron heating for both ohmic and neutral beam heated target plasmas; (2) alteration of MHD behavior using ECH; (3) identification of the trapped electron population with ECH; and (4) signature of velocity-space time evolution during ECH. In the best heating results obtained, Thomson scattering data indicated a central temperature increase from less than or equal to 1.5 keV to greater than or equal to 2.5 keV. This occurred with an average density of about 10 13 cm -3 and approximately 80 kW outside-launch ordinary-mode heating

  2. The PowerAtlas: a power and sample size atlas for microarray experimental design and research

    Directory of Open Access Journals (Sweden)

    Wang Jelai

    2006-02-01

    Full Text Available Abstract Background Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies. Results To address this challenge, we have developed a Microrarray PowerAtlas 1. The atlas enables estimation of statistical power by allowing investigators to appropriately plan studies by building upon previous studies that have similar experimental characteristics. Currently, there are sample sizes and power estimates based on 632 experiments from Gene Expression Omnibus (GEO. The PowerAtlas also permits investigators to upload their own pilot data and derive power and sample size estimates from these data. This resource will be updated regularly with new datasets from GEO and other databases such as The Nottingham Arabidopsis Stock Center (NASC. Conclusion This resource provides a valuable tool for investigators who are planning efficient microarray studies and estimating required sample sizes.

  3. Extraction of High Charge Electron Bunch from the ELSA RF Injector Comparison Between Simulation and Experiment

    CERN Document Server

    Lemaire, J; Binet, A; Lagniel, J M; Le Flanchec, V; Pichoff, N

    2004-01-01

    A new scheme based on a photoinjector and a RF linear accelerator operating at 352 MHz has been recently proposed as a versatile radiographic facility. Beam pulses of 60 ns duration contain 20 succesive electron bunches which will be extracted at 2.5 MeV from a photoinjector then accelerated through the next structure to the final energy of 51 MeV. Bunches carrying 100 nC are required for this purpose. As a first demonstrating step, 50 nC electron bunches have been produced and accelerated to 2.5 MeV with the 144 MHz ELSA photoinjector at Bruyères le Chatel. For this experiment, we compare the results and the numerical simulations made with PARMELA, MAGIC and MAFIA codes.

  4. Measurements of electron density and temperature profiles in a gas blanket experiment

    International Nuclear Information System (INIS)

    Kuthy, A.

    1979-02-01

    Radial profiles of electron density, temperature and H sub(β) intensity are presented for the rotating plasma device F-1. The hydrogen filling pressure, the average magnetic field strength at the midplane, and the power input to the discharge have been varied in the ranges 10-100 mTorr, 0.25-0.5 Tesla, and 0.1 to 1.5 MW, respectively. These experiments have been performed with the main purpose of studying the gas blanket (cold-mantle) state of the plasma. It is shown, that a simple spectroscopic method can be used to derive the radial distribution of the electron temperature in such plasmas. The observed peak temperatures and densities are in agreement with earlier theoretical estimates. (author)

  5. Trigger electronics of the new Fluorescence Detectors of the Telescope Array Experiment

    International Nuclear Information System (INIS)

    Tameda, Yuichiro; Taketa, Akimichi; Smith, Jeremy D.; Tanaka, Manobu; Fukushima, Masaki; Jui, Charles C.H.; Kadota, Ken'ichi; Kakimoto, Fumio; Matsuda, Takeshi; Matthews, John N.; Ogio, Shoichi; Sagawa, Hiroyuki; Sakurai, Nobuyuki; Shibata, Tatsunobu; Takeda, Masahiro; Thomas, Stanton B.; Tokuno, Hisao; Tsunesada, Yoshiki

    2009-01-01

    The Telescope Array Project is an experiment designed to observe Ultra High Energy Cosmic Rays via a 'hybrid' detection technique utilizing both fluorescence light detectors (FDs) and scintillator surface particle detectors (SDs). We have installed three FD stations and 507 SDs in the Utah desert, and initiated observations from March 2008. The northern FD station reuses 14 telescopes from the High Resolution Fly's Eye, HiRes-I station. Each of the two southern FD stations contains 12 new telescopes utilizing new FADC electronics. Each telescope is instrumented with a camera composed of 256 PMTs. Since the detectors are composed of many PMTs and each PMT detects fluorescence photons together with the vast amount of night sky background, a sophisticated triggering system is required. In this paper, we describe the trigger electronics of these new FD stations. We also discuss performance of the FDs with this triggering system, in terms of efficiencies and apertures for various detector configurations.

  6. The SAMPLE experiment: Parity-violating electron scattering from the proton and deuteron

    International Nuclear Information System (INIS)

    Pitt, M.; Arrington, J.; Beck, D.; Beise, E.; Candell, E.; Cardman, L.; Carr, R.; Dodson, G.; Dow, K.; Duncan, F.; Farkhondeh, M.; Filippone, B.; Forest, T.; Gao, H.; Korsch, W.; Kowalski, S.; Lung, A.; McKeown, R.; Mohring, R.; Mueller, B.; Napolitano, J.; Simicevic, N.; Terburg, B.; Witkowski, M.

    1995-01-01

    Recent experimental evidence on nucleon structure has provided indications that some strange quark matrix elements can be comparable to those involving up and down quarks. The SAMPLE experiment will determine the strange magnetic form factor G s M at Q 2 =0.1 (GeV/c) 2 from a measurement of the asymmetry in the scattering of polarized electrons from the proton. The error on the extraction of G s M is ultimately limited by a theoretical uncertainty---the uncertain electroweak hadronic radiative correction to the axial form factor, R T=1 A . To address this issue, the collaboration is also approved to measure the asymmetry in parity-violating quasielastic electron scattering from the deuteron. The combination of the proton and deuteron measurements will yield a value of G s M that is almost completely free of the uncertainty in R T=1 A

  7. Subharmonic buncher for the Los Alamos free-electron laser oscillator experiment

    International Nuclear Information System (INIS)

    Fraser, J.S.

    1983-01-01

    A high efficiency free-electron laser oscillator experiment is being constructed at Los Alamos National Laboratory. A buncher system has been designed to deliver 30-ps, 5-nC electron bunches to a 20-MeV standing-wave linac at the 60th subharmonic of the 1300-MHz accelerator frequency. The first 108.3-MHz buncher cavity accepts a 5-ns, 5-A peak current pulse from a triode gun. Following a 120-cm drift space, a second 108.3-MHz cavity is used, primarily to enhance the bunching of the trailing half of the bunch. A 1300-MHz cavity with 20-cm drift spaces at the each end completes the beamline components. The bunching process continues into the linac's first three accelerating cells. Two thin iron-shielded lenses and several large-diameter solenoids provide axial magnetic fields for radial focusing

  8. An extreme ultraviolet Michelson interferometer for experiments at free-electron lasers

    International Nuclear Information System (INIS)

    Hilbert, Vinzenz; Fuchs, Silvio; Paulus, Gerhard G.; Zastrau, Ulf; Blinne, Alexander; Feigl, Torsten; Kämpfer, Tino; Rödel, Christian; Uschmann, Ingo; Wünsche, Martin; Förster, Eckhart

    2013-01-01

    We present a Michelson interferometer for 13.5 nm soft x-ray radiation. It is characterized in a proof-of-principle experiment using synchrotron radiation, where the temporal coherence is measured to be 13 fs. The curvature of the thin-film beam splitter membrane is derived from the observed fringe pattern. The applicability of this Michelson interferometer at intense free-electron lasers is investigated, particularly with respect to radiation damage. This study highlights the potential role of such Michelson interferometers in solid density plasma investigations using, for instance, extreme soft x-ray free-electron lasers. A setup using the Michelson interferometer for pseudo-Nomarski-interferometry is proposed

  9. An extreme ultraviolet Michelson interferometer for experiments at free-electron lasers.

    Science.gov (United States)

    Hilbert, Vinzenz; Blinne, Alexander; Fuchs, Silvio; Feigl, Torsten; Kämpfer, Tino; Rödel, Christian; Uschmann, Ingo; Wünsche, Martin; Paulus, Gerhard G; Förster, Eckhart; Zastrau, Ulf

    2013-09-01

    We present a Michelson interferometer for 13.5 nm soft x-ray radiation. It is characterized in a proof-of-principle experiment using synchrotron radiation, where the temporal coherence is measured to be 13 fs. The curvature of the thin-film beam splitter membrane is derived from the observed fringe pattern. The applicability of this Michelson interferometer at intense free-electron lasers is investigated, particularly with respect to radiation damage. This study highlights the potential role of such Michelson interferometers in solid density plasma investigations using, for instance, extreme soft x-ray free-electron lasers. A setup using the Michelson interferometer for pseudo-Nomarski-interferometry is proposed.

  10. Experiments on continuum electron capture in atomic hydrogen and collisional interaction of trapped ions. Progress report

    International Nuclear Information System (INIS)

    Sellin, I.A.; Elston, S.B.

    1981-01-01

    This section describes the background and scope of as well as progress made on experiments designed to test the present theory of charge exchange to continuum for the case of bare nuclei on atomic hydrogen. The charge transfer process is well known to be an essential ingredient of any attempt to understand the ionization of gaseous media traversed by highly-charged energetic ions. Surprisingly, a sometimes dominant contribution to such ionization remained undiscovered until the past decade. This process, known as charge transfer to the continuum, involves the ionization of electrons from the target species into unbound states closely matched in exit direction and speed to the charged particles which generate them. Subsequent measurements of the resultant forward electron production, performed by University of Tennessee searchers at Oak Ridge and Brookhaven National Laboratories, were unique in employing more highly charged projectiles than previously

  11. Dielectrophoretic Manipulation and Separation of Microparticles Using Microarray Dot Electrodes

    Directory of Open Access Journals (Sweden)

    Bashar Yafouz

    2014-04-01

    Full Text Available This paper introduces a dielectrophoretic system for the manipulation and separation of microparticles. The system is composed of five layers and utilizes microarray dot electrodes. We validated our system by conducting size-dependent manipulation and separation experiments on 1, 5 and 15 μm polystyrene particles. Our findings confirm the capability of the proposed device to rapidly and efficiently manipulate and separate microparticles of various dimensions, utilizing positive and negative dielectrophoresis (DEP effects. Larger size particles were repelled and concentrated in the center of the dot by negative DEP, while the smaller sizes were attracted and collected by the edge of the dot by positive DEP.

  12. High throughput production of mouse monoclonal antibodies using antigen microarrays

    DEFF Research Database (Denmark)

    De Masi, Federico; Chiarella, P.; Wilhelm, H.

    2005-01-01

    Recent advances in proteomics research underscore the increasing need for high-affinity monoclonal antibodies, which are still generated with lengthy, low-throughput antibody production techniques. Here we present a semi-automated, high-throughput method of hybridoma generation and identification....... Monoclonal antibodies were raised to different targets in single batch runs of 6-10 wk using multiplexed immunisations, automated fusion and cell-culture, and a novel antigen-coated microarray-screening assay. In a large-scale experiment, where eight mice were immunized with ten antigens each, we generated...

  13. Discovering biological progression underlying microarray samples.

    Directory of Open Access Journals (Sweden)

    Peng Qiu

    2011-04-01

    Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

  14. Integrated Numerical Experiments (INEX) and the Free-Electron Laser Physical Process Code (FELPPC)

    International Nuclear Information System (INIS)

    Thode, L.E.; Chan, K.C.D.; Schmitt, M.J.; McKee, J.; Ostic, J.; Elliott, C.J.; McVey, B.D.

    1990-01-01

    The strong coupling of subsystem elements, such as the accelerator, wiggler, and optics, greatly complicates the understanding and design of a free electron laser (FEL), even at the conceptual level. To address the strong coupling character of the FEL the concept of an Integrated Numerical Experiment (INEX) was proposed. Unique features of the INEX approach are consistency and numerical equivalence of experimental diagnostics. The equivalent numerical diagnostics mitigates the major problem of misinterpretation that often occurs when theoretical and experimental data are compared. The INEX approach has been applied to a large number of accelerator and FEL experiments. Overall, the agreement between INEX and the experiments is very good. Despite the success of INEX, the approach is difficult to apply to trade-off and initial design studies because of the significant manpower and computational requirements. On the other hand, INEX provides a base from which realistic accelerator, wiggler, and optics models can be developed. The Free Electron Laser Physical Process Code (FELPPC) includes models developed from INEX, provides coupling between the subsystem models, and incorporates application models relevant to a specific trade-off or design study. In other words, FELPPC solves the complete physical process model using realistic physics and technology constraints. Because FELPPC provides a detailed design, a good estimate for the FEL mass, cost, and size can be made from a piece-part count of the FEL. FELPPC requires significant accelerator and FEL expertise to operate. The code can calculate complex FEL configurations including multiple accelerator and wiggler combinations

  15. Electronics, trigger, data acquisition, and computing working group on future B physics experiments

    International Nuclear Information System (INIS)

    Geer, S.

    1993-01-01

    Electronics, trigger, data acquisition, and computing: this is a very broad list of topics. Nevertheless in a modern particle physics experiment one thinks in terms of a data pipeline in which the front end electronics, the trigger and data acquisition, and the offline reconstruction are linked together. In designing any piece of this pipeline it is necessary to understand the bigger picture of the data flow, data rates and volume, and the input rate, output rate, and latencies for each part of the pipeline. All of this needs to be developed with a clear understanding of the requirements imposed by the physics goals of the experiment; the signal efficiencies, background rates, and the amount of recorded information that needs to be propagated through the pipeline to select and analyse the events of interest. The technology needed to meet the demanding high data volume needs of the next round of B physics experiments appears to be available, now or within a couple of years. This seems to be the case for both fixed target and collider B physics experiments. Although there are many differences between the various data pipelines that are being proposed, there are also striking similarities. All experiments have a multi-level trigger scheme (most have levels 1, 2, and 3) where the final level consists of a computing farm that can run offline-type code and reduce the data volume by a factor of a few. Finally, the ability to reconstruct large data volumes offline in a reasonably short time, and making large data volumes available to many physicists for analysis, imposes severe constraints on the foreseen data pipelines, and a significant uncertainty in evaluating the various approaches proposed

  16. Experiments on melting in classical and quantum two dimensional electron systems

    International Nuclear Information System (INIS)

    Williams, F.I.B.

    1991-01-01

    ''Two dimensional electron system'' (2DES) here refers to electrons whose dynamics is free in 2 dimensions but blocked in the third. Experiments have been performed in two limiting situations: the classical, low density, limit realised by electrons deposited on a liquid helium surface and the quantum, high density, limit realised by electrons at an interface between two epitaxially matched semiconductors. In the classical system, where T Q c so that the thermodynamic state is determined by the competition between the temperature and the Coulomb interaction, melting is induced either by raising the temperature at constant density or by lowering the density at finite temperature. In the quantum system, it is not possible to lower the density below about 100n W without the Coulomb interaction losing out to the random field representing the extrinsic disorder imposed by the semiconductor host. Instead one has to induce crystallisation with the help of the Lorentz force, by applying a perpendicular magnetic field B [2] . As the quantum magnetic length l c = (Planck constant c/eB) 1/2 is reduced with respect to the interelectronic spacing a, expressed by the filling factor ν 2l c 2 /a 2 , the system exhibits the quantum Hall effect (QHE), first for integer then for fractional values of ν. The fractional quantum Hall effect (FQHE) is a result of Coulomb induced correlation in the quantum liquid, but as ν is decreased still further the correlations are expected to take on long-range crystal-like periodicity accompanied by elastic shear rigidity. Such a state can nonetheless be destroyed by the disordering effect of temperature, giving rise to a phase boundary in a (T, B) plane. The aim of experiment is first to determine the phase diagram and then to help elucidate the mechanism of the melting. (author)

  17. Investigation of Electron Density Profile in the ionospheric D and E region by Kagoshima rocket experiment

    Science.gov (United States)

    Ashihara, Y.; Ishisaka, K.; Miyake, T.; Okada, T.; Nagano, I.; Abe, T.; Ono, T.

    2007-12-01

    The radio wave propagation characteristic in the lower ionosphere is important because of its effect on commercial radio communication, navigation, and broadcast services. The electron density is of primary interest in this region because the high ion-neutral collision frequencies result in radio wave absorption. In order to investigate the ionization structure in the ionospheric D and E region by using the propagation characteristics of MF-band and LF-band radio waves, S-310-37 and S-520-23 sounding rocket experiments have been carried out at Uchinoura Space Center (USC). S-310-37 sounding rocket was launched at 11:20 LT on January 16, 2007. The apex of rocket trajectory was about 138 km. Then S-520-23 sounding rocket was launched at 19:20 LT on September 2, 2007. The apex was about 279 km. As a common measurement, these sounding rockets measure the fields intensities and the waveform of radio waves from NHK Kumamoto broadcasting station (873kHz, 500kW) and JJY signals from Haganeyama LF radio station (60kHz, 50kW). The approximate electron density profile can be determined from the comparison between these experimental results and propagation characteristics calculated by the full wave method. We will get the most probable electron density profile in the ionosphere. In presentation, we will show the propagation characteristic of LF/MF radio waves measured by two sounding rocket experiments. Then we will discuss the analysis method and the estimated electron density profile in the ionosphere.

  18. The use of microarrays in microbial ecology

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  19. 3D Biomaterial Microarrays for Regenerative Medicine

    DEFF Research Database (Denmark)

    Gaharwar, Akhilesh K.; Arpanaei, Ayyoob; Andresen, Thomas Lars

    2015-01-01

    Three dimensional (3D) biomaterial microarrays hold enormous promise for regenerative medicine because of their ability to accelerate the design and fabrication of biomimetic materials. Such tissue-like biomaterials can provide an appropriate microenvironment for stimulating and controlling stem...... for tissue engineering and drug screening applications....... cell differentiation into tissue-specifi c lineages. The use of 3D biomaterial microarrays can, if optimized correctly, result in a more than 1000-fold reduction in biomaterials and cells consumption when engineering optimal materials combinations, which makes these miniaturized systems very attractive...

  20. Plasma heating by relativistic electron beams: correlations between experiment and theory

    International Nuclear Information System (INIS)

    Thode, L.E.; Godfrey, B.B.

    1975-01-01

    The streaming instability is the primary heating mechanism in most, if not all, experiments in which the beam is injected into partially or fully ionized gas. In plasma heating experiments, the relativistic beam must traverse an anode foil before interacting with the plasma. The linear theory for such a scattered beam is discussed, including a criterion for the onset of the kinetic interaction. A nonlinear model of the two-stream instability for a scattered beam is developed. Using this model, data from ten experiments are unfolded to obtain the following correlations: (i) for a fixed anode foil, the dependence of the plasma heating on the beam-to-plasma density ratio is due to anode foil scattering, (ii) for a fixed beam-to-plasma density ratio, the predicted change in the magnitude of plasma heating as a function of the anode foil is in agreement with experiment, and (iii) the plasma heating tentatively appears to be proportional to the beam kinetic energy density and beam pulse length. For a fixed anode foil, theory also predicts that the energy deposition is improved by increasing the beam electron energy γmc 2 . Presently, no experiment has been performed to confirm this aspect of the theory

  1. Excitation of rare gases in an electron-beam-controlled discharge: report on preliminary experiments

    International Nuclear Information System (INIS)

    Bingham, F.W.

    1976-05-01

    Data from the preliminary phase of a study of rare-gas-excimer production in an electron-beam-controlled discharge are presented. The results indicate that it is possible to maintain an arc-free discharge in preionized Ar and Xe gas for a period of several microseconds at applied external E/p values up to 5 V/cm/Torr. In these experiments ultraviolet radiation emitted during the discharge signaled the presence of excited rare-gas molecules. Application of the external electric field significantly enhanced the ultraviolet intensity from xenon-gas discharges but produced little enhancement from argon-gas discharges

  2. Conceptual design of a laser-plasma accelerator driven free-electron laser demonstration experiment

    International Nuclear Information System (INIS)

    Seggebrock, Thorben

    2015-01-01

    Up to now, short-wavelength free-electron lasers (FEL) have been systems on the scale of hundreds of meters up to multiple kilometers. Due to the advancements in laser-plasma acceleration in the recent years, these accelerators have become a promising candidate for driving a fifth-generation synchrotron light source - a lab-scale free-electron laser. So far, demonstration experiments have been hindered by the broad energy spread typical for this type of accelerator. This thesis addresses the most important challenges of the conceptual design for a first lab-scale FEL demonstration experiment using analytical considerations as well as simulations. The broad energy spread reduces the FEL performance directly by weakening the microbunching and indirectly via chromatic emittance growth, caused by the focusing system. Both issues can be mitigated by decompressing the electron bunch in a magnetic chicane, resulting in a sorting by energies. This reduces the local energy spread as well as the local chromatic emittance growth and also lowers performance degradations caused by the short bunch length. Moreover, the energy dependent focus position leads to a focus motion within the bunch, which can be synchronized with the radiation pulse, maximizing the current density in the interaction region. This concept is termed chromatic focus matching. A comparison shows the advantages of the longitudinal decompression concept compared to the alternative approach of transverse dispersion. When using typical laser-plasma based electron bunches, coherent synchrotron radiation and space-charge contribute in equal measure to the emittance growth during decompression. It is shown that a chicane for this purpose must not be as weak and long as affordable to reduce coherent synchrotron radiation, but that an intermediate length is required. Furthermore, the interplay of the individual concepts and components is assessed in a start-to-end simulation, confirming the feasibility of the

  3. Perampanel: An audit of clinical experience using the epilepsy electronic patient record.

    LENUS (Irish Health Repository)

    Ryan, E

    2016-07-01

    Perampanel is a non-competitive antagonist of AMPA glutamate receptors on post synaptic neurons. The aim of this study was to conduct an audit of the experience of perampanel treatment in Ireland based on the interrogation of the national epilepsy electronic patient record (EPR). A retrospective audit was compiled which reviewed the progress of patients who had been treated across two regional epilepsy centres. The EPR was used to identify patients and collect information relevant to their perampanel therapy. Collected data was entered into a statistical package for social sciences for analysis using descriptive statistics.\\r\

  4. Conceptual design of a laser-plasma accelerator driven free-electron laser demonstration experiment

    Energy Technology Data Exchange (ETDEWEB)

    Seggebrock, Thorben

    2015-07-08

    Up to now, short-wavelength free-electron lasers (FEL) have been systems on the scale of hundreds of meters up to multiple kilometers. Due to the advancements in laser-plasma acceleration in the recent years, these accelerators have become a promising candidate for driving a fifth-generation synchrotron light source - a lab-scale free-electron laser. So far, demonstration experiments have been hindered by the broad energy spread typical for this type of accelerator. This thesis addresses the most important challenges of the conceptual design for a first lab-scale FEL demonstration experiment using analytical considerations as well as simulations. The broad energy spread reduces the FEL performance directly by weakening the microbunching and indirectly via chromatic emittance growth, caused by the focusing system. Both issues can be mitigated by decompressing the electron bunch in a magnetic chicane, resulting in a sorting by energies. This reduces the local energy spread as well as the local chromatic emittance growth and also lowers performance degradations caused by the short bunch length. Moreover, the energy dependent focus position leads to a focus motion within the bunch, which can be synchronized with the radiation pulse, maximizing the current density in the interaction region. This concept is termed chromatic focus matching. A comparison shows the advantages of the longitudinal decompression concept compared to the alternative approach of transverse dispersion. When using typical laser-plasma based electron bunches, coherent synchrotron radiation and space-charge contribute in equal measure to the emittance growth during decompression. It is shown that a chicane for this purpose must not be as weak and long as affordable to reduce coherent synchrotron radiation, but that an intermediate length is required. Furthermore, the interplay of the individual concepts and components is assessed in a start-to-end simulation, confirming the feasibility of the

  5. Study of the thermal and suprathermal electron density fluctuations of the plasma in the Focus experiment

    International Nuclear Information System (INIS)

    Jolas, A.

    1981-10-01

    An experiment on Thomson scattering of ruby laser light by the electrons of a plasma produced by an intense discharge between the electrodes of a coaxial gun in a gas at low pressure has been carried out. It is shown that the imploding plasma is made up of layers with different characteristics: a dense plasma layer where the density fluctuations are isotropic and have a thermal level, and a tenuous plasma layer where the fluctuations are anisotropic, and strongly suprathermal. The suprathermal fluctuations are attributed to microscopic instabilities generated by the electric current circulating in the transition zone where the magnetic field penetrates the plasma [fr

  6. Valence electronic structure of the indene molecule: Experiment vs. GW calculations

    Energy Technology Data Exchange (ETDEWEB)

    Umari, P.; Stenuit, G. [CNR-IOM DEMOCRITOS Theory Elettra Group, Basovizza, Trieste (Italy); Castellarin-Cudia, C.; Feyer, V.; Di Santo, G.; Goldoni, A. [Sincrotrone Trieste S.C.p.A., Basovizza, Trieste (Italy); Borghetti, P.; Sangaletti, L. [Dipartimento di Matematica e Fisica, Universita Cattolica del Sacro Cuore, Brescia (Italy)

    2011-04-15

    We investigate the valence electronic properties in the gas phase of the indene molecule, which is one of the simplest polycyclic aromatic hydrocarbons, with photoemission spectroscopy using synchrotron light and through first-principles calculations using a many-body perturbation theory GW approach. We found an excellent agreement between theory and experiment. This allows us to assign to the peaks appearing in the photoemission spectrum the calculated molecular orbitals. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Experiments on resonator concept of plasma wakefield accelerator driven by a train of relativistic electron bunches

    International Nuclear Information System (INIS)

    Kiselev, V.A.; Linnik, A.F.; Mirny, V. I; Onishchenko, I.N.; Uskov, V.V.

    2008-01-01

    The experimental installation was elaborated to increase plasma wakefield amplitude by means of using plasma resonator that allows all bunches of the train to participate in wakefield build-up contrary to waveguide case, in which due to group velocity effect only a part of the bunches participates. Experiments on plasma producing with resonant density, at which a coincidence of the plasma frequency and bunch repetition frequency is provided, are carried out. The first results of the measurements of beam energy loss on plasma wakefield excitation and energy gain by accelerated electrons are presented

  8. Interference experiment with asymmetric double slit by using 1.2-MV field emission transmission electron microscope.

    Science.gov (United States)

    Harada, Ken; Akashi, Tetsuya; Niitsu, Kodai; Shimada, Keiko; Ono, Yoshimasa A; Shindo, Daisuke; Shinada, Hiroyuki; Mori, Shigeo

    2018-01-17

    Advanced electron microscopy technologies have made it possible to perform precise double-slit interference experiments. We used a 1.2-MV field emission electron microscope providing coherent electron waves and a direct detection camera system enabling single-electron detections at a sub-second exposure time. We developed a method to perform the interference experiment by using an asymmetric double-slit fabricated by a focused ion beam instrument and by operating the microscope under a "pre-Fraunhofer" condition, different from the Fraunhofer condition of conventional double-slit experiments. Here, pre-Fraunhofer condition means that each single-slit observation was performed under the Fraunhofer condition, while the double-slit observations were performed under the Fresnel condition. The interference experiments with each single slit and with the asymmetric double slit were carried out under two different electron dose conditions: high-dose for calculation of electron probability distribution and low-dose for each single electron distribution. Finally, we exemplified the distribution of single electrons by color-coding according to the above three types of experiments as a composite image.

  9. Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

    Science.gov (United States)

    Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

    2012-06-08

    Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

  10. Experiment study on four button electrode used to monitor position of high current electron-beam

    International Nuclear Information System (INIS)

    Xu Tiezheng; Wang Huacen; Xie Yutong; Zhang Wenwei

    2004-01-01

    The button electrode is one that widely used in high energy accelerators, such as storage ring, and the button electrode has many merit like high accuracy, high resolution, resisting magnetic field, simple machinery, without magnetic core and low cost, etc. It's helpful that the button electrode is used as the beam position monitor in the linear induction accelerator. The experimental facilities have been designed and set up and it can simulate the beam of linear induction accelerator. The button electrode beam position monitor experiment have been done on the experimental facilities. The result of the experiment prove that the button electrode has an accuracy of 0.5 mm, and can reflect the wave of electron-beam accurately

  11. First lasing of a high-gain harmonic generation free-electron laser experiment.

    Energy Technology Data Exchange (ETDEWEB)

    Babzien, M.; Ben-Zvi, I.; Biedron, S. G.; DiMauro, L. F.; Douryan, A.; Galayda, J. N.; Gluskin, E.; Graves, W.; Jagger, J.; Johnson, E.; Krinsky, S.; Malone, R.; Pogorelsky, I.; Rakowsky, G.; Sajaev, V.; Skaritka, J.; Solomon, L.; Vasserman, I.; Wang, X. L.; Woodle, M.; Yakimenko, V.; Yu, L.-H.

    1999-09-11

    We report on the first lasing of a high-gain harmonic generation (HGHG) free-electron laser (FEL). The experiment was conducted at the Accelerator Test Facility (ATF) at Brookhaven National Laboratory (BNL). This is a BNL experiment in collaboration with the Advanced Photon Source (APS) at Argonne National Laboratory. A preliminary measurement gives a high-gain harmonic generation (HGHG) pulse energy that is 2 x 10{sup 7} times larger than the spontaneous radiation, In a purely self-amplified spontaneous emission (SASE) mode of operation, the signal was measured as 10 times larger than the spontaneous radiation in the same distance ({approximately}2 m) through the same wiggler. This means the HGHG signal is 2 x 10{sup 6} times larger than the SASE signal. To obtain the same saturated output power by the SASE process, the radiator would have to be 3 times longer (6 m).

  12. Detecting Outlier Microarray Arrays by Correlation and Percentage of Outliers Spots

    Directory of Open Access Journals (Sweden)

    Song Yang

    2006-01-01

    Full Text Available We developed a quality assurance (QA tool, namely microarray outlier filter (MOF, and have applied it to our microarray datasets for the identification of problematic arrays. Our approach is based on the comparison of the arrays using the correlation coefficient and the number of outlier spots generated on each array to reveal outlier arrays. For a human universal reference (HUR dataset, which is used as a technical control in our standard hybridization procedure, 3 outlier arrays were identified out of 35 experiments. For a human blood dataset, 12 outlier arrays were identified from 185 experiments. In general, arrays from human blood samples displayed greater variation in their gene expression profiles than arrays from HUR samples. As a result, MOF identified two distinct patterns in the occurrence of outlier arrays. These results demonstrate that this methodology is a valuable QA practice to identify questionable microarray data prior to downstream analysis.

  13. Observing Muon Neutrino to Electron Neutrino Oscillations in the NOνA Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Xin, Tian [Iowa State U.

    2016-01-01

    Neutrino oscillations offers an insight on new physics beyond the Standard Model. The three mixing angles (θ12, θ13 and θ23) and the two mass splittings (Δm2 and Αm2 ) have been measured by different neutrino oscillation experiments. Some other parameters including the mass ordering of different neutrino mass eigenstates and the CP violation phase are still unknown. NOνA is a long-baseline accelerator neutrino experiment, using neutrinos from the NuMI beam at Fermilab. The experiment is equipped with two functionally identical detectors about 810 kilometers apart and 14 mrad off the beam axis. In this configuration, the muon neutrinos from the NuMI beam reach the disappearance maximum in the far detector and a small fraction of that oscillates into electron neutrinos. The sensitivity to the mass ordering and CP viola- tion phase determination is greately enhanced. This thesis presents the νeappearance analysis using the neutrino data collected with the NOνA experiment between February 2014 and May 2015, which corresponds to 3.45 ×1020 protons-on-target (POT). The νe appearance analysis is performed by comparing the observed νe CC-like events to the estimated background at the far detector. The total background is predicted to be 0.95 events with 0.89 originated from beam events and 0.06 from cosmic ray events. The beam background is obtained by extrapolating near detector data through different oscillation channels, while the cosmic ray background is calculated based on out-of-time NuMI trigger data. A total of 6 electron neutrino candidates are observed in the end at the far detector which represents 3.3 σ excess over the predicted background. The NOνA result disfavors inverted mass hierarchy for δcp ϵ [0, 0.6π] at 90% C.L.

  14. MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data

    Directory of Open Access Journals (Sweden)

    Rahman Fatimah

    2005-11-01

    Full Text Available Abstract Background The generation of large amounts of microarray data presents challenges for data collection, annotation, exchange and analysis. Although there are now widely accepted formats, minimum standards for data content and ontologies for microarray data, only a few groups are using them together to build and populate large-scale databases. Structured environments for data management are crucial for making full use of these data. Description The MiMiR database provides a comprehensive infrastructure for microarray data annotation, storage and exchange and is based on the MAGE format. MiMiR is MIAME-supportive, customised for use with data generated on the Affymetrix platform and includes a tool for data annotation using ontologies. Detailed information on the experiment, methods, reagents and signal intensity data can be captured in a systematic format. Reports screens permit the user to query the database, to view annotation on individual experiments and provide summary statistics. MiMiR has tools for automatic upload of the data from the microarray scanner and export to databases using MAGE-ML. Conclusion MiMiR facilitates microarray data management, annotation and exchange, in line with international guidelines. The database is valuable for underpinning research activities and promotes a systematic approach to data handling. Copies of MiMiR are freely available to academic groups under licence.

  15. Cryogenic systems for proof of the principle experiment of coherent electron cooling at RHIC

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuenian; Belomestnykh, Sergey; Brutus, Jean Clifford; Lederle, Dewey; Orfin, Paul; Skaritka, John; Soria, Victor; Tallerico, Thomas; Than, Roberto [Collider Accelerator Department, Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2014-01-29

    The Coherent electron Cooling (CeC) Proof of Principle (PoP) experiment is proposed to be installed in the Relativistic Heavy Ion Collider (RHIC) to demonstrate proton and ion beam cooling with this new technique that may increase the beam luminosity in certain cases, by as much as tenfold. Within the scope of this project, a 112 MHz, 2MeV Superconducting Radio Frequency (SRF) electron gun and a 704 MHz 20MeV 5-cell SRF cavity will be installed at IP2 in the RHIC ring. The superconducting RF electron gun will be cooled in a liquid helium bath at 4.4 K. The 704 MHz 5-cell SRF cavity will be cooled in a super-fluid helium bath at 2.0 K. This paper discusses the cryogenic systems designed for both cavities. For the 112 MHz cavity cryogenic system, a condenser/boiler heat exchanger is used to isolate the cavity helium bath from pressure pulses and microphonics noise sources. For the 704 MHz 5-cell SRF cavity, a heat exchanger is also used to isolate the SRF cavity helium bath from noise sources in the sub-atmospheric pumping system operating at room temperature. Detailed designs, thermal analyses and discussions for both systems will be presented in this paper.

  16. Electronically excited states of chloroethylenes: Experiment and DFT calculations in comparison

    International Nuclear Information System (INIS)

    Khvostenko, O.G.

    2014-01-01

    Highlights: • B3LYP/6-311 + G(d,p) calculations of chloroethylenes molecules were performed. • Calculations were correlated with experiment on the molecules ground and excited states. • The general pattern of electron structure of chloroethylenes was obtained. • Necessity of this data for chloroethylenes negative ions study was noted. - Abstract: B3LYP/6-311 + G(d,p) calculations of ground and electronically excited states of ethylene, chloroethylene, 1,1-dichloroethylene, 1,2-dichloroethylene-cis, 1,2-dichloroethylene-trans trichloroethylene and tetrachloroethylene molecules have been performed. Molecular orbitals images and orbital correlation diagram are given. The calculation results for chloroethylenes electronically excited states were compared with experimental data from the energy-loss spectra obtained and generally considered previously by C.F. Koerting, K.N. Walzl and A. Kupperman. Several new additional triplet and singlet transitions were pointed out in these spectra considering the calculation results. The finding of the additional transitions was supported by the UV absorption spectrum of trichloroethylene recorded in big cuvette (10 cm), where the first three triplet and two low-intensive forbidden singlet transitions were registered. The first triplet of this compound was recorded to be at the same energy as was found with the energy-loss spectroscopy

  17. Electronically excited states of chloroethylenes: Experiment and DFT calculations in comparison

    Energy Technology Data Exchange (ETDEWEB)

    Khvostenko, O.G., E-mail: khv@mail.ru

    2014-08-15

    Highlights: • B3LYP/6-311 + G(d,p) calculations of chloroethylenes molecules were performed. • Calculations were correlated with experiment on the molecules ground and excited states. • The general pattern of electron structure of chloroethylenes was obtained. • Necessity of this data for chloroethylenes negative ions study was noted. - Abstract: B3LYP/6-311 + G(d,p) calculations of ground and electronically excited states of ethylene, chloroethylene, 1,1-dichloroethylene, 1,2-dichloroethylene-cis, 1,2-dichloroethylene-trans trichloroethylene and tetrachloroethylene molecules have been performed. Molecular orbitals images and orbital correlation diagram are given. The calculation results for chloroethylenes electronically excited states were compared with experimental data from the energy-loss spectra obtained and generally considered previously by C.F. Koerting, K.N. Walzl and A. Kupperman. Several new additional triplet and singlet transitions were pointed out in these spectra considering the calculation results. The finding of the additional transitions was supported by the UV absorption spectrum of trichloroethylene recorded in big cuvette (10 cm), where the first three triplet and two low-intensive forbidden singlet transitions were registered. The first triplet of this compound was recorded to be at the same energy as was found with the energy-loss spectroscopy.

  18. Principles of gene microarray data analysis.

    Science.gov (United States)

    Mocellin, Simone; Rossi, Carlo Riccardo

    2007-01-01

    The development of several gene expression profiling methods, such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE), and gene microarray, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complex cascade of molecular events leading to tumor development and progression. The availability of such large amounts of information has shifted the attention of scientists towards a nonreductionist approach to biological phenomena. High throughput technologies can be used to follow changing patterns of gene expression over time. Among them, gene microarray has become prominent because it is easier to use, does not require large-scale DNA sequencing, and allows for the parallel quantification of thousands of genes from multiple samples. Gene microarray technology is rapidly spreading worldwide and has the potential to drastically change the therapeutic approach to patients affected with tumor. Therefore, it is of paramount importance for both researchers and clinicians to know the principles underlying the analysis of the huge amount of data generated with microarray technology.

  19. Detection of selected plant viruses by microarrays

    OpenAIRE

    HRABÁKOVÁ, Lenka

    2013-01-01

    The main aim of this master thesis was the simultaneous detection of four selected plant viruses ? Apple mosaic virus, Plum pox virus, Prunus necrotic ringspot virus and Prune harf virus, by microarrays. The intermediate step in the process of the detection was optimizing of multiplex polymerase chain reaction (PCR).

  20. LNA-modified isothermal oligonucleotide microarray for ...

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... the advent of DNA microarray techniques (Lee et al. 2007). ... atoms of ribose to form a bicyclic ribosyl structure. It is the .... 532 nm and emission at 570 nm. The signal ..... sis and validation using real-time PCR. Nucleic Acids ...

  1. Gene Expression Analysis Using Agilent DNA Microarrays

    DEFF Research Database (Denmark)

    Stangegaard, Michael

    2009-01-01

    Hybridization of labeled cDNA to microarrays is an intuitively simple and a vastly underestimated process. If it is not performed, optimized, and standardized with the same attention to detail as e.g., RNA amplification, information may be overlooked or even lost. Careful balancing of the amount ...

  2. Microarrays (DNA Chips) for the Classroom Laboratory

    Science.gov (United States)

    Barnard, Betsy; Sussman, Michael; BonDurant, Sandra Splinter; Nienhuis, James; Krysan, Patrick

    2006-01-01

    We have developed and optimized the necessary laboratory materials to make DNA microarray technology accessible to all high school students at a fraction of both cost and data size. The primary component is a DNA chip/array that students "print" by hand and then analyze using research tools that have been adapted for classroom use. The…

  3. Comparing transformation methods for DNA microarray data

    NARCIS (Netherlands)

    Thygesen, Helene H.; Zwinderman, Aeilko H.

    2004-01-01

    Background: When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include

  4. A Low Cost Implementation of an Existing Hands-on Laboratory Experiment in Electronic Engineering

    Directory of Open Access Journals (Sweden)

    Clement Onime

    2014-10-01

    Full Text Available In engineering the pedagogical content of most formative programmes includes a significant amount of practical laboratory hands-on activity designed to deliver knowledge acquisition from actual experience alongside traditional face-to-face classroom based lectures and tutorials; this hands-on aspect is not always adequately addressed by current e-learning platforms. An innovative approach to e-learning in engineering, named computer aided engineering education (CAEE is about the use of computer aids for the enhanced, interactive delivery of educational materials in different fields of engineering through two separate but related components; one for classroom and another for practical hands-on laboratory work. The component for hands-on laboratory practical work focuses on the use of mixed reality (video-based augmented reality tools on mobile devices/platforms. This paper presents the computer aided engineering education (CAEE implementation of a laboratory experiment in micro-electronics that highlights some features such as the ability to closely implement an existing laboratory based hands-on experiment with lower associated costs and the ability to conduct the experiment off-line while maintaining existing pedagogical contents and standards.

  5. Very large solid angle spectrometer for single arm electron scattering experiments

    International Nuclear Information System (INIS)

    Leconte, P.

    1981-01-01

    Major information about short range behavior of nuclear forces should be obtained through electron scattering experiments at high momentum transfer. Cross sections will be very low as is usually the case in electron scattering. In order to reach them, the solid angle of the detection system will have to be enlarged. Traditional optics cannot give correct answer to the problem. For very large apertures, it is impossible to obtain good focussing properties which provide accurate momentum/position correlation with no dependence on the entrance angles. Furthermore, the experiment will require the measurement of these angles. It means that the final system will be equipped with a complete set of position sensitive detectors able to measure positions and angles of trajectories in both planes. Then, the question arises: is it really necessary to provide good focussing, or more precisely: is it possible to get all the required information without the help of a sophisticated predetermined magnetic optics. We try to answer this question and then to sketch from a new point of view the best spectrometer we could think of

  6. Comments on advanced, time-resolved imaging techniques for free-electron laser (FEL) experiments

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A.H.

    1992-01-01

    An extensive set of time-resolved imaging experiments has been performed on rf-linac driven free-electron lasers (FELs) over the past few years. These experiments have addressed both micropulse and macropulse timescales on both the charged-particle beam and the wiggler/undulator outputs (spontaneous emission and lasing). A brief review of first measurements on photoinjecter micropulse elongation, submacropulse phase slew in drive lasers, submacropulse wavelength shifts in lasers, etc. is presented. This is followed by discussions of new measurements of 35-MeV electron beam micropulse bunch length (<10 ps) using optical transition radiation, some of the first single bend synchrotron radiation beam profile measurements at gamma <80, and comments on the low-jitter synchroscan streak camera tuner. These techniques will be further developed on the 200-650 MeV linac test stand at the Advanced Photon Source (APS) in the next few years. Such techniques should be adaptable to many of the present FEL designs and to some aspects of the next generation of light sources.

  7. Comments on advanced, time-resolved imaging techniques for free-electron laser (FEL) experiments

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A.H.

    1992-11-01

    An extensive set of time-resolved imaging experiments has been performed on rf-linac driven free-electron lasers (FELs) over the past few years. These experiments have addressed both micropulse and macropulse timescales on both the charged-particle beam and the wiggler/undulator outputs (spontaneous emission and lasing). A brief review of first measurements on photoinjecter micropulse elongation, submacropulse phase slew in drive lasers, submacropulse wavelength shifts in lasers, etc. is presented. This is followed by discussions of new measurements of 35-MeV electron beam micropulse bunch length (<10 ps) using optical transition radiation, some of the first single bend synchrotron radiation beam profile measurements at gamma <80, and comments on the low-jitter synchroscan streak camera tuner. These techniques will be further developed on the 200-650 MeV linac test stand at the Advanced Photon Source (APS) in the next few years. Such techniques should be adaptable to many of the present FEL designs and to some aspects of the next generation of light sources.

  8. Vehicle charging and return current measurements during electron-beam emission experiments from the Shuttle Orbiter

    International Nuclear Information System (INIS)

    Hawkins, J.G.

    1988-01-01

    The prime objective of this research was to investigate the electro-dynamic response of the Shuttle Orbiter during electron beam emission from the payload bay. This investigation has been conducted by examining data collected by the Vehicle Charging And Potential (VCAP) Experiment. The VCAP experiment has flown on two Shuttle missions with a Fast Pulse Electron Generator (FPEG) capable of emitting a 100 mA beam of 1 keV electrons. Diagnostics of the charging and return current during beam emission were provided by a combined Charge and Current Probe (CCP) located in the payload bay of the Orbiter. The CCP measurements were used to conduct a parametric study of the vehicle charging and return current as a function of vehicle attitude, ambient plasma parameters, and emitted beam current. In particular, the CCP measurements were found to depend strongly on the ambient plasma density. The vehicle charging during a 100 mA beam emission was small when the predicted ambient plasma density was greater than 3 x 10 5 cm -3 , but appreciable charging occurred when the density was less than this value. These observations indicated that the effective current-collecting area of the Orbiter is approximately 42 m 2 , consistent with estimates for the effective area of the Orbiter's engine nozzles. The operation of the Orbiter's Reaction Control System thrusters can create perturbations in the Orbiter's neutral and plasma environment that affect the CCP measurements. The CCP signatures of thruster firings are quite complex, but in general they are consistent with the depletion of plasma density in the ram direction and the enhancement of plasma density in the Orbiter's wake

  9. A silicon microstrip detector in a magnetic spectrometer for high-resolution electron scattering experiments at the S-DALINAC

    International Nuclear Information System (INIS)

    Lenhardt, A.W.; Bonnes, U.; Burda, O.; Neumann-Cosel, P. von; Platz, M.; Richter, A.; Watzlawik, S.

    2006-01-01

    A silicon microstrip detector was developed as focal plane detector of the 169.7 deg. magic angle double-focussing spectrometer at the superconducting Darmstadt electron linear accelerator (S-DALINAC). It allows experiments with minimum ionizing electrons at data rates up to 100 kHz, utilizing the maximum resolution of the spectrometer achievable in dispersion-matching mode

  10. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  11. The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data

    Directory of Open Access Journals (Sweden)

    Hyunseok P Kang

    2010-01-01

    Full Text Available Background: Tissue microarrays (TMAs are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF provides a flexible method to represent knowledge in triples, which take the form Subject- Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs, which are global in scope. We present an OWL (Web Ontology Language schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration. Methods: A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format. Results: We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES to OWL. Conclusion: By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.

  12. Reconstructing the temporal ordering of biological samples using microarray data.

    Science.gov (United States)

    Magwene, Paul M; Lizardi, Paul; Kim, Junhyong

    2003-05-01

    Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.

  13. Temperature Gradient Effect on Gas Discrimination Power of a Metal-Oxide Thin-Film Sensor Microarray

    Directory of Open Access Journals (Sweden)

    Joachim Goschnick

    2004-05-01

    Full Text Available Abstract: The paper presents results concerning the effect of spatial inhomogeneous operating temperature on the gas discrimination power of a gas-sensor microarray, with the latter based on a thin SnO2 film employed in the KAMINA electronic nose. Three different temperature distributions over the substrate are discussed: a nearly homogeneous one and two temperature gradients, equal to approx. 3.3 oC/mm and 6.7 oC/mm, applied across the sensor elements (segments of the array. The gas discrimination power of the microarray is judged by using the Mahalanobis distance in the LDA (Linear Discrimination Analysis coordinate system between the data clusters obtained by the response of the microarray to four target vapors: ethanol, acetone, propanol and ammonia. It is shown that the application of a temperature gradient increases the gas discrimination power of the microarray by up to 35 %.

  14. Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jianping Hua

    2004-01-01

    Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

  15. AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

    Directory of Open Access Journals (Sweden)

    Xia Yuannan

    2006-12-01

    Full Text Available Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes of interest onto the Gene Ontology (GO space; and interfaces to run Cluster, a program for clustering analysis, and GenMAPP, a program for pathway analysis. AffyMiner has been used for analyzing the GeneChip data and the results were presented in several publications. Conclusion AffyMiner fills an important gap in finding differentially expressed genes in Affymetrix GeneChip microarray data. AffyMiner effectively deals with multiple replicates in the experiment and takes into account both quantitative and qualitative data in identifying significant genes. AffyMiner reduces the time and effort needed to compare data from multiple arrays and to interpret the possible biological implications associated with significant changes in a gene's expression.

  16. The capacitor banks for the text diagnostic neutral beam and electron cyclotron heating experiments

    International Nuclear Information System (INIS)

    Nelin, K.; Jagger, J.; Baker, M.; Ourou, A.; De Turk, P.

    1986-01-01

    The Texas Experimental Tokamak (TEXT) has been operational since November of 1980. Since that time, many experimental systems have been added to the machine. Currently, two major experiments are being added to compliment the diagnostics already online. These systems, the Diagnostic Neutral Beam (DNB) and the Electron Cyclotron Heating (ECH) experiments are described in separate papers. A set of five modular, bipolar capacitor banks are used to power both the DNB and the ECH. The total capacitance of the banks is 92μF. The stored energy is about 500kJ at+or-100kV. The banks are built as five identical, interchangeable modules. One module is adequate to run the DNB. Up to four banks are used to power the ECH. The banks are portable so that they can be moved to the open end of the laboratory for maintenance. This gives much better access for repair work and allows the experiments to continue to run with the remaining banks. Due to budgetary constraints, these banks were constructed in the most economical manner possible consistent with worker safety and long term reliability. The capacitors themselves are on loan from Los Alamos National Labs. They are rated at 1.85μF at 60kV. Our application requires that they be used in a series/parallel configuration with a peak voltage of 50kV each. This paper describes the electrical, mechanical and control design considerations required to achieve a working set of banks

  17. Web based electronic logbook and experiment run database viewer for Alcator C-Mod

    International Nuclear Information System (INIS)

    Fredian, T.W.; Stillerman, J.A.

    2006-01-01

    Since 1991, the scientists and engineers at the Alcator C-Mod experiment at MIT have been recording text entries about the experiments being performed in an electronic logbook. In addition, separate documents such as run plans, run summaries and experimental proposals have been created and stored in a variety of formats in computer files. This information has now been organized and made available via any modern web browser. The new web based interface permits the user to browse through all the logbook entries, run information and even view some key data traces of the experiment. Since this information is being catalogued by Internet search engines, these tools can also be used to quickly locate information. The web based logbook and run information interface provides some additional capabilities. Once logged into the web site, users can add, delete or modify logbook entries directly from their browser. The logbook window on their browser also provides dynamic updating when any new logbook entries are made. There is also live C-Mod operation status information with optional audio announcements available. The user can receive the same state change announcements such as 'entering init' or 'entering pulse' as they would if they were sitting in the C-Mod control room. This paper will describe the functionality of the web based logbook and how it was implemented

  18. Phased-array antenna system for electron Bernstein wave heating and current drive experiments in QUEST

    International Nuclear Information System (INIS)

    Idei, H.; Sakaguchi, M.; Kalinnikova, E.I.

    2010-11-01

    The phased-array antenna system for Electron Bernstein Wave Heating and Current Drive (EBWH/CD) experiments has been developed in the QUEST. The antenna was designed to excite a pure O-mode wave in the oblique injection for the EBWH/CD experiments, and was tested at a low power level. The measured two orthogonal fields were in excellent agreements with the fields evaluated by a developed Kirchhoff code. The heat load and thermal stress in CW 200 kW operation were analyzed with finite element codes. The phased array has been fast scanned [∼10 4 degree/s] to control the incident polarization and angle to follow time evolutions of the plasma current and density. The RF startup and sustainment experiments were conducted using the developed antenna system. The plasma current (< ∼15 kA) with an aspect ratio of 1.5 was started up and sustained by only RF injection. The long pulse discharge of 10 kA was attained for 40 s with the 30 kW injection. (author)

  19. Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data.

    Science.gov (United States)

    Tan, Qihua; Thomassen, Mads; Burton, Mark; Mose, Kristian Fredløv; Andersen, Klaus Ejner; Hjelmborg, Jacob; Kruse, Torben

    2017-06-06

    Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

  20. Extended analysis of benchmark datasets for Agilent two-color microarrays

    Directory of Open Access Journals (Sweden)

    Kerr Kathleen F

    2007-10-01

    Full Text Available Abstract Background As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC project reported the results of experiments using External RNA Controls (ERCs on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consideration of different methods for processing the data from the Agilent two-color platform. While this omission is understandable given the scale of the project, it can create the false impression that there is consensus about the best way to process Agilent two-color data. It is also important to consider whether ERCs are representative of all the probes on a microarray. Results A comparison of different methods of processing Agilent two-color data shows substantial differences among methods for low-intensity genes. The sensitivity and specificity for detecting differentially expressed genes varies substantially for different methods. Analysis also reveals that the ERCs in the MAQC data only span the upper half of the intensity range, and therefore cannot be representative of all genes on the microarray. Conclusion Although ERCs demonstrate good agreement between observed and expected log-ratios on the Agilent two-color platform, such an analysis is incomplete. Simple loess normalization outperformed data processing with Agilent's Feature Extraction software for accurate identification of differentially expressed genes. Results from studies using ERCs should not be over-generalized when ERCs are not representative of all probes on a microarray.

  1. IsoGeneGUI : Multiple approaches for dose-response analysis of microarray data using R

    NARCIS (Netherlands)

    Otava, Martin; Sengupta, Rudradev; Shkedy, Ziv; Lin, Dan; Pramana, Setia; Verbeke, Tobias; Haldermans, Philippe; Hothorn, Ludwig A.; Gerhard, Daniel; Kuiper, Rebecca M.; Klinglmueller, Florian; Kasim, Adetayo

    2017-01-01

    The analysis of transcriptomic experiments with ordered covariates, such as dose-response data, has become a central topic in bioinformatics, in particular in omics studies. Consequently, multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various perspectives

  2. Electron electric dipole moment experiment using electric-fieldquantized slow cesium atoms

    Energy Technology Data Exchange (ETDEWEB)

    Amini, Jason M.; Munger Jr., Charles T.; Gould, Harvey.

    2007-04-05

    A proof-of-principle electron electric dipole moment (e-EDM)experiment using slow cesium atoms, nulled magnetic fields, and electricfield quantization has been performed. With the ambient magnetic fieldsseen by the atoms reduced to less than 200 pT, an electric field of 6MV/m lifts the degeneracy between states of unequal lbar mF rbar and,along with the low (approximately 3 m/s) velocity, suppresses thesystematic effect from the motional magnetic field. The low velocity andsmall residual magnetic field have made it possible to induce transitionsbetween states and to perform state preparation, analysis, and detectionin regions free of applied static magnetic and electric fields. Thisexperiment demonstrates techniques that may be used to improve the e-EDMlimit by two orders of magnitude, but it is not in itself a sensitivee-EDM search, mostly due to limitations of the laser system.

  3. A long electromagnetic wiggler for the paladin free-electron laser experiments

    International Nuclear Information System (INIS)

    Deis, G.A.; Harvey, A.R.; Parkison, C.D.; Prosnitz, D.; Rego, J.; Scharlemann, E.T.; Halbach, K.

    1987-01-01

    We have designed, built, and tested a 25.6-m-long wiggler for a free-electron-laser (FEL) experiment. It is a DC iron-core electromagnetic wiggler that incorporates a number of important and unique features. Permanent magnets are used to suppress saturation in the iron and extend the linear operating range. Steering-free excitation allows real-time adjustment of the field taper without causing beam steering. Wiggle-plane focusing is produced by curved pole tips. The magnitude of random pole-to-pole field errors is minimized by a mechanical design concept that reduces tolerance stackup in critical locations. To date, we have tested 15 m of this wiggler, and our measurements have shown exceptionally low levels of random errors. 8 refs

  4. Spectrometer for X-ray emission experiments at FERMI free-electron-laser

    International Nuclear Information System (INIS)

    Poletto, L.; Frassetto, F.; Miotti, P.; Di Cicco, A.; Iesari, F.; Finetti, P.; Grazioli, C.; Kivimäki, A.; Stagira, S.; Coreno, M.

    2014-01-01

    A portable and compact photon spectrometer to be used for photon in-photon out experiments, in particular x-ray emission spectroscopy, is presented. The instrument operates in the 25–800 eV energy range to cover the full emissions of the FEL1 and FEL2 stages of FERMI. The optical design consists of two interchangeable spherical varied-lined-spaced gratings and a CCD detector. Different input sections can be accommodated, with/without an entrance slit and with/without an additional relay mirror, that allow to mount the spectrometer in different end-stations and at variable distances from the target area both at synchrotron and at free-electron-laser beamlines. The characterization on the Gas Phase beamline at ELETTRA Synchrotron (Italy) is presented

  5. An Ensemble of Neural Networks for Online Electron Filtering at the ATLAS Experiment.

    CERN Document Server

    Da Fonseca Pinto, Joao Victor; The ATLAS collaboration

    2018-01-01

    In 2017 the ATLAS experiment implemented an ensemble of neural networks (NeuralRinger algorithm) dedicated to improving the performance of filtering events containing electrons in the high-input rate online environment of the Large Hadron Collider at CERN, Geneva. The ensemble employs a concept of calorimetry rings. The training procedure and final structure of the ensemble are used to minimize fluctuations from detector response, according to the particle energy and position of incidence. A detailed study was carried out to assess profile distortions in crucial offline quantities through the usage of statistical tests and residual analysis. These details and the online performance of this algorithm during the 2017 data-taking will be presented.

  6. First results of the University of Maryland electron beam transport experiment

    International Nuclear Information System (INIS)

    Namkung, W.; Loschialpo, P.; Reiser, M.; Suter, J.; Lawson, J.D.

    1981-01-01

    A study is made of emittance growth in periodically focused intense beams. For initial studies, the electron gun consists of a 1-cm diam., dispenser-type cathode and an anode covered with a wire mesh. To avoid neutralization, 5 /mu/s, 60 Hz pulses are used and the current is 230 mA at 5 kV. By varying the voltage from 10 kV to 500 volts the space charge depression, /omega/sub //omega/sub //o, of the particle oscillation frequencies in the focusing channel can be changed from approximately 0.04 to approximately 0.2. Further increase of /omega/sub //omega/sub //o should be possible with modified guns and the use of emittance control grids. Four prototype solenoids have been built, and the results of experiments with the first two are presented. 8 refs

  7. Low voltage powering of on-detector electronics for HL-LHC experiments upgrades

    CERN Document Server

    Bobillier, Vincent; Vasey, Francois; Karmakar, Sabyasachi; Maity, Manas; Roy, Subhasish; Kundu, Tapas Kumar

    2018-01-01

    All LHC experiments will be upgraded during the next LHC long shutdowns (LS2 and LS3). The increase in resolution and luminosity and the use of more advanced CMOS technology nodes typically implies higher current consumption of the on-detector electronics. In this context, and in view of limiting the cable voltage drop, point-of-load DC-DC converters will be used on detector. This will have a direct impact on the existing powering scheme, implying new AC-DC and/or DC-DC stages as well as changes in the power cabling infrastructure. This paper presents the first results obtained while evaluating different LV powering schemes and distribution layouts for HL-LHC trackers. The precise low voltage power source requirements are being assessed and understood using the CMS tracker upgrade as a use-case.

  8. Emittance growth caused by bends in the Los Alamos free-electron laser energy recovery experiment

    International Nuclear Information System (INIS)

    Carlsten, B.E.

    1987-01-01

    Experimentally transporting the beam from the wiggler to the decelerators in the energy recovery experiment (ERX) at the Los Alamos National Laboratory free-electron laser was more difficult than expected because of the large initial emittance in the beam. This emittance was apparently caused in an early 60 0 achromatic bend. To get this beam through subsequent bends without wall interception, the quadrupole focusing had to be changed from the design amount; as a result, the emittance grew further. This paper discusses various mechanisms for this emittance growth in the 60 0 bend, including effects caused by path changes in the bend resulting from wake-field-induced energy changes of particles in the beam and examines emittance filters, ranging from a simple aperture near a beam crossover to more complicated telescope schemes designed to regain the original emittance before the 60 0 bend

  9. A search for muon neutrino to electron neutrino oscillations in the MINOS Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ochoa Ricoux, Juan Pedro [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2009-01-01

    We perform a search for vμ → ve oscillations, a process which would manifest a nonzero value of the θ13 mixing angle, in the MINOS long-baseline neutrino oscillation experiment. The analysis consists of searching for an excess of ve charged-current candidate events over the predicted backgrounds, made mostly of neutral-current events with high electromagnetic content. A novel technique to select electron neutrino events is developed, which achieves an improved separation between the signal and the backgrounds, and which consequently yields a better reach in θ13. The backgrounds are predicted in the Far Detector from Near Detector measurements. An excess is observed in the Far Detector data over the predicted backgrounds, which is consistent with the background-only hypothesis at 1.2 standard deviations.

  10. Beam experiments with the Grenoble test electron cyclotron resonance ion source at iThemba LABS

    Energy Technology Data Exchange (ETDEWEB)

    Thomae, R., E-mail: rthomae@tlabs.ac.za; Conradie, J.; Fourie, D.; Mira, J.; Nemulodi, F. [iThemba LABS, P.O. Box 722, Somerset West 7130 (South Africa); Kuechler, D.; Toivanen, V. [CERN, BE/ABP/HSL, 1211 Geneva 23 (Switzerland)

    2016-02-15

    At iThemba Laboratory for Accelerator Based Sciences (iThemba LABS) an electron cyclotron ion source was installed and commissioned. This source is a copy of the Grenoble Test Source (GTS) for the production of highly charged ions. The source is similar to the GTS-LHC at CERN and named GTS2. A collaboration between the Accelerators and Beam Physics Group of CERN and the Accelerator and Engineering Department of iThemba LABS was proposed in which the development of high intensity argon and xenon beams is envisaged. In this paper, we present beam experiments with the GTS2 at iThemba LABS, in which the results of continuous wave and afterglow operation of xenon ion beams with oxygen as supporting gases are presented.

  11. Autoregressive-model-based missing value estimation for DNA microarray time series data.

    Science.gov (United States)

    Choong, Miew Keen; Charbit, Maurice; Yan, Hong

    2009-01-01

    Missing value estimation is important in DNA microarray data analysis. A number of algorithms have been developed to solve this problem, but they have several limitations. Most existing algorithms are not able to deal with the situation where a particular time point (column) of the data is missing entirely. In this paper, we present an autoregressive-model-based missing value estimation method (ARLSimpute) that takes into account the dynamic property of microarray temporal data and the local similarity structures in the data. ARLSimpute is especially effective for the situation where a particular time point contains many missing values or where the entire time point is missing. Experiment results suggest that our proposed algorithm is an accurate missing value estimator in comparison with other imputation methods on simulated as well as real microarray time series datasets.

  12. How the RNA isolation method can affect microRNA microarray results

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

    2011-01-01

    RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

  13. Experiments on electron temperature profile resilience in FTU tokamak with continuous and modulated ECRH

    International Nuclear Information System (INIS)

    Cirant, S.

    2002-01-01

    Experiments performed on FTU tokamak, aiming at validation of physics-based transport models of the electron temperature profile resilience, are presented. ECRH is used to probe transport features, both in steady-state and in response to perturbations, while ECCD and LHCD are used for current density profile shaping. Observed confinement behaviour shows agreement with a critical temperature gradient length modelling. Central, low gradient plasma is characterized by low stiffness and low electron thermal diffusivity. Strong stiffness and high conduction are found in the confinement region. Resilience is experimentally characterized by an index of the resistance of the profile to adapt its shape to localized ECRH, while the diffusivity and its low-high transition are measured both by power balance and heat pulse propagation analysis. A particular attention is given to the investigation of the transition layer between low-high diffusivity and low-high stiffness regions. A dependence of LTc on magnetic shear, similar to what found in Tore Supra, and consistent with ETG based anomalous transport, is found. (author)

  14. VME as a front-end electronics system in high energy physics experiments

    International Nuclear Information System (INIS)

    Ohska, T.K.

    1990-01-01

    It is only a few years since the VME became a standard system, yet the VME system is already so much more popular than other systems. The VME system was developed for industrial applications and not for the scientific research, and high energy physics field is a tiny market when compared with the industrial market. Considerations made here indicate that the VME system would be a good one for a rear-end system, but would not be a good candidate for front-end electronics in physics experiments. Furthermore, there is a fear that the VXI bus could become popular in this field of instrumentation since the VXI system is backed up by major suppliers of instrumentation in the high energy physics field. VXI would not be an adequate system for front-end electronics, yet advertised to be one. It would be worse to see the VXI system to become a standard system for high energy physics instrumentation than the VME system to be one. The VXI system would do a mediocre job so that people might be misled to think that the VXI system can be used as front-end system. (N.K.)

  15. Runaway electron mitigation by 3D fields in the ASDEX-Upgrade experiment

    Science.gov (United States)

    Gobbin, M.; Li, L.; Liu, Y. Q.; Marrelli, L.; Nocente, M.; Papp, G.; Pautasso, G.; Piovesan, P.; Valisa, M.; Carnevale, D.; Esposito, B.; Giacomelli, L.; Gospodarczyk, M.; McCarthy, P. J.; Martin, P.; Suttrop, W.; Tardocchi, M.; Teschke, M.; the ASDEX Upgrade Team; the EUROfusion MST1 Team

    2018-01-01

    Disruption-generated runaway electron (RE) beams represent a severe threat for tokamak plasma-facing components in high current devices like ITER, thus motivating the search of mitigation techniques. The application of 3D fields might aid this purpose and recently was investigated also in the ASDEX Upgrade experiment by using the internal active saddle coils (termed B-coils). Resonant magnetic perturbations (RMPs) with dominant toroidal mode number n = 1 have been applied by the B-coils, in a RE specific scenario, before and during disruptions, which are deliberately created via massive gas injection. The application of RMPs affects the electron temperature profile and seemingly changes the dynamics of the disruption; this results in a significantly reduced current and lifetime of the generated RE beam. A similar effect is observed also in the hard-x-ray (HXR) spectrum, associated to RE emission, characterized by a partial decrease of the energy content below 1 MeV when RMPs are applied. The strength of the observed effects strongly depends on the upper-to-lower B-coil phasing, i.e. on the poloidal spectrum of the applied RMPs, which has been reconstructed including the plasma response by the code MARS-F. A crude vacuum approximation fails in the interpretation of the experimental findings: despite the relatively low β (< 0.5 % ) of these discharges, a modest amplification (factor of 2) of the edge kink response occurs, which has to be considered to explain the observed suppression effects.

  16. IN-SITU EXPERIMENTS OF VACUUM DISCHARGE USING SCANNING ELECTRON MICROSCOPES

    CERN Document Server

    Muranaka, T; Leifer, K; Ziemann, V

    2011-01-01

    The fundamental understanding of vacuum discharge mechanisms and induced surface damage is indispensable for the CLIC feasibility study. We have been conducting dc sparc experiments inside a Scanning Electron Microscope (SEM) at Uppsala university in order to investigate localized breakdown phenomena. By using a SEM, we achieve the resolution of the electron probe in the few-nm range, which is of great advantage as the surface roughness of the polished accelerating structures is in the same scale. The high accelerating field of 1 GV/m is realized by biasing an electrode with 1 kV set above the sample with a gap of sub μm. Furthermore, a second SEM equipped with a Focused Ion Beam (FIB) is used to modify the topography of sample surfaces thus the geometrical dependence of field emissions and vacuum discharges can be studied. The FIB can be used for the surface damage analysis as well. We have demonstrated subsurface damage observations by using FIB to sputter a rectangular recess into the sample in the breakd...

  17. Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Cannataro, Mario

    2013-08-01

    A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

  18. Electron Bernstein wave emission based diagnostic on National Spherical Torus Experiment (invited)

    International Nuclear Information System (INIS)

    Diem, S.; Taylor, G.; Caughman, John B.; Efthimion, P.C.; Kugel, H.; LeBlanc, B.; Preinhaelter, J.; Sabbagh, S.A.; Urban, J.

    2008-01-01

    National Spherical Torus Experiment (NSTX) is a spherical tokamak (ST) that operates with n(e) up to 10(20) m(-3) and B-T less than 0.6 T, cutting off low harmonic electron cyclotron (EC) emission widely used for T-e measurements on conventional aspect ratio tokamaks. The electron Bernstein wave (EBW) can propagate in ST plasmas and is emitted at EC harmonics. These properties suggest thermal EBW emission (EBE) may be used for local T-e measurements in the ST. Practically, a robust T-e(R,t) EBE diagnostic requires EBW transmission efficiencies of >90% for a wide range of plasma conditions. EBW emission and coupling physics were studied on NSTX with an obliquely viewing EBW to O-mode (B-X-O) diagnostic with two remotely steered antennas, coupled to absolutely calibrated radiometers. While T-e(R,t) measurements with EBW emission on NSTX were possible, they were challenged by several issues. Rapid fluctuations in edge n(e) scale length resulted in >20% changes in the low harmonic B-X-O transmission efficiency. Also, B-X-O transmission efficiency during H modes was observed to decay by a factor of 5-10 to less than a few percent. The B-X-O transmission behavior during H modes was reproduced by EBE simulations that predict that EBW collisional damping can significantly reduce emission when T-e < 30 eV inside the B-X-O mode conversion (MC) layer. Initial edge lithium conditioning experiments during H modes have shown that evaporated lithium can increase T-e inside the B-X-O MC layer, significantly increasing B-X-O transmission.

  19. Electron Bernstein Wave Emission Based Diagnostic on National Spherical Torus Experiment

    International Nuclear Information System (INIS)

    Diem, S.; Taylor, G.; Caughman, John B.; Efthimion, P.C.; Kugel, H.; LeBlanc, B.; Preinhaelter, J.; Sabbagh, S.A.; Urban, J.; Wilgen, John B.

    2008-01-01

    National Spherical Torus Experiment (NSTX) is a spherical tokamak (ST) that operates with n(e) up to 10(20) m(-3) and B(T) less than 0.6 T, cutting off low harmonic electron cyclotron (EC) emission widely used for T(e) measurements on conventional aspect ratio tokamaks. The electron Bernstein wave (EBW) can propagate in ST plasmas and is emitted at EC harmonics. These properties suggest thermal EBW emission (EBE) may be used for local T(e) measurements in the ST. Practically, a robust T(e)(R,t) EBE diagnostic requires EBW transmission efficiencies of >90% for a wide range of plasma conditions. EBW emission and coupling physics were studied on NSTX with an obliquely viewing EBW to O-mode (B-X-O) diagnostic with two remotely steered antennas, coupled to absolutely calibrated radiometers. While T(e)(R,t) measurements with EBW emission on NSTX were possible, they were challenged by several issues. Rapid fluctuations in edge n(e) scale length resulted in >20% changes in the low harmonic B-X-O transmission efficiency. Also, B-X-O transmission efficiency during H modes was observed to decay by a factor of 5-10 to less than a few percent. The B-X-O transmission behavior during H modes was reproduced by EBE simulations that predict that EBW collisional damping can significantly reduce emission when T(e)< 30 eV inside the B-X-O mode conversion (MC) layer. Initial edge lithium conditioning experiments during H modes have shown that evaporated lithium can increase T(e) inside the B-X-O MC layer, significantly increasing B-X-O transmission.

  20. DNA Microarrays in Comparative Genomics and Transcriptomics

    DEFF Research Database (Denmark)

    Willenbrock, Hanni

    2007-01-01

    at identifying the exact breakpoints where DNA has been gained or lost. In this thesis, three popular methods are compared and a realistic simulation model is presented for generating artificial data with known breakpoints and known DNA copy number. By using simulated data, we obtain a realistic evaluation......During the past few years, innovations in the DNA sequencing technology has led to an explosion in available DNA sequence information. This has revolutionized biological research and promoted the development of high throughput analysis methods that can take advantage of the vast amount of sequence...... data. For this, the DNA microarray technology has gained enormous popularity due to its ability to measure the presence or the activity of thousands of genes simultaneously. Microarrays for high throughput data analyses are not limited to a few organisms but may be applied to everything from bacteria...

  1. Facilitating RNA structure prediction with microarrays.

    Science.gov (United States)

    Kierzek, Elzbieta; Kierzek, Ryszard; Turner, Douglas H; Catrina, Irina E

    2006-01-17

    Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.

  2. Plasmonically amplified fluorescence bioassay with microarray format

    Science.gov (United States)

    Gogalic, S.; Hageneder, S.; Ctortecka, C.; Bauch, M.; Khan, I.; Preininger, Claudia; Sauer, U.; Dostalek, J.

    2015-05-01

    Plasmonic amplification of fluorescence signal in bioassays with microarray detection format is reported. A crossed relief diffraction grating was designed to couple an excitation laser beam to surface plasmons at the wavelength overlapping with the absorption and emission bands of fluorophore Dy647 that was used as a label. The surface of periodically corrugated sensor chip was coated with surface plasmon-supporting gold layer and a thin SU8 polymer film carrying epoxy groups. These groups were employed for the covalent immobilization of capture antibodies at arrays of spots. The plasmonic amplification of fluorescence signal on the developed microarray chip was tested by using interleukin 8 sandwich immunoassay. The readout was performed ex situ after drying the chip by using a commercial scanner with high numerical aperture collecting lens. Obtained results reveal the enhancement of fluorescence signal by a factor of 5 when compared to a regular glass chip.

  3. Tissue Microarray Analysis Applied to Bone Diagenesis

    OpenAIRE

    Barrios Mello, Rafael; Regis Silva, Maria Regina; Seixas Alves, Maria Teresa; Evison, Martin; Guimarães, Marco Aurélio; Francisco, Rafaella Arrabaça; Dias Astolphi, Rafael; Miazato Iwamura, Edna Sadayo

    2017-01-01

    Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens....

  4. Microarrays for the evaluation of cell-biomaterial surface interactions

    Science.gov (United States)

    Thissen, H.; Johnson, G.; McFarland, G.; Verbiest, B. C. H.; Gengenbach, T.; Voelcker, N. H.

    2007-01-01

    The evaluation of cell-material surface interactions is important for the design of novel biomaterials which are used in a variety of biomedical applications. While traditional in vitro test methods have routinely used samples of relatively large size, microarrays representing different biomaterials offer many advantages, including high throughput and reduced sample handling. Here, we describe the simultaneous cell-based testing of matrices of polymeric biomaterials, arrayed on glass slides with a low cell-attachment background coating. Arrays were constructed using a microarray robot at 6 fold redundancy with solid pins having a diameter of 375 μm. Printed solutions contained at least one monomer, an initiator and a bifunctional crosslinker. After subsequent UV polymerisation, the arrays were washed and characterised by X-ray photoelectron spectroscopy. Cell culture experiments were carried out over 24 hours using HeLa cells. After labelling with CellTracker ® Green for the final hour of incubation and subsequent fixation, the arrays were scanned. In addition, individual spots were also viewed by fluorescence microscopy. The evaluation of cell-surface interactions in high-throughput assays as demonstrated here is a key enabling technology for the effective development of future biomaterials.

  5. Harshlight: a "corrective make-up" program for microarray chips

    Directory of Open Access Journals (Sweden)

    Wittkowski Knut M

    2005-12-01

    Full Text Available Abstract Background Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs, few tools are available to help with the detection of those defects. Results We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip. Conclusion We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated.

  6. Classification of mislabelled microarrays using robust sparse logistic regression.

    Science.gov (United States)

    Bootkrajang, Jakramate; Kabán, Ata

    2013-04-01

    Previous studies reported that labelling errors are not uncommon in microarray datasets. In such cases, the training set may become misleading, and the ability of classifiers to make reliable inferences from the data is compromised. Yet, few methods are currently available in the bioinformatics literature to deal with this problem. The few existing methods focus on data cleansing alone, without reference to classification, and their performance crucially depends on some tuning parameters. In this article, we develop a new method to detect mislabelled arrays simultaneously with learning a sparse logistic regression classifier. Our method may be seen as a label-noise robust extension of the well-known and successful Bayesian logistic regression classifier. To account for possible mislabelling, we formulate a label-flipping process as part of the classifier. The regularization parameter is automatically set using Bayesian regularization, which not only saves the computation time that cross-validation would take, but also eliminates any unwanted effects of label noise when setting the regularization parameter. Extensive experiments with both synthetic data and real microarray datasets demonstrate that our approach is able to counter the bad effects of labelling errors in terms of predictive performance, it is effective at identifying marker genes and simultaneously it detects mislabelled arrays to high accuracy. The code is available from http://cs.bham.ac.uk/∼jxb008. Supplementary data are available at Bioinformatics online.

  7. Building a national electronic medical record exchange system - experiences in Taiwan.

    Science.gov (United States)

    Li, Yu-Chuan Jack; Yen, Ju-Chuan; Chiu, Wen-Ta; Jian, Wen-Shan; Syed-Abdul, Shabbir; Hsu, Min-Huei

    2015-08-01

    There are currently 501 hospitals and about 20,000 clinics in Taiwan. The National Health Insurance (NHI) system, which is operated by the NHI Administration, uses a single-payer system and covers 99.9% of the nation's total population of 23,000,000. Taiwan's NHI provides people with a high degree of freedom in choosing their medical care options. However, there is the potential concern that the available medical resources will be overused. The number of doctor consultations per person per year is about 15. Duplication of laboratory tests and prescriptions are not rare either. Building an electronic medical record exchange system is a good method of solving these problems and of improving continuity in health care. In November 2009, Taiwan's Executive Yuan passed the 'Plan for accelerating the implementation of electronic medical record systems in medical institutions' (2010-2012; a 3-year plan). According to this plan, a patient can, at any hospital in Taiwan, by using his/her health insurance IC card and physician's medical professional IC card, upon signing a written agreement, retrieve all important medical records for the past 6 months from other participating hospitals. The focus of this plan is to establish the National Electronic Medical Record Exchange Centre (EEC). A hospital's information system will be connected to the EEC through an electronic medical record (EMR) gateway. The hospital will convert the medical records for the past 6 months in its EMR system into standardized files and save them on the EMR gateway. The most important functions of the EEC are to generate an index of all the XML files on the EMR gateways of all hospitals, and to provide search and retrieval services for hospitals and clinics. The EEC provides four standard inter-institution EMR retrieval services covering medical imaging reports, laboratory test reports, discharge summaries, and outpatient records. In this system, we adopted the Health Level 7 (HL7) Clinical Document

  8. Geiger mode avalanche photodiodes for microarray systems

    Science.gov (United States)

    Phelan, Don; Jackson, Carl; Redfern, R. Michael; Morrison, Alan P.; Mathewson, Alan

    2002-06-01

    New Geiger Mode Avalanche Photodiodes (GM-APD) have been designed and characterized specifically for use in microarray systems. Critical parameters such as excess reverse bias voltage, hold-off time and optimum operating temperature have been experimentally determined for these photon-counting devices. The photon detection probability, dark count rate and afterpulsing probability have been measured under different operating conditions. An active- quench circuit (AQC) is presented for operating these GM- APDs. This circuit is relatively simple, robust and has such benefits as reducing average power dissipation and afterpulsing. Arrays of these GM-APDs have already been designed and together with AQCs open up the possibility of having a solid-state microarray detector that enables parallel analysis on a single chip. Another advantage of these GM-APDs over current technology is their low voltage CMOS compatibility which could allow for the fabrication of an AQC on the same device. Small are detectors have already been employed in the time-resolved detection of fluorescence from labeled proteins. It is envisaged that operating these new GM-APDs with this active-quench circuit will have numerous applications for the detection of fluorescence in microarray systems.

  9. Angle selective backscattered electron contrast in the low-voltage scanning electron microscope: Simulation and experiment for polymers

    Energy Technology Data Exchange (ETDEWEB)

    Wan, Q., E-mail: qwan2@sheffield.ac.uk [Department of Material Science and Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom); Masters, R.C. [Department of Material Science and Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom); Lidzey, D. [Department of Physics and Astronomy, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom); Abrams, K.J. [Department of Material Science and Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom); Dapor, M. [European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT-FBK) and Trento Institute for Fundamental Physics and Applications (TIFPA-INFN), via Sommarive 18, I-38123 Trento (Italy); Plenderleith, R.A. [Department of Material Science and Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom); Rimmer, S. [Department of Chemistry, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom); Claeyssens, F.; Rodenburg, C. [Department of Material Science and Engineering, University of Sheffield, Western Bank, Sheffield S10 2TN (United Kingdom)

    2016-12-15

    Recently developed detectors can deliver high resolution and high contrast images of nanostructured carbon based materials in low voltage scanning electron microscopes (LVSEM) with beam deceleration. Monte Carlo Simulations are also used to predict under which exact imaging conditions purely compositional contrast can be obtained and optimised. This allows the prediction of the electron signal intensity in angle selective conditions for back-scattered electron (BSE) imaging in LVSEM and compares it to experimental signals. Angle selective detection with a concentric back scattered (CBS) detector is considered in the model in the absence and presence of a deceleration field, respectively. The validity of the model prediction for both cases was tested experimentally for amorphous C and Cu and applied to complex nanostructured carbon based materials, namely a Poly(N-isopropylacrylamide)/Poly(ethylene glycol) Diacrylate (PNIPAM/PEGDA) semi-interpenetration network (IPN) and a Poly(3-hexylthiophene-2,5-diyl) (P3HT) film, to map nano-scale composition and crystallinity distribution by avoiding experimental imaging conditions that lead to a mixed topographical and compositional contrast - Highlights: • An optimised model for nano-scale analysis of beam sensitive materials by LVSEM. • Simulation and separation of composition and topography in a CBS detector. • Selective angle backscattered electron collection for mapping of polymers.

  10. Angle selective backscattered electron contrast in the low-voltage scanning electron microscope: Simulation and experiment for polymers

    International Nuclear Information System (INIS)

    Wan, Q.; Masters, R.C.; Lidzey, D.; Abrams, K.J.; Dapor, M.; Plenderleith, R.A.; Rimmer, S.; Claeyssens, F.; Rodenburg, C.

    2016-01-01

    Recently developed detectors can deliver high resolution and high contrast images of nanostructured carbon based materials in low voltage scanning electron microscopes (LVSEM) with beam deceleration. Monte Carlo Simulations are also used to predict under which exact imaging conditions purely compositional contrast can be obtained and optimised. This allows the prediction of the electron signal intensity in angle selective conditions for back-scattered electron (BSE) imaging in LVSEM and compares it to experimental signals. Angle selective detection with a concentric back scattered (CBS) detector is considered in the model in the absence and presence of a deceleration field, respectively. The validity of the model prediction for both cases was tested experimentally for amorphous C and Cu and applied to complex nanostructured carbon based materials, namely a Poly(N-isopropylacrylamide)/Poly(ethylene glycol) Diacrylate (PNIPAM/PEGDA) semi-interpenetration network (IPN) and a Poly(3-hexylthiophene-2,5-diyl) (P3HT) film, to map nano-scale composition and crystallinity distribution by avoiding experimental imaging conditions that lead to a mixed topographical and compositional contrast - Highlights: • An optimised model for nano-scale analysis of beam sensitive materials by LVSEM. • Simulation and separation of composition and topography in a CBS detector. • Selective angle backscattered electron collection for mapping of polymers.

  11. Electronics

    Science.gov (United States)

    2001-01-01

    International Acer Incorporated, Hsin Chu, Taiwan Aerospace Industrial Development Corporation, Taichung, Taiwan American Institute of Taiwan, Taipei, Taiwan...Singapore and Malaysia .5 - 4 - The largest market for semiconductor products is the high technology consumer electronics industry that consumes up...Singapore, and Malaysia . A new semiconductor facility costs around $3 billion to build and takes about two years to become operational

  12. ELSA - one year of experience with the Bonn Electron Stretcher Accelerator

    International Nuclear Information System (INIS)

    Althoff, K.H.; Drachenfels, W.v.; Dreist, A.; Husmann, D.; Neckenig, M.; Nuhn, H.D.; Schillo, M.; Schittko, F.J.; Wermelskirchen, C.

    1990-01-01

    One and a half year ago the Bonn Electron Stretcher Accelerator ELSA came into operation. Since then detailed machine studies have been performed between 0.5 and 2 GeV. The control system proved to be a valuable tool for operating the machine. Injection into ELSA including the fast extraction out of the 2.5 GeV booster-synchrotron has been investigated. The adjustment of dipoles and quadrupoles has been checked by closed orbit measurements. The slow extraction at a third integer resonance has been studied in detail. Extraction times up to 200 msec with a duty factor of about 35% are possible. For synchrotron radiation experiments the accumulation and storage of high currents up to 275 mA in ELSA was tested. The beam lifetime (1/e point) at 30 mA is in the order of 15 min. (due to vacuum limitations). Since one year the three experiments have been supplied with external beams. (author) 3 refs., 2 figs., 1 tab

  13. Studies of scintillator optical properties, electronics simulation and data analysis for the BOREXINO neutrino experiment

    International Nuclear Information System (INIS)

    Lewke, Timo

    2013-01-01

    Borexino is a state-of-the-art low-energy neutrino detector. Many results, like the first real-time measurement of 7 Be neutrinos and the detection of pep neutrinos, could be reported. However, still some parts of the solar neutrino spectrum remain unseen. With a better detector understanding and monitoring these unexploited regions could be investigated. The results achieved in course of the present thesis account for accomplishing these improvements. First, the ionization quenching for electrons in liquid scintillators is investigated using a specially designed and build experiment. This effect is especially interesting for low-energy events and, therefore, has a direct influence on the possibility to detect CNO and pp neutrinos. With a coincidence circuit and the properties of Compton scattering the quenching is analysed. Further, the so-called Birks factor kB is measured for the scintillator used in the running Borexino experiment. As the Birks factor is also an important input parameter to simulations of the future large scale neutrino experiment LENA, the Birks factor of LENA's most probable scintillator is determined as well. Second, as muons are responsible for a large amount of background, an excellent working muon veto is essential. During this thesis, it was achieved to monitor the muon tagging stability and efficiency for a long period of time. Further, to verify the muon track reconstruction Monte Carlo simulations are needed. For the Inner Detector of Borexino the simulation is fully operable. In course of this thesis the complete electronics system of the Outer Detector is included into the simulation tool. In this way, a functioning simulation mimicking real physical events is generated. In addition, the output of the simulation can now be accessed and evaluated by the normal data handling system of Borexino. A comparison to real data and, therefore, validating the muon track reconstruction is now possible. Last, to check the neutron tagging, CNGS

  14. Studies of scintillator optical properties, electronics simulation and data analysis for the BOREXINO neutrino experiment

    Energy Technology Data Exchange (ETDEWEB)

    Lewke, Timo

    2013-10-18

    Borexino is a state-of-the-art low-energy neutrino detector. Many results, like the first real-time measurement of {sup 7}Be neutrinos and the detection of pep neutrinos, could be reported. However, still some parts of the solar neutrino spectrum remain unseen. With a better detector understanding and monitoring these unexploited regions could be investigated. The results achieved in course of the present thesis account for accomplishing these improvements. First, the ionization quenching for electrons in liquid scintillators is investigated using a specially designed and build experiment. This effect is especially interesting for low-energy events and, therefore, has a direct influence on the possibility to detect CNO and pp neutrinos. With a coincidence circuit and the properties of Compton scattering the quenching is analysed. Further, the so-called Birks factor kB is measured for the scintillator used in the running Borexino experiment. As the Birks factor is also an important input parameter to simulations of the future large scale neutrino experiment LENA, the Birks factor of LENA's most probable scintillator is determined as well. Second, as muons are responsible for a large amount of background, an excellent working muon veto is essential. During this thesis, it was achieved to monitor the muon tagging stability and efficiency for a long period of time. Further, to verify the muon track reconstruction Monte Carlo simulations are needed. For the Inner Detector of Borexino the simulation is fully operable. In course of this thesis the complete electronics system of the Outer Detector is included into the simulation tool. In this way, a functioning simulation mimicking real physical events is generated. In addition, the output of the simulation can now be accessed and evaluated by the normal data handling system of Borexino. A comparison to real data and, therefore, validating the muon track reconstruction is now possible. Last, to check the neutron

  15. Electron microprobe analyses of selected samples from deep rock disposal experiment No. 1

    International Nuclear Information System (INIS)

    Hlava, P.F.; Chambers, W.F.

    1976-04-01

    Deep Rock Disposal Experiment No. 1 was designed to provide information about the interaction between a molten, glass-based, nuclear waste simulant and rock material. Selected samples from this experiment were examined by optical microscopy and electron probe microanalysis. Analysis of the homogenized material in the convection cell that was created in the central portion of the melt region shows that an amount of rock equal to about one-half of the original amount of waste simulant was incorporated in the melt during the experiment. Stagnant melt at the sides of the cell formed a glass with large compositional gradients. A white band separated the convected and stagnant materials. The color of the band is attributed to light scattering by small crystallites formed during cooling. Four types of crystallites grew from the melt: two oxides, a Mg--Fe borate, and a silicate. Spinel (MgO, Cr 2 O 3 , FeO (Fe 2 O 3 ), and NiO) was the most common crystallite in the glass. The spinel crystallites found within the convection cell displayed skeletal morphology and oscillatory zoning which indicates growth at varying temperatures as they were carried along by convection. A single cluster of nonskeletal (Fe,Cr) 2 O 3 crystallites was found at the bottom of the melt zone where convection did not occur. Mg--Fe borate crystallites grew in clusters in the central portion of the convection cell after convection ceased. A silicate similar to Fe-rich diopside (CaMgSi 2 O 6 ) with unusual amounts of Ce 2 O 3 and other heavy metal oxides formed as larger crystallites in the stagnant melt at the side of the convection cell and as many very small crystallites in the white band

  16. ON EXPERIENCE OF THE ELECTRONIC DOCUMENT MANAGEMENT SYSTEM IMPLEMENTATION IN THE MEDICAL UNIVERSITY

    OpenAIRE

    A. V. Semenets; V. Yu. Kovalok

    2015-01-01

    An importance of the application of the electronic document management to the Ukraine healthcare is shown. The electronic document management systems market overview is presented. Example of the usage of the open-source electronic document management system in the Ternopil State Medical University by I. Ya. Horbachevsky is shown. The implementation capabilities of the electronic document management system within a cloud services are shown. The electronic document management features of the Mi...

  17. 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

  18. The experiments of high power electron beam emission by the K-9M-57 and K-9M-58 rockets

    International Nuclear Information System (INIS)

    Kaneko, Osamu; Sasaki, Susumu; Yamori, Akira; Hagiwara, Michinobu; Kawashima, Nobuki

    1977-01-01

    Active experiments have been conducted to obtain the precise picture of the ionosphere and magnetosphere. As the turbulence source of the active experiment by the authors, electron beam was employed, and the variation of the rocket potential, wave excitation and turbulence of peripheral plasma were investigated. The rated voltage and current of the present electron gun were 6 kV and 500 mA, respectively. The Langmuir probe, floating probe, optical detector and wave receiver were used for the measurement of various phenomena associated with electron beam emission. The experimental data on the voltage-current characteristics of the electron gun, the rocket potential, total light emission and plasma density and temperature were obtained by the K-9M-57 and K-9M-58 rockets. (Yoshimori, M.)

  19. The role of secondary electrons in some experiments determining fluorescence emission from nitrogen C3Πu levels

    International Nuclear Information System (INIS)

    Blanco, F.; Arqueros, F.

    2005-01-01

    The processes involved in fluorescence emission from C 3 Π u levels of N 2 molecule by electron impact are studied. Secondary electrons are shown to play an important role in typical experiments for the measurement of emission cross sections and fluorescence yields, dominating at high impact energies. A simple model is proposed which accounts for fluorescence measurements in a wide range of experimental conditions, and in particular for some recent results up to 1 GeV energies

  20. Wave excitation in the experiment with an electron beam at the Dzhajkiken Exos-B Japanese satellite

    International Nuclear Information System (INIS)

    Kavashima, N.

    1985-01-01

    An experiment on investigation of beam-plasma interaction in the magnetosphere is carried out at the ''Dzhajkiken (Exos-B)'' japanese satellite. 100-200 eV and 0.25-1 μA electron beam was injected into the magnetosphere. Using LF and HF detectors in low altitude range waves with the frequencies close to the upper hybrid and electron frequencies are recorded. Beyond the plasmapause the satellite was charged to the potential corresponding to the beam energy

  1. Serious limitations of the QTL/Microarray approach for QTL gene discovery

    Directory of Open Access Journals (Sweden)

    Warden Craig H

    2010-07-01

    Full Text Available Abstract Background It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL. However, the effectiveness of this approach has not been assessed. Results Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons between congenic and background strains. Three studies led to the identification of an underlying QTL gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of QTL regulated in cis (cis eQTL showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP. Conclusions The literature shows limited successes from the QTL/microarray approach to identify QTL genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select cis-eQTL over trans-eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false cis-eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes

  2. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

    Science.gov (United States)

    Stokes, Todd H; Torrance, JT; Li, Henry; Wang, May D

    2008-01-01

    Background A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers

  3. ON EXPERIENCE OF THE ELECTRONIC DOCUMENT MANAGEMENT SYSTEM IMPLEMENTATION IN THE MEDICAL UNIVERSITY

    Directory of Open Access Journals (Sweden)

    A. V. Semenets

    2015-05-01

    Full Text Available An importance of the application of the electronic document management to the Ukraine healthcare is shown. The electronic document management systems market overview is presented. Example of the usage of the open-source electronic document management system in the Ternopil State Medical University by I. Ya. Horbachevsky is shown. The implementation capabilities of the electronic document management system within a cloud services are shown. The electronic document management features of the Microsoft Office 365 and Google Apps For Education are compared. Some results of the usage of the Google Apps For Education inTSMUas electronic document management system are presented.

  4. Physicians’ experience adopting the electronic transfer of care communication tool: barriers and opportunities

    Directory of Open Access Journals (Sweden)

    de Grood C

    2015-01-01

    Full Text Available Chloe de Grood, Katherine Eso, Maria Jose Santana Department of Community Health Sciences, W21C Research and Innovation Centre, Institute of Public Health, University of Calgary, Calgary, AB, Canada Purpose: The purpose of this study was to assess physicians' perceptions on a newly developed electronic transfer of care (e-TOC communication tool and identify barriers and opportunities toward its adoption. Participants and methods: The study was conducted in a tertiary care teaching center as part of a randomized controlled trial assessing the efficacy of an e-TOC communication tool. The e-TOC technology was developed through iterative consultation with stakeholders. This e-TOC summary was populated by acute care physicians (AcPs and communicated electronically to community care physicians (CcPs. The AcPs consisted of attending physicians, resident trainees, and medical students rotating through the Medical Teaching Unit. The CcPs were health care providers caring for patients discharged from hospital to the community. AcPs and CcPs completed validated surveys assessing their experience with the newly developed e-TOC tool. Free text questions were added to gather general comments from both groups of physicians. Units of analysis were individual physicians. Data from the surveys were analyzed using mixed methods. Results: AcPs completed 138 linked pre- and post-rotation surveys. At post-rotation, each AcP completed an average of six e-TOC summaries, taking an average of 37 minutes per e-TOC summary. Over 100 CcPs assessed the quality of the TOC summaries, with an overall rating of 8.3 (standard deviation: 1.48; on a scale of 1–10. Thematic analyses revealed barriers and opportunities encountered by physicians toward the adoption of the e-TOC tool. While the AcPs highlighted issues with timeliness, usability, and presentation, the CcPs identified barriers accessing the web-based TOC summaries, emphasizing that the summaries were timely and the

  5. Lower hybrid heating data on the Wega experiment revisited using ion stochastic heating and electron Landau damping theories

    International Nuclear Information System (INIS)

    Gormezano, C.; Hess, W.; Ichtchenko, G.

    1980-07-01

    The already obtained data on the Wega Tokamak by lower hybrid heating (f=500 MHz - Psub(HF)=130 KW) are revisited in the light of recent theories on ion stochastic heating and quasi-linear electron Landau damping. It is possible to correctly estimate with these theories the fast ion mean energy, the H.F. power density coupled to the ions and that coupled to the electrons. The values of the parallel index of refraction, Nsub(//), which are necessary to obtain a good quantitative agreement between experiment and theoretical estimates, are the same for the ions and for the electrons, even though at higher values than expected

  6. A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy

    Directory of Open Access Journals (Sweden)

    Archer Kellie J

    2008-02-01

    Full Text Available Abstract Background With the popularity of DNA microarray technology, multiple groups of researchers have studied the gene expression of similar biological conditions. Different methods have been developed to integrate the results from various microarray studies, though most of them rely on distributional assumptions, such as the t-statistic based, mixed-effects model, or Bayesian model methods. However, often the sample size for each individual microarray experiment is small. Therefore, in this paper we present a non-parametric meta-analysis approach for combining data from independent microarray studies, and illustrate its application on two independent Affymetrix GeneChip studies that compared the gene expression of biopsies from kidney transplant recipients with chronic allograft nephropathy (CAN to those with normal functioning allograft. Results The simulation study comparing the non-parametric meta-analysis approach to a commonly used t-statistic based approach shows that the non-parametric approach has better sensitivity and specificity. For the application on the two CAN studies, we identified 309 distinct genes that expressed differently in CAN. By applying Fisher's exact test to identify enriched KEGG pathways among those genes called differentially expressed, we found 6 KEGG pathways to be over-represented among the identified genes. We used the expression measurements of the identified genes as predictors to predict the class labels for 6 additional biopsy samples, and the predicted results all conformed to their pathologist diagnosed class labels. Conclusion We present a new approach for combining data from multiple independent microarray studies. This approach is non-parametric and does not rely on any distributional assumptions. The rationale behind the approach is logically intuitive and can be easily understood by researchers not having advanced training in statistics. Some of the identified genes and pathways have been

  7. Elastic and inelastic electrons in the double-slit experiment: A variant of Feynman's which-way set-up.

    Science.gov (United States)

    Frabboni, Stefano; Gazzadi, Gian Carlo; Grillo, Vincenzo; Pozzi, Giulio

    2015-07-01

    Modern nanotechnology tools allowed us to prepare slits of 90 nm width and 450 nm spacing in a screen almost completely opaque to 200 keV electrons. Then by covering both slits with a layer of amorphous material and carrying out the experiment in a conventional transmission electron microscope equipped with an energy filter we can demonstrate that the diffraction pattern, taken by selecting the elastically scattered electrons, shows the presence of interference fringes, but with a bimodal envelope which can be accounted for by taking into account the non-constant thickness of the deposited layer. However, the intensity of the inelastically scattered electrons in the diffraction plane is very broad and at the limit of detectability. Therefore the experiment was repeated using an aluminum film and a microscope also equipped with a Schottky field emission gun. It was thus possible to observe also the image due to the inelastically scattered electron, which does not show interference phenomena both in the Fraunhofer or Fresnel regimes. If we assume that inelastic scattering through the thin layer covering the slits provides the dissipative process of interaction responsible for the localization mechanism, then these experiments can be considered a variant of the Feynman which-way thought experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Accurate detection of carcinoma cells by use of a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shohei Yamamura

    Full Text Available BACKGROUND: Accurate detection and analysis of circulating tumor cells plays an important role in the diagnosis and treatment of metastatic cancer treatment. METHODS AND FINDINGS: A cell microarray chip was used to detect spiked carcinoma cells among leukocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene; and the formation of monolayers of leukocytes in the microchambers was observed. Cultured human T lymphoblastoid leukemia (CCRF-CEM cells were used to examine the potential of the cell microarray chip for the detection of spiked carcinoma cells. A T lymphoblastoid leukemia suspension was dispersed on the chip surface, followed by 15 min standing to allow the leukocytes to settle down into the microchambers. Approximately 29 leukocytes were found in each microchamber when about 600,000 leukocytes in total were dispersed onto a cell microarray chip. Similarly, when leukocytes isolated from human whole blood were used, approximately 89 leukocytes entered each microchamber when about 1,800,000 leukocytes in total were placed onto the cell microarray chip. After washing the chip surface, PE-labeled anti-cytokeratin monoclonal antibody and APC-labeled anti-CD326 (EpCAM monoclonal antibody solution were dispersed onto the chip surface and allowed to react for 15 min; and then a microarray scanner was employed to detect any fluorescence-positive cells within 20 min. In the experiments using spiked carcinoma cells (NCI-H1650, 0.01 to 0.0001%, accurate detection of carcinoma cells was achieved with PE-labeled anti-cytokeratin monoclonal antibody. Furthermore, verification of carcinoma cells in the microchambers was performed by double staining with the above monoclonal antibodies. CONCLUSION: The potential application of the cell microarray chip for the detection of CTCs was shown, thus demonstrating accurate detection by double staining for cytokeratin and EpCAM at the single carcinoma cell level.

  9. Exploring the use of internal and externalcontrols for assessing microarray technical performance

    Directory of Open Access Journals (Sweden)

    Game Laurence

    2010-12-01

    Full Text Available Abstract Background The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. Results A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes" was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification. External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC metrics. Conclusions These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray

  10. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets

    Directory of Open Access Journals (Sweden)

    Cohen Aaron

    2009-02-01

    Full Text Available Abstract Background Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarkers for disease and discover novel types of therapeutics and the task of finding information in journal articles on sets of genes is common for translational researchers working with microarray data. However, manually searching and scanning the literature references returned from PubMed is a time-consuming task for scientists. We built and evaluated an automatic summarizer of information on genes studied in microarray experiments. The Gene Information Clustering and Summarization System (GICSS is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering. The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. Results The clusters generated by GICSS were validated by scientists during their microarray analysis process. In addition, presenting sentences in the abstract provided significantly more important information to the users than just showing the title in the default PubMed format. Conclusion The evaluation results suggest that GICSS can be useful for researchers in genomic area. In addition, the hybrid evaluation method, partway between intrinsic and extrinsic system evaluation, may enable researchers to gauge the true usefulness of the tool for the scientists in their natural analysis workflow and also elicit suggestions for future enhancements. Availability GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html

  11. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam

    2016-10-09

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  12. Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

    KAUST Repository

    Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

    2016-01-01

    High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

  13. A function-behavior-structure framework for quantification and reproduction of emotional haptic experience in using an electronic device

    International Nuclear Information System (INIS)

    Bae, Il Ju; Lee, Soo Hong; Ok, Hyung Seok; Lee, Jae In

    2013-01-01

    A user's haptic experience in using an electronic device is related to the continuous and dynamic variances of the structural state of the device. Since the changes of the structural component cause complex changes of the dynamics, it is difficult to predict the user's experience. We propose a function-behavior-structure framework to predict and improve the user's experience. The framework consists of the function layer model, the behavior layer model, and the structure layer model. Especially, the independent behavior model to the device is based on a physical phenomenon. Finally, an optimized structure which produces an ideal haptic experience for a cell phone is suggested.

  14. Controlled molecules for X-ray diffraction experiments at free-electron lasers

    International Nuclear Information System (INIS)

    Stern, Stephan

    2013-12-01

    X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

  15. Pharmacy Customers’ Experiences With Electronic Prescriptions: Cross-Sectional Survey on Nationwide Implementation in Finland

    Science.gov (United States)

    Timonen, Johanna; Ahonen, Riitta

    2018-01-01

    Background One of the forerunners in electronic health, Finland has introduced electronic prescriptions (ePrescriptions) nationwide by law. This has led to significant changes for pharmacy customers. Despite the worldwide ambition to develop ePrescription services, there are few reports of nationally adopted systems and particularly on the experiences of pharmacy customers. Objective The aim of this study was to investigate Finnish pharmacy customers’ (1) experiences with purchasing medicines with ePrescriptions; (2) experiences with renewing ePrescriptions and acting on behalf of someone else at the pharmacy; (3) ways in which customers keep up to date with their ePrescriptions; and (4) overall satisfaction with ePrescriptions. Methods Questionnaires were distributed to 2913 pharmacy customers aged ≥18 years purchasing prescription medicines for themselves with an ePrescription in 18 community pharmacies across Finland in autumn 2015. Customers’ experiences were explored with 10 structured questions. The data were stored in SPSS for Windows and subjected to descriptive analysis, chi-square, Fisher exact, Kolmogorov-Smirnov, the Mann-Whitney U, and Kruskal-Wallis tests. Results Completed questionnaires were returned by 1288 customers, a response rate of 44.19% (1288/2913). The majority of the respondents did not encounter any problems during pharmacy visits (1161/1278, 90.85%) and were informed about the current status of their ePrescriptions after their medication was dispensed (1013/1276, 79.44%). Over half of the respondents had usually received a patient instruction sheet from their physician (752/1255, 59.92%), and nearly all of them regarded its content as clear (711/724, 98.2%). Half of the respondents had renewed their ePrescriptions through the pharmacy (645/1281, 50.35%), and one-third of them had acted on behalf of someone else with ePrescriptions (432/1280, 33.75%). Problems were rarely encountered in the renewal process (49/628, 7.8%) or when

  16. Pharmacy Customers' Experiences With Electronic Prescriptions: Cross-Sectional Survey on Nationwide Implementation in Finland.

    Science.gov (United States)

    Lämsä, Elina; Timonen, Johanna; Ahonen, Riitta

    2018-02-23

    One of the forerunners in electronic health, Finland has introduced electronic prescriptions (ePrescriptions) nationwide by law. This has led to significant changes for pharmacy customers. Despite the worldwide ambition to develop ePrescription services, there are few reports of nationally adopted systems and particularly on the experiences of pharmacy customers. The aim of this study was to investigate Finnish pharmacy customers' (1) experiences with purchasing medicines with ePrescriptions; (2) experiences with renewing ePrescriptions and acting on behalf of someone else at the pharmacy; (3) ways in which customers keep up to date with their ePrescriptions; and (4) overall satisfaction with ePrescriptions. Questionnaires were distributed to 2913 pharmacy customers aged ≥18 years purchasing prescription medicines for themselves with an ePrescription in 18 community pharmacies across Finland in autumn 2015. Customers' experiences were explored with 10 structured questions. The data were stored in SPSS for Windows and subjected to descriptive analysis, chi-square, Fisher exact, Kolmogorov-Smirnov, the Mann-Whitney U, and Kruskal-Wallis tests. Completed questionnaires were returned by 1288 customers, a response rate of 44.19% (1288/2913). The majority of the respondents did not encounter any problems during pharmacy visits (1161/1278, 90.85%) and were informed about the current status of their ePrescriptions after their medication was dispensed (1013/1276, 79.44%). Over half of the respondents had usually received a patient instruction sheet from their physician (752/1255, 59.92%), and nearly all of them regarded its content as clear (711/724, 98.2%). Half of the respondents had renewed their ePrescriptions through the pharmacy (645/1281, 50.35%), and one-third of them had acted on behalf of someone else with ePrescriptions (432/1280, 33.75%). Problems were rarely encountered in the renewal process (49/628, 7.8%) or when acting on behalf of another person (25

  17. Controlled molecules for X-ray diffraction experiments at free-electron lasers

    Energy Technology Data Exchange (ETDEWEB)

    Stern, Stephan

    2013-12-15

    X-ray diffractive imaging is at the very heart of materials science and has been utilized for decades to solve unknown molecular structures. Nowadays, it serves as the key method of structural biology to solve molecular structures of large biological molecules comprising several thousand or even millions of atoms. However, X-ray diffraction from isolated molecules is very weak. Therefore, the regular and periodic arrangement of a huge number of identical copies of a certain molecule of interest within a crystal lattice has been a necessary condition in order to exploit Bragg diffraction of X-rays. This results in a huge increase in scattered signal and a strongly improved signal-to-noise ratio compared to diffraction from non-crystalline samples. The major bottleneck of structural biology is that many of biologically interesting molecules refuse to form crystals of sufficient size to be used at synchrotron X-ray lightsources. However, novel X-ray free-electron lasers (XFELs), which became operational very recently, promise to address this issue. X-ray pulses provided by XFELs are many orders of magnitude more intense than X-ray pulses from a synchrotron source and at the same time as short as only several tens of femtoseconds. Combined with wavelengths in the nm-pm range, XFELs are well-suited to study ultrafast atomic and molecular dynamics. Additionally, the ultrashort pulses can be utilized to circumvent the damage threshold which set a limit to the incident intensity in X-ray diffraction experiments before. At XFELs, though eventually destroying the investigated sample, no significant sample deterioration happens on the ultrashort timescale of the XFEL pulse and the measured diffraction pattern is due to an (almost) unharmed sample. In the framework of this thesis, the approach of utilizing the highly intense XFEL pulses for X-ray diffraction of weakly-scattering non-crystalline samples was taken to the limit of small isolated molecules. X-ray diffraction was

  18. A study of muon neutrino to electron neutrino oscillations in the MINOS experiment

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Tingjun [Stanford Univ., CA (United States)

    2009-03-01

    The observation of neutrino oscillations (neutrino changing from one flavor to another) has provided compelling evidence that the neutrinos have non-zero masses and that leptons mix, which is not part of the original Standard Model of particle physics. The theoretical framework that describes neutrino oscillation involves two mass scales (Δmatm2 and Δmsol2), three mixing angles (θ12, θ23, and θ13) and one CP violating phase (δCP). Both mass scales and two of the mixing angles (θ12 and θ23) have been measured by many neutrino experiments. The mixing angle θ13, which is believed to be very small, remains unknown. The current best limit on θ13 comes from the CHOOZ experiment: θ13 < 11° at 90% C.L. at the atmospheric mass scale. δCP is also unknown today. MINOS, the Main Injector Neutrino Oscillation Search, is a long baseline neutrino experiment based at Fermi National Accelerator Laboratory. The experiment uses a muon neutrino beam, which is measured 1 km downstream from its origin in the Near Detector at Fermilab and then 735 km later in the Far Detector at the Soudan mine. By comparing these two measurements, MINOS can obtain parameters in the atmospheric sector of neutrino oscillations. MINOS has published results on the precise measurement of Δmatm2 and θ23 through the disappearance of muon neutrinos in the Far Detector and on a search for sterile neutrinos by looking for a deficit in the number of neutral current interactions seen in the Far Detector. MINOS also has the potential to improve the limit on the neutrino mixing angle θ13 or make the first measurement of its value by searching for an electron neutrino appearance signal in the Far Detector. This is the focus of the study presented in this thesis. We developed a neural network based algorithm to

  19. Pixel array detector for X-ray free electron laser experiments

    Energy Technology Data Exchange (ETDEWEB)

    Philipp, Hugh T., E-mail: htp2@cornell.edu [Department of Physics, Laboratory of Solid State Physics, Cornell University, Ithaca, NY 14853 (United States); Hromalik, Marianne [Electrical and Computer Engineering, SUNY Oswego, Oswego, NY 13126 (United States); Tate, Mark; Koerner, Lucas [Department of Physics, Laboratory of Solid State Physics, Cornell University, Ithaca, NY 14853 (United States); Gruner, Sol M. [Department of Physics, Laboratory of Solid State Physics, Cornell University, Ithaca, NY 14853 (United States); Wilson Laboratory, Cornell University, CHESS, Ithaca, NY 14853 (United States)

    2011-09-01

    X-ray free electron lasers (XFELs) promise to revolutionize X-ray science with extremely high peak brilliances and femtosecond X-ray pulses. This will require novel detectors to fully realize the potential of these new sources. There are many current detector development projects aimed at the many challenges of meeting the XFEL requirements . This paper describes a pixel array detector (PAD) that has been developed for the Coherent X-ray Imaging experiment at the Linac Coherent Light Source (LCLS) at the SLAC National Laboratory . The detector features 14-bit in-pixel digitization; a 2-level in-pixel gain setting that can be used to make an arbitrary 2-D gain pattern that is adaptable to a particular experiment; the ability to handle instantaneous X-ray flux rates of 10{sup 17} photons per second; and continuous frames rates in excess of 120 Hz. The detector uses direct detection of X-rays in a silicon diode. The charge produced by the diode is integrated in a pixilated application specific integrated circuit (ASIC) which digitizes collected holes with single X-ray photon capability. Each ASIC is 194x185 pixels, each pixel is 110{mu}mx110{mu}m on a side. Each pixel can detect up to 2500 X-rays per frame in low-gain mode, yet easily detects single photons at high-gain. Cooled, single-chip detectors have been built and meet all the required specifications. SLAC National Laboratory is engaged in constructing a tiled, multi-chip 1516x1516 pixel detector.

  20. Introducing sexual orientation and gender identity into the electronic health record: one academic health center's experience.

    Science.gov (United States)

    Callahan, Edward J; Sitkin, Nicole; Ton, Hendry; Eidson-Ton, W Suzanne; Weckstein, Julie; Latimore, Darin

    2015-02-01

    Many U.S. populations experience significant health disparities. Increasing health care providers' awareness of and education about sexual orientation (SO) and gender identity (GI) diversity could help reduce health disparities among lesbian, gay, bisexual, and transgender (LGBT) patients. The authors share the University of California, Davis, Health System's (UCDHS's) experience as it became the first U.S. academic health center to formally introduce patient SO/GI demographic data into its electronic health record (EHR) as a step toward reducing LGBT health disparities. Adding these data to the EHR initially met with resistance. The authors, members of the UCDHS Task Force for Inclusion of SO/GI in the EHR, viewed this resistance as an invitation to educate leaders, providers, and staff about LGBT health disparities and to expose providers to techniques for discussing SO/GI with patients. They describe the strategies they employed to effect institutional culture change, including involvement of senior leadership, key informant interviews, educational outreach via grand rounds and resident workshops, and creation of a patient safety net through inviting providers to self-identify as welcoming LGBT patients. The ongoing cultural change process has inspired spin-off projects contributing to an improved climate for LGBT individuals at UCDHS, including an employee organization supporting SO/GI diversity, support for and among LGBT medical learners through events and listservs, development and implementation of an LGBT health curriculum, and creation of peer navigator programs for LGBT patients with cancer. The authors reflect on lessons learned and on institutional pride in and commitment to providing quality care for LGBT patients.

  1. Injection Methods and Instrumentation for Serial X-ray Free Electron Laser Experiments

    Science.gov (United States)

    James, Daniel

    Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques. The XFEL is characterized by high intensity pulses, which are only about 50 femtoseconds in duration. The intensity allows for scattering from microscopic particles, while the short pulses offer a way to outrun radiation damage. XFELs are powerful enough to obliterate most samples in a single pulse. While this allows for a "diffract and destroy" methodology, it also requires instrumentation that can position microscopic particles into the X-ray beam (which may also be microscopic), continuously renew the sample after each pulse, and maintain sample viability during data collection. Typically these experiments have used liquid microjets to continuously renew sample. The high flow rate associated with liquid microjets requires large amounts of sample, most of which runs to waste between pulses. An injector designed to stream a viscous gel-like material called lipidic cubic phase (LCP) was developed to address this problem. LCP, commonly used as a growth medium for membrane protein crystals, lends itself to low flow rate jetting and so reduces the amount of sample wasted significantly. This work discusses sample delivery and injection for XFEL experiments. It reviews the liquid microjet method extensively, and presents the LCP injector as a novel device for serial crystallography, including detailed protocols for the LCP injector and anti-settler operation.

  2. Meaningful Use of Electronic Health Records: Experiences From the Field and Future Opportunities.

    Science.gov (United States)

    Slight, Sarah Patricia; Berner, Eta S; Galanter, William; Huff, Stanley; Lambert, Bruce L; Lannon, Carole; Lehmann, Christoph U; McCourt, Brian J; McNamara, Michael; Menachemi, Nir; Payne, Thomas H; Spooner, S Andrew; Schiff, Gordon D; Wang, Tracy Y; Akincigil, Ayse; Crystal, Stephen; Fortmann, Stephen P; Bates, David W

    2015-09-18

    With the aim of improving health care processes through health information technology (HIT), the US government has promulgated requirements for "meaningful use" (MU) of electronic health records (EHRs) as a condition for providers receiving financial incentives for the adoption and use of these systems. Considerable uncertainty remains about the impact of these requirements on the effective application of EHR systems. The Agency for Healthcare Research and Quality (AHRQ)-sponsored Centers for Education and Research in Therapeutics (CERTs) critically examined the impact of the MU policy relating to the use of medications and jointly developed recommendations to help inform future HIT policy. We gathered perspectives from a wide range of stakeholders (N=35) who had experience with MU requirements, including academicians, practitioners, and policy makers from different health care organizations including and beyond the CERTs. Specific issues and recommendations were discussed and agreed on as a group. Stakeholders' knowledge and experiences from implementing MU requirements fell into 6 domains: (1) accuracy of medication lists and medication reconciliation, (2) problem list accuracy and the shift in HIT priorities, (3) accuracy of allergy lists and allergy-related standards development, (4) support of safer and effective prescribing for children, (5) considerations for rural communities, and (6) general issues with achieving MU. Standards are needed to better facilitate the exchange of data elements between health care settings. Several organizations felt that their preoccupation with fulfilling MU requirements stifled innovation. Greater emphasis should be placed on local HIT configurations that better address population health care needs. Although MU has stimulated adoption of EHRs, its effects on quality and safety remain uncertain. Stakeholders felt that MU requirements should be more flexible and recognize that integrated models may achieve information

  3. DAQ system for testing RPC front-end electronics of the INO experiment

    International Nuclear Information System (INIS)

    Hari Prasad, K.; Sukhwani, Menka; Kesarkar, Tushar A.; Kumar, Sandeep; Chandratre, V.B.; Das, D.; Shinde, R.R.; Satyanarayana, B.

    2015-01-01

    The Resistive Plate Chamber (RPC) is the active detector element in the INO experiment. The in-house developed ANUSPARSH-III ASICs are being used as front-end electronics of the detector. The 2 m X 2 m RPC being used has 64-readout channels on X-side and 64-readout channels on Y-side. In order to test and validate the FE along with the RPC, a 64-channel DAQ system has been designed and developed. The detector parameters to be measured are noise rate, efficiency, hit pattern register and time resolution. The salient features of the DAQ system are: 64-channel LVDS receiver in FPGA, FPGA based parameter calculations and a micro controller for acquiring the processed data from FPGAs and sent through Ethernet and USB interfaces. The DAQ system consists of following parts: Two FPGAs each receiving 32 LVDS channels, FPGA firm-ware, micro controller firm-ware, Ethernet interface, embedded web server hosting data analysis software, USB interface, and Lab-windows based data analysis software. The DAQ system has been tested at TIFR with 1 m X 1 m RPC

  4. Smart Trigger Pre-Processor Custom Electronics for the PHENIX Experiment

    International Nuclear Information System (INIS)

    Nagle, James L.

    2003-01-01

    OAK-B135 The document provides a final technical report on activities and accomplishments of the experimental relativistic heavy ion physics group at the University of Colorado at Boulder as supported by the Outstanding Junior Investigator Program, Division of Nuclear Physics at the Department of Energy. All of the goals of the grant proposal were achieved during this last year of the Outstanding Junior Investigator funding period. The development of a Smart Trigger Pre-Processor module for fast trigger primitive calculations in the PHENIX experiment has been completed. We finalized the board design, constructed and tested two prototype modules, and with additional funding from the PHENIX project, we fabricated a full set of 15 modules for the Muon Tracking system. During Run-4 at RHIC:, we have begun the process of integrating these modules into the PHENIX data acquisition system, Additionally, we put a large Effort into developing new trigger and fast-track analysis methods for J j J data filtering and reconstruction. These algorithms make use of the trigger primitivE∼s generated via the new electronics

  5. Refrigerant flow through electronic expansion valve: Experiment and neural network modeling

    International Nuclear Information System (INIS)

    Cao, Xiang; Li, Ze-Yu; Shao, Liang-Liang; Zhang, Chun-Lu

    2016-01-01

    Highlights: • Experimental data from different sources were used in comparison of EEV models. • Artificial neural network in EEV modeling is superior to literature correlations. • Artificial neural network with 4-4-1 structure and S function is recommended. • Artificial neural network is flexible for EEV mass flow rate and opening prediction. - Abstract: Electronic expansion valve (EEV) plays a crucial role in controlling refrigerant mass flow rate of refrigeration or heat pump systems for energy savings. However, complexities in two-phase throttling process and geometry make accurate modeling of EEV flow characteristics more difficult. This paper developed an artificial neural network (ANN) model using refrigerant inlet and outlet pressures, inlet subcooling, EEV opening as ANN inputs, refrigerant mass flow rate as ANN output. Both linear and nonlinear transfer functions in hidden layer were used and compared to each other. Experimental data from multiple sources including in-house experiments of one EEV with R410A were used for ANN training and test. In addition, literature correlations were compared with ANN as well. Results showed that the ANN model with nonlinear transfer function worked well in all cases and it is much accurate than the literature correlations. In all cases, nonlinear ANN predicted refrigerant mass flow rates within ±0.4% average relative deviation (A.D.) and 2.7% standard deviation (S.D.), meanwhile it predicted the EEV opening at 0.1% A.D. and 2.1% S.D.

  6. Measuring $\\theta_{13}$ via Muon Neutrino to Electron Neutrino Oscillations in the MINOS Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Toner, Ruth B. [Univ. of Cambridge (United Kingdom). Pembroke College

    2011-01-01

    One of the primary goals in neutrino physics at the present moment is to make a measurement of the neutrino oscillation parameter $\\theta_{13}$. This parameter, in addition to being unknown, could potentially allow for the introduction of CP violation into the lepton sector. The MINOS long-baseline neutrino oscillation experiment has the ability to make a measurement of this parameter, by looking for the oscillation of muon neutrinos to electron neutrinos between a Near and Far Detector over a distance of 735 km. This thesis discusses the development of an analysis framework to search for this oscillation mode. Two major improvements to pre-existing analysis techniques have been implemented by the author. First, a novel particle ID technique based on strip topology, known as the Library Event Matching (LEM) method, is optimized for use in MINOS. Second, a multiple bin likelihood method is developed to fit the data. These two improvements, when combined, increase MINOS' sensitivity to $\\sin^2(2\\theta_{13})$ by 27\\% over previous analyses. This thesis sees a small excess over background in the Far Detector. A Frequentist interpretation of the data rules out $\\theta_{13}=0$ at 91\\%. A Bayesian interpretation of the data is also presented, placing the most stringent upper boundary on the oscillation parameter to date, at $\\sin^2(2\\theta_{13})<0.09(0.015)$ for the Normal (Inverted) Hierarchy and $\\delta_{CP}=0$.

  7. Electronic Health Record (EHR) Organizational Change: Explaining Resistance Through Profession, Organizational Experience, and EHR Communication Quality.

    Science.gov (United States)

    Barrett, Ashley K

    2018-04-01

    The American Recovery and Reinvestment Act passed by the U.S. government in 2009 mandates that all healthcare organizations adopt a certified electronic health record (EHR) system by 2015. Failure to comply will result in Medicare reimbursement penalties, which steadily increase with each year of delinquency. There are several repercussions of this seemingly top-down, rule-bound organizational change-one of which is employee resistance. Given the penalties for violating EHR meaningful use standards are ongoing, resistance to this mandate presents a serious issue for healthcare organizations. This study surveyed 345 employees in one healthcare organization that recently implemented an EHR. Analysis of variance results offer theoretical and pragmatic contributions by demonstrating physicians, nurses, and employees with more experience in their organization are the most resistant to EHR change. The job characteristics model is used to explain these findings. Hierarchical regression analyses also demonstrate the quality of communication surrounding EHR implementation-from both formal and informal sources-is negatively associated with EHR resistance and positively associated with perceived EHR implementation success and EHR's perceived relative advantage.

  8. 1-MeV electron beam propagation experiments in neutral gas

    International Nuclear Information System (INIS)

    Greenspan, M.A.; Rose, E.A.

    1984-01-01

    Experiments were performed studying the propagation of a 1-MeV, 10-ns electron beam at currents of 2-8 kA. Propagation was studied in a 7.6-cm-diam glass guide tube, the same tube with a conducting screen inside, and in a 3.4-m-diam chamber. In the guide tube with the screen, ion-focused propagation is observed at low pressures (≤ 40 Pa) with net current equal to beam current. At higher pressures (55-130 Pa), a notch in beam current is observed for pressure time products of ≅ 100 Pa-ns. Between 270 Pa and 1070 Pa, good propagation is again observed with net currents of 50-70% of the beam current. The net current fraction of beam current increases with increasing pressure and with decreasing beam current. At pressure above 1070 Pa, hose instability occurs, and net current nearly equal to beam current is observed. The hose frequency is in reasonable accord with theory. Nose erosion is minimized at pressures for 1000-2000 Pa depending on beam current, and increases at lower and higher pressures

  9. Gaussian mixture clustering and imputation of microarray data.

    Science.gov (United States)

    Ouyang, Ming; Welsh, William J; Georgopoulos, Panos

    2004-04-12

    In microarray experiments, missing entries arise from blemishes on the chips. In large-scale studies, virtually every chip contains some missing entries and more than 90% of the genes are affected. Many analysis methods require a full set of data. Either those genes with missing entries are excluded, or the missing entries are filled with estimates prior to the analyses. This study compares methods of missing value estimation. Two evaluation metrics of imputation accuracy are employed. First, the root mean squared error measures the difference between the true values and the imputed values. Second, the number of mis-clustered genes measures the difference between clustering with true values and that with imputed values; it examines the bias introduced by imputation to clustering. The Gaussian mixture clustering with model averaging imputation is superior to all other imputation methods, according to both evaluation metrics, on both time-series (correlated) and non-time series (uncorrelated) data sets.

  10. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  11. Design of a covalently bonded glycosphingolipid microarray

    DEFF Research Database (Denmark)

    Arigi, Emma; Blixt, Klas Ola; Buschard, Karsten

    2012-01-01

    , the major classes of plant and fungal GSLs. In this work, a prototype "universal" GSL-based covalent microarray has been designed, and preliminary evaluation of its potential utility in assaying protein-GSL binding interactions investigated. An essential step in development involved the enzymatic release...... of the fatty acyl moiety of the ceramide aglycone of selected mammalian GSLs with sphingolipid N-deacylase (SCDase). Derivatization of the free amino group of a typical lyso-GSL, lyso-G(M1), with a prototype linker assembled from succinimidyl-[(N-maleimidopropionamido)-diethyleneglycol] ester and 2...

  12. Development of a high repetition rate laser-plasma accelerator for ultra-fast electron diffraction experiments

    International Nuclear Information System (INIS)

    Beaurepaire, B.

    2009-01-01

    Electronic microscopy and electron diffraction allowed the understanding of the organization of atoms in matter. Using a temporally short source, one can measure atomic displacements or modifications of the electronic distribution in matter. To date, the best temporal resolution for time resolved diffraction experiments is of the order of a hundred femto-seconds (fs). Laser accelerators are good candidates to reach the femtosecond temporal resolution in electron diffraction experiments. Such accelerators used to work at a low repetition rate, so that it was necessary to develop a new one operating at a high repetition rate in order to accumulate a large amount of data. In this thesis, a laser-plasma accelerator operating at the kHz repetition rate was developed and built. This source generates electron bunches at 100 keV from 3 mJ and 25 fs laser pulses. The physics of the acceleration has been studied, and the effect of the laser wavefront on the electron transverse distribution has been demonstrated. (author)

  13. Design of an Enterobacteriaceae Pan-genome Microarray Chip

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Ussery, David

    2010-01-01

    -density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability...... to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination...

  14. Experiments on the injection, confinement, and ejection of electron clouds in a magnetic mirror

    International Nuclear Information System (INIS)

    Eckhouse, S.; Fisher, A.; Rostoker, N.

    1978-01-01

    A cloud of (5 to 10 keV) electrons is injected into a magnetic mirror field. The magnetic field rises in 40--120 μsec to a maximum of 10 kG. Two methods of injection were tried: In the first, the injector is located at the mirror midplane and electrons are injected perpendicular to the magnetic field lines. In the second scheme, the injector is located near the mirror maximum. Up to about 10 11 electrons were trapped in both schemes with a mean kinetic energy of 0.3 MeV. Measured confinement time is limited only by the magnetic field decay time. The compressed electron cloud executes electrostatic oscillations. The frequency of the oscillation is proportional to the number of electrons trapped, and it is independent of the value of the magnetic field and the initial electron energy. The electron cloud was ejected along the mirror axis and properties of the ejected electron cloud were measured by x-ray pulses from bremstrahlung of electrons on the vacuum system wall and by collecting electrons on a Faraday cup

  15. Nonlinear two-stream interaction between a cold, relativistic electron beam and a collisional plasma-Astron experiment

    International Nuclear Information System (INIS)

    Newberger, B.S.; Thode, L.E.

    1979-05-01

    Experiments on the two-stream instability of a relativistic electron beam propagating through a neutral gas, carried out with the Lawrence Livermore Laboratory Astron beam, have been analyzed using a nonlinear saturation model for a cold beam. The behavior of the observed microwave emission due to the instability is in good agreement with that of the beam energy loss. Collisions on the plasma electrons weaken the nonlinear state of the instability but do not stabilize the mode. The beam essentially acts as if it were cold, a result substantiated by linear theory for waves propagating along the beam. In order to predict the effect of both beam momentum scatter and plasma electron collisions on the stability of the mode in future experiments a full two-dimensional linear theory must be developed

  16. Measurement of the polarisation of Jefferson Laboratory electron beam by Compton effect for the HAPPEX parity violation experiment in elastic electron-proton scattering

    International Nuclear Information System (INIS)

    Baylac, Maud

    2000-01-01

    This research thesis reports and describes the first measurements of polarisation of the Jlab electron beam by using the Compton polarimeter, and the exploitation of these measurements by the HAPPEX experiment which aims at determining the contribution of strange quarks to nucleon electromagnetic shape factors. The author first presents these shape factors and their compositions in terms of quarks. He describes the experimental installation used by the HAPPEX experiment for the measurement of the parity violation asymmetry. He presents the principle of Compton polarimetry and the experimental installation used at Jlab. Then, he addresses the main part of his research work which addresses the processing and analysis of data acquired during the HAPPEX experiment: measurement of the experimental asymmetry, and determination of the analysis power. HAPPEX results are finally presented and discussed [fr

  17. First observations of acceleration of injected electrons in a laser plasma beatwave experiment

    International Nuclear Information System (INIS)

    Ebrahim, N.A.; Martin, F.; Bordeur, P.; Heighway, E.A.; Matte, J.P.; Pepin, H.; Lavigne, P.

    1986-01-01

    The first experimental observations of acceleration of injected electrons in a laser driven plasma beatwave are presented. The plasma waves were excited in an ionized gas jet, using a short pulse high intensity CO 2 laser with two collinearly propagating beams (at λ = 9.6 μm and 10.6 μm) to excite a fast wave (v/sub p/ = c). The source of electrons was a laser plasma produced on an aluminum slab target by a third, synchronized CO 2 laser beam. A double-focusing dipole magnet was used to energy select and inject electrons into the beatwave, and a second magnetic spectrograph was used to analyze the accelerated electrons. Electron acceleration was only observed when the appropriate resonant plasma density was produced (∼ 10 17 cm -3 ), the two laser lines were incident on the plasma, and electrons were injected into this plasma from an external source

  18. Computer experiments on the imaging of point defects with the conventional transmission electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Krakow, W [Xerox Corp., Rochester, N.Y. (USA)

    1978-02-01

    To aid in the interpretation of high resolution electron micrographs of defect structures in crystals, computer-simulated dark-field electron micrographs have been obtained for a variety of point defects in metals. Interpretation of these images in terms of atomic positions and atom correlations becomes straightforward, and it is a simple matter to distinguish between real structural information and image artifacts produced by the phase contrast mechanism in the electron optical imaging process.

  19. Pharmacy customers' experiences with the national online service for viewing electronic prescriptions in Finland.

    Science.gov (United States)

    Lämsä, Elina; Timonen, Johanna; Mäntyselkä, Pekka; Ahonen, Riitta

    2017-01-01

    To investigate (1) Finnish pharmacy customers' familiarity with My Kanta, the national online service for viewing electronic prescriptions (ePrescriptions), (2) how commonly My Kanta is used, (3) who the typical users are, and (4) users' experiences of the usability of My Kanta. A survey was conducted among pharmacy customers (aged ≥18) purchasing medicines for themselves. Questionnaires (N=2915) were distributed from 18 community pharmacies across Finland in autumn 2015. The data obtained was stored in SPSS for Windows and subjected to descriptive analysis, chi-square tests and logistic regression analysis. In total, 1288 respondents were included (response rate 44%). Most (62%) of the customers were familiar with My Kanta. The majority of them (78%) were using it to view their ePrescriptions. My Kanta was perceived as clear, easy to use and to provide a good overall picture of the prescribed medications. Familiarity with My Kanta was associated with a higher education than basic school, regular use of prescription medicines, and sufficient information received about ePrescriptions. Men used My Kanta more often than women. Respondents aged 75 or older were less likely to be familiar with and to use the service compared to 18-34year olds. Most of the Finnish pharmacy customers were familiar with the national online service, My Kanta, for viewing ePrescriptions. Service users perceived it as easy to use and beneficial in managing their overall medication. Customers under 75, those educated beyond basic school, those using prescription medicines regularly, and those who had obtained sufficient information about ePrescriptions were most likely to be familiar with My Kanta. Men and customers under 75 were the typical users of the service. Some customers, however, were unaware of the service, or unable or reluctant to use it. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. Electronic data capture in a rural African setting: evaluating experiences with different systems in Malawi.

    Science.gov (United States)

    King, Carina; Hall, Jenny; Banda, Masford; Beard, James; Bird, Jon; Kazembe, Peter; Fottrell, Ed

    2014-01-01

    As hardware for electronic data capture (EDC), such as smartphones or tablets, becomes cheaper and more widely available, the potential for using such hardware as data capture tools in routine healthcare and research is increasing. We aim to highlight the advantages and disadvantages of four EDC systems being used simultaneously in rural Malawi: two for Android devices (CommCare and ODK Collect), one for PALM and Windows OS (Pendragon), and a custom-built application for Android (Mobile InterVA--MIVA). We report on the personal field and development experience of fieldworkers, project managers, and EDC system developers. Fieldworkers preferred using EDC to paper-based systems, although some struggled with the technology at first. Highlighted features include in-built skip patterns for all systems, and specifically the 'case' function that CommCare offers. MIVA as a standalone app required considerably more time and expertise than the other systems to create and could not be customised for our specific research needs; however, it facilitates standardised routine data collection. CommCare and ODK Collect both have user-friendly web-interfaces for form development and good technical support. CommCare requires Internet to build an application and download it to a device, whereas all steps can be done offline with ODK Collect, a desirable feature in low connectivity settings. Pendragon required more complex programming of logic, using a Microsoft Access application, and generally had less technical support. Start-up costs varied between systems, and all were considered more expensive than setting up a paper-based system; however running costs were generally low and therefore thought to be cost-effective over the course of our projects. EDC offers many opportunities for efficient data collection, but brings some issues requiring consideration when designing a study; the decision of which hardware and software to use should be informed by the aim of data collection