WorldWideScience

Sample records for genome scanning method

  1. An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans.

    Science.gov (United States)

    Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B

    2006-08-01

    Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.

  2. The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance in F1 Hybrids

    Directory of Open Access Journals (Sweden)

    Tomoko Takamiya

    2009-01-01

    Full Text Available We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath of rice (Oryza sativa L. using restriction landmark genome scanning (RLGS, and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the applicability of RLGS for scanning of non-Mendelian inheritance of DNA methylation and biased allelic expression.

  3. Genome-wide DNA polymorphism analyses using VariScan

    Directory of Open Access Journals (Sweden)

    Vilella Albert J

    2006-09-01

    Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

  4. Scanning apparatus and method

    International Nuclear Information System (INIS)

    Brunnett, C.J.

    1980-01-01

    A novel method is described for processing the analogue signals from the photomultiplier tubes in a tomographic X-ray scanner. The system produces a series of pulses whose instantaneous frequency depends on the detected intensity of the X-radiation. A timer unit is used to determine the segment scan intervals and also to deduce the average radiation intensity detected during this interval. The overall system is claimed to possess the advantageous properties of low time delay, wide bandwidth and relative low cost. (U.K.)

  5. Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods.

    Directory of Open Access Journals (Sweden)

    Yuri Tani Utsunomiya

    Full Text Available As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP data generated from dairy and beef cattle (taurine and indicine. The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10(-7 population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3 in Brown Swiss (P = 3.82×10(-12, and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.

  6. Uninformative polymorphisms bias genome scans for signatures of selection

    Directory of Open Access Journals (Sweden)

    Roesti Marius

    2012-06-01

    Full Text Available Abstract Background With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular. Methods and Results On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these ‘uninformative’ polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artifacts in the data (PCR and sequencing errors, as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations. Conclusions We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation.

  7. A Genome-Wide Breast Cancer Scan in African Americans

    Science.gov (United States)

    2010-06-01

    SNPs from the African American breast cancer scan to COGs , a European collaborative study which is has designed a SNP array with that will be genotyped...Award Number: W81XWH-08-1-0383 TITLE: A Genome-wide Breast Cancer Scan in African Americans PRINCIPAL INVESTIGATOR: Christopher A...SUBTITLE A Genome-wide Breast Cancer Scan in African Americans 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-08-1-0383 5c. PROGRAM

  8. Scanning tunneling microscope nanoetching method

    Science.gov (United States)

    Li, Yun-Zhong; Reifenberger, Ronald G.; Andres, Ronald P.

    1990-01-01

    A method is described for forming uniform nanometer sized depressions on the surface of a conducting substrate. A tunneling tip is used to apply tunneling current density sufficient to vaporize a localized area of the substrate surface. The resulting depressions or craters in the substrate surface can be formed in information encoding patterns readable with a scanning tunneling microscope.

  9. Footwear scanning systems and methods

    Science.gov (United States)

    Fernandes, Justin L.; McMakin, Douglas L.; Sheen, David M.; Tedeschi, Jonathan R.

    2017-07-25

    Methods and apparatus for scanning articles, such as footwear, to provide information regarding the contents of the articles are described. According to one aspect, a footwear scanning system includes a platform configured to contact footwear to be scanned, an antenna array configured to transmit electromagnetic waves through the platform into the footwear and to receive electromagnetic waves from the footwear and the platform, a transceiver coupled with antennas of the antenna array and configured to apply electrical signals to at least one of the antennas to generate the transmitted electromagnetic waves and to receive electrical signals from at least another of the antennas corresponding to the electromagnetic waves received by the others of the antennas, and processing circuitry configured to process the received electrical signals from the transceiver to provide information regarding contents within the footwear.

  10. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi

    2009-06-01

    Full Text Available Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS, which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20 of gastric cancer cell lines (8–18-fold amplification and 4.7% (4/86 of primary gastric tumors (8–50-fold amplification. KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild

  11. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    International Nuclear Information System (INIS)

    Mita, Hiroaki; Yanagihara, Kazuyoshi; Fujita, Masahiro; Hosokawa, Masao; Kusano, Masanobu; Sabau, Sorin Vasile; Tatsumi, Haruyuki; Imai, Kohzoh; Shinomura, Yasuhisa; Tokino, Takashi; Toyota, Minoru; Aoki, Fumio; Akashi, Hirofumi; Maruyama, Reo; Sasaki, Yasushi; Suzuki, Hiromu; Idogawa, Masashi; Kashima, Lisa

    2009-01-01

    Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS), which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20) of gastric cancer cell lines (8–18-fold amplification) and 4.7% (4/86) of primary gastric tumors (8–50-fold amplification). KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild-type KRAS resulted in the inhibition of cell growth and

  12. Statistical Methods in Integrative Genomics

    Science.gov (United States)

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

  13. Genome scan for linkage to Gilles de la Tourette syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Barr, C.L.; Livingston, J.; Williamson, R. [and others

    1994-09-01

    Gilles de la Tourette Syndrome (TS) is a familial, neuropsychiatric disorder characterized by chronic, intermittent motor and vocal tics. In addition to tics, affected individuals frequently display symptoms such as attention-deficit hyperactivity disorder and/or obsessive compulsive disorder. Genetic analyses of family data have suggested that susceptibility to the disorder is most likely due to a single genetic locus with a dominant mode of transmission and reduced penetrance. In the search for genetic linkage for TS, we have collected well-characterized pedigrees with multiple affected individuals on whom extensive diagnostic evaluations have been done. The first stage of our study is to scan the genome systematically using a panel of uniformly spaced (10 to 20 cM), highly polymorphic, microsatellite markers on 5 families segregating TS. To date, 290 markers have been typed and 3,660 non-overlapping cM of the genome have been excluded for possible linkage under the assumption of genetic homogeneity. Because of the possibility of locus heterogeneity overall summed exclusion is not considered tantamount to absolute exclusion of a disease locus in that region. The results from each family are carefully evaluated and a positive lod score in a single family is followed up by typing closely linked markers. Linkage to TS was examined by two-point analysis using the following genetic model: single autosomal dominant gene with gene frequency .003 and maximum penetrance of .99. An age-of-onset correction is included using a linear function increasing from age 2 years to 21 years. A small rate of phenocopies is also incorporated into the model. Only individuals with TS or CMT according to DSM III-R criteria were regarded as affected for the purposes of this summary. Additional markers are being tested to provide coverage at 5 cM intervals. Moreover, we are currently analyzing the data non-parametrically using the Affected-Pedigree-Member Method of linkage analysis.

  14. Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach.

    Science.gov (United States)

    Fariello, María Inés; Boitard, Simon; Mercier, Sabine; Robelin, David; Faraut, Thomas; Arnould, Cécile; Recoquillay, Julien; Bouchez, Olivier; Salin, Gérald; Dehais, Patrice; Gourichon, David; Leroux, Sophie; Pitel, Frédérique; Leterrier, Christine; SanCristobal, Magali

    2017-07-01

    Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal. Using computer simulations, we demonstrate that this approach detects selection with higher power than several state-of-the-art single-marker, windowing or haplotype-based approaches. We illustrate this on two benchmark data sets including individual genotypes, for which we obtain similar results with the local score and one haplotype-based approach. Finally, we apply the local score approach to Pool-Seq data obtained from a divergent selection experiment on behaviour in quail and obtain precise and biologically coherent selection signals: while competing methods fail to highlight any clear selection signature, our method detects several regions involving genes known to act on social responsiveness or autistic traits. Although we focus here on the detection of positive selection from multiple population data, the local score approach is general and can be applied to other genome scans for selection or other genomewide analyses such as GWAS. © 2017 John Wiley & Sons Ltd.

  15. A genome scan for positive selection in thoroughbred horses.

    Science.gov (United States)

    Gu, Jingjing; Orr, Nick; Park, Stephen D; Katz, Lisa M; Sulimova, Galina; MacHugh, David E; Hill, Emmeline W

    2009-06-02

    Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (F(ST)). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; PThoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease.

  16. Sample preparation method for scanning force microscopy

    CERN Document Server

    Jankov, I R; Szente, R N; Carreno, M N P; Swart, J W; Landers, R

    2001-01-01

    We present a method of sample preparation for studies of ion implantation on metal surfaces. The method, employing a mechanical mask, is specially adapted for samples analysed by Scanning Force Microscopy. It was successfully tested on polycrystalline copper substrates implanted with phosphorus ions at an acceleration voltage of 39 keV. The changes of the electrical properties of the surface were measured by Kelvin Probe Force Microscopy and the surface composition was analysed by Auger Electron Spectroscopy.

  17. A genome scan for positive selection in thoroughbred horses.

    Directory of Open Access Journals (Sweden)

    Jingjing Gu

    2009-06-01

    Full Text Available Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1 deviations from expected heterozygosity (Ewens-Watterson test in Thoroughbred (n = 112 and (2 global differentiation among four geographically diverse horse populations (F(ST. We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01, insulin receptor signalling (5.0-fold enrichment; P<0.01 and lipid transport (2.2-fold enrichment; P<0.05 genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05 and focal adhesion pathway (1.9-fold enrichment; P<0.01 genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1, ACTA1 (actin, alpha 1, skeletal muscle, ACTN2 (actinin, alpha 2, ADHFE1 (alcohol dehydrogenase, iron containing, 1, MTFR1 (mitochondrial fission regulator 1, PDK4 (pyruvate dehydrogenase kinase, isozyme 4 and TNC (tenascin C. Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes

  18. Internal scanning method as unique imaging method of optical vortex scanning microscope

    Science.gov (United States)

    Popiołek-Masajada, Agnieszka; Masajada, Jan; Szatkowski, Mateusz

    2018-06-01

    The internal scanning method is specific for the optical vortex microscope. It allows to move the vortex point inside the focused vortex beam with nanometer resolution while the whole beam stays in place. Thus the sample illuminated by the focused vortex beam can be scanned just by the vortex point. We show that this method enables high resolution imaging. The paper presents the preliminary experimental results obtained with the first basic image recovery procedure. A prospect of developing more powerful tools for topography recovery with the optical vortex scanning microscope is discussed shortly.

  19. SCANNING AND TRACKING MONITORING APPARATUS AND METHOD

    DEFF Research Database (Denmark)

    2017-01-01

    Disclosed is a scanning monitoring apparatus for medical imaging, the scanning monitoring apparatus comprising a controller unit and a display, wherein the controller unit during a scanning session is configured to obtain tracking data (102) of a subject in a medical scanner, obtain scanner data ...

  20. Genome scan of M. tuberculosis infection and disease in Ugandans.

    Directory of Open Access Journals (Sweden)

    Catherine M Stein

    Full Text Available Tuberculosis (TB, caused by Mycobacterium tuberculosis (Mtb, is an enduring public health problem globally, particularly in sub-Saharan Africa. Several studies have suggested a role for host genetic susceptibility in increased risk for TB but results across studies have been equivocal. As part of a household contact study of Mtb infection and disease in Kampala, Uganda, we have taken a unique approach to the study of genetic susceptibility to TB, by studying three phenotypes. First, we analyzed culture confirmed TB disease compared to latent Mtb infection (LTBI or lack of Mtb infection. Second, we analyzed resistance to Mtb infection in the face of continuous exposure, defined by a persistently negative tuberculin skin test (PTST-; this outcome was contrasted to LTBI. Third, we analyzed an intermediate phenotype, tumor necrosis factor-alpha (TNFalpha expression in response to soluble Mtb ligands enriched with molecules secreted from Mtb (culture filtrate. We conducted a full microsatellite genome scan, using genotypes generated by the Center for Medical Genetics at Marshfield. Multipoint model-free linkage analysis was conducted using an extension of the Haseman-Elston regression model that includes half sibling pairs, and HIV status was included as a covariate in the model. The analysis included 803 individuals from 193 pedigrees, comprising 258 full sibling pairs and 175 half sibling pairs. Suggestive linkage (p<10(-3 was observed on chromosomes 2q21-2q24 and 5p13-5q22 for PTST-, and on chromosome 7p22-7p21 for TB; these findings for PTST- are novel and the chromosome 7 region contains the IL6 gene. In addition, we replicated recent linkage findings on chromosome 20q13 for TB (p = 0.002. We also observed linkage at the nominal alpha = 0.05 threshold to a number of promising candidate genes, SLC11A1 (PTST- p = 0.02, IL-1 complex (TB p = 0.01, IL12BR2 (TNFalpha p = 0.006, IL12A (TB p = 0.02 and IFNGR2 (TNFalpha p = 0.002. These results confirm

  1. Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.

    Science.gov (United States)

    Gautier, Mathieu

    2015-12-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier

  2. Scanning probe methods applied to molecular electronics

    Energy Technology Data Exchange (ETDEWEB)

    Pavlicek, Niko

    2013-08-01

    Scanning probe methods on insulating films offer a rich toolbox to study electronic, structural and spin properties of individual molecules. This work discusses three issues in the field of molecular and organic electronics. An STM head to be operated in high magnetic fields has been designed and built up. The STM head is very compact and rigid relying on a robust coarse approach mechanism. This will facilitate investigations of the spin properties of individual molecules in the future. Combined STM/AFM studies revealed a reversible molecular switch based on two stable configurations of DBTH molecules on ultrathin NaCl films. AFM experiments visualize the molecular structure in both states. Our experiments allowed to unambiguously determine the pathway of the switch. Finally, tunneling into and out of the frontier molecular orbitals of pentacene molecules has been investigated on different insulating films. These experiments show that the local symmetry of initial and final electron wave function are decisive for the ratio between elastic and vibration-assisted tunneling. The results can be generalized to electron transport in organic materials.

  3. Evaluation of processing methods for static radioisotope scan images

    International Nuclear Information System (INIS)

    Oakberg, J.A.

    1976-12-01

    Radioisotope scanning in the field of nuclear medicine provides a method for the mapping of a radioactive drug in the human body to produce maps (images) which prove useful in detecting abnormalities in vital organs. At best, radioisotope scanning methods produce images with poor counting statistics. One solution to improving the body scan images is using dedicated small computers with appropriate software to process the scan data. Eleven methods for processing image data are compared

  4. A Genome Scan for Quantitative Trait Loci Affecting Average Daily ...

    Indian Academy of Sciences (India)

    reviewer

    Sari, P.O. Box -578, Iran .... (2015) identified one SNP with genome wide significance effect within SYNE1 gene on ..... analysis of thirty one production, health, reproduction and body conformation traits in contemporary US Holstein cows. ... Problems involved in breeding for efficiency of food utilization. Proc .... 131, 210-216.

  5. Benchmarking of methods for genomic taxonomy

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Lukjancenko, Oksana

    2014-01-01

    . Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene...

  6. prokaryote genome annotation with GeneScan and GLIMMER

    Indian Academy of Sciences (India)

    Unknown

    The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a ... on whether they need to be trained on a set of genes in order to ..... FP has partial matches to the kdpA gene in C. jejuni.

  7. Radar Scan Methods in Modern Multifunctional Radars

    Directory of Open Access Journals (Sweden)

    V. N. Skosyrev

    2014-01-01

    overview in elevation plane ray beam with high directivity and electronic scanning. This method is preferable from the viewpoint of the anti-jamming passive and active interference, as well as reducing electromagnetic visibility.

  8. Genomic methods take the plunge

    DEFF Research Database (Denmark)

    Cammen, Kristina M.; Andrews, Kimberly R.; Carroll, Emma L.

    2016-01-01

    The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent...

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

    Science.gov (United States)

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

    2012-01-01

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

  10. A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data

    Directory of Open Access Journals (Sweden)

    Scherer Stephen W

    2011-05-01

    Full Text Available Abstract Background Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. Results We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wide association data for rare copy-number variations, which have been strongly implicated in common diseases. Application of our method to a simulated dataset demonstrated the high accuracy of this method in detecting disease-associated gene clusters in a whole gene pathway. Conclusions The scan statistic approach proposed here shows a high level of accuracy in detecting gene clusters in a whole gene pathway. This study has provided a sound statistical framework for analyzing genome-wide rare CNV data by incorporating topological information on the gene pathway.

  11. Huffman and linear scanning methods with statistical language models.

    Science.gov (United States)

    Roark, Brian; Fried-Oken, Melanie; Gibbons, Chris

    2015-03-01

    Current scanning access methods for text generation in AAC devices are limited to relatively few options, most notably row/column variations within a matrix. We present Huffman scanning, a new method for applying statistical language models to binary-switch, static-grid typing AAC interfaces, and compare it to other scanning options under a variety of conditions. We present results for 16 adults without disabilities and one 36-year-old man with locked-in syndrome who presents with complex communication needs and uses AAC scanning devices for writing. Huffman scanning with a statistical language model yielded significant typing speedups for the 16 participants without disabilities versus any of the other methods tested, including two row/column scanning methods. A similar pattern of results was found with the individual with locked-in syndrome. Interestingly, faster typing speeds were obtained with Huffman scanning using a more leisurely scan rate than relatively fast individually calibrated scan rates. Overall, the results reported here demonstrate great promise for the usability of Huffman scanning as a faster alternative to row/column scanning.

  12. AFLP genome scans suggest divergent selection on colour patterning in allopatric colour morphs of a cichlid fish.

    Science.gov (United States)

    Mattersdorfer, Karin; Koblmüller, Stephan; Sefc, Kristina M

    2012-07-01

    Genome scan-based tests for selection are directly applicable to natural populations to study the genetic and evolutionary mechanisms behind phenotypic differentiation. We conducted AFLP genome scans in three distinct geographic colour morphs of the cichlid fish Tropheus moorii to assess whether the extant, allopatric colour pattern differentiation can be explained by drift and to identify markers mapping to genomic regions possibly involved in colour patterning. The tested morphs occupy adjacent shore sections in southern Lake Tanganyika and are separated from each other by major habitat barriers. The genome scans revealed significant genetic structure between morphs, but a very low proportion of loci fixed for alternative AFLP alleles in different morphs. This high level of polymorphism within morphs suggested that colour pattern differentiation did not result exclusively from neutral processes. Outlier detection methods identified six loci with excess differentiation in the comparison between a bluish and a yellow-blotch morph and five different outlier loci in comparisons of each of these morphs with a red morph. As population expansions and the genetic structure of Tropheus make the outlier approach prone to false-positive signals of selection, we examined the correlation between outlier locus alleles and colour phenotypes in a genetic and phenotypic cline between two morphs. Distributions of allele frequencies at one outlier locus were indeed consistent with linkage to a colour locus. Despite the challenges posed by population structure and demography, our results encourage the cautious application of genome scans to studies of divergent selection in subdivided and recently expanded populations. © 2012 Blackwell Publishing Ltd.

  13. Scanning tunneling microscopy III theory of STM and related scanning probe methods

    CERN Document Server

    Güntherodt, Hans-Joachim

    1996-01-01

    Scanning Tunneling Microscopy III provides a unique introduction to the theoretical foundations of scanning tunneling microscopy and related scanning probe methods. The different theoretical concepts developed in the past are outlined, and the implications of the theoretical results for the interpretation of experimental data are discussed in detail. Therefore, this book serves as a most useful guide for experimentalists as well as for theoreticians working in the filed of local probe methods. In this second edition the text has been updated and new methods are discussed.

  14. AFLP genome scanning reveals divergent selection in natural populations of Liriodendron chinense (Magnoliaceae along a latitudinal transect

    Directory of Open Access Journals (Sweden)

    Aihong eYang

    2016-05-01

    Full Text Available Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined AFLP genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Two complementary methods (Dfdist and BayeScan and association analysis between AFLP loci and climate factors were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity towards the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.

  15. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder

    NARCIS (Netherlands)

    Zhou, K.; Dempfle, A.; Arcos-Burgos, M.; Bakker, S.C.; Banaschewski, T.; Biederman, J; Buitelaar, J.K.; Castellanos, F.X.; Doyle, A.; Ebstein, R.; Ekholm, J.; Forabosco, P.; Franke, F.; Freitag, C.; Friedel, S.; Gill, M.; Hebebrand, J.; Hinney, A.; Jacob, C.; Lesch, K.P.; Loo, S.K.; Lopera, F.; McCracken, J.T.; McGough, J.J.; Meyer, J.; Mick, E.; Miranda, A.; Muenkel, M.; Mulas, F.; Nelson, S.F.; Nguyen, T.T.; Oades, R.D.; Ogdie, M.N.; Palacio, J.D.; Pineda, D.; Reif, A.; Renner, T.J.; Roeyers, H.; Romanos, M.; Rothenberger, A.; Schäfer, H.; Sergeant, J.A.; Sinke, R.J.; Smalley, S.L.; Sonuga-Barke, E.; Steinhausen, H.C.; van der Meulen, E.; Walitza, S.; Warnke, A.; Lewis, C.M.; Faraone, S.V.; Asherson, P.

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies,

  16. Meta-analysis of genome-wide linkage scans of attention deficit hyperactivity disorder.

    NARCIS (Netherlands)

    Zhou, K.; Dempfle, A.; Arcos-Burgos, M.; Bakker, S.C.; Banaschewski, T.; Biederman, J.; Buitelaar, J.K.; Castellanos, F.X.; Doyle, A.; Ebstein, R.P.; Ekholm, J.; Forabosco, P.; Franke, B.; Freitag, C.; Friedel, S.; Gill, M.; Hebebrand, J.; Hinney, A.; Jacob, C.; Lesch, K.P.; Loo, S.K.; Lopera, F.; McCracken, J.T.; McGough, J.J.; Meyer, J.; Mick, E.; Miranda, A.; Muenke, M.; Mulas, F.; Nelson, S.F.; Nguyen, T.T.; Oades, R.D.; Ogdie, M.N.; Palacio, J.D.; Pineda, D.; Reif, A.; Renner, T.J.; Roeyers, H.; Romanos, M.; Rothenberger, A.; Schafer, H.; Sergeant, J.A.; Sinke, R.J.; Smalley, S.L.; Sonuga-Barke, E.J.S.; Steinhausen, H.C.; Meulen, E. van der; Walitza, S.; Warnke, A.; Lewis, C.M.; Faraone, S.V.; Asherson, P.

    2008-01-01

    Genetic contribution to the development of attention deficit hyperactivity disorder (ADHD) is well established. Seven independent genome-wide linkage scans have been performed to map loci that increase the risk for ADHD. Although significant linkage signals were identified in some of the studies,

  17. Genomic scans for selective sweeps using SNP data

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob

    2005-01-01

    of the selection coefficient. To illustrate the method, we apply our approach to data from the Seattle SNP project and to Chromosome 2 data from the HapMap project. In Chromosome 2, the most extreme signal is found in the lactase gene, which previously has been shown to be undergoing positive selection. Evidence...

  18. A Genome-wide Breast Cancer Scan in African Americans

    Science.gov (United States)

    2012-06-01

    Contraceptive and Reproductive Experiences (CARE) Study. The CARE Study is a large multi-center, population-based case–control study that was designed to examine...Malone, K.E., Strom, B.L., Norman, S.A., Weiss, L.K. et al. (2002) The NICHD Women’s Contraceptive and Reproductive Experiences Study: methods and...PMV Research Group at the Department of Child and Adolescent Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany 51 Division of

  19. Method for Surface Scanning in Medical Imaging and Related Apparatus

    DEFF Research Database (Denmark)

    2015-01-01

    A method and apparatus for surface scanning in medical imaging is provided. The surface scanning apparatus comprises an image source, a first optical fiber bundle comprising first optical fibers having proximal ends and distal ends, and a first optical coupler for coupling an image from the image...

  20. Method of estimation of scanning system quality

    Science.gov (United States)

    Larkin, Eugene; Kotov, Vladislav; Kotova, Natalya; Privalov, Alexander

    2018-04-01

    Estimation of scanner parameters is an important part in developing electronic document management system. This paper suggests considering the scanner as a system that contains two main channels: a photoelectric conversion channel and a channel for measuring spatial coordinates of objects. Although both of channels consist of the same elements, the testing of their parameters should be executed separately. The special structure of the two-dimensional reference signal is offered for this purpose. In this structure, the fields for testing various parameters of the scanner are sp atially separated. Characteristics of the scanner are associated with the loss of information when a document is digitized. The methods to test grayscale transmitting ability, resolution and aberrations level are offered.

  1. DETECTING SELECTION IN NATURAL POPULATIONS: MAKING SENSE OF GENOME SCANS AND TOWARDS ALTERNATIVE SOLUTIONS

    Science.gov (United States)

    Haasl, Ryan J.; Payseur, Bret A.

    2016-01-01

    Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example FST, cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach. PMID:26224644

  2. A laser sheet self-calibration method for scanning PIV

    Science.gov (United States)

    Knutsen, Anna N.; Lawson, John M.; Dawson, James R.; Worth, Nicholas A.

    2017-10-01

    Knowledge of laser sheet position, orientation, and thickness is a fundamental requirement of scanning PIV and other laser-scanning methods. This paper describes the development and evaluation of a new laser sheet self-calibration method for stereoscopic scanning PIV, which allows the measurement of these properties from particle images themselves. The approach is to fit a laser sheet model by treating particles as randomly distributed probes of the laser sheet profile, whose position is obtained via a triangulation procedure enhanced by matching particle images according to their variation in brightness over a scan. Numerical simulations and tests with experimental data were used to quantify the sensitivity of the method to typical experimental error sources and validate its performance in practice. The numerical simulations demonstrate the accurate recovery of the laser sheet parameters over range of different seeding densities and sheet thicknesses. Furthermore, they show that the method is robust to significant image noise and camera misalignment. Tests with experimental data confirm that the laser sheet model can be accurately reconstructed with no impairment to PIV measurement accuracy. The new method is more efficient and robust in comparison with the standard (self-) calibration approach, which requires an involved, separate calibration step that is sensitive to experimental misalignments. The method significantly improves the practicality of making accurate scanning PIV measurements and broadens its potential applicability to scanning systems with significant vibrations.

  3. Whole genome PCR scanning reveals the syntenic genome structure of toxigenic Vibrio cholerae strains in the O1/O139 population.

    Directory of Open Access Journals (Sweden)

    Bo Pang

    Full Text Available Vibrio cholerae is commonly found in estuarine water systems. Toxigenic O1 and O139 V. cholerae strains have caused cholera epidemics and pandemics, whereas the nontoxigenic strains within these serogroups only occasionally lead to disease. To understand the differences in the genome and clonality between the toxigenic and nontoxigenic strains of V. cholerae serogroups O1 and O139, we employed a whole genome PCR scanning (WGPScanning method, an rrn operon-mediated fragment rearrangement analysis and comparative genomic hybridization (CGH to analyze the genome structure of different strains. WGPScanning in conjunction with CGH revealed that the genomic contents of the toxigenic strains were conservative, except for a few indels located mainly in mobile elements. Minor nucleotide variation in orthologous genes appeared to be the major difference between the toxigenic strains. rrn operon-mediated rearrangements were infrequent in El Tor toxigenic strains tested using I-CeuI digested pulsed-field gel electrophoresis (PFGE analysis and PCR analysis based on flanking sequence of rrn operons. Using these methods, we found that the genomic structures of toxigenic El Tor and O139 strains were syntenic. The nontoxigenic strains exhibited more extensive sequence variations, but toxin coregulated pilus positive (TCP+ strains had a similar structure. TCP+ nontoxigenic strains could be subdivided into multiple lineages according to the TCP type, suggesting the existence of complex intermediates in the evolution of toxigenic strains. The data indicate that toxigenic O1 El Tor and O139 strains were derived from a single lineage of intermediates from complex clones in the environment. The nontoxigenic strains with non-El Tor type TCP may yet evolve into new epidemic clones after attaining toxigenic attributes.

  4. Combined amplification and hybridization techniques for genome scanning in vegetatively propagated crops

    Energy Technology Data Exchange (ETDEWEB)

    Kahl, G; Ramser, J; Terauchi, R [Biocentre, University of Frankfurt, Frankfurt am Main (Germany); Lopez-Peralta, C [IRGP, Colegio de Postgraduados, Montecillo, Edo. de Mexico, Texcoco (Mexico); Asemota, H N [Biotechnology Centre, University of the West Indies, Mona, Kingston (Jamaica); Weising, K [School of Biological Sciences, University of Auckland, Auckland (New Zealand)

    1998-10-01

    A combination of PCR- and hybridization-based genome scanning techniques and sequence comparisons between non-coding chloroplast DNA flanking tRNA genes has been employed to screen Dioscorea species for intra- and interspecific genetic diversity. This methodology detected extensive polymorphisms within Dioscorea bulbifera L., and revealed taxonomic and phylogenetic relationships among cultivated Guinea yams varieties and their potential wild progenitors. Finally, screening of yam germplasm grown in Jamaica permitted reliable discrimination between all major cultivars. Genome scanning by micro satellite-primed PCR (MP-PCR) and random amplified polymorphic DNA (RAPD) analysis in combination with the novel random amplified micro satellite polymorphisms (RAMPO) hybridization technique has shown high potential for the genetic analysis of yams, and holds promise for other vegetatively propagated orphan crops. (author) 46 refs, 3 figs, 3 tabs

  5. Combined amplification and hybridization techniques for genome scanning in vegetatively propagated crops

    International Nuclear Information System (INIS)

    Kahl, G.; Ramser, J.; Terauchi, R.; Lopez-Peralta, C.; Asemota, H.N.; Weising, K.

    1998-01-01

    A combination of PCR- and hybridization-based genome scanning techniques and sequence comparisons between non-coding chloroplast DNA flanking tRNA genes has been employed to screen Dioscorea species for intra- and interspecific genetic diversity. This methodology detected extensive polymorphisms within Dioscorea bulbifera L., and revealed taxonomic and phylogenetic relationships among cultivated Guinea yams varieties and their potential wild progenitors. Finally, screening of yam germplasm grown in Jamaica permitted reliable discrimination between all major cultivars. Genome scanning by micro satellite-primed PCR (MP-PCR) and random amplified polymorphic DNA (RAPD) analysis in combination with the novel random amplified micro satellite polymorphisms (RAMPO) hybridization technique has shown high potential for the genetic analysis of yams, and holds promise for other vegetatively propagated orphan crops. (author)

  6. Method and apparatus for scanning x-ray tomography

    International Nuclear Information System (INIS)

    Albert, R.D.

    1988-01-01

    In a method of producing a tomographic image of a subject that includes the steps of generating X-rays at a moving origin point by directing a charged particle beam to a target surface, deflecting the charged particle beam to travel the origin point through a predetermined raster scan at the surface, detecting variations of X-ray intensity during the course of the raster scan at spaced apart detection points situated at the opposite side of the subject from the origin point, generating a first sequence of data values that is indicative of variations of X-ray intensity at a first of the detection points at successive times during the course of the raster scan and generating at least a second sequence of data values that is indicative of variations of X-ray intensity at a second of the detection points at successive times during the course of the same raster scan, the improvement is described comprising: combining successive individual data values of the first sequence that are generated by X-rays from successive particular locations in the raster scan with at least individual data values of the second sequence that are generated by X-rays from predetermined successive different locations in the same raster scan in order to produce a composite sequence of data values, and producing an image corresponding to at least a portion of the raster scan which depicts variations of the magnitude of successive data values of the composite sequence

  7. Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae.

    Science.gov (United States)

    Laiba, Efrat; Glikaite, Ilana; Levy, Yael; Pasternak, Zohar; Fridman, Eyal

    2016-04-01

    The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.

  8. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...... represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders....

  9. Improved coating and fixation methods for scanning electron microscope autoradiography

    International Nuclear Information System (INIS)

    Weiss, R.L.

    1984-01-01

    A simple apparatus for emulsion coating is described. The apparatus is inexpensive and easily assembled in a standard glass shop. Emulsion coating for scanning electron microscope autoradiography with this apparatus consistently yields uniform layers. When used in conjunction with newly described fixation methods, this new approach produces reliable autoradiographs of undamaged specimens

  10. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity

    Science.gov (United States)

    Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P.; Nir, Talia M.; Toga, Arthur W.; Jack, Clifford R.; Saykin, Andrew J.; Green, Robert C.; Weiner, Michael W.; Medland, Sarah E.; Montgomery, Grant W.; Hansell, Narelle K.; McMahon, Katie L.; de Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.; Weiner, Michael; Aisen, Paul; Weiner, Michael; Aisen, Paul; Petersen, Ronald; Jack, Clifford R.; Jagust, William; Trojanowski, John Q.; Toga, Arthur W.; Beckett, Laurel; Green, Robert C.; Saykin, Andrew J.; Morris, John; Liu, Enchi; Green, Robert C.; Montine, Tom; Petersen, Ronald; Aisen, Paul; Gamst, Anthony; Thomas, Ronald G.; Donohue, Michael; Walter, Sarah; Gessert, Devon; Sather, Tamie; Beckett, Laurel; Harvey, Danielle; Gamst, Anthony; Donohue, Michael; Kornak, John; Jack, Clifford R.; Dale, Anders; Bernstein, Matthew; Felmlee, Joel; Fox, Nick; Thompson, Paul; Schuff, Norbert; Alexander, Gene; DeCarli, Charles; Jagust, William; Bandy, Dan; Koeppe, Robert A.; Foster, Norm; Reiman, Eric M.; Chen, Kewei; Mathis, Chet; Morris, John; Cairns, Nigel J.; Taylor-Reinwald, Lisa; Trojanowki, J.Q.; Shaw, Les; Lee, Virginia M.Y.; Korecka, Magdalena; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Saykin, Andrew J.; Foroud, Tatiana M.; Potkin, Steven; Shen, Li; Khachaturian, Zaven; Frank, Richard; Snyder, Peter J.; Molchan, Susan; Kaye, Jeffrey; Quinn, Joseph; Lind, Betty; Dolen, Sara; Schneider, Lon S.; Pawluczyk, Sonia; Spann, Bryan M.; Brewer, James; Vanderswag, Helen; Heidebrink, Judith L.; Lord, Joanne L.; Petersen, Ronald; Johnson, Kris; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Morris, John C.; Ances, Beau; Carroll, Maria; Leon, Sue; Mintun, Mark A.; Schneider, Stacy; Marson, Daniel; Griffith, Randall; Clark, David; Grossman, Hillel; Mitsis, Effie; Romirowsky, Aliza; deToledo-Morrell, Leyla; Shah, Raj C.; Duara, Ranjan; Varon, Daniel; Roberts, Peggy; Albert, Marilyn; Onyike, Chiadi; Kielb, Stephanie; Rusinek, Henry; de Leon, Mony J.; Glodzik, Lidia; De Santi, Susan; Doraiswamy, P. Murali; Petrella, Jeffrey R.; Coleman, R. Edward; Arnold, Steven E.; Karlawish, Jason H.; Wolk, David; Smith, Charles D.; Jicha, Greg; Hardy, Peter; Lopez, Oscar L.; Oakley, MaryAnn; Simpson, Donna M.; Porsteinsson, Anton P.; Goldstein, Bonnie S.; Martin, Kim; Makino, Kelly M.; Ismail, M. Saleem; Brand, Connie; Mulnard, Ruth A.; Thai, Gaby; Mc-Adams-Ortiz, Catherine; Womack, Kyle; Mathews, Dana; Quiceno, Mary; Diaz-Arrastia, Ramon; King, Richard; Weiner, Myron; Martin-Cook, Kristen; DeVous, Michael; Levey, Allan I.; Lah, James J.; Cellar, Janet S.; Burns, Jeffrey M.; Anderson, Heather S.; Swerdlow, Russell H.; Apostolova, Liana; Lu, Po H.; Bartzokis, George; Silverman, Daniel H.S.; Graff-Radford, Neill R.; Parfitt, Francine; Johnson, Heather; Farlow, Martin R.; Hake, Ann Marie; Matthews, Brandy R.; Herring, Scott; van Dyck, Christopher H.; Carson, Richard E.; MacAvoy, Martha G.; Chertkow, Howard; Bergman, Howard; Hosein, Chris; Black, Sandra; Stefanovic, Bojana; Caldwell, Curtis; Hsiung, Ging-Yuek Robin; Feldman, Howard; Mudge, Benita; Assaly, Michele; Kertesz, Andrew; Rogers, John; Trost, Dick; Bernick, Charles; Munic, Donna; Kerwin, Diana; Mesulam, Marek-Marsel; Lipowski, Kristina; Wu, Chuang-Kuo; Johnson, Nancy; Sadowsky, Carl; Martinez, Walter; Villena, Teresa; Turner, Raymond Scott; Johnson, Kathleen; Reynolds, Brigid; Sperling, Reisa A.; Johnson, Keith A.; Marshall, Gad; Frey, Meghan; Yesavage, Jerome; Taylor, Joy L.; Lane, Barton; Rosen, Allyson; Tinklenberg, Jared; Sabbagh, Marwan; Belden, Christine; Jacobson, Sandra; Kowall, Neil; Killiany, Ronald; Budson, Andrew E.; Norbash, Alexander; Johnson, Patricia Lynn; Obisesan, Thomas O.; Wolday, Saba; Bwayo, Salome K.; Lerner, Alan; Hudson, Leon; Ogrocki, Paula; Fletcher, Evan; Carmichael, Owen; Olichney, John; DeCarli, Charles; Kittur, Smita; Borrie, Michael; Lee, T.-Y.; Bartha, Rob; Johnson, Sterling; Asthana, Sanjay; Carlsson, Cynthia M.; Potkin, Steven G.; Preda, Adrian; Nguyen, Dana; Tariot, Pierre; Fleisher, Adam; Reeder, Stephanie; Bates, Vernice; Capote, Horacio; Rainka, Michelle; Scharre, Douglas W.; Kataki, Maria; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Pearlson, Godfrey D.; Blank, Karen; Anderson, Karen; Saykin, Andrew J.; Santulli, Robert B.; Schwartz, Eben S.; Sink, Kaycee M.; Williamson, Jeff D.; Garg, Pradeep; Watkins, Franklin; Ott, Brian R.; Querfurth, Henry; Tremont, Geoffrey; Salloway, Stephen; Malloy, Paul; Correia, Stephen; Rosen, Howard J.; Miller, Bruce L.; Mintzer, Jacobo; Longmire, Crystal Flynn; Spicer, Kenneth; Finger, Elizabeth; Rachinsky, Irina; Rogers, John; Kertesz, Andrew; Drost, Dick

    2013-01-01

    Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer’s disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, high-angular resolution diffusion MRI. We adapted GWASs to screen the brain’s connectivity pattern, allowing us to discover genetic variants that affect the human brain’s wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer’s disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases. PMID:23471985

  11. Combined genome scans for body stature in 6,602 European twins

    DEFF Research Database (Denmark)

    Perola, Markus; Sammalisto, Sampo; Hiekkalinna, Tero

    2007-01-01

    combined and related to the sequence positions using software developed by us, which is publicly available (https://apps.bioinfo.helsinki.fi/software/cartographer.aspx). Variance component linkage analysis was performed with age, sex, and country of origin as covariates. The covariate adjusted heritability....... Several cohorts contributed to the identified loci, suggesting an evolutionarily old genetic variant having effects on stature in European-based populations. To facilitate the genetic studies of stature we have also set up a website that lists all stature genome scans published and their most significant...

  12. PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.

    Science.gov (United States)

    Ambrosini, Giovanna; Groux, Romain; Bucher, Philipp

    2018-03-05

    Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or TF binding site model from a public database. The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively. giovanna.ambrosini@epfl.ch. SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE.

  13. Nanometrology using a through-focus scanning optical microscopy method

    International Nuclear Information System (INIS)

    Attota, Ravikiran; Silver, Richard

    2011-01-01

    We present an initial review of a novel through-focus scanning optical microscopy (TSOM pronounced as 'tee-som') imaging method that produces nanometer-dimensional measurement sensitivity using a conventional bright-field optical microscope. In the TSOM method a target is scanned through the focus of an optical microscope, acquiring conventional optical images at different focal positions. The TSOM images are constructed using the through-focus optical images. A TSOM image is unique under given experimental conditions and is sensitive to changes in the dimensions of a target in a distinct way. We use this characteristic for nanoscale-dimensional metrology. This technique can be used to identify the dimension which is changing between two nanosized targets and to determine the dimensions using a library-matching method. This methodology has potential utility for a wide range of target geometries and application areas, including nanometrology, nanomanufacturing, defect analysis, inspection, process control and biotechnology

  14. Genome-wide association scan for variants associated with early-onset prostate cancer.

    Directory of Open Access Journals (Sweden)

    Ethan M Lange

    Full Text Available Prostate cancer is the most common non-skin cancer and the second leading cause of cancer related mortality for men in the United States. There is strong empirical and epidemiological evidence supporting a stronger role of genetics in early-onset prostate cancer. We performed a genome-wide association scan for early-onset prostate cancer. Novel aspects of this study include the focus on early-onset disease (defined as men with prostate cancer diagnosed before age 56 years and use of publically available control genotype data from previous genome-wide association studies. We found genome-wide significant (p<5×10(-8 evidence for variants at 8q24 and 11p15 and strong supportive evidence for a number of previously reported loci. We found little evidence for individual or systematic inflated association findings resulting from using public controls, demonstrating the utility of using public control data in large-scale genetic association studies of common variants. Taken together, these results demonstrate the importance of established common genetic variants for early-onset prostate cancer and the power of including early-onset prostate cancer cases in genetic association studies.

  15. Apparatus and method for nuclear magnetic resonance scanning and mapping

    International Nuclear Information System (INIS)

    Damadian, R.V.

    1983-01-01

    An improved apparatus and method is disclosed for analyzing the chemical and structural composition of a specimen including whole-body specimens which may include, for example, living mammals, utilizing nuclear magnetic resonance (NMR) techniques. A magnetic field space necessary to obtain an NMR signal characteristic of the chemical structure of the specimen is focused to provide a resonance domain of selectable size, which may then be moved in a pattern with respect to the specimen to scan the specimen

  16. Scanning tunneling microscopy III theory of STM and related scanning probe methods

    CERN Document Server

    Güntherodt, Hans-Joachim

    1993-01-01

    While the first two volumes on Scanning Tunneling Microscopy (STM) and its related scanning probe (SXM) methods have mainly concentrated on intro­ ducing the experimental techniques, as well as their various applications in different research fields, this third volume is exclusively devoted to the theory of STM and related SXM methods. As the experimental techniques including the reproducibility of the experimental results have advanced, more and more theorists have become attracted to focus on issues related to STM and SXM. The increasing effort in the development of theoretical concepts for STM/SXM has led to considerable improvements in understanding the contrast mechanism as well as the experimental conditions necessary to obtain reliable data. Therefore, this third volume on STM/SXM is not written by theorists for theorists, but rather for every scientist who is not satisfied by just obtaining real­ space images of surface structures by STM/SXM. After a brief introduction (Chap. 1), N. D. Lang first co...

  17. Classication Methods for CT-Scanned Carcass Midsections

    DEFF Research Database (Denmark)

    Skytte, Jacob Lercke; Dahl, Anders Lindbjerg; Larsen, Rasmus

    2011-01-01

    Computed tomography (CT) has successfully been applied in medical environments for decades. In recent years CT has also made its entry to the industrial environments, including the slaughterhouses. In this paper we investigate classication methods for an online CT system, in order to assist...... in the segmentation of the outer fat layer in the mid- section of CT-scanned pig carcasses. Prior information about the carcass composition can potentially be applied for a fully automated solution, in order to optimize the slaughter line. The methods comprise Markov Random Field and contextual Bayesian classication...

  18. Gamma Ray Tomographic Scan Method for Large Scale Industrial Plants

    International Nuclear Information System (INIS)

    Moon, Jin Ho; Jung, Sung Hee; Kim, Jong Bum; Park, Jang Geun

    2011-01-01

    The gamma ray tomography systems have been used to investigate a chemical process for last decade. There have been many cases of gamma ray tomography for laboratory scale work but not many cases for industrial scale work. Non-tomographic equipment with gamma-ray sources is often used in process diagnosis. Gamma radiography, gamma column scanning and the radioisotope tracer technique are examples of gamma ray application in industries. In spite of many outdoor non-gamma ray tomographic equipment, the most of gamma ray tomographic systems still remained as indoor equipment. But, as the gamma tomography has developed, the demand on gamma tomography for real scale plants also increased. To develop the industrial scale system, we introduced the gamma-ray tomographic system with fixed detectors and rotating source. The general system configuration is similar to 4 th generation geometry. But the main effort has been made to actualize the instant installation of the system for real scale industrial plant. This work would be a first attempt to apply the 4th generation industrial gamma tomographic scanning by experimental method. The individual 0.5-inch NaI detector was used for gamma ray detection by configuring circular shape around industrial plant. This tomographic scan method can reduce mechanical complexity and require a much smaller space than a conventional CT. Those properties make it easy to get measurement data for a real scale plant

  19. A genome-wide scan in families with maturity-onset diabetes of the young

    DEFF Research Database (Denmark)

    Frayling, Timothy M; Lindgren, Cecilia M; Chevre, Jean Claude

    2003-01-01

    Maturity-onset diabetes of the young (MODY) is a heterogeneous single gene disorder characterized by non-insulin-dependent diabetes, an early onset and autosomal dominant inheritance. Mutations in six genes have been shown to cause MODY. Approximately 15-20% of families fitting MODY criteria do...... not have mutations in any of the known genes. These families provide a rich resource for the identification of new MODY genes. This will potentially enable further dissection of clinical heterogeneity and bring new insights into mechanisms of beta-cell dysfunction. To facilitate the identification of novel...... MODY loci, we combined the results from three genome-wide scans on a total of 23 families fitting MODY criteria. We used both a strict parametric model of inheritance with heterogeneity and a model-free analysis. We did not identify any single novel locus but provided putative evidence for linkage...

  20. A genome scan conducted in a multigenerational pedigree with convergent strabismus supports a complex genetic determinism.

    Directory of Open Access Journals (Sweden)

    Anouk Georges

    Full Text Available A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.

  1. A genome scan conducted in a multigenerational pedigree with convergent strabismus supports a complex genetic determinism.

    Science.gov (United States)

    Georges, Anouk; Cambisano, Nadine; Ahariz, Naïma; Karim, Latifa; Georges, Michel

    2013-01-01

    A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.

  2. Cardiac imaging systems and methods employing computerized tomographic scanning

    International Nuclear Information System (INIS)

    Richey, J.B.; Wake, R.H.; Walters, R.G.; Hunt, W.F.; Cool, S.L.

    1980-01-01

    The invention relates to cardiac imaging systems and methods employing computerised tomographic scanning. Apparatus is described which allows an image of the radiation attenuation of the heart at a desired phase of the cardiac cycle. The patients ECG signal can be used in a transverse-and-rotate type CT scanner as a time base, so that the beam reaches the heart at a desired phase of the cardiac cycle, or, in a purely rotational-type CT scanner continuously generated scan data is only stored for corresponding phases of successive cardiac cycles. Alternatively, gating of the beams themselves by shuttering or switching the power supply can be controlled by the ECG signal. A pacemaker is used to stabilize the cardiac period. Also used is a system for recognising unacceptable variations in the cardiac period and discarding corresponding scan data. In a transverse-and-rotate type fan-beam CT scanner, the effective beam width is narrowed to reduce the duration of the traverse of the heart. (U.K.)

  3. method and container for production of diagnostic scanning agents

    International Nuclear Information System (INIS)

    Ruddock, C.F.

    1979-01-01

    The pertechnetate ion containing the technetium-99m isotope has limited applications in diagnostic scanning because it does not readily form complexes with materials which locate in specific parts of the body. Stannous salts have been widely used to reduce the pertechnetate to a form which readily complexes with materials. In the present invention, both a container and a more suitable metal reducing agent are discussed for transforming the technetium in pertechnetate for diagnostic scanning use. The vessel contains tin or a tin-containing alloy as a reducing agent for the pertechnetate and a complexant for the reduced technetium; all contents are sterile and dry. The present invention is advantageous over the stannous salts method since (1) problems of stannous salt instability during production, storage and after labelling are eliminated; (2) production procedures are simplified; (3) it is not essential to nitrogen purge vials before sterilisation; (4) it reduces toxicity; (5) the shelf life of diagnostic scanning kits may be dramatically improved; (6) the metal reducing agent may be sterilised by γ-irradiation without deteriorating; (7) the labelling technique can be performed over a wide pH range; and (8) the technique should be unaffected by technetium-99 in the technetium-99m. (U.K.)

  4. A Testable Design Method for Memories by Boundary Scan Technique

    Directory of Open Access Journals (Sweden)

    Qiao Guo-Hui

    2016-01-01

    Full Text Available This paper presents a design for test the embedded flash in an object System-on-a-chip (SoC. The feature of the Flash TAP (Test Access Port complies with the IEEE std.1149.1, and it can select different scan chains and other control registers for other test. By the trade-off between the test time and the circuit area, an IST (In System Test circuit is designed in the SoC. Experiment results on the embedded memory have shown that the proposed method costs small testing timing by the use of IST.

  5. Performance of analytical methods for tomographic gamma scanning

    International Nuclear Information System (INIS)

    Prettyman, T.H.; Mercer, D.J.

    1997-01-01

    The use of gamma-ray computerized tomography for nondestructive assay of radioactive materials has led to the development of specialized analytical methods. Over the past few years, Los Alamos has developed and implemented a computer code, called ARC-TGS, for the analysis of data obtained by tomographic gamma scanning (TGS). ARC-TGS reduces TGS transmission and emission tomographic data, providing the user with images of the sample contents, the activity or mass of selected radionuclides, and an estimate of the uncertainty in the measured quantities. The results provided by ARC-TGS can be corrected for self-attenuation when the isotope of interest emits more than one gamma-ray. In addition, ARC-TGS provides information needed to estimate TGS quantification limits and to estimate the scan time needed to screen for small amounts of radioactivity. In this report, an overview of the analytical methods used by ARC-TGS is presented along with an assessment of the performance of these methods for TGS

  6. Method and apparatus for scanning a transverse field

    International Nuclear Information System (INIS)

    Stoddart, H.F.

    1978-01-01

    A transverse radionuclide scan-field imaging apparatus is described for use in scanning with particular reference to the brain. It comprises a plurality of highly focussed collimators surrounding and being focussed inwardly with respect to the scan-field and means for imparting movement to the collimators. Adjacent collimators can be stepped in radially opposite directions after each tangential scan, so that the focal point of each collimator scans at least one half of the scan-field. Each collimator is associated with a scintillator crystal and photodetector whose output is used to calculate the radioactive emission intensity at a number of points in the scan-field. (author)

  7. Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan

    NARCIS (Netherlands)

    Sonuga-Barke, E.; Lasky-Su, J.; Neale, B.; Oades, R.D.; Chen, W.; Franke, B.; Buitelaar, J.K.; Banaschewski, T.; Ebstein, R.; Gill, M.; Anney, R.J.; Miranda, A.; Mulas, F.; Roeyers, H.; Rothenberger, A.; Sergeant, J.A.; Steinhausen, H.C.; Thompson, M.; Asherson, P.; Faraone, S.V.

    2008-01-01

    Studies of gene x environment (G x E) interaction in ADHD have previously focused on known risk genes for ADHD and environmentally mediated biological risk. Here we use G x E analysis in the context of a genome-wide association scan to identify novel genes whose effects on ADHD symptoms and comorbid

  8. Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan.

    NARCIS (Netherlands)

    Sonuga-Barke, E.J.S.; Lasky-Su, J.; Neale, B.; Oades, R.D.; Chen, W.; Franke, B.; Buitelaar, J.K.; Banaschewski, T.; Ebstein, R.P.; Gill, M.; Anney, R.; Miranda, A.; Mulas, F.; Roeyers, H.; Rothenberger, A.; Sergeant, J.A.; Steinhausen, H.C.; Thompson, M.; Asherson, P.; Faraone, S.V.

    2008-01-01

    Studies of gene x environment (G x E) interaction in ADHD have previously focused on known risk genes for ADHD and environmentally mediated biological risk. Here we use G x E analysis in the context of a genome-wide association scan to identify novel genes whose effects on ADHD symptoms and comorbid

  9. Genome-wide association scan in HIV-1-infected individuals identifying variants influencing disease course.

    Directory of Open Access Journals (Sweden)

    Daniëlle van Manen

    Full Text Available BACKGROUND: AIDS develops typically after 7-11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (15 years. To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. METHODS: The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. RESULTS: Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. CONCLUSIONS: Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection.

  10. Genome-Wide Association Scan in HIV-1-Infected Individuals Identifying Variants Influencing Disease Course

    Science.gov (United States)

    van Manen, Daniëlle; Delaneau, Olivier; Kootstra, Neeltje A.; Boeser-Nunnink, Brigitte D.; Limou, Sophie; Bol, Sebastiaan M.; Burger, Judith A.; Zwinderman, Aeilko H.; Moerland, Perry D.; van 't Slot, Ruben; Zagury, Jean-François; van 't Wout, Angélique B.; Schuitemaker, Hanneke

    2011-01-01

    Background AIDS develops typically after 7–11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (15 years). To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS) in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. Methods The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. Results Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. Conclusions Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection. PMID:21811574

  11. Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data.

    Directory of Open Access Journals (Sweden)

    Abigail Bigham

    2010-09-01

    Full Text Available High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2, shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association

  12. SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.

    Science.gov (United States)

    Mao, Hongliang; Wang, Hao

    2017-03-01

    Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux. wangh8@fudan.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  13. Measurement of gastric emptying rate in humans. Simplified scanning method

    Energy Technology Data Exchange (ETDEWEB)

    Holt, S.; Colliver, J.; Guram, M.; Neal, C.; Verhulst, S.J.; Taylor, T.V. (Univ. of South Carolina School of Medicine, Columbia (USA))

    1990-11-01

    Simultaneous measurements of the gastric emptying rate of the solid and liquid phase of a dual-isotope-labeled test meal were made using a gamma camera and a simple scintillation detector, similar to that used in a hand-held probe. A simple scanning apparatus, similar to that used in a hand-held scintillation probe, was compared with simultaneous measurements made by a gamma camera in 16 healthy males. A dual-labeled test meal was utilized to measure liquid and solid emptying simultaneously. Anterior and posterior scans were taken at intervals up to 120 min using both a gamma camera and the scintillation probe. Good relative agreement between the methods was obtained both for solid-phase (correlation range 0.92-0.99, mean 0.97) and for liquid-phase data (correlation range 0.93-0.99, mean 0.97). For solid emptying data regression line slopes varied from 0.75 to 1.03 (mean 0.84). Liquid emptying data indicated that slopes ranged from 0.71 to 1.06 (mean 0.87). These results suggested that an estimate of the gamma measurement could be obtained by multiplying the scintillation measurement by a factor of 0.84 for the solid phase and 0.87 for the liquid phase. Correlation between repeat studies was 0.97 and 0.96 for solids and liquids, respectively. The application of a hand-held probe technique provides a noninvasive and inexpensive method for accurately assessing solid- and liquid-phase gastric emptying from the human stomach that correlates well with the use of a gamma camera, within the range of gastric emptying rate in the normal individuals in this study.

  14. Measurement of gastric emptying rate in humans. Simplified scanning method

    International Nuclear Information System (INIS)

    Holt, S.; Colliver, J.; Guram, M.; Neal, C.; Verhulst, S.J.; Taylor, T.V.

    1990-01-01

    Simultaneous measurements of the gastric emptying rate of the solid and liquid phase of a dual-isotope-labeled test meal were made using a gamma camera and a simple scintillation detector, similar to that used in a hand-held probe. A simple scanning apparatus, similar to that used in a hand-held scintillation probe, was compared with simultaneous measurements made by a gamma camera in 16 healthy males. A dual-labeled test meal was utilized to measure liquid and solid emptying simultaneously. Anterior and posterior scans were taken at intervals up to 120 min using both a gamma camera and the scintillation probe. Good relative agreement between the methods was obtained both for solid-phase (correlation range 0.92-0.99, mean 0.97) and for liquid-phase data (correlation range 0.93-0.99, mean 0.97). For solid emptying data regression line slopes varied from 0.75 to 1.03 (mean 0.84). Liquid emptying data indicated that slopes ranged from 0.71 to 1.06 (mean 0.87). These results suggested that an estimate of the gamma measurement could be obtained by multiplying the scintillation measurement by a factor of 0.84 for the solid phase and 0.87 for the liquid phase. Correlation between repeat studies was 0.97 and 0.96 for solids and liquids, respectively. The application of a hand-held probe technique provides a noninvasive and inexpensive method for accurately assessing solid- and liquid-phase gastric emptying from the human stomach that correlates well with the use of a gamma camera, within the range of gastric emptying rate in the normal individuals in this study

  15. Specific surface area evaluation method by using scanning electron microscopy

    International Nuclear Information System (INIS)

    Petrescu, Camelia; Petrescu, Cristian; Axinte, Adrian

    2000-01-01

    Ceramics are among the most interesting materials for a large category of applications, including both industry and health. Among the characteristic of the ceramic materials, the specific surface area is often difficult to evaluate.The paper presents a method of evaluation for the specific surface area of two ceramic powders by means of scanning electron microscopy measurements and an original method of computing the specific surface area.Cumulative curves are used to calculate the specific surface area under assumption that the values of particles diameters follow a normal logarithmic distribution. For two powder types, X7R and NPO the results are the following: - for the density ρ (g/cm 2 ), 5.5 and 6.0, respectively; - for the average diameter D bar (μm), 0.51 and 0.53, respectively; - for σ, 1.465 and 1.385, respectively; - for specific surface area (m 2 /g), 1.248 and 1.330, respectively. The obtained results are in good agreement with the values measured by conventional methods. (authors)

  16. System and method for compressive scanning electron microscopy

    Science.gov (United States)

    Reed, Bryan W

    2015-01-13

    A scanning transmission electron microscopy (STEM) system is disclosed. The system may make use of an electron beam scanning system configured to generate a plurality of electron beam scans over substantially an entire sample, with each scan varying in electron-illumination intensity over a course of the scan. A signal acquisition system may be used for obtaining at least one of an image, a diffraction pattern, or a spectrum from the scans, the image, diffraction pattern, or spectrum representing only information from at least one of a select subplurality or linear combination of all pixel locations comprising the image. A dataset may be produced from the information. A subsystem may be used for mathematically analyzing the dataset to predict actual information that would have been produced by each pixel location of the image.

  17. Band excitation method applicable to scanning probe microscopy

    Science.gov (United States)

    Jesse, Stephen [Knoxville, TN; Kalinin, Sergei V [Knoxville, TN

    2010-08-17

    Methods and apparatus are described for scanning probe microscopy. A method includes generating a band excitation (BE) signal having finite and predefined amplitude and phase spectrum in at least a first predefined frequency band; exciting a probe using the band excitation signal; obtaining data by measuring a response of the probe in at least a second predefined frequency band; and extracting at least one relevant dynamic parameter of the response of the probe in a predefined range including analyzing the obtained data. The BE signal can be synthesized prior to imaging (static band excitation), or adjusted at each pixel or spectroscopy step to accommodate changes in sample properties (adaptive band excitation). An apparatus includes a band excitation signal generator; a probe coupled to the band excitation signal generator; a detector coupled to the probe; and a relevant dynamic parameter extractor component coupled to the detector, the relevant dynamic parameter extractor including a processor that performs a mathematical transform selected from the group consisting of an integral transform and a discrete transform.

  18. Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs.

    Directory of Open Access Journals (Sweden)

    Kunzhe Dong

    Full Text Available High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP that is well adapted to the high altitude and Dahe pig (DHP that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19 for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16 were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9 were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.

  19. GenoSets: visual analytic methods for comparative genomics.

    Directory of Open Access Journals (Sweden)

    Aurora A Cain

    Full Text Available Many important questions in biology are, fundamentally, comparative, and this extends to our analysis of a growing number of sequenced genomes. Existing genomic analysis tools are often organized around literal views of genomes as linear strings. Even when information is highly condensed, these views grow cumbersome as larger numbers of genomes are added. Data aggregation and summarization methods from the field of visual analytics can provide abstracted comparative views, suitable for sifting large multi-genome datasets to identify critical similarities and differences. We introduce a software system for visual analysis of comparative genomics data. The system automates the process of data integration, and provides the analysis platform to identify and explore features of interest within these large datasets. GenoSets borrows techniques from business intelligence and visual analytics to provide a rich interface of interactive visualizations supported by a multi-dimensional data warehouse. In GenoSets, visual analytic approaches are used to enable querying based on orthology, functional assignment, and taxonomic or user-defined groupings of genomes. GenoSets links this information together with coordinated, interactive visualizations for both detailed and high-level categorical analysis of summarized data. GenoSets has been designed to simplify the exploration of multiple genome datasets and to facilitate reasoning about genomic comparisons. Case examples are included showing the use of this system in the analysis of 12 Brucella genomes. GenoSets software and the case study dataset are freely available at http://genosets.uncc.edu. We demonstrate that the integration of genomic data using a coordinated multiple view approach can simplify the exploration of large comparative genomic data sets, and facilitate reasoning about comparisons and features of interest.

  20. Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa

    2014-01-01

    BACKGROUND:  Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS:  We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used......, an area of high malaria transmission. Allele frequency-based tests provided evidence of recent population growth in Malawi and detected potential targets of host immunity and candidate vaccine antigens. Comparison of the sequence variation between isolates from Malawi and those from 5 geographically...... dispersed countries (Kenya, Burkina Faso, Mali, Cambodia, and Thailand) detected population genetic differences between Africa and Asia, within Southeast Asia, and within Africa. Haplotype-based tests of selection to sequence data from all 6 populations identified signals of directional selection at known...

  1. Circular mode: a new scanning probe microscopy method for investigating surface properties at constant and continuous scanning velocities.

    Science.gov (United States)

    Nasrallah, Hussein; Mazeran, Pierre-Emmanuel; Noël, Olivier

    2011-11-01

    In this paper, we introduce a novel scanning probe microscopy mode, called the circular mode, which offers expanded capabilities for surface investigations especially for measuring physical properties that require high scanning velocities and/or continuous displacement with no rest periods. To achieve these specific conditions, we have implemented a circular horizontal displacement of the probe relative to the sample plane. Thus the relative probe displacement follows a circular path rather than the conventional back and forth linear one. The circular mode offers advantages such as high and constant scanning velocities, the possibility to be combined with other classical operating modes, and a simpler calibration method of the actuators generating the relative displacement. As application examples of this mode, we report its ability to (1) investigate the influence of scanning velocity on adhesion forces, (2) measure easily and instantly the friction coefficient, and (3) generate wear tracks very rapidly for tribological investigations. © 2011 American Institute of Physics

  2. Uniform irradiation system using beam scanning method for cyclotron

    International Nuclear Information System (INIS)

    Agematsu, Takashi; Okumura, Susumu; Arakawa, Kazuo

    1994-03-01

    JAERI AVF-cyclotron is equipped with an ion beam scanner for large area irradiation. The two-dimensional fluence distribution of ion beam obtained using cellulose triacetate film dosimeter was not uniform. This is resulted from the distortion of excitation current for electromagnet of the scanner. So, the beam scanning condition, i.e., the relation between the ion species, the beam profile and the scanning width, was extremely limited to make a good uniformity. We have developed a beam scanning simulator to get fluence distributions by calculation and then compared the simulated distributions with the measured ones. It was revealed that the both of them are in good agreement and the beam scanning condition to get good uniformity was led by using this simulator. On the basis of these results, the power supply of scanner was improved. A good uniformity of beam distribution was available. (author)

  3. Translate rotate scanning method for X-ray imaging

    International Nuclear Information System (INIS)

    Eberhard, J.W.; Kwog Cheong Tam.

    1990-01-01

    Rapid x-ray inspection of objects larger than an x-ray detector array is based on a translate rotate scanning motion of the object related to the fan beam source and detector. The scan for computerized tomography imaging is accomplished by rotating the object through 360 degrees at two or more positions relative to the source and detector array, in moving to another position the object is rotated and the object or source and detector are translated. A partial set of x-ray data is acquired at every position which are combined to obtain a full data set for complete image reconstruction. X-ray data for digital radiography imaging is acquired by scanning the object vertically at a first position at one view angle, rotating and translating the object relative to the source and detector to a second position, scanning vertically, and so on to cover the object field of view, and combining the partial data sets. (author)

  4. Method for HEPA filter leak scanning with differentiating aerosol detector

    Energy Technology Data Exchange (ETDEWEB)

    Kovach, B.J.; Banks, E.M.; Wikoff, W.O. [NUCON International, Inc., Columbus, OH (United States)

    1997-08-01

    While scanning HEPA filters for leaks with {open_quotes}Off the Shelf{close_quote} aerosol detection equipment, the operator`s scanning speed is limited by the time constant and threshold sensitivity of the detector. This is based on detection of the aerosol density, where the maximum signal is achieved when the scanning probe resides over the pinhole longer than several detector time-constants. Since the differential value of the changing signal can be determined by observing only the first small fraction of the rising signal, using a differentiating amplifier will speed up the locating process. The other advantage of differentiation is that slow signal drift or zero offset will not interfere with the process of locating the leak, since they are not detected. A scanning hand-probe attachable to any NUCON{reg_sign} Aerosol Detector displaying the combination of both aerosol density and differentiated signal was designed. 3 refs., 1 fig.

  5. Genomics protocols [Methods in molecular biology, v. 175

    National Research Council Canada - National Science Library

    Starkey, Michael P; Elaswarapu, Ramnath

    2001-01-01

    ... exploiting the potential of gene therapy. Highlights include methods for the analysis of differential gene expression, SNP detection, comparative genomic hybridization, and the functional analysis of genes, as well as the use of bio...

  6. Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations

    Directory of Open Access Journals (Sweden)

    David Jean-Philippe

    2009-11-01

    Full Text Available Abstract Background Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s or mutation(s targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito Aedes aegypti with the aim to look for candidate genes involved in resistance to Bacillus thuringiensis subsp. israelensis (Bti insecticidal toxins. Results The genome of a Bti-resistant and a Bti-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the Aedes aegypti genome sequence. Several good candidate genes for Bti-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations, as well as a significant under-expression compared to the susceptible strain. Conclusion Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to Bti is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with Bti resistance in Ae. aegypti. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full

  7. Univariate/multivariate genome-wide association scans using data from families and unrelated samples.

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2009-08-01

    Full Text Available As genome-wide association studies (GWAS are becoming more popular, two approaches, among others, could be considered in order to improve statistical power for identifying genes contributing subtle to moderate effects to human diseases. The first approach is to increase sample size, which could be achieved by combining both unrelated and familial subjects together. The second approach is to jointly analyze multiple correlated traits. In this study, by extending generalized estimating equations (GEEs, we propose a simple approach for performing univariate or multivariate association tests for the combined data of unrelated subjects and nuclear families. In particular, we correct for population stratification by integrating principal component analysis and transmission disequilibrium test strategies. The proposed method allows for multiple siblings as well as missing parental information. Simulation studies show that the proposed test has improved power compared to two popular methods, EIGENSTRAT and FBAT, by analyzing the combined data, while correcting for population stratification. In addition, joint analysis of bivariate traits has improved power over univariate analysis when pleiotropic effects are present. Application to the Genetic Analysis Workshop 16 (GAW16 data sets attests to the feasibility and applicability of the proposed method.

  8. Genome-wide linkage scan for colorectal cancer susceptibility genes supports linkage to chromosome 3q

    Directory of Open Access Journals (Sweden)

    Velculescu Victor E

    2008-04-01

    Full Text Available Abstract Background Colorectal cancer is one of the most common causes of cancer-related mortality. The disease is clinically and genetically heterogeneous though a strong hereditary component has been identified. However, only a small proportion of the inherited susceptibility can be ascribed to dominant syndromes, such as Hereditary Non-Polyposis Colorectal Cancer (HNPCC or Familial Adenomatous Polyposis (FAP. In an attempt to identify novel colorectal cancer predisposing genes, we have performed a genome-wide linkage analysis in 30 Swedish non-FAP/non-HNPCC families with a strong family history of colorectal cancer. Methods Statistical analysis was performed using multipoint parametric and nonparametric linkage. Results Parametric analysis under the assumption of locus homogeneity excluded any common susceptibility regions harbouring a predisposing gene for colorectal cancer. However, several loci on chromosomes 2q, 3q, 6q, and 7q with suggestive linkage were detected in the parametric analysis under the assumption of locus heterogeneity as well as in the nonparametric analysis. Among these loci, the locus on chromosome 3q21.1-q26.2 was the most consistent finding providing positive results in both parametric and nonparametric analyses Heterogeneity LOD score (HLOD = 1.90, alpha = 0.45, Non-Parametric LOD score (NPL = 2.1. Conclusion The strongest evidence of linkage was seen for the region on chromosome 3. Interestingly, the same region has recently been reported as the most significant finding in a genome-wide analysis performed with SNP arrays; thus our results independently support the finding on chromosome 3q.

  9. High-speed X-ray phase tomography with Talbot interferometer and fringe scanning method

    International Nuclear Information System (INIS)

    Kibayashi, Shunsuke; Harasse, Sébastien; Yashiro, Wataru; Momose, Atsushi

    2012-01-01

    High-speed X-ray phase tomography based on the Fourier-transform method has been demonstrated with an X-ray Talbot interferometer using white synchrotron radiation. We report the experimental results of high-speed X-ray phase tomography with fringe-scanning method instead of Fourier-transform method to improve spatial resolution without a considerable increase of scan time. To apply fringe-scanning method to high speed tomography, we tested a scan that is a synchronous combination of one-way continuous movements of the sample rotation and the grating displacement. When this scanning method was combined with X-ray phase tomography, we were able to obtain a scan time of 5 s. A comparison of the image quality derived with the conventional approach and with the proposed approach using the fringe-scanning method showed that the latter had better spatial resolution.

  10. Finding function: evaluation methods for functional genomic data

    Directory of Open Access Journals (Sweden)

    Barrett Daniel R

    2006-07-01

    Full Text Available Abstract Background Accurate evaluation of the quality of genomic or proteomic data and computational methods is vital to our ability to use them for formulating novel biological hypotheses and directing further experiments. There is currently no standard approach to evaluation in functional genomics. Our analysis of existing approaches shows that they are inconsistent and contain substantial functional biases that render the resulting evaluations misleading both quantitatively and qualitatively. These problems make it essentially impossible to compare computational methods or large-scale experimental datasets and also result in conclusions that generalize poorly in most biological applications. Results We reveal issues with current evaluation methods here and suggest new approaches to evaluation that facilitate accurate and representative characterization of genomic methods and data. Specifically, we describe a functional genomics gold standard based on curation by expert biologists and demonstrate its use as an effective means of evaluation of genomic approaches. Our evaluation framework and gold standard are freely available to the community through our website. Conclusion Proper methods for evaluating genomic data and computational approaches will determine how much we, as a community, are able to learn from the wealth of available data. We propose one possible solution to this problem here but emphasize that this topic warrants broader community discussion.

  11. A Two-stage Improvement Method for Robot Based 3D Surface Scanning

    Science.gov (United States)

    He, F. B.; Liang, Y. D.; Wang, R. F.; Lin, Y. S.

    2018-03-01

    As known that the surface of unknown object was difficult to measure or recognize precisely, hence the 3D laser scanning technology was introduced and used properly in surface reconstruction. Usually, the surface scanning speed was slower and the scanning quality would be better, while the speed was faster and the quality would be worse. In this case, the paper presented a new two-stage scanning method in order to pursuit the quality of surface scanning in a faster speed. The first stage was rough scanning to get general point cloud data of object’s surface, and then the second stage was specific scanning to repair missing regions which were determined by chord length discrete method. Meanwhile, a system containing a robotic manipulator and a handy scanner was also developed to implement the two-stage scanning method, and relevant paths were planned according to minimum enclosing ball and regional coverage theories.

  12. Statistical image reconstruction methods for simultaneous emission/transmission PET scans

    International Nuclear Information System (INIS)

    Erdogan, H.; Fessler, J.A.

    1996-01-01

    Transmission scans are necessary for estimating the attenuation correction factors (ACFs) to yield quantitatively accurate PET emission images. To reduce the total scan time, post-injection transmission scans have been proposed in which one can simultaneously acquire emission and transmission data using rod sources and sinogram windowing. However, since the post-injection transmission scans are corrupted by emission coincidences, accurate correction for attenuation becomes more challenging. Conventional methods (emission subtraction) for ACF computation from post-injection scans are suboptimal and require relatively long scan times. We introduce statistical methods based on penalized-likelihood objectives to compute ACFs and then use them to reconstruct lower noise PET emission images from simultaneous transmission/emission scans. Simulations show the efficacy of the proposed methods. These methods improve image quality and SNR of the estimates as compared to conventional methods

  13. Comparison of demons deformable registration-based methods for texture analysis of serial thoracic CT scans

    Science.gov (United States)

    Cunliffe, Alexandra R.; Al-Hallaq, Hania A.; Fei, Xianhan M.; Tuohy, Rachel E.; Armato, Samuel G.

    2013-02-01

    To determine how 19 image texture features may be altered by three image registration methods, "normal" baseline and follow-up computed tomography (CT) scans from 27 patients were analyzed. Nineteen texture feature values were calculated in over 1,000 32x32-pixel regions of interest (ROIs) randomly placed in each baseline scan. All three methods used demons registration to map baseline scan ROIs to anatomically matched locations in the corresponding transformed follow-up scan. For the first method, the follow-up scan transformation was subsampled to achieve a voxel size identical to that of the baseline scan. For the second method, the follow-up scan was transformed through affine registration to achieve global alignment with the baseline scan. For the third method, the follow-up scan was directly deformed to the baseline scan using demons deformable registration. Feature values in matched ROIs were compared using Bland- Altman 95% limits of agreement. For each feature, the range spanned by the 95% limits was normalized to the mean feature value to obtain the normalized range of agreement, nRoA. Wilcoxon signed-rank tests were used to compare nRoA values across features for the three methods. Significance for individual tests was adjusted using the Bonferroni method. nRoA was significantly smaller for affine-registered scans than for the resampled scans (p=0.003), indicating lower feature value variability between baseline and follow-up scan ROIs using this method. For both of these methods, however, nRoA was significantly higher than when feature values were calculated directly on demons-deformed followup scans (p<0.001). Across features and methods, nRoA values remained below 26%.

  14. A bi-dimensional genome scan for prolificacy traits in pigs shows the existence of multiple epistatic QTL

    Directory of Open Access Journals (Sweden)

    Bidanel Jean P

    2009-12-01

    Full Text Available Abstract Background Prolificacy is the most important trait influencing the reproductive efficiency of pig production systems. The low heritability and sex-limited expression of prolificacy have hindered to some extent the improvement of this trait through artificial selection. Moreover, the relative contributions of additive, dominant and epistatic QTL to the genetic variance of pig prolificacy remain to be defined. In this work, we have undertaken this issue by performing one-dimensional and bi-dimensional genome scans for number of piglets born alive (NBA and total number of piglets born (TNB in a three generation Iberian by Meishan F2 intercross. Results The one-dimensional genome scan for NBA and TNB revealed the existence of two genome-wide highly significant QTL located on SSC13 (P SSC17 (P P P P P Conclusions The complex inheritance of prolificacy traits in pigs has been evidenced by identifying multiple additive (SSC13 and SSC17, dominant and epistatic QTL in an Iberian × Meishan F2 intercross. Our results demonstrate that a significant fraction of the phenotypic variance of swine prolificacy traits can be attributed to first-order gene-by-gene interactions emphasizing that the phenotypic effects of alleles might be strongly modulated by the genetic background where they segregate.

  15. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

  16. Indoor Map Acquisition System Using Global Scan Matching Method and Laser Range Scan Data

    Science.gov (United States)

    Hisanaga, Satoshi; Kase, Takaaki

    Simultaneous localization and mapping (SLAM) is the latest technique for constructing indoor maps. In indoor environment, a localization method using the features of the walls as landmarks has been studied in the past. The past study has a drawback. It cannot localize in spaces surrounded by featureless walls or walls on which similar features are repeated. To overcome this drawback, we developed an accuracy localization method that ignores the features of the walls. We noted the fact that the walls in a building are aligned along only two orthogonal directions. By considering a specific wall to be a reference wall, the location of a robot was expressed by using the distance between the robot and the reference wall. We developed the robot in order to evaluate the mapping accuracy of our method and carried out an experiment to map a corridor (40m long) that contained featureless parts. The map obtained had a margin of error of less than 2%.

  17. Nuclear emulsion scanning in opera: methods and results

    CERN Document Server

    Bozza, C.

    2008-01-01

    The design of the OPERA experiment was also motivated and justified by the revival of nuclear emulsion handling and scanning in a modem, automatic fashion, as it took previously place, although at a smaller scale, for the CHORUS experiment. Nuclear emulsions are still the only detector to allow a very detailed topological study of an interaction/decay vertex at the sub-micrometer level. They are most suitable in experiments where topology is a non-ambiguous signature of a certain class of events. This is for instance the case of neutrino oscillation detection and measurement by the study of a tau-appearance signal. The design and performance of the two different scanning systems used in OPERA (ESS and S-UTS) are discussed. Their unique features in terms of speed, precision, background suppression, particle identification, and kinematical reconstruction are shown in close connection with the technical details that make them possible. Unequalled precision, almost vanishing background, and a wealth of informati...

  18. A surface refractive index scanning system and method

    DEFF Research Database (Denmark)

    2015-01-01

    The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction, and a s......The invention relates to a surface refractive index scanning system for characterization of a sample. The system comprises a grating device for holding or receiving the sample, the device comprising at least a first grating region having a first grating width along a transverse direction...... a grating period Λ2 in the longitudinal direction, where the longitudinal direction is orthogonal to the transverse direction. A grating period spacing ΔΛ = Λ1 - Λ2 is finite. Further, the first and second grating periods are chosen to provide optical resonances for light respectively in a first...... wavelength band and a second wavelength band, light is being emitted, transmitted, or reflected in an out-of-plane direction, wherein the first wavelength band and the second wavelength band are at least partially non-overlapping in wavelength. The system further comprises a light source for illuminating...

  19. Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan

    OpenAIRE

    Sonuga-Barke, E.; Lasky-Su, J.; Neale, B.; Oades, R.D.; Chen, W.; Franke, B.; Buitelaar, J.K.; Banaschewski, T.; Ebstein, R.; Gill, M.; Anney, R.J.; Miranda, A.; Mulas, F.; Roeyers, H.; Rothenberger, A.

    2008-01-01

    Studies of gene x environment (G x E) interaction in ADHD have previously focused on known risk genes for ADHD and environmentally mediated biological risk. Here we use G x E analysis in the context of a genome-wide association scan to identify novel genes whose effects on ADHD symptoms and comorbid conduct disorder are moderated by high maternal expressed emotion (EE). SNPs (600,000) were genotyped in 958 ADHD proband-parent trios. After applying data cleaning procedures we examined 429,981 ...

  20. Allergic rhinitis - a total genome-scan for susceptibility genes suggests a locus on chromosome 4q24-q27

    DEFF Research Database (Denmark)

    Haagerup, A; Bjerke, T; Schøitz, P O

    2001-01-01

    Allergic rhinitis is a common disease of complex inheritance and is characterised by mucosal inflammation caused by allergen exposure. The genetics of closely related phenotypes such as asthma, atopy and to some extend atopic dermatitis has attracted attention in recent years. Genetic reports...... of allergic rhinitis on the contrary have as yet been most sparse. To identify candidate regions holding genes for allergic rhinitis we performed a total genome-scan on affected sib-pair families. From 100 Danish sib-pair families selected for allergy, families containing sib-pairs matching a phenotype...

  1. A tailing genome walking method suitable for genomes with high local GC content.

    Science.gov (United States)

    Liu, Taian; Fang, Yongxiang; Yao, Wenjuan; Guan, Qisai; Bai, Gang; Jing, Zhizhong

    2013-10-15

    The tailing genome walking strategies are simple and efficient. However, they sometimes can be restricted due to the low stringency of homo-oligomeric primers. Here we modified their conventional tailing step by adding polythymidine and polyguanine to the target single-stranded DNA (ssDNA). The tailed ssDNA was then amplified exponentially with a specific primer in the known region and a primer comprising 5' polycytosine and 3' polyadenosine. The successful application of this novel method for identifying integration sites mediated by φC31 integrase in goat genome indicates that the method is more suitable for genomes with high complexity and local GC content. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Kernel methods for large-scale genomic data analysis

    Science.gov (United States)

    Xing, Eric P.; Schaid, Daniel J.

    2015-01-01

    Machine learning, particularly kernel methods, has been demonstrated as a promising new tool to tackle the challenges imposed by today’s explosive data growth in genomics. They provide a practical and principled approach to learning how a large number of genetic variants are associated with complex phenotypes, to help reveal the complexity in the relationship between the genetic markers and the outcome of interest. In this review, we highlight the potential key role it will have in modern genomic data processing, especially with regard to integration with classical methods for gene prioritizing, prediction and data fusion. PMID:25053743

  3. Genome analysis methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Genome analysis... methods Data detail Data name Genome analysis methods DOI 10.18908/lsdba.nbdc01194-01-005 De...scription of data contents The current status and related information of the genomic analysis about each org...anism (March, 2014). In the case of organisms carried out genomic analysis, the d...e File name: pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip File URL: ftp://ftp.biosciencedbc.j

  4. Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution

    NARCIS (Netherlands)

    C.M. Lindgren (Cecilia); I.M. Heid (Iris); J.C. Randall (Joshua); C. Lamina (Claudia); V. Steinthorsdottir (Valgerdur); L. Qi (Lu); E.K. Speliotes (Elizabeth); G. Thorleifsson (Gudmar); C.J. Willer (Cristen); B.M. Herrera (Blanca); A.U. Jackson (Anne); N. Lim (Noha); P. Scheet (Paul); N. Soranzo (Nicole); N. Amin (Najaf); Y.S. Aulchenko (Yurii); J.C. Chambers (John); A. Drong (Alexander); J. Luan; H.N. Lyon (Helen); F. Rivadeneira Ramirez (Fernando); S. Sanna (Serena); N.J. Timpson (Nicholas); M.C. Zillikens (Carola); H.Z. Jing; P. Almgren (Peter); S. Bandinelli (Stefania); A.J. Bennett (Amanda); R.N. Bergman (Richard); L.L. Bonnycastle (Lori); S. Bumpstead (Suzannah); S.J. Chanock (Stephen); L. Cherkas (Lynn); P.S. Chines (Peter); L. Coin (Lachlan); C. Cooper (Charles); G. Crawford (Gabe); A. Doering (Angela); A. Dominiczak (Anna); A.S.F. Doney (Alex); S. Ebrahim (Shanil); P. Elliott (Paul); M.R. Erdos (Michael); K. Estrada Gil (Karol); L. Ferrucci (Luigi); G. Fischer (Guido); N.G. Forouhi (Nita); C. Gieger (Christian); H. Grallert (Harald); C.J. Groves (Christopher); S.M. Grundy (Scott); C. Guiducci (Candace); D. Hadley (David); A. Hamsten (Anders); A.S. Havulinna (Aki); A. Hofman (Albert); R. Holle (Rolf); J.W. Holloway (John); T. Illig (Thomas); B. Isomaa (Bo); L.C. Jacobs (Leonie); K. Jameson (Karen); P. Jousilahti (Pekka); F. Karpe (Fredrik); J. Kuusisto (Johanna); J. Laitinen (Jaana); G.M. Lathrop (Mark); D.A. Lawlor (Debbie); M. Mangino (Massimo); W.L. McArdle (Wendy); T. Meitinger (Thomas); M.A. Morken (Mario); A.P. Morris (Andrew); P. Munroe (Patricia); N. Narisu (Narisu); A. Nordström (Anna); B.A. Oostra (Ben); C.N.A. Palmer (Colin); F. Payne (Felicity); J. Peden (John); I. Prokopenko (Inga); F. Renström (Frida); A. Ruokonen (Aimo); V. Salomaa (Veikko); M.S. Sandhu (Manjinder); L.J. Scott (Laura); A. Scuteri (Angelo); K. Silander (Kaisa); K. Song (Kijoung); X. Yuan (Xin); H.M. Stringham (Heather); A.J. Swift (Amy); T. Tuomi (Tiinamaija); M. Uda (Manuela); P. Vollenweider (Peter); G. Waeber (Gérard); C. Wallace (Chris); G.B. Walters (Bragi); M.N. Weedon (Michael); J.C.M. Witteman (Jacqueline); C. Zhang (Cuilin); M. Caulfield (Mark); F.S. Collins (Francis); G.D. Smith; I.N.M. Day (Ian); P.W. Franks (Paul); A.T. Hattersley (Andrew); F.B. Hu (Frank); M.-R. Jarvelin (Marjo-Riitta); A. Kong (Augustine); J.S. Kooner (Jaspal); M. Laakso (Markku); E. Lakatta (Edward); V. Mooser (Vincent); L. Peltonen (Leena Johanna); N.J. Samani (Nilesh); T.D. Spector (Timothy); D.P. Strachan (David); T. Tanaka (Toshiko); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); P. Tikka-Kleemola (Päivi); N.J. Wareham (Nick); H. Watkins (Hugh); D. Waterworth (Dawn); M. Boehnke (Michael); P. Deloukas (Panagiotis); L. Groop (Leif); D.J. Hunter (David); U. Thorsteinsdottir (Unnur); D. Schlessinger (David); H.E. Wichmann (Erich); T.M. Frayling (Timothy); G.R. Abecasis (Gonçalo); J.N. Hirschhorn (Joel); R.J.F. Loos (Ruth); J-A. Zwart (John-Anker); K.L. Mohlke (Karen); I.E. Barroso (Inês); M.I. McCarthy (Mark)

    2009-01-01

    textabstractTo identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the

  5. SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C.; Nielsen, Morten; Lamberth, K.

    2004-01-01

    . Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly, from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS...

  6. Improvement of chirped pulse contrast using electro-optic birefringence scanning filter method

    International Nuclear Information System (INIS)

    Zeng Shuguang; Wang Xianglin; Wang Qishan; Zhang Bin; Sun Nianchun; Wang Fei

    2013-01-01

    A method using scanning filter to improve the contrast of chirped pulse is proposed, and the principle of this method is analyzed. The scanning filter is compared with the existing pulse-picking technique and nonlinear filtering technique. The scanning filter is a temporal gate that is independent on the intensity of the pulses, but on the instantaneous wavelengths of light. Taking the electro-optic birefringence scanning filter as an example, the application of scanning filter methods is illustrated. Based on numerical simulation and experimental research, it is found that the electro-optic birefringence scanning filter can eliminate a prepulse which is several hundred picoseconds before the main pulse, and the main pulse can maintain a high transmissivity. (authors)

  7. Reliability testing of tendon disease using two different scanning methods in patients with rheumatoid arthritis

    DEFF Research Database (Denmark)

    Bruyn, George A W; Möller, Ingrid; Garrido, Jesus

    2012-01-01

    To assess the intra- and interobserver reliability of musculoskeletal ultrasonography (US) in detecting inflammatory and destructive tendon abnormalities in patients with RA using two different scanning methods.......To assess the intra- and interobserver reliability of musculoskeletal ultrasonography (US) in detecting inflammatory and destructive tendon abnormalities in patients with RA using two different scanning methods....

  8. GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.

    Science.gov (United States)

    Lu, Bingxin; Leong, Hon Wai

    2016-02-01

    Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.

  9. A universal, rapid, and inexpensive method for genomic DNA ...

    Indian Academy of Sciences (India)

    MOHAMMED BAQUR SAHIB A. AL-SHUHAIB

    gels, containing 7% glycerol, and 1×TBE buffer. The gels were run under 200 .... Inc. Germany, GeneaidTM DNA Isolation Kit, Geneaid. Biotech., New Taipei City, .... C. L. and Arsenos G. 2015 Comparison of eleven methods for genomic DNA ...

  10. Methods to compute reliabilities for genomic predictions of feed intake

    Science.gov (United States)

    For new traits without historical reference data, cross-validation is often the preferred method to validate reliability (REL). Time truncation is less useful because few animals gain substantial REL after the truncation point. Accurate cross-validation requires separating genomic gain from pedigree...

  11. Genome-wide scans for delineation of candidate genes regulating seed-protein content in chickpea

    Directory of Open Access Journals (Sweden)

    Hari Deo eUpadhyaya

    2016-03-01

    Full Text Available Identification of potential genes/alleles governing complex seed-protein content (SPC trait is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study, high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150-200 kb LD (linkage disequilibrium decay] was utilized. This led to identification of seven most effective genomic loci (genes associated [10 to 20% with 41% combined PVE (phenotypic variation explained] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line mapping population (ICC 12299 x ICC 4958 by selective genotyping. The seed-specific expression, including differential up-regulation (> 4-fold of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with high level of contrasting seed-protein content (21-22% was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait

  12. Uniform irradiation using rotational-linear scanning method for narrow synchrotron radiation beam

    International Nuclear Information System (INIS)

    Nariyama, N.; Ohnishi, S.; Odano, N.

    2004-01-01

    At SPring-8, photon intensity monitors for synchrotron radiation have been developed. Using these monitors, the responses of radiation detectors and dosimeters to monoenergetic photons can be measured. In most cases, uniform irradiation to the sample is necessary. Here, two scanning methods are proposed. One is an XZ-linear scanning method, which moves the sample simultaneously in both the X and Z direction, that is, in zigzag fashion. The other is a rotational-linear scanning method, which rotates the sample moving in the X direction. To investigate the validity of the two methods, thermoluminescent dosimeters were irradiated with a broad synchrotron-radiation beam, and the readings from the two methods were compared with that of the dosimeters fixed in the beam. The results for both scanning methods virtually agreed with that of the fixed method. The advantages of the rotational-linear scanning method are that low- and medium-dose irradiation is possible, uniformity is excellent and the load to the scanning equipment is light: hence, this method is superior to the XZ-linear scanning method for most applications. (author)

  13. A simplified method for scanning electron microscopy (SEM) autoradiography

    International Nuclear Information System (INIS)

    Shahar, A.; Lasher, R.

    1980-01-01

    The combination of autoradiography with SEM provides a valuable tool for the study of labeled biological materials, but the previously described methods are complicated because they call first for the removal of gelatin from the film emulsion and this is then followed by deposition of gold vapor on the specimen. The authors describe a much simpler method which can easily be adapted to routine examination of cell cultures. In this method, gelatin is not removed; the film is coated with vaporized carbon only. This procedure permits visualization of both cellular image and distribution of silver grains. (Auth.)

  14. Genomic Selection in Plant Breeding: Methods, Models, and Perspectives.

    Science.gov (United States)

    Crossa, José; Pérez-Rodríguez, Paulino; Cuevas, Jaime; Montesinos-López, Osval; Jarquín, Diego; de Los Campos, Gustavo; Burgueño, Juan; González-Camacho, Juan M; Pérez-Elizalde, Sergio; Beyene, Yoseph; Dreisigacker, Susanne; Singh, Ravi; Zhang, Xuecai; Gowda, Manje; Roorkiwal, Manish; Rutkoski, Jessica; Varshney, Rajeev K

    2017-11-01

    Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. A genome-wide scan for selection signatures in Nellore cattle.

    Science.gov (United States)

    Somavilla, A L; Sonstegard, T S; Higa, R H; Rosa, A N; Siqueira, F; Silva, L O C; Torres Júnior, R A A; Coutinho, L L; Mudadu, M A; Alencar, M M; Regitano, L C A

    2014-12-01

    Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777,000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty-one significant regions (P meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high-density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome. © 2014 Stichting International Foundation for Animal Genetics.

  16. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Science.gov (United States)

    Amambua-Ngwa, Alfred; Tetteh, Kevin K A; Manske, Magnus; Gomez-Escobar, Natalia; Stewart, Lindsay B; Deerhake, M Elizabeth; Cheeseman, Ian H; Newbold, Christopher I; Holder, Anthony A; Knuepfer, Ellen; Janha, Omar; Jallow, Muminatou; Campino, Susana; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Conway, David J

    2012-01-01

    Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now

  17. Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Directory of Open Access Journals (Sweden)

    Alfred Amambua-Ngwa

    Full Text Available Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3, and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%, indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing

  18. SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C; Nielsen, M; Lamberth, K

    2004-01-01

    . Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS...... of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design....

  19. SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C.; Nielsen, Morten; Lamberth, K.

    2004-01-01

    . Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly, from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS...... of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design....

  20. A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Bustamente, Carlos; Clark, Andrew G.

    2005-01-01

    Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect...... such evolutionary changes to leave a noticeable signature throughout the genome. We here compare 13,731 annotated genes from humans to their chimpanzee orthologs to identify genes that show evidence of positive selection. Many of the genes that present a signature of positive selection tend to be involved...

  1. A method for crack profiles identification in eddy current testing by the multi-directional scan

    International Nuclear Information System (INIS)

    Kojima, Fumio; Ikeda, Takuya; Nguyen, Doung

    2006-01-01

    This paper is concerned with a method for identification of crack shape in conducting materials. Multi-directional scanning strategies using Eddy Current Testing is performed for sizing complex natural crackings. Two dimensional measurements by means of multi-directional scan are used in a output least square identifications. (author)

  2. A genome-wide scan for common alleles affecting risk for autism

    Science.gov (United States)

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

    2010-01-01

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C. PMID:20663923

  3. A scan for positively selected genes in the genomes of humans and chimpanzees.

    Directory of Open Access Journals (Sweden)

    Rasmus Nielsen

    2005-06-01

    Full Text Available Since the divergence of humans and chimpanzees about 5 million years ago, these species have undergone a remarkable evolution with drastic divergence in anatomy and cognitive abilities. At the molecular level, despite the small overall magnitude of DNA sequence divergence, we might expect such evolutionary changes to leave a noticeable signature throughout the genome. We here compare 13,731 annotated genes from humans to their chimpanzee orthologs to identify genes that show evidence of positive selection. Many of the genes that present a signature of positive selection tend to be involved in sensory perception or immune defenses. However, the group of genes that show the strongest evidence for positive selection also includes a surprising number of genes involved in tumor suppression and apoptosis, and of genes involved in spermatogenesis. We hypothesize that positive selection in some of these genes may be driven by genomic conflict due to apoptosis during spermatogenesis. Genes with maximal expression in the brain show little or no evidence for positive selection, while genes with maximal expression in the testis tend to be enriched with positively selected genes. Genes on the X chromosome also tend to show an elevated tendency for positive selection. We also present polymorphism data from 20 Caucasian Americans and 19 African Americans for the 50 annotated genes showing the strongest evidence for positive selection. The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations.

  4. Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

    Directory of Open Access Journals (Sweden)

    Mahmood Gholami

    Full Text Available An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red, genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10. We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

  5. A genome-wide scan for common alleles affecting risk for autism.

    LENUS (Irish Health Repository)

    Anney, Richard

    2010-10-15

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner\\'s curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

  6. A genome-wide scan for signatures of directional selection in domesticated pigs.

    Science.gov (United States)

    Moon, Sunjin; Kim, Tae-Hun; Lee, Kyung-Tai; Kwak, Woori; Lee, Taeheon; Lee, Si-Woo; Kim, Myung-Jick; Cho, Kyuho; Kim, Namshin; Chung, Won-Hyong; Sung, Samsun; Park, Taesung; Cho, Seoae; Groenen, Martien Am; Nielsen, Rasmus; Kim, Yuseob; Kim, Heebal

    2015-02-25

    Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

  7. A genome-wide scan for common alleles affecting risk for autism.

    Science.gov (United States)

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

    2010-10-15

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

  8. Error analysis of motion correction method for laser scanning of moving objects

    Science.gov (United States)

    Goel, S.; Lohani, B.

    2014-05-01

    The limitation of conventional laser scanning methods is that the objects being scanned should be static. The need of scanning moving objects has resulted in the development of new methods capable of generating correct 3D geometry of moving objects. Limited literature is available showing development of very few methods capable of catering to the problem of object motion during scanning. All the existing methods utilize their own models or sensors. Any studies on error modelling or analysis of any of the motion correction methods are found to be lacking in literature. In this paper, we develop the error budget and present the analysis of one such `motion correction' method. This method assumes availability of position and orientation information of the moving object which in general can be obtained by installing a POS system on board or by use of some tracking devices. It then uses this information along with laser scanner data to apply correction to laser data, thus resulting in correct geometry despite the object being mobile during scanning. The major application of this method lie in the shipping industry to scan ships either moving or parked in the sea and to scan other objects like hot air balloons or aerostats. It is to be noted that the other methods of "motion correction" explained in literature can not be applied to scan the objects mentioned here making the chosen method quite unique. This paper presents some interesting insights in to the functioning of "motion correction" method as well as a detailed account of the behavior and variation of the error due to different sensor components alone and in combination with each other. The analysis can be used to obtain insights in to optimal utilization of available components for achieving the best results.

  9. Two methods for isolating the lung area of a CT scan for density information

    International Nuclear Information System (INIS)

    Hedlund, L.W.; Anderson, R.F.; Goulding, P.L.; Beck, J.W.; Effmann, E.L.; Putman, C.E.

    1982-01-01

    Extracting density information from irregularly shaped tissue areas of CT scans requires automated methods when many scans are involved. We describe two computer methods that automatically isolate the lung area of a CT scan. Each starts from a single, operator specified point in the lung. The first method follows the steep density gradient boundary between lung and adjacent tissues; this tracking method is useful for estimating the overall density and total area of lung in a scan because all pixels within the lung area are available for statistical sampling. The second method finds all contiguous pixels of lung that are within the CT number range of air to water and are not a part of strong density gradient edges; this method is useful for estimating density and area of the lung parenchyma. Structures within the lung area that are surrounded by strong density gradient edges, such as large blood vessels, airways and nodules, are excluded from the lung sample while lung areas with diffuse borders, such as an area of mild or moderate edema, are retained. Both methods were tested on scans from an animal model of pulmonary edema and were found to be effective in isolating normal and diseased lungs. These methods are also suitable for isolating other organ areas of CT scans that are bounded by density gradient edges

  10. Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

    Science.gov (United States)

    Jiang, Y; Slager, S L; Huang, J

    2001-01-01

    We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

  11. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...

  12. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Directory of Open Access Journals (Sweden)

    Chiao-Ling Lo

    2016-08-01

    Full Text Available Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP. This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross resulted in small haplotype blocks (HB with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS, were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50% of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284 and intronic regions (169 with the least in exon's (4, suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a, excitatory receptors (Grin2a, Gria3, Grip1, neurotransmitters (Pomc, and synapses (Snap29. This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  13. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Science.gov (United States)

    Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M

    2016-08-01

    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  14. Genome-wide scans between two honeybee populations reveal putative signatures of human-mediated selection.

    Science.gov (United States)

    Parejo, M; Wragg, D; Henriques, D; Vignal, A; Neuditschko, M

    2017-12-01

    Human-mediated selection has left signatures in the genomes of many domesticated animals, including the European dark honeybee, Apis mellifera mellifera, which has been selected by apiculturists for centuries. Using whole-genome sequence information, we investigated selection signatures in spatially separated honeybee subpopulations (Switzerland, n = 39 and France, n = 17). Three different test statistics were calculated in windows of 2 kb (fixation index, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio) and combined into a recently developed composite selection score. Applying a stringent false discovery rate of 0.01, we identified six significant selective sweeps distributed across five chromosomes covering eight genes. These genes are associated with multiple molecular and biological functions, including regulation of transcription, receptor binding and signal transduction. Of particular interest is a selection signature on chromosome 1, which corresponds to the WNT4 gene, the family of which is conserved across the animal kingdom with a variety of functions. In Drosophila melanogaster, WNT4 alleles have been associated with differential wing, cross vein and abdominal phenotypes. Defining phenotypic characteristics of different Apis mellifera ssp., which are typically used as selection criteria, include colour and wing venation pattern. This signal is therefore likely to be a good candidate for human mediated-selection arising from different applied breeding practices in the two managed populations. © 2017 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

  15. Marginal and internal fit of zirconia copings obtained using different digital scanning methods

    Directory of Open Access Journals (Sweden)

    Lorena Oliveira PEDROCHE

    Full Text Available Abstract The objective of this study was to evaluate the marginal and internal fit of zirconia copings obtained with different digital scanning methods. A human mandibular first molar was set in a typodont with its adjacent and antagonist teeth and prepared for an all-ceramic crown. Digital impressions were made using an intraoral scanner (3Shape. Polyvinyl siloxane impressions and Type IV gypsum models were also obtained and scanned with a benchtop laboratory scanner (3Shape D700. Ten zirconia copings were fabricated for each group using CAD-CAM technology. The marginal and internal fit of the zirconia copings was assessed by the silicone replica technique. Four sections of each replica were obtained, and each section was evaluated at four points: marginal gap (MG, axial wall (AW, axio-occlusal edge (AO and centro-occlusal wall (CO, using an image analyzing software. The data were submitted to one-way ANOVA and Tukey’s test (α = 0.05. They showed statistically significant differences for MG, AO and CO. Regarding MG, intraoral scanning showed lower gap values, whereas gypsum model scanning showed higher gap values. Regarding AO and CO, intraoral digital scanning showed lower gap values. Polyvinyl siloxane impression scanning and gypsum model scanning showed higher gap values and were statistically similar. It can be concluded that intraoral digital scanning provided a lower mean gap value, in comparison with conventional impressions and gypsum casts scanned with a standard benchtop laboratory scanner.

  16. Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture.

    Science.gov (United States)

    Bhatia, Gaurav; Tandon, Arti; Patterson, Nick; Aldrich, Melinda C; Ambrosone, Christine B; Amos, Christopher; Bandera, Elisa V; Berndt, Sonja I; Bernstein, Leslie; Blot, William J; Bock, Cathryn H; Caporaso, Neil; Casey, Graham; Deming, Sandra L; Diver, W Ryan; Gapstur, Susan M; Gillanders, Elizabeth M; Harris, Curtis C; Henderson, Brian E; Ingles, Sue A; Isaacs, William; De Jager, Phillip L; John, Esther M; Kittles, Rick A; Larkin, Emma; McNeill, Lorna H; Millikan, Robert C; Murphy, Adam; Neslund-Dudas, Christine; Nyante, Sarah; Press, Michael F; Rodriguez-Gil, Jorge L; Rybicki, Benjamin A; Schwartz, Ann G; Signorello, Lisa B; Spitz, Margaret; Strom, Sara S; Tucker, Margaret A; Wiencke, John K; Witte, John S; Wu, Xifeng; Yamamura, Yuko; Zanetti, Krista A; Zheng, Wei; Ziegler, Regina G; Chanock, Stephen J; Haiman, Christopher A; Reich, David; Price, Alkes L

    2014-10-02

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  17. Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana.

    Science.gov (United States)

    Gould, Billie A; Stinchcombe, John R

    2017-01-01

    A long-standing question in evolutionary biology is whether the evolution of convergent phenotypes results from selection on the same heritable genetic components. Using whole-genome sequencing and genome scans, we tested whether the evolution of parallel longitudinal flowering time clines in the native and introduced ranges of Arabidopsis thaliana has a similar genetic basis. We found that common variants of large effect on flowering time in the native range do not appear to have been under recent strong selection in the introduced range. We identified a set of 38 new candidate genes that are putatively linked to the evolution of flowering time. A high degree of conditional neutrality of flowering time variants between the native and introduced range may preclude parallel evolution at the level of genes. Overall, neither gene pleiotropy nor available standing genetic variation appears to have restricted the evolution of flowering time to high-frequency variants from the native range or to known flowering time pathway genes. © 2016 John Wiley & Sons Ltd.

  18. Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms.

    Science.gov (United States)

    Chávez-Galarza, Julio; Henriques, Dora; Johnston, J Spencer; Azevedo, João C; Patton, John C; Muñoz, Irene; De la Rúa, Pilar; Pinto, M Alice

    2013-12-01

    Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST -based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST -based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes. © 2013 John Wiley & Sons Ltd.

  19. Predicting human height by Victorian and genomic methods.

    Science.gov (United States)

    Aulchenko, Yurii S; Struchalin, Maksim V; Belonogova, Nadezhda M; Axenovich, Tatiana I; Weedon, Michael N; Hofman, Albert; Uitterlinden, Andre G; Kayser, Manfred; Oostra, Ben A; van Duijn, Cornelia M; Janssens, A Cecile J W; Borodin, Pavel M

    2009-08-01

    In the Victorian era, Sir Francis Galton showed that 'when dealing with the transmission of stature from parents to children, the average height of the two parents, ... is all we need care to know about them' (1886). One hundred and twenty-two years after Galton's work was published, 54 loci showing strong statistical evidence for association to human height were described, providing us with potential genomic means of human height prediction. In a population-based study of 5748 people, we find that a 54-loci genomic profile explained 4-6% of the sex- and age-adjusted height variance, and had limited ability to discriminate tall/short people, as characterized by the area under the receiver-operating characteristic curve (AUC). In a family-based study of 550 people, with both parents having height measurements, we find that the Galtonian mid-parental prediction method explained 40% of the sex- and age-adjusted height variance, and showed high discriminative accuracy. We have also explored how much variance a genomic profile should explain to reach certain AUC values. For highly heritable traits such as height, we conclude that in applications in which parental phenotypic information is available (eg, medicine), the Victorian Galton's method will long stay unsurpassed, in terms of both discriminative accuracy and costs. For less heritable traits, and in situations in which parental information is not available (eg, forensics), genomic methods may provide an alternative, given that the variants determining an essential proportion of the trait's variation can be identified.

  20. Genome-wide scan in Hispanics highlights candidate loci for brain white matter hyperintensities.

    Science.gov (United States)

    Beecham, Ashley; Dong, Chuanhui; Wright, Clinton B; Dueker, Nicole; Brickman, Adam M; Wang, Liyong; DeCarli, Charles; Blanton, Susan H; Rundek, Tatjana; Mayeux, Richard; Sacco, Ralph L

    2017-10-01

    To investigate genetic variants influencing white matter hyperintensities (WMHs) in the understudied Hispanic population. Using 6.8 million single nucleotide polymorphisms (SNPs), we conducted a genome-wide association study (GWAS) to identify SNPs associated with WMH volume (WMHV) in 922 Hispanics who underwent brain MRI as a cross-section of 2 community-based cohorts in the Northern Manhattan Study and the Washington Heights-Inwood Columbia Aging Project. Multiple linear modeling with PLINK was performed to examine the additive genetic effects on ln(WMHV) after controlling for age, sex, total intracranial volume, and principal components of ancestry. Gene-based tests of association were performed using VEGAS. Replication was performed in independent samples of Europeans, African Americans, and Asians. From the SNP analysis, a total of 17 independent SNPs in 7 genes had suggestive evidence of association with WMHV in Hispanics ( p < 1 × 10 -5 ) and 5 genes from the gene-based analysis with p < 1 × 10 -3 . One SNP (rs9957475 in GATA6 ) and 1 gene ( UBE2C ) demonstrated evidence of association ( p < 0.05) in the African American sample. Four SNPs with p < 1 × 10 -5 were shown to affect binding of SPI1 using RegulomeDB. This GWAS of 2 community-based Hispanic cohorts revealed several novel WMH-associated genetic variants. Further replication is needed in independent Hispanic samples to validate these suggestive associations, and fine mapping is needed to pinpoint causal variants.

  1. A genome scan for quantitative trait loci affecting the Salmonella carrier-state in the chicken

    Directory of Open Access Journals (Sweden)

    Bumstead Nat

    2005-09-01

    Full Text Available Abstract Selection for increased resistance to Salmonella colonisation and excretion could reduce the risk of foodborne Salmonella infection. In order to identify potential loci affecting resistance, differences in resistance were identified between the N and 61 inbred lines and two QTL research performed. In an F2 cross, the animals were inoculated at one week of age with Salmonella enteritidis and cloacal swabs were carried out 4 and 5 wk post inoculation (thereafter called CSW4F2 and CSW4F2 and caecal contamination (CAECF2 was assessed 1 week later. The animals from the (N × 61 × N backcross were inoculated at six weeks of age with Salmonella typhimurium and cloacal swabs were studied from wk 1 to 4 (thereafter called CSW1BC to CSW4BC. A total of 33 F2 and 46 backcross progeny were selectively genotyped for 103 and 135 microsatellite markers respectively. The analysis used least-squares-based and non-parametric interval mapping. Two genome-wise significant QTL were observed on Chromosome 1 for CSW2BC and on Chromosome 2 for CSW4F2, and four suggestive QTL for CSW5F2 on Chromosome 2, for CSW5F2 and CSW2BC on chromosome 5 and for CAECF2 on chromosome 16. These results suggest new regions of interest and the putative role of SAL1.

  2. Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

    Directory of Open Access Journals (Sweden)

    Cecilia M Lindgren

    2009-06-01

    Full Text Available To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580 informative for adult waist circumference (WC and waist-hip ratio (WHR. We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11 and MSRA (WC, P = 8.9x10(-9. A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8. The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

  3. Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

    Science.gov (United States)

    Tycko, Josh; Myer, Vic E.; Hsu, Patrick D.

    2016-01-01

    Summary Advances in the development of delivery, repair, and specificity strategies for the CRISPR-Cas9 genome engineering toolbox are helping researchers understand gene function with unprecedented precision and sensitivity. CRISPR-Cas9 also holds enormous therapeutic potential for the treatment of genetic disorders by directly correcting disease-causing mutations. Although the Cas9 protein has been shown to bind and cleave DNA at off-target sites, the field of Cas9 specificity is rapidly progressing with marked improvements in guide RNA selection, protein and guide engineering, novel enzymes, and off-target detection methods. We review important challenges and breakthroughs in the field as a comprehensive practical guide to interested users of genome editing technologies, highlighting key tools and strategies for optimizing specificity. The genome editing community should now strive to standardize such methods for measuring and reporting off-target activity, while keeping in mind that the goal for specificity should be continued improvement and vigilance. PMID:27494557

  4. Scanning laser topography and scanning laser polarimetry: comparing both imaging methods at same distances from the optic nerve head.

    Science.gov (United States)

    Kremmer, Stephan; Keienburg, Marcus; Anastassiou, Gerasimos; Schallenberg, Maurice; Steuhl, Klaus-Peter; Selbach, J Michael

    2012-01-01

    To compare the performance of scanning laser topography (SLT) and scanning laser polarimetry (SLP) on the rim of the optic nerve head and its surrounding area and thereby to evaluate whether these imaging technologies are influenced by other factors beyond the thickness of the retinal nerve fiber layer (RNFL). A total of 154 eyes from 5 different groups were examined: young healthy subjects (YNorm), old healthy subjects (ONorm), patients with normal tension glaucoma (NTG), patients with open-angle glaucoma and early glaucomatous damage (OAGE) and patients with open-angle glaucoma and advanced glaucomatous damage (OAGA). SLT and SLP measurements were taken. Four concentric circles were superimposed on each of the images: the first one measuring at the rim of the optic nerve head (1.0 ONHD), the next measuring at 1.25 optic nerve head diameters (ONHD), at 1.5 ONHD and at 1.75 ONHD. The aligned images were analyzed using GDx/NFA software. Both methods showed peaks of RNFL thickness in the superior and inferior segments of the ONH. The maximum thickness, registered by the SLT device was at the ONH rim where the SLP device tended to measure the lowest values. SLT measurements at the ONH were influenced by other tissues besides the RNFL like blood vessels and glial tissues. SLT and SLP were most strongly correlated at distances of 1.25 and 1.5 ONHD. While both imaging technologies are valuable tools in detecting glaucoma, measurements at the ONH rim should be interpreted critically since both methods might provide misleading results. For the assessment of the retinal nerve fiber layer we would like to recommend for both imaging technologies, SLT and SLP, measurements in 1.25 and 1.5 ONHD distance of the rim of the optic nerve head.

  5. Genome-wide linkage scan for factors of metabolic syndrome in a Chinese population

    Directory of Open Access Journals (Sweden)

    Chan Juliana CN

    2010-02-01

    Full Text Available Abstract Background Shared genetic factors may contribute to the phenotypic clustering of different components of the metabolic syndrome (MES. This study aims to identify genetic loci that contribute to individual or multiple factors related to MES. Results We studied 478 normoglycemic subjects ascertained through 163 families participating in the Hong Kong Family Diabetes Study. Factor analysis on 15 MES-related traits yielded 6 factors including adiposity factor (body mass index, waist and hip circumferences, insulin factor (fasting insulin and insulin AUC during OGTT, glucose factor (fasting glucose and glucose AUC during OGTT, TC-LDLC factor (total cholesterol and LDL-cholesterol, blood pressure factor (systolic and diastolic blood pressure and TG-HDLC factor (triglycerides and HDL-cholesterol. Genome-wide linkage analyses were performed on these factors using variance component approach. Suggestive evidence for linkage (LOD = 1.24 - 2.46 were observed for adiposity factor (chromosome 1 at 187 cM, chromosome 9 at 34 cM and chromosome 17 at 10 cM, insulin factor (chromosome 2 at 128 cM, chromosome 5 at 21 cM and chromosome 12 at 7 cM, glucose factor (chromosome 7 at 155 cM, TC-LDLC factor (chromosome 7 at 151 cM and chromosome 13 at 15 cM and TG-HDLC factor (chromosome 7 at 155 cM. Conclusions In summary, our findings suggest the presence of susceptibility loci that influence either single (chromosomes 1, 2, 5, 9, 12, 13 and 17 or multiple factors (chromosome 7 for MES in Hong Kong Chinese without diabetes.

  6. A simple and inexpensive method for genomic restriction mapping analysis

    International Nuclear Information System (INIS)

    Huang, C.H.; Lam, V.M.S.; Tam, J.W.O.

    1988-01-01

    The Southern blotting procedure for the transfer of DNA fragments from agarose gels to nitrocellulose membranes has revolutionized nucleic acid detection methods, and it forms the cornerstone of research in molecular biology. Basically, the method involves the denaturation of DNA fragments that have been separated on an agarose gel, the immobilization of the fragments by transfer to a nitrocellulose membrane, and the identification of the fragments of interest through hybridization to /sup 32/P-labeled probes and autoradiography. While the method is sensitive and applicable to both genomic and cloned DNA, it suffers from the disadvantages of being time consuming and expensive, and fragments of greater than 15 kb are difficult to transfer. Moreover, although theoretically the nitrocellulose membrane can be washed and hybridized repeatedly using different probes, in practice, the membrane becomes brittle and difficult to handle after a few cycles. A direct hybridization method for pure DNA clones was developed in 1975 but has not been widely exploited. The authors report here a modification of their procedure as applied to genomic DNA. The method is simple, rapid, and inexpensive, and it does not involve transfer to nitrocellulose membranes

  7. Concurrent Driving Method with Fast Scan Rate for Large Mutual Capacitance Touch Screens

    Directory of Open Access Journals (Sweden)

    Mohamed Gamal Ahmed Mohamed

    2015-01-01

    Full Text Available A novel touch screen control technique is introduced, which scans each frame in two steps of concurrent multichannel driving and differential sensing. The proposed technique substantially increases the scan rate and reduces the ambient noise effectively. It is also extended to a multichip architecture to support excessively large touch screens with great scan rate improvement. The proposed method has been implemented using 0.18 μm CMOS TowerJazz process and tested with FPGA and AFE board connecting a 23-inch touch screen. Experimental results show a scan rate improvement of up to 23.8 times and an SNR improvement of 24.6 dB over the conventional method.

  8. Will genomic selection be a practical method for plant breeding?

    Science.gov (United States)

    Nakaya, Akihiro; Isobe, Sachiko N

    2012-11-01

    Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory.

  9. Spectrum scanning and reserve channel methods for link maintenance in cognitive radio systems

    OpenAIRE

    Subramani, S; Armour, SMD; Kaleshi, D; Fan, Z

    2008-01-01

    Underutilization of the limited spectrum sparked the need for dynamic spectrum access and flexible spectrum policies. Accurate estimation of spectrum occupancy is an essential step for spectrum access in distributed networks. This paper analyzes a bidirectional and dual scanning method that scans multiple spectrum bands to find a suitable free-channel. Moreover, secondary users' access to available spectrum could be interrupted by the arrival of primary spectrum users, forcing the well-behave...

  10. Genome-wide scan for visceral leishmaniasis in mixed-breed dogs identifies candidate genes involved in T helper cells and macrophage signaling

    Science.gov (United States)

    We conducted a genome-wide scan for visceral leishmaniasis in mixed-breed dogs from a highly endemic area in Brazil using 149,648 single nucleotide polymorphism (SNP) markers genotyped in 20 cases and 28 controls. Using a mixed model approach, we found two candidate loci on canine autosomes 1 and 2....

  11. A whole-genome scan in 164 Dutch sib pairs with attention-deficit/hyperactivity disorder : Suggestive evidence for linkage on chromosomes 7p and 15q

    NARCIS (Netherlands)

    Bakker, SC; van der Meulen, EM; Buitelaar, JK; Sandkuijl, LA; Pauls, DL; Monsuur, AJ; van't Slot, R; Minderaa, RB; Gunning, WB; Pearson, PL; Sinke, RJ

    A genome scan was performed on 164 Dutch affected sib pairs (ASPs) with attention-deficit/hyperactivity disorder (ADHD). All subjects were white and of Dutch descent and were phenotyped according to criteria set out in the Diagnostic and Statistical Manual Of Mental Disorders, 4th edition.

  12. Whole Genome Scan to Detect Chromosomal Regions Affecting Multiple Traits in Dairy Cattle

    NARCIS (Netherlands)

    Schrooten, C.; Bink, M.C.A.M.; Bovenhuis, H.

    2004-01-01

    Chromosomal regions affecting multiple traits ( multiple trait quantitative trait regions or MQR) in dairy cattle were detected using a method based on results from single trait analyses to detect quantitative trait loci (QTL). The covariance between contrasts for different traits in single trait

  13. Genome scan identifies a locus affecting gamma-globin expression in human beta-cluster YAC transgenic mice

    Energy Technology Data Exchange (ETDEWEB)

    Lin, S.D.; Cooper, P.; Fung, J.; Weier, H.U.G.; Rubin, E.M.

    2000-03-01

    Genetic factors affecting post-natal g-globin expression - a major modifier of the severity of both b-thalassemia and sickle cell anemia, have been difficult to study. This is especially so in mice, an organism lacking a globin gene with an expression pattern equivalent to that of human g-globin. To model the human b-cluster in mice, with the goal of screening for loci affecting human g-globin expression in vivo, we introduced a human b-globin cluster YAC transgene into the genome of FVB mice . The b-cluster contained a Greek hereditary persistence of fetal hemoglobin (HPFH) g allele resulting in postnatal expression of human g-globin in transgenic mice. The level of human g-globin for various F1 hybrids derived from crosses between the FVB transgenics and other inbred mouse strains was assessed. The g-globin level of the C3HeB/FVB transgenic mice was noted to be significantly elevated. To map genes affecting postnatal g-globin expression, a 20 centiMorgan (cM) genome scan of a C3HeB/F VB transgenics [prime] FVB backcross was performed, followed by high-resolution marker analysis of promising loci. From this analysis we mapped a locus within a 2.2 cM interval of mouse chromosome 1 at a LOD score of 4.2 that contributes 10.4% of variation in g-globin expression level. Combining transgenic modeling of the human b-globin gene cluster with quantitative trait analysis, we have identified and mapped a murine locus that impacts on human g-globin expression in vivo.

  14. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits.

    Directory of Open Access Journals (Sweden)

    Angelo Scuteri

    2007-07-01

    Full Text Available The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 showed the strongest association with BMI (p = 8.6 x10(-7, hip circumference (p = 3.4 x 10(-8, and weight (p = 9.1 x 10(-7. In Sardinia, homozygotes for the rare "G" allele of this SNP (minor allele frequency = 0.46 were 1.3 BMI units heavier than homozygotes for the common "A" allele. Within the PFKP gene, rs6602024 showed very strong association with BMI (p = 4.9 x 10(-6. Homozygotes for the rare "A" allele of this SNP (minor allele frequency = 0.12 were 1.8 BMI units heavier than homozygotes for the common "G" allele. To replicate our findings, we genotyped these two SNPs in the GenNet study. In European Americans (N = 1,496 and in Hispanic Americans (N = 839, we replicated significant association between rs9930506 in the FTO gene and BMI (p-value for meta-analysis of European American and Hispanic American follow-up samples, p = 0.001, weight (p = 0.001, and hip circumference (p = 0.0005. We did not replicate association between rs6602024 and obesity-related traits in the GenNet sample, although we found that in European Americans, Hispanic Americans, and African Americans, homozygotes for the rare "A" allele were, on average, 1.0-3.0 BMI units heavier than homozygotes for the more common "G" allele. In summary, we have completed a whole genome-association scan for

  15. 3D scan line method for identifying void fabric of granular materials

    Directory of Open Access Journals (Sweden)

    Theocharis Alexandros I.

    2017-01-01

    Full Text Available Among other processes measuring the void phase of porous or fractured media, scan line approach is a simplified “graphical” method, mainly used in image processing related procedures. In soil mechanics, the application of scan line method is related to the soil fabric, which is important in characterizing the anisotropic mechanical response of soils. Void fabric is of particular interest, since graphical approaches are well defined experimentally and most of them can also be easily used in numerical experiments, like the scan line method. This is in contrast to the definition of fabric based on contact normal vectors that are extremely difficult to determine, especially considering physical experiments. The scan line method has been proposed by Oda et al [1] and implemented again by Ghedia and O’Sullivan [2]. A modified method based on DEM analysis instead of image measurements of fabric has been previously proposed and implemented by the authors in a 2D scheme [3-4]. In this work, a 3D extension of the modified scan line definition is presented using PFC 3D®. The results show clearly similar trends with the 2D case and the same behaviour of fabric anisotropy is presented.

  16. In Silico Genome Mismatch Scanning to Map Breast Cancer Genes in Extended Pedigrees

    Science.gov (United States)

    2009-07-01

    of ASPM, a Brain Size Determinant in Homo sapiens . This manuscript was prepared with the AAS LATEX macros v5.2. – 14 – 6. Figures and Tables – 15...Cai et al. 2009) describing, and ex- plaining, some anomalous features that could have let to false positive results if left unin- vestigated. This...are well behaved, tractable and flexible. This class is defined and the main features of estimation methods are described below. The Markov graph of a

  17. In Silico Genome Mismatch Scanning to Map Breast Cancer Genes in Extended Pedigrees

    Science.gov (United States)

    2008-07-01

    University College London Annals of Human Genetics (2008) 72,279–287 279 A. Thomas et al. Methods IBD sharing in pedigrees There is considerable literature...is sufficient to maintain interest in the region. 282 Annals of Human Genetics (2008) 72,279–287 C© 2007 The Authors Journal compilation C© 2007...for observed IBS instead of IBD, and for sporadic cases reducing the number of meioses, pedigrees with meiosis count d in the 25 to 30 range are

  18. Method for quantifying percentage wood failure in block-shear specimens by a laser scanning profilometer

    Science.gov (United States)

    C. T. Scott; R. Hernandez; C. Frihart; R. Gleisner; T. Tice

    2005-01-01

    A new method for quantifying percentage wood failure of an adhesively bonded block-shear specimen has been developed. This method incorporates a laser displacement gage with an automated two-axis positioning system that functions as a highly sensitive profilometer. The failed specimen is continuously scanned across its width to obtain a surface failure profile. The...

  19. A comparison of multivariate genome-wide association methods

    DEFF Research Database (Denmark)

    Galesloot, Tessel E; Van Steen, Kristel; Kiemeney, Lambertus A L M

    2014-01-01

    Joint association analysis of multiple traits in a genome-wide association study (GWAS), i.e. a multivariate GWAS, offers several advantages over analyzing each trait in a separate GWAS. In this study we directly compared a number of multivariate GWAS methods using simulated data. We focused on six...... methods that are implemented in the software packages PLINK, SNPTEST, MultiPhen, BIMBAM, PCHAT and TATES, and also compared them to standard univariate GWAS, analysis of the first principal component of the traits, and meta-analysis of univariate results. We simulated data (N = 1000) for three...... for scenarios with an opposite sign of genetic and residual correlation. All multivariate analyses resulted in a higher power than univariate analyses, even when only one of the traits was associated with the QTL. Hence, use of multivariate GWAS methods can be recommended, even when genetic correlations between...

  20. Research on Method of Photoelectric Measurement for Tilt Angle of Scanning Mirror of Infrared Earth Sensor

    Energy Technology Data Exchange (ETDEWEB)

    Xu, X P; Zhang, G Y; Zhang, N; Wang, L Y [Changchun University of Science and Technology, 130022, Changchun (China)

    2006-10-15

    Tilt angle of scanning mirror is one of the important qualifications of performance measurement on the earth surface for swing scanning mode infrared the earth sensor. In order to settle the problem of measuring the tilt angle of scanning mirror in dynamic, real-time and non-contact, based on laser inspecting technology and CCD probing technology, a method of laser dynamical measurement for tilt angle of scanning mirror of the infrared earth sensor is presented. The measurement system developed in this paper can accomplish the dynamic and static laser non-contact measurement for the parameters of scanning mirror such as tilt angle, swing frequency, etc. In this paper the composition and overall structure of system are introduced. Emphasis on analyzing and discussing the theory of dynamically measuring tilt angle of scanning mirror, the problems of data processing and error correction are settled by established mathematic model of system. The accuracy of measurement system is verified by experiment, the results indicated that measurement range of system for tilt angle is 0{approx}{+-}12{sup 0}, accuracy of dynamic and static measurement is less than {+-}0.05{sup 0}, this method of dynamically measuring tilt angle is suitable.

  1. Change Analysis in Structural Laser Scanning Point Clouds: The Baseline Method.

    Science.gov (United States)

    Shen, Yueqian; Lindenbergh, Roderik; Wang, Jinhu

    2016-12-24

    A method is introduced for detecting changes from point clouds that avoids registration. For many applications, changes are detected between two scans of the same scene obtained at different times. Traditionally, these scans are aligned to a common coordinate system having the disadvantage that this registration step introduces additional errors. In addition, registration requires stable targets or features. To avoid these issues, we propose a change detection method based on so-called baselines. Baselines connect feature points within one scan. To analyze changes, baselines connecting corresponding points in two scans are compared. As feature points either targets or virtual points corresponding to some reconstructable feature in the scene are used. The new method is implemented on two scans sampling a masonry laboratory building before and after seismic testing, that resulted in damages in the order of several centimeters. The centres of the bricks of the laboratory building are automatically extracted to serve as virtual points. Baselines connecting virtual points and/or target points are extracted and compared with respect to a suitable structural coordinate system. Changes detected from the baseline analysis are compared to a traditional cloud to cloud change analysis demonstrating the potential of the new method for structural analysis.

  2. Change Analysis in Structural Laser Scanning Point Clouds: The Baseline Method

    Directory of Open Access Journals (Sweden)

    Yueqian Shen

    2016-12-01

    Full Text Available A method is introduced for detecting changes from point clouds that avoids registration. For many applications, changes are detected between two scans of the same scene obtained at different times. Traditionally, these scans are aligned to a common coordinate system having the disadvantage that this registration step introduces additional errors. In addition, registration requires stable targets or features. To avoid these issues, we propose a change detection method based on so-called baselines. Baselines connect feature points within one scan. To analyze changes, baselines connecting corresponding points in two scans are compared. As feature points either targets or virtual points corresponding to some reconstructable feature in the scene are used. The new method is implemented on two scans sampling a masonry laboratory building before and after seismic testing, that resulted in damages in the order of several centimeters. The centres of the bricks of the laboratory building are automatically extracted to serve as virtual points. Baselines connecting virtual points and/or target points are extracted and compared with respect to a suitable structural coordinate system. Changes detected from the baseline analysis are compared to a traditional cloud to cloud change analysis demonstrating the potential of the new method for structural analysis.

  3. Adaptive and robust statistical methods for processing near-field scanning microwave microscopy images.

    Science.gov (United States)

    Coakley, K J; Imtiaz, A; Wallis, T M; Weber, J C; Berweger, S; Kabos, P

    2015-03-01

    Near-field scanning microwave microscopy offers great potential to facilitate characterization, development and modeling of materials. By acquiring microwave images at multiple frequencies and amplitudes (along with the other modalities) one can study material and device physics at different lateral and depth scales. Images are typically noisy and contaminated by artifacts that can vary from scan line to scan line and planar-like trends due to sample tilt errors. Here, we level images based on an estimate of a smooth 2-d trend determined with a robust implementation of a local regression method. In this robust approach, features and outliers which are not due to the trend are automatically downweighted. We denoise images with the Adaptive Weights Smoothing method. This method smooths out additive noise while preserving edge-like features in images. We demonstrate the feasibility of our methods on topography images and microwave |S11| images. For one challenging test case, we demonstrate that our method outperforms alternative methods from the scanning probe microscopy data analysis software package Gwyddion. Our methods should be useful for massive image data sets where manual selection of landmarks or image subsets by a user is impractical. Published by Elsevier B.V.

  4. Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods.

    Science.gov (United States)

    Oldfield, Lauren M; Grzesik, Peter; Voorhies, Alexander A; Alperovich, Nina; MacMath, Derek; Najera, Claudia D; Chandra, Diya Sabrina; Prasad, Sanjana; Noskov, Vladimir N; Montague, Michael G; Friedman, Robert M; Desai, Prashant J; Vashee, Sanjay

    2017-10-17

    Here, we present a transformational approach to genome engineering of herpes simplex virus type 1 (HSV-1), which has a large DNA genome, using synthetic genomics tools. We believe this method will enable more rapid and complex modifications of HSV-1 and other large DNA viruses than previous technologies, facilitating many useful applications. Yeast transformation-associated recombination was used to clone 11 fragments comprising the HSV-1 strain KOS 152 kb genome. Using overlapping sequences between the adjacent pieces, we assembled the fragments into a complete virus genome in yeast, transferred it into an Escherichia coli host, and reconstituted infectious virus following transfection into mammalian cells. The virus derived from this yeast-assembled genome, KOS YA , replicated with kinetics similar to wild-type virus. We demonstrated the utility of this modular assembly technology by making numerous modifications to a single gene, making changes to two genes at the same time and, finally, generating individual and combinatorial deletions to a set of five conserved genes that encode virion structural proteins. While the ability to perform genome-wide editing through assembly methods in large DNA virus genomes raises dual-use concerns, we believe the incremental risks are outweighed by potential benefits. These include enhanced functional studies, generation of oncolytic virus vectors, development of delivery platforms of genes for vaccines or therapy, as well as more rapid development of countermeasures against potential biothreats.

  5. Simulation of scanning geometry for Shadow Shield counter using Monte Carlo method

    International Nuclear Information System (INIS)

    Deepu, R.; Manohari, M.; Mathiyarasu, R.

    2018-01-01

    The whole body counting facility at RSD, IGCAR employs a Shadow Shield Counter (SSC) for the assessment of internal exposure of radiation workers from fission and activation products. The SSC system is routinely calibrated using an in-house built Masonite cut sheet phantom, loaded with standard point sources, in scanning mode. The system is capable of measuring gamma energy from 200 keV to 3 MeV. The standard sources available have energies in the range of 300 - 1500 keV. In order to extend the energy range, numerical simulation can be carried out. As, numerical methods cannot simulate scanning mode directly, a novel scheme is attempted to generate the efficiency value for scanning mode through the use of multiple static mode. The same method was also verified through measurement. The efficiency values of the simulation as well two measurements techniques were compared

  6. X-CT imaging method for large objects using double offset scan mode

    International Nuclear Information System (INIS)

    Fu Jian; Lu Hongnian; Li Bing; Zhang Lei; Sun Jingjing

    2007-01-01

    In X-ray computed tomography (X-CT) inspection, rotate-only scanner is commonly used because this configuration offers the highest imaging speed and best utilization of X-ray dose. But it requires that the imaging region of the scanned object must fit within the X-ray beam. Another configuration, transverse-rotate scanner, has a bigger field of view, but it is much more time consuming. In this paper, a two-dimensional X-CT imaging method for large objects is proposed to overcome the existing disadvantages. The scan principle of this method has been described and the reconstruction algorithm has been deduced. The results of the computer simulation and the experiments show the validity of the new method. Analysis shows that the scan field of view of this method is 1.8 times larger than that of rotate-only X-CT. The scan speed of this method is also much quicker than transverse-rotate X-CT

  7. Scatter measurement and correction method for cone-beam CT based on single grating scan

    Science.gov (United States)

    Huang, Kuidong; Shi, Wenlong; Wang, Xinyu; Dong, Yin; Chang, Taoqi; Zhang, Hua; Zhang, Dinghua

    2017-06-01

    In cone-beam computed tomography (CBCT) systems based on flat-panel detector imaging, the presence of scatter significantly reduces the quality of slices. Based on the concept of collimation, this paper presents a scatter measurement and correction method based on single grating scan. First, according to the characteristics of CBCT imaging, the scan method using single grating and the design requirements of the grating are analyzed and figured out. Second, by analyzing the composition of object projection images and object-and-grating projection images, the processing method for the scatter image at single projection angle is proposed. In addition, to avoid additional scan, this paper proposes an angle interpolation method of scatter images to reduce scan cost. Finally, the experimental results show that the scatter images obtained by this method are accurate and reliable, and the effect of scatter correction is obvious. When the additional object-and-grating projection images are collected and interpolated at intervals of 30 deg, the scatter correction error of slices can still be controlled within 3%.

  8. Fast beam cut-off method in RF-knockout extraction for spot-scanning

    CERN Document Server

    Furukawa, T

    2002-01-01

    An irradiation method with magnetic scanning has been developed in order to provide accurate irradiation even for an irregular target shape. The scanning method has strongly required a lower ripple of the beam spill and a faster response to beam-on/off in slow extraction from a synchrotron ring. At HIMAC, RF-knockout extraction has utilized a bunched beam to reduce the beam-spill ripple. Therefore, particles near the resonance can be spilled out from the separatrices by synchrotron oscillation as well as by a transverse RF field. From this point of view, a fast beam cut-off method has been proposed and verified by both simulations and experiments. The maximum delay from the beam cut-off signal to beam-off has been improved to around 60 mu s from 700 mu s by a usual method. Unwanted dose has been considerably reduced by around a factor of 10 compared with that by the usual method.

  9. An assessment on epitope prediction methods for protozoa genomes

    Directory of Open Access Journals (Sweden)

    Resende Daniela M

    2012-11-01

    Full Text Available Abstract Background Epitope prediction using computational methods represents one of the most promising approaches to vaccine development. Reduction of time, cost, and the availability of completely sequenced genomes are key points and highly motivating regarding the use of reverse vaccinology. Parasites of genus Leishmania are widely spread and they are the etiologic agents of leishmaniasis. Currently, there is no efficient vaccine against this pathogen and the drug treatment is highly toxic. The lack of sufficiently large datasets of experimentally validated parasites epitopes represents a serious limitation, especially for trypanomatids genomes. In this work we highlight the predictive performances of several algorithms that were evaluated through the development of a MySQL database built with the purpose of: a evaluating individual algorithms prediction performances and their combination for CD8+ T cell epitopes, B-cell epitopes and subcellular localization by means of AUC (Area Under Curve performance and a threshold dependent method that employs a confusion matrix; b integrating data from experimentally validated and in silico predicted epitopes; and c integrating the subcellular localization predictions and experimental data. NetCTL, NetMHC, BepiPred, BCPred12, and AAP12 algorithms were used for in silico epitope prediction and WoLF PSORT, Sigcleave and TargetP for in silico subcellular localization prediction against trypanosomatid genomes. Results A database-driven epitope prediction method was developed with built-in functions that were capable of: a removing experimental data redundancy; b parsing algorithms predictions and storage experimental validated and predict data; and c evaluating algorithm performances. Results show that a better performance is achieved when the combined prediction is considered. This is particularly true for B cell epitope predictors, where the combined prediction of AAP12 and BCPred12 reached an AUC value

  10. A Novel Complementary Method for the Point-Scan Nondestructive Tests Based on Lamb Waves

    Directory of Open Access Journals (Sweden)

    Rahim Gorgin

    2014-01-01

    Full Text Available This study presents a novel area-scan damage identification method based on Lamb waves which can be used as a complementary method for point-scan nondestructive techniques. The proposed technique is able to identify the most probable locations of damages prior to point-scan test which lead to decreasing the time and cost of inspection. The test-piece surface was partitioned with some smaller areas and the damage probability presence of each area was evaluated. A0 mode of Lamb wave was generated and collected using a mobile handmade transducer set at each area. Subsequently, a damage presence probability index (DPPI based on the energy of captured responses was defined for each area. The area with the highest DPPI value highlights the most probable locations of damages in test-piece. Point-scan nondestructive methods can then be used once these areas are found to identify the damage in detail. The approach was validated by predicting the most probable locations of representative damages including through-thickness hole and crack in aluminum plates. The obtained experimental results demonstrated the high potential of developed method in defining the most probable locations of damages in structures.

  11. A robust method for processing scanning probe microscopy images and determining nanoobject position and dimensions

    NARCIS (Netherlands)

    Silly, F.

    2009-01-01

    P>Processing of scanning probe microscopy (SPM) images is essential to explore nanoscale phenomena. Image processing and pattern recognition techniques are developed to improve the accuracy and consistency of nanoobject and surface characterization. We present a robust and versatile method to

  12. Technetium-99m labeled radiodiagnostic agents for liver and bone marrow scanning and method of preparation

    International Nuclear Information System (INIS)

    Molinski, V.J.; Peacock, F.R.

    1977-01-01

    An improved technetium-99m labeled colloid and method of preparation comprising reducing technetium-99m with stannous oxalate and stabilizing with sodium phytate are described. This radiodiagnostic agent is useful in the scintigraphic examination of the reticuloendothelial system, particularly the liver. In addition, by autoclaving this product with saline, it becomes a superior bone marrow scanning agent

  13. Virtual teeth: a 3D method for editing and visualizing small structures in CT scans

    DEFF Research Database (Denmark)

    Bro-Nielsen, Morten; Larsen, Per; Kreiborg, Sven

    1996-01-01

    The paper presents an interactive method for segmentation and visualization of small structures in CT scans. A combination of isosurface generation, spatial region growing and interactive graphics tools are used to extract small structures interactively. A practical example of segmentation of the...

  14. Genomic prediction based on data from three layer lines: a comparison between linear methods

    NARCIS (Netherlands)

    Calus, M.P.L.; Huang, H.; Vereijken, J.; Visscher, J.; Napel, ten J.; Windig, J.J.

    2014-01-01

    Background The prediction accuracy of several linear genomic prediction models, which have previously been used for within-line genomic prediction, was evaluated for multi-line genomic prediction. Methods Compared to a conventional BLUP (best linear unbiased prediction) model using pedigree data, we

  15. Some elaborating methods of gamma scanning results on irradiated nuclear fuels

    International Nuclear Information System (INIS)

    Sternini, E.

    1979-01-01

    Gamma scanning, as a post-irradiation examination, is a technique which provides a large number of informations on irradiated nuclear fuels. Power profile, fission products distribution, average and local burn-up of single elements structural and nuclear behaviour of fuel materials are examples of the obtained informations. In the present work experimental methods and theoretical calculations used at the CNEN hot cell laboratory for the mentioned purposes are described. Errors arising from the application of the gamma scanning technique are also discussed

  16. A novel method of genomic DNA extraction for Cactaceae1

    Science.gov (United States)

    Fehlberg, Shannon D.; Allen, Jessica M.; Church, Kathleen

    2013-01-01

    • Premise of the study: Genetic studies of Cactaceae can at times be impeded by difficult sampling logistics and/or high mucilage content in tissues. Simplifying sampling and DNA isolation through the use of cactus spines has not previously been investigated. • Methods and Results: Several protocols for extracting DNA from spines were tested and modified to maximize yield, amplification, and sequencing. Sampling of and extraction from spines resulted in a simplified protocol overall and complete avoidance of mucilage as compared to typical tissue extractions. Sequences from one nuclear and three plastid regions were obtained across eight genera and 20 species of cacti using DNA extracted from spines. • Conclusions: Genomic DNA useful for amplification and sequencing can be obtained from cactus spines. The protocols described here are valuable for any cactus species, but are particularly useful for investigators interested in sampling living collections, extensive field sampling, and/or conservation genetic studies. PMID:25202521

  17. Genome scan of human systemic lupus erythematosus: Evidence for linkage on chromosome 1q in African-American pedigrees

    Science.gov (United States)

    Moser, Kathy L.; Neas, Barbara R.; Salmon, Jane E.; Yu, Hua; Gray-McGuire, Courtney; Asundi, Neeraj; Bruner, Gail R.; Fox, Jerome; Kelly, Jennifer; Henshall, Stephanie; Bacino, Debra; Dietz, Myron; Hogue, Robert; Koelsch, Gerald; Nightingale, Lydia; Shaver, Tim; Abdou, Nabih I.; Albert, Daniel A.; Carson, Craig; Petri, Michelle; Treadwell, Edward L.; James, Judith A.; Harley, John B.

    1998-01-01

    Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by production of autoantibodies against intracellular antigens including DNA, ribosomal P, Ro (SS-A), La (SS-B), and the spliceosome. Etiology is suspected to involve genetic and environmental factors. Evidence of genetic involvement includes: associations with HLA-DR3, HLA-DR2, Fcγ receptors (FcγR) IIA and IIIA, and hereditary complement component deficiencies, as well as familial aggregation, monozygotic twin concordance >20%, λs > 10, purported linkage at 1q41–42, and inbred mouse strains that consistently develop lupus. We have completed a genome scan in 94 extended multiplex pedigrees by using model-based linkage analysis. Potential [log10 of the odds for linkage (lod) > 2.0] SLE loci have been identified at chromosomes 1q41, 1q23, and 11q14–23 in African-Americans; 14q11, 4p15, 11q25, 2q32, 19q13, 6q26–27, and 12p12–11 in European-Americans; and 1q23, 13q32, 20q13, and 1q31 in all pedigrees combined. An effect for the FcγRIIA candidate polymorphism) at 1q23 (lod = 3.37 in African-Americans) is syntenic with linkage in a murine model of lupus. Sib-pair and multipoint nonparametric analyses also support linkage (P 2.0). Our results are consistent with the presumed complexity of genetic susceptibility to SLE and illustrate racial origin is likely to influence the specific nature of these genetic effects. PMID:9843982

  18. The grid-scan. A novel method for a less biased broadband SED modeling

    Energy Technology Data Exchange (ETDEWEB)

    Doert, Marlene [Ruhr-Universitaet Bochum (Germany); Paneque, David [Max-Planck-Institut fuer Physik, Muenchen (Germany)

    2016-07-01

    We present a novel strategy for the modeling of blazar SEDs in the scope of current emission models: the grid-scan modeling. With an unbiased and uniform scan of the multi-dimensional parameter space of current emission models, e.g. the SSC model, and an a posteriori evaluation of the model-to-data agreement, independent sets of equally good model representations can be found. This variety of models generally includes different valid physical scenarios, which offer a more complete picture than single ''best'' solutions found by minimizers or the often-practised ''eyeball-fit''. Additionally, the grid-scan also allows to quantify how well the individual model parameters get constrained by any given experimental data set. The method will be introduced using the example of multi-wavelength spectral measurements of the blazar Markarian 501.

  19. Data Based Parameter Estimation Method for Circular-scanning SAR Imaging

    Directory of Open Access Journals (Sweden)

    Chen Gong-bo

    2013-06-01

    Full Text Available The circular-scanning Synthetic Aperture Radar (SAR is a novel working mode and its image quality is closely related to the accuracy of the imaging parameters, especially considering the inaccuracy of the real speed of the motion. According to the characteristics of the circular-scanning mode, a new data based method for estimating the velocities of the radar platform and the scanning-angle of the radar antenna is proposed in this paper. By referring to the basic conception of the Doppler navigation technique, the mathematic model and formulations for the parameter estimation are firstly improved. The optimal parameter approximation based on the least square criterion is then realized in solving those equations derived from the data processing. The simulation results verified the validity of the proposed scheme.

  20. Acquiring 4D thoracic CT scans using a multislice helical method

    International Nuclear Information System (INIS)

    Keall, P J; Starkschall, G; Shukla, H; Forster, K M; Ortiz, V; Stevens, C W; Vedam, S S; George, R; Guerrero, T; Mohan, R

    2004-01-01

    Respiratory motion degrades anatomic position reproducibility during imaging, necessitates larger margins during radiotherapy planning and causes errors during radiation delivery. Computed tomography (CT) scans acquired synchronously with the respiratory signal can be used to reconstruct 4D CT scans, which can be employed for 4D treatment planning to explicitly account for respiratory motion. The aim of this research was to develop, test and clinically implement a method to acquire 4D thoracic CT scans using a multislice helical method. A commercial position-monitoring system used for respiratory-gated radiotherapy was interfaced with a third generation multislice scanner. 4D cardiac reconstruction methods were modified to allow 4D thoracic CT acquisition. The technique was tested on a phantom under different conditions: stationary, periodic motion and non-periodic motion. 4D CT was also implemented for a lung cancer patient with audio-visual breathing coaching. For all cases, 4D CT images were successfully acquired from eight discrete breathing phases, however, some limitations of the system in terms of respiration reproducibility and breathing period relative to scanner settings were evident. Lung mass for the 4D CT patient scan was reproducible to within 2.1% over the eight phases, though the lung volume changed by 20% between end inspiration and end expiration (870 cm 3 ). 4D CT can be used for 4D radiotherapy, respiration-gated radiotherapy, 'slow' CT acquisition and tumour motion studies

  1. Measuring the plutonium distribution in fuel elements by the gamma scanning method

    International Nuclear Information System (INIS)

    Gorobets, A.K.; Leshchenko, Yu.I.; Semenov, A.L.

    1982-01-01

    An on-line system designed for measuring Pu distribution in the length of fresh fuel elements with vibrocompacted UO 2 -PuO 2 fuel rods by the γ-scanning method is described. An algorithm for measurement result processing and the procedure of determination of calibration parameters necessary for the valid signal separat.ion by means of a two-channel analyzer and for evaluation of the self-absorption effect are considered. The device scanning unit consists of two NaI(Tl) detectors simultaneously detecting γ-radiation from the opposite sides of a measured fuel rod section. The cesium source with Esub(γ)=660 keV is used for fuel scanning. On the base of the analysis of the results obtained when studying the BOR-60 experimental fuel elements with fuel rods of 400 mm long by means of the described device clusion is made that fuel element scanning during 20 min (scanning step is 4 mm, measuring time at each step is 10 s) makes it possible to determine Pu distribution with the error less than +-4% at the confidence probability of 0.68

  2. A METHOD OF SECURITY SCANNING OF CARRY-ON ITEMS, AND A CARRY-ON ITEMS SECURITY SCANNING SYSTEM

    DEFF Research Database (Denmark)

    2017-01-01

    A security scanning system (1) comprises a first stage module (3) having at least one X-ray source (6) and at least three first detectors (7) that are line-shaped and arranged in mutually different orientations and have at least dual energy resolution. A group of carry-on items (4) on a carrier...

  3. Development of a Method for Tool Wear Analysis Using 3D Scanning

    Directory of Open Access Journals (Sweden)

    Hawryluk Marek

    2017-12-01

    Full Text Available The paper deals with evaluation of a 3D scanning method elaborated by the authors, by applying it to the analysis of the wear of forging tools. The 3D scanning method in the first place consists in the application of scanning to the analysis of changes in geometry of a forging tool by way of comparing the images of a worn tool with a CAD model or an image of a new tool. The method was evaluated in the context of the important measurement problems resulting from the extreme conditions present during the industrial hot forging processes. The method was used to evaluate wear of tools with an increasing wear degree, which made it possible to determine the wear characteristics in a function of the number of produced forgings. The following stage was the use it for a direct control of the quality and geometry changes of forging tools (without their disassembly by way of a direct measurement of the geometry of periodically collected forgings (indirect method based on forgings. The final part of the study points to the advantages and disadvantages of the elaborated method as well as the potential directions of its further development.

  4. Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method

    DEFF Research Database (Denmark)

    Steen, Hanno; Pandey, Akhilesh; Andersen, Jens S

    2002-01-01

    mechanism for activating or inhibiting enzymes and for the assembly of multiprotein complexes. Here, we describe a mass spectrometry-based phosphotyrosine-specific immonium ion scanning (PSI scanning) method for selective detection of tyrosine-phosphorylated peptides. Once the tyrosine....... Because of its simplicity and specificity, PSI scanning is likely to become an important tool in proteomic studies of pathways involving tyrosine phosphorylation....

  5. Genomics protocols [Methods in molecular biology, v. 175

    National Research Council Canada - National Science Library

    Starkey, Michael P; Elaswarapu, Ramnath

    2001-01-01

    ... to the larger community of researchers who have recognized the potential of genomics research and may themselves be beginning to explore the technologies involved. Some of the techniques described in Genomics Protocols are clearly not restricted to the genomics field; indeed, a prerequisite for many procedures in this discipline is that they require an extremely high throughput, beyond the scope of the average investigator. However, what we have endeavored here to achieve is both to compile a collection of...

  6. Will genomic selection be a practical method for plant breeding?

    OpenAIRE

    Nakaya, Akihiro; Isobe, Sachiko N.

    2012-01-01

    Background Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information avail...

  7. Genomics protocols [Methods in molecular biology, v. 175

    National Research Council Canada - National Science Library

    Starkey, Michael P; Elaswarapu, Ramnath

    2001-01-01

    .... Drawing on emerging technologies in the fields of bioinformatics and proteomics, these protocols cover not only those traditionally recognized as genomics, but also early therapeutich approaches...

  8. Genome-wide scan for serum ghrelin detects linkage on chromosome 1p36 in Hispanic children: results from the Viva La Familia study.

    Science.gov (United States)

    Voruganti, V Saroja; Göring, Harald H H; Diego, Vincent P; Cai, Guowen; Mehta, Nitesh R; Haack, Karin; Cole, Shelley A; Butte, Nancy F; Comuzzie, Anthony G

    2007-10-01

    This study was conducted to investigate genetic influence on serum ghrelin and its relationship with adiposity-related phenotypes in Hispanic children (n=1030) from the Viva La Familia study (VFS). Anthropometric measurements and levels of serum ghrelin were estimated and genetic analyses conducted according to standard procedures. Mean age, body mass index (BMI), and serum ghrelin were 11+/-0.13 y, 25+/-0.24 kg/m2 and 38+/-0.5 ng/mL, respectively. Significant heritabilities (p<0.001) were obtained for BMI, weight, fat mass, percent fat, waist circumference, waist-to-height ratio, and ghrelin. Bivariate analyses of ghrelin with adiposity traits showed significant negative genetic correlations (p<0.0001) with weight, BMI, fat mass, percent fat, waist circumference, and waist-to-height ratio. A genome-wide scan for ghrelin detected significant linkage on chromosome 1p36.2 between STR markers D1S2697 and D1S199 (LOD=3.2). The same region on chromosome 1 was the site of linkage for insulin (LOD=3.3), insulinlike growth factor binding protein 1 (IGFBP1) (LOD=3.4), homeostatic model assessment method (HOMA) (LOD=2.9), and C-peptide (LOD=2.0). Several family-based studies have reported linkages for obesity-related phenotypes in the region of 1p36. These results indicate the importance of this region in relation to adiposity in children from the VFS.

  9. A Novel Real-Time Reference Key Frame Scan Matching Method

    Directory of Open Access Journals (Sweden)

    Haytham Mohamed

    2017-05-01

    Full Text Available Unmanned aerial vehicles represent an effective technology for indoor search and rescue operations. Typically, most indoor missions’ environments would be unknown, unstructured, and/or dynamic. Navigation of UAVs in such environments is addressed by simultaneous localization and mapping approach using either local or global approaches. Both approaches suffer from accumulated errors and high processing time due to the iterative nature of the scan matching method. Moreover, point-to-point scan matching is prone to outlier association processes. This paper proposes a low-cost novel method for 2D real-time scan matching based on a reference key frame (RKF. RKF is a hybrid scan matching technique comprised of feature-to-feature and point-to-point approaches. This algorithm aims at mitigating errors accumulation using the key frame technique, which is inspired from video streaming broadcast process. The algorithm depends on the iterative closest point algorithm during the lack of linear features which is typically exhibited in unstructured environments. The algorithm switches back to the RKF once linear features are detected. To validate and evaluate the algorithm, the mapping performance and time consumption are compared with various algorithms in static and dynamic environments. The performance of the algorithm exhibits promising navigational, mapping results and very short computational time, that indicates the potential use of the new algorithm with real-time systems.

  10. Genome analysis methods: Sorghum bicolor [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

    Lifescience Database Archive (English)

    Full Text Available Sorghum bicolor Finished 2n=20 760 Mb 2009 Sanger (Clone-based) 10,717,203 reads 7...30 Mb 8.5x Arachne2 v.20060705 3,304 12,873 BLAST, GenomeScan 34,496 (Sbi1.4) JGI; http://www.phytozome.net/sorghum Sbi1 Sbi1.4 10.1038/nature07723 19189423 ...

  11. Accuracy of optical scanning methods of the Cerec®3D system in the process of making ceramic inlays

    Directory of Open Access Journals (Sweden)

    Trifković Branka

    2010-01-01

    Full Text Available Background/Aim. One of the results of many years of Cerec® 3D CAD/CAM system technological development is implementation of one intraoral and two extraoral optical scanning methods which, depending on the current indications, are applied in making fixed restorations. The aim of this study was to determine the degree of precision of optical scanning methods by the use of the Cerec®3D CAD/CAM system in the process of making ceramic inlays. Methods. The study was conducted in three experimental groups of inlays prepared using the procedure of three methods of scanning Cerec ®3D system. Ceramic inlays made by conventional methodology were the control group. The accuracy of optical scanning methods of the Cerec®3D system computer aided designcomputer aided manufacturing (CAD/CAM was indirectly examined by measuring a marginal gap size between inlays and demarcation preparation by scanning electron microscope (SEM. Results. The results of the study showed a difference in the accuracy of the existing methods of scanning dental CAD/CAM systems. The highest level of accuracy was achieved by the extraoral optical superficial scanning technique. The value of marginal gap size inlays made with the technique of extraoral optical superficial scanning was 32.97 ± 13.17 μ. Techniques of intraoral optical superficial and extraoral point laser scanning showed a lower level of accuracy (40.29 ± 21.46 μ for inlays of intraoral optical superficial scanning and 99.67 ± 37.25 μ for inlays of extraoral point laser scanning. Conclusion. Optical scanning methods in dental CAM/CAM technologies are precise methods of digitizing the spatial models; application of extraoral optical scanning methods provides the hightest precision.

  12. An elastography method based on the scanning contact resonance of a piezoelectric cantilever

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Ji; Li, Faxin, E-mail: lifaxin@pku.edu.cn [State Key Lab for Turbulence and Complex Systems, College of Engineering, Peking University, Beijing 100871, China and HEDPS, Center for Applied Physics and Technologies, Peking University, Beijing 100871 (China)

    2013-12-15

    Purpose: Most tissues may become significantly stiffer than their normal states when there are lesions inside. The tissue's modulus can then act as an identification parameter for clinic diagnosis of tumors or fibrosis, which leads to elastography. This study introduces a novel elastography method that can be used for modulus imaging of superficial organs. Methods: This method is based on the scanning contact-resonance of a unimorph piezoelectric cantilever. The cantilever vibrates in its bending mode with the tip pressed tightly on the sample. The contact resonance frequency of the cantilever-sample system is tracked at each scanning point, from which the sample's modulus can be derived based on a beam dynamic model and a contact mechanics model. Scanning is performed by a three-dimensional motorized stage and the whole system is controlled by a homemade software program based on LabVIEW. Results: Testing onin vitro beef tissues indicates that the fat and the muscle can be easily distinguished using this system, and the accuracy of the modulus measurement can be comparable with that of nanoindentation. Imaging on homemade gelatin phantoms shows that the depth information of the abnormalities can be qualitatively obtained by varying the pressing force. The detection limit of this elastography method is specially examined both experimentally and numerically. Results show that it can detect the typical lesions in superficial organs with the depth of several centimeters. The lateral resolution of this elastography method/system is better than 0.5 mm, and could be further enhanced by using more scanning points. Conclusions: The proposed elastography system can be regarded as a sensitive palpation robot, which may be very promising in early diagnosis of tumors in superficial organs such as breast and thyroid.

  13. Study on scan timing using a test injection method in head CTA

    International Nuclear Information System (INIS)

    Sekito, Yuichi; Sanada, Hidenori

    2005-01-01

    In head computed tomographic angiography (CTA), circulation from arterial phase to venous phase is more rapid than that in other regions. Therefore, it is necessary to determine correct scan timing to obtain ideal CTA images. A test injection method makes it possible to set correct scan timing from the time density curve (TDC) for each subject. The method, however, has a weak point that is a time lag in an arrival time at peak point of contrast medium on TDC between the test injection and the primary examination because of the difference in total volume of contrast medium used. The purpose of this study calculated the delay time on the TDC in both scans. We used the test injection method and the bolus tracking method in the primary examination. The average errors in start time (Δt1) and slope change time (Δt2) of the contrast medium on the TDC between test injection and primary examination were 0.15 sec and 3.05 sec, respectively. The results indicated that it was important to grasp the delay time in start time and peak arrival time of the contrast medium between test injection and primary examination to obtain ideal images in head CTA. (author)

  14. Genomic breeding value prediction:methods and procedures

    NARCIS (Netherlands)

    Calus, M.P.L.

    2010-01-01

    Animal breeding faces one of the most significant changes of the past decades – the implementation of genomic selection. Genomic selection uses dense marker maps to predict the breeding value of animals with reported accuracies that are up to 0.31 higher than those of pedigree indexes, without the

  15. Evaluation of positional plagiocephaly: Conventional anthropometric measurement versus laser scanning method.

    Science.gov (United States)

    Nahles, Susanne; Klein, Martin; Yacoub, Anke; Neyer, Julia

    2018-01-01

    The incidence of plagiocephaly has increased in the 25 years since the "Back to Sleep" campaign in 1991 to prevent sudden infant death. Plagiocephaly is not considered to be a pathological condition. It is more of an esthetic impairment and could have potentially negative psychological or psychosocial consequences; therefore, treatment is recommended. The aim of this study is to compare conventional anthropometry and laser scanning - two different measurement methods - as diagnostic instruments for plagiocephaly. The present study also tests the measurement time of both methods and whether one method is easier on the patient than the other. A total of 44 children (21 girls, 23 boys) with a mean age of 8.8 months were involved in the present study. Of all patients, the following parameters were routinely evaluated using a standard protocol with the conventional anthropometric method and the scan method: head circumference, head length, head width, head diagonals, and distances ex-t. Furthermore, the time required to obtain measurements and the behavior of the children during measurement were documented. For statistical analysis, a t-test and a Wilcoxon test were used to analyze differences between the two methods. The results for head circumference showed a mean of 441.5 mm for the anthropometric measurements and 441.6 mm for the scan method, with no significant difference between the two methods. A significant difference was found regarding the head width, head length, diagonals, and distance ex-t. The measurement process using the scan method needed a mean of 579.6 s in contrast to the manual anthropometric method, which required a mean time of 180.5 s. In comparison with the conventional anthropometric method, measurements made with a 3D laser scanner yield inconsistent results. Moreover, the current state of technology of 3D cephalometry has no advantages compared with the conventional anthropometric method. Disadvantages worth mentioning appear to be the

  16. Methods for studying biofilm formation: flow cells and confocal laser scanning microscopy

    DEFF Research Database (Denmark)

    Tolker-Nielsen, Tim; Sternberg, Claus

    2014-01-01

    In this chapter methods for growing and analyzing biofilms under hydrodynamic conditions in flow cells are described. Use of flow cells allows for direct microscopic investigation of biofilm formation. The flow in these chambers is essentially laminar, which means that the biofilms can be grown u......, inoculation of the flow cells, running of the system, confocal laser scanning microscopy and image analysis, and disassembly and cleaning of the system....

  17. Single-step electrochemical method for producing very sharp Au scanning tunneling microscopy tips

    International Nuclear Information System (INIS)

    Gingery, David; Buehlmann, Philippe

    2007-01-01

    A single-step electrochemical method for making sharp gold scanning tunneling microscopy tips is described. 3.0M NaCl in 1% perchloric acid is compared to several previously reported etchants. The addition of perchloric acid to sodium chloride solutions drastically shortens etching times and is shown by transmission electron microscopy to produce very sharp tips with a mean radius of curvature of 15 nm

  18. Automatic calibration method of voxel size for cone-beam 3D-CT scanning system

    International Nuclear Information System (INIS)

    Yang Min; Wang Xiaolong; Wei Dongbo; Liu Yipeng; Meng Fanyong; Li Xingdong; Liu Wenli

    2014-01-01

    For a cone-beam three-dimensional computed tomography (3D-CT) scanning system, voxel size is an important indicator to guarantee the accuracy of data analysis and feature measurement based on 3D-CT images. Meanwhile, the voxel size changes with the movement of the rotary stage along X-ray direction. In order to realize the automatic calibration of the voxel size, a new and easily-implemented method is proposed. According to this method, several projections of a spherical phantom are captured at different imaging positions and the corresponding voxel size values are calculated by non-linear least-square fitting. Through these interpolation values, a linear equation is obtained that reflects the relationship between the voxel size and the rotary stage translation distance from its nominal zero position. Finally, the linear equation is imported into the calibration module of the 3D-CT scanning system. When the rotary stage is moving along X-ray direction, the accurate value of the voxel size is dynamically exported. The experimental results prove that this method meets the requirements of the actual CT scanning system, and has virtues of easy implementation and high accuracy. (authors)

  19. Highly Accurate Tree Models Derived from Terrestrial Laser Scan Data: A Method Description

    Directory of Open Access Journals (Sweden)

    Jan Hackenberg

    2014-05-01

    Full Text Available This paper presents a method for fitting cylinders into a point cloud, derived from a terrestrial laser-scanned tree. Utilizing high scan quality data as the input, the resulting models describe the branching structure of the tree, capable of detecting branches with a diameter smaller than a centimeter. The cylinders are stored as a hierarchical tree-like data structure encapsulating parent-child neighbor relations and incorporating the tree’s direction of growth. This structure enables the efficient extraction of tree components, such as the stem or a single branch. The method was validated both by applying a comparison of the resulting cylinder models with ground truth data and by an analysis between the input point clouds and the models. Tree models were accomplished representing more than 99% of the input point cloud, with an average distance from the cylinder model to the point cloud within sub-millimeter accuracy. After validation, the method was applied to build two allometric models based on 24 tree point clouds as an example of the application. Computation terminated successfully within less than 30 min. For the model predicting the total above ground volume, the coefficient of determination was 0.965, showing the high potential of terrestrial laser-scanning for forest inventories.

  20. A landmark-based method for the geometrical 3D calibration of scanning microscopes

    Energy Technology Data Exchange (ETDEWEB)

    Ritter, M.

    2007-04-27

    This thesis presents a new strategy and a spatial method for the geometric calibration of 3D measurement devices at the micro-range, based on spatial reference structures with nanometersized landmarks (nanomarkers). The new method was successfully applied for the 3D calibration of scanning probe microscopes (SPM) and confocal laser scanning microscopes (CLSM). Moreover, the spatial method was also used for the photogrammetric self-calibration of scanning electron microscopes (SEM). In order to implement the calibration strategy to all scanning microscopes used, the landmark-based principle of reference points often applied at land survey or at close-range applications has been transferred to the nano- and micro-range in the form of nanomarker. In order to function as a support to the nanomarkers, slope-shaped step pyramids have been developed and fabricated by focused ion beam (FIB) induced metal deposition. These FIB produced 3D microstructures have been sized to embrace most of the measurement volume of the scanning microscopes. Additionally, their special design allows the homogenous distribution of the nanomarkers. The nanomarkers were applied onto the support and the plateaus of the slope-step pyramids by FIB etching (milling) as landmarks with as little as several hundreds of nanometers in diameter. The nanomarkers are either of point-, or ring-shaped design. They are optimized so that they can be spatially measured by SPM and CLSM, and, imaged and photogrammetrically analyzed on the basis of SEM data. The centre of the each nanomarker serves as reference point in the measurement data or images. By applying image processing routines, the image (2D) or object (3D) coordinates of each nanomarker has been determined with subpixel accuracy. The correlative analysis of the SPM, CLSM and photogrammetric SEM measurement data after 3D calibration resulted in mean residues in the measured coordinates of as little as 13 nm. Without the coupling factors the mean

  1. An elastography method based on the scanning contact resonance of a piezoelectric cantilever.

    Science.gov (United States)

    Fu, Ji; Li, Faxin

    2013-12-01

    Most tissues may become significantly stiffer than their normal states when there are lesions inside. The tissue's modulus can then act as an identification parameter for clinic diagnosis of tumors or fibrosis, which leads to elastography. This study introduces a novel elastography method that can be used for modulus imaging of superficial organs. This method is based on the scanning contact-resonance of a unimorph piezoelectric cantilever. The cantilever vibrates in its bending mode with the tip pressed tightly on the sample. The contact resonance frequency of the cantilever-sample system is tracked at each scanning point, from which the sample's modulus can be derived based on a beam dynamic model and a contact mechanics model. Scanning is performed by a three-dimensional motorized stage and the whole system is controlled by a homemade software program based on LabVIEW. Testing on in vitro beef tissues indicates that the fat and the muscle can be easily distinguished using this system, and the accuracy of the modulus measurement can be comparable with that of nanoindentation. Imaging on homemade gelatin phantoms shows that the depth information of the abnormalities can be qualitatively obtained by varying the pressing force. The detection limit of this elastography method is specially examined both experimentally and numerically. Results show that it can detect the typical lesions in superficial organs with the depth of several centimeters. The lateral resolution of this elastography method∕system is better than 0.5 mm, and could be further enhanced by using more scanning points. The proposed elastography system can be regarded as a sensitive palpation robot, which may be very promising in early diagnosis of tumors in superficial organs such as breast and thyroid.

  2. A new method of CT scanning for the diagnosis of mandibular fractures

    International Nuclear Information System (INIS)

    Tsukagoshi, Taku; Satoh, Kaneshige; Onizuka, Takuya

    1990-01-01

    The condylar neck of the mandible is one of the most common fracture sites in the facial skeleton. Such a fracture is routinely diagnosed by A-P, lateral oblique, and Towne projection roentgenography or orthopantomography. Despite the combination of these films, fracture of the neck of the mandible is still difficult to diagnose definitely. Therefore, a new CT scanning method was developed for diagnosing fractures of the neck of the condylar mandible. The CT axis is projected along the length of the mandible, extending from the condyle to the symphysis. This projection visualizes both the condyle and the mandibular symphysis in the same plane. The patient is placed in a supine position with the head fully extended. The base line, a line extending from the midpoint of the glenoid fossa to the menton, is determined with a lateral facial cephalogram. CT scanning with a 5 mm window is performed in parallel with and 2 cm anterior to and 2 cm posterior to the base line. When CT scanning was performed in a healthy volunteer, the condition of the condyle and the condylar neck of the mandible was clearly shown, and the view extended from the condyle to the symphysis. For automobile accident patients in whom fracture of the neck of the mandible was associated with fracture of the symphysis, two fractures were found in the same plane. A newly developed CT scanning technique is useful in the diagnosis of fractures of the condylar neck of the mandible and in the identification of fractures at other mandibular sites. It also allows scanning of patients in a supine position, which may aid in managing patients with multiple traumas. (N.K.)

  3. Method of composing two-dimensional scanned spectra observed by the New Vacuum Solar Telescope

    Science.gov (United States)

    Cai, Yun-Fang; Xu, Zhi; Chen, Yu-Chao; Xu, Jun; Li, Zheng-Gang; Fu, Yu; Ji, Kai-Fan

    2018-04-01

    In this paper we illustrate the technique used by the New Vacuum Solar Telescope (NVST) to increase the spatial resolution of two-dimensional (2D) solar spectroscopy observations involving two dimensions of space and one of wavelength. Without an image stabilizer at the NVST, large scale wobble motion is present during the spatial scanning, whose instantaneous amplitude can reach 1.3″ due to the Earth’s atmosphere and the precision of the telescope guiding system, and seriously decreases the spatial resolution of 2D spatial maps composed with scanned spectra. We make the following effort to resolve this problem: the imaging system (e.g., the TiO-band) is used to record and detect the displacement vectors of solar image motion during the raster scan, in both the slit and scanning directions. The spectral data (e.g., the Hα line) which are originally obtained in time sequence are corrected and re-arranged in space according to those displacement vectors. Raster scans are carried out in several active regions with different seeing conditions (two rasters are illustrated in this paper). Given a certain spatial sampling and temporal resolution, the spatial resolution of the composed 2D map could be close to that of the slit-jaw image. The resulting quality after correction is quantitatively evaluated with two methods. A physical quantity, such as the line-of-sight velocities in multiple layers of the solar atmosphere, is also inferred from the re-arranged spectrum, demonstrating the advantage of this technique.

  4. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

    Science.gov (United States)

    Eoche-Bosy, D; Gautier, M; Esquibet, M; Legeai, F; Bretaudeau, A; Bouchez, O; Fournet, S; Grenier, E; Montarry, J

    2017-09-01

    Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaV vrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability. © 2017 John Wiley & Sons Ltd.

  5. A scanning tunneling microscope break junction method with continuous bias modulation.

    Science.gov (United States)

    Beall, Edward; Yin, Xing; Waldeck, David H; Wierzbinski, Emil

    2015-09-28

    Single molecule conductance measurements on 1,8-octanedithiol were performed using the scanning tunneling microscope break junction method with an externally controlled modulation of the bias voltage. Application of an AC voltage is shown to improve the signal to noise ratio of low current (low conductance) measurements as compared to the DC bias method. The experimental results show that the current response of the molecule(s) trapped in the junction and the solvent media to the bias modulation can be qualitatively different. A model RC circuit which accommodates both the molecule and the solvent is proposed to analyze the data and extract a conductance for the molecule.

  6. Frequency scanning-based stability analysis method for grid-connected inverter system

    DEFF Research Database (Denmark)

    Wang, Yanbo; Wang, Xiongfei; Blaabjerg, Frede

    2017-01-01

    This paper proposes a frequency scanning-based impedance analysis for stability assessment of grid-connected inverter system, which is able to perform stability assessment without using system mathematical models and inherit the superior feature of impedance-based stability criterion with conside......This paper proposes a frequency scanning-based impedance analysis for stability assessment of grid-connected inverter system, which is able to perform stability assessment without using system mathematical models and inherit the superior feature of impedance-based stability criterion...... with consideration of the inverter nonlinearities. Small current disturbance is injected into grid-connected inverter system in a particular frequency range, and the impedance is computed according to the harmonic-frequency response using Fourier analysis, and then the stability is predicted on the basis...... of the impedance stability criterion. The stability issues of grid-connected inverters with grid-current feedback and the converter-current feedback are addressed using the proposed method. The results obtained from simulation and experiments validate the effectiveness of the method. The frequency scanning...

  7. Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

    Directory of Open Access Journals (Sweden)

    Gray Joanna

    2010-11-01

    Full Text Available Abstract Background We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism microarrays and DNA pooling (SNP-MaP employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations. The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes. Findings In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods. Conclusions Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

  8. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

    Science.gov (United States)

    Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

    2014-01-01

    Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

  9. Segmented gamma scanning method for measuring holdup in the spherical container

    International Nuclear Information System (INIS)

    Deng Jingshan; Li Ze; Gan Lin; Lu Wenguang; Dong Mingli

    2007-01-01

    Some special nuclear material (SNM) is inevitably deposited in the facilities (mixer, reactor) of nuclear material process line. Exactly knowing the quantity of nuclear material holdup is very important for nuclear material accountability and critical safety. This paper presents segmented gamma scanning method for SNM holdup measurement of spherical container, at the left, right and back of which other equipments exist so that the detectors can be put at the only front of container for measurement. The nuclear material deposited in the spherical container can be looked as spherical shell source, which is divided into many layers. The detectors scanning spherical shell source are moved layer by layer from the top to the bottom to obtain projection data, with which deposited material distribution can be reconstructed by using Least Square (LS) method or Maximum Likelihood (ML) method. With these methods accurate total holdup can be obtained by summing up all the segmental values reconstructed. In this paper this measurement method for holdup in the spherical container was verified with Monte-Carlo simulation calculation and experiment. (authors)

  10. Diagnosis of spatial resolution for microbeam scanning PIXE using STIM method and CR-39 track detector in PASTA

    International Nuclear Information System (INIS)

    Hamano, T.; Imaseki, H.; Yukawa, M.; Ishikawa, T.; Iso, H.; Matsumoto, K.

    2003-01-01

    In PIXE analysis system and Tandem Accelerator facility (PASTA) of NIRS, we are using Scanning Transmission Ion Microscopy (STIM) method and solid track detector to diagnose the spatial resolution of scanning microbeam PIXE analysis system. These methods are widely used by many microbeam facilities. (author)

  11. Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods

    DEFF Research Database (Denmark)

    Bohlin, Jon; Snipen, Lars; Cloeckaert, Axel

    2010-01-01

    BACKGROUND: Classification of bacteria within the genus Brucella has been difficult due in part to considerable genomic homogeneity between the different species and biovars, in spite of clear differences in phenotypes. Therefore, many different methods have been used to assess Brucella taxonomy....... In the current work, we examine 32 sequenced genomes from genus Brucella representing the six classical species, as well as more recently described species, using bioinformatical methods. Comparisons were made at the level of genomic DNA using oligonucleotide based methods (Markov chain based genomic signatures...... between the oligonucleotide based methods used. Whilst the Markov chain based genomic signatures grouped the different species in genus Brucella according to host preference, the codon and amino acid frequencies based methods reflected small differences between the Brucella species. Only minor differences...

  12. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  13. A simple and effective method for construction of Escherichia coli strains proficient for genome engineering.

    Directory of Open Access Journals (Sweden)

    Young Shin Ryu

    Full Text Available Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the λ Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.

  14. Real-time dose compensation methods for scanned ion beam therapy of moving tumors

    International Nuclear Information System (INIS)

    Luechtenborg, Robert

    2012-01-01

    Scanned ion beam therapy provides highly tumor-conformal treatments. So far, only tumors showing no considerable motion during therapy have been treated as tumor motion and dynamic beam delivery interfere, causing dose deteriorations. One proposed technique to mitigate these deteriorations is beam tracking (BT), which adapts the beam position to the moving tumor. Despite application of BT, dose deviations can occur in the case of non-translational motion. In this work, real-time dose compensation combined with beam tracking (RDBT) has been implemented into the control system to compensate these dose changes by adaptation of nominal particle numbers during irradiation. Compared to BT, significantly reduced dose deviations were measured using RDBT. Treatment planning studies for lung cancer patients including the increased biological effectiveness of ions revealed a significantly reduced over-dose level (3/5 patients) as well as significantly improved dose homogeneity (4/5 patients) for RDBT. Based on these findings, real-time dose compensated re-scanning (RDRS) has been proposed that potentially supersedes the technically complex fast energy adaptation necessary for BT and RDBT. Significantly improved conformity compared to re-scanning, i.e., averaging of dose deviations by repeated irradiation, was measured in film irradiations. Simulations comparing RDRS to BT revealed reduced under- and overdoses of the former method.

  15. Digital radiography of scoliosis with a scanning method: radiation dose optimization

    Energy Technology Data Exchange (ETDEWEB)

    Geijer, Haakan; Andersson, Torbjoern [Department of Radiology, Oerebro University Hospital, 701 85 Oerebro (Sweden); Verdonck, Bert [Philips Medical Systems, P.O. Box 10,000, 5680 Best (Netherlands); Beckman, Karl-Wilhelm; Persliden, Jan [Department of Medical Physics, Oerebro University Hospital, 701 85 Oerebro (Sweden)

    2003-03-01

    The aim of this study was optimization of the radiation dose-image quality relationship for a digital scanning method of scoliosis radiography. The examination is performed as a digital multi-image translation scan that is reconstructed to a single image in a workstation. Entrance dose was recorded with thermoluminescent dosimeters placed dorsally on an Alderson phantom. At the same time, kerma area product (KAP) values were recorded. A Monte Carlo calculation of effective dose was also made. Image quality was evaluated with a contrast-detail phantom and Visual Grading. The radiation dose was reduced by lowering the image intensifier entrance dose request, adjusting pulse frequency and scan speed, and by raising tube voltage. The calculated effective dose was reduced from 0.15 to 0.05 mSv with reduction of KAP from 1.07 to 0.25 Gy cm{sup 2} and entrance dose from 0.90 to 0.21 mGy. The image quality was reduced with the Image Quality Figure going from 52 to 62 and a corresponding reduction in image quality as assessed with Visual Grading. The optimization resulted in a dose reduction to 31% of the original effective dose with an acceptable reduction in image quality considering the intended use of the images for angle measurements. (orig.)

  16. Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

    Science.gov (United States)

    Behura, Susanta K; Severson, David W

    2013-02-01

    Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

  17. A New, Simple Method for Estimating Pleural Effusion Size on CT Scans

    Science.gov (United States)

    Moy, Matthew P.; Berko, Netanel S.; Godelman, Alla; Jain, Vineet R.; Haramati, Linda B.

    2013-01-01

    Background: There is no standardized system to grade pleural effusion size on CT scans. A validated, systematic grading system would improve communication of findings and may help determine the need for imaging guidance for thoracentesis. Methods: CT scans of 34 patients demonstrating a wide range of pleural effusion sizes were measured with a volume segmentation tool and reviewed for qualitative and simple quantitative features related to size. A classification rule was developed using the features that best predicted size and distinguished among small, moderate, and large effusions. Inter-reader agreement for effusion size was assessed on the CT scans for three groups of physicians (radiology residents, pulmonologists, and cardiothoracic radiologists) before and after implementation of the classification rule. Results: The CT imaging features found to best classify effusions as small, moderate, or large were anteroposterior (AP) quartile and maximum AP depth measured at the midclavicular line. According to the decision rule, first AP-quartile effusions are small, second AP-quartile effusions are moderate, and third or fourth AP-quartile effusions are large. In borderline cases, AP depth is measured with 3-cm and 10-cm thresholds for the upper limit of small and moderate, respectively. Use of the rule improved interobserver agreement from κ = 0.56 to 0.79 for all physicians, 0.59 to 0.73 for radiology residents, 0.54 to 0.76 for pulmonologists, and 0.74 to 0.85 for cardiothoracic radiologists. Conclusions: A simple, two-step decision rule for sizing pleural effusions on CT scans improves interobserver agreement from moderate to substantial levels. PMID:23632863

  18. A method for the reconstruction of four-dimensional synchronized CT scans acquired during free breathing

    International Nuclear Information System (INIS)

    Low, Daniel A.; Nystrom, Michelle; Kalinin, Eugene; Parikh, Parag; Dempsey, James F.; Bradley, Jeffrey D.; Mutic, Sasa; Wahab, Sasha H.; Islam, Tareque; Christensen, Gary; Politte, David G.; Whiting, Bruce R.

    2003-01-01

    Breathing motion is a significant source of error in radiotherapy treatment planning for the thorax and upper abdomen. Accounting for breathing motion has a profound effect on the size of conformal radiation portals employed in these sites. Breathing motion also causes artifacts and distortions in treatment planning computed tomography (CT) scans acquired during free breathing and also causes a breakdown of the assumption of the superposition of radiation portals in intensity-modulated radiation therapy, possibly leading to significant dose delivery errors. Proposed voluntary and involuntary breath-hold techniques have the potential for reducing or eliminating the effects of breathing motion, however, they are limited in practice, by the fact that many lung cancer patients cannot tolerate holding their breath. We present an alternative solution to accounting for breathing motion in radiotherapy treatment planning, where multislice CT scans are collected simultaneously with digital spirometry over many free breathing cycles to create a four-dimensional (4-D) image set, where tidal lung volume is the additional dimension. An analysis of this 4-D data leads to methods for digital-spirometry, based elimination or accounting of breathing motion artifacts in radiotherapy treatment planning for free breathing patients. The 4-D image set is generated by sorting free-breathing multislice CT scans according to user-defined tidal-volume bins. A multislice CT scanner is operated in the cine mode, acquiring 15 scans per couch position, while the patient undergoes simultaneous digital-spirometry measurements. The spirometry is used to retrospectively sort the CT scans by their correlated tidal lung volume within the patient's normal breathing cycle. This method has been prototyped using data from three lung cancer patients. The actual tidal lung volumes agreed with the specified bin volumes within standard deviations ranging between 22 and 33 cm 3 . An analysis of sagittal and

  19. Accuracy and reliability of a novel method for fusion of digital dental casts and Cone Beam Computed Tomography scans.

    Directory of Open Access Journals (Sweden)

    Frits A Rangel

    Full Text Available Several methods have been proposed to integrate digital models into Cone Beam Computed Tomography scans. Since all these methods have some drawbacks such as radiation exposure, soft tissue deformation and time-consuming digital handling processes, we propose a new method to integrate digital dental casts into Cone Beam Computed Tomography scans. Plaster casts of 10 patients were randomly selected and 5 titanium markers were glued to the upper and lower plaster cast. The plaster models were scanned, impressions were taken from the plaster models and the impressions were also scanned. Linear measurements were performed on all three models, to assess accuracy and reproducibility. Besides that, matching of the scanned plaster models and scanned impressions was done, to assess the accuracy of the matching procedure. Results show that all measurement errors are smaller than 0.2 mm, and that 81% is smaller than 0.1 mm. Matching of the scanned plaster casts and scanned impressions show a mean error between the two surfaces of the upper arch of 0.14 mm and for the lower arch of 0.18 mm. The time needed for reconstructing the CBCT scans to a digital patient, where the impressions are integrated into the CBCT scan of the patient takes about 15 minutes, with little variance between patients. In conclusion, we can state that this new method is a reliable method to integrate digital dental casts into CBCT scans. As far as radiation exposure, soft tissue deformation and digital handling processes are concerned, it is a significant improvement compared to the previously published methods.

  20. Accuracy and Reliability of a Novel Method for Fusion of Digital Dental Casts and Cone Beam Computed Tomography Scans

    Science.gov (United States)

    Rangel, Frits A.; Maal, Thomas J. J.; Bronkhorst, Ewald M.; Breuning, K. Hero; Schols, Jan G. J. H.; Bergé, Stefaan J.; Kuijpers-Jagtman, Anne Marie

    2013-01-01

    Several methods have been proposed to integrate digital models into Cone Beam Computed Tomography scans. Since all these methods have some drawbacks such as radiation exposure, soft tissue deformation and time-consuming digital handling processes, we propose a new method to integrate digital dental casts into Cone Beam Computed Tomography scans. Plaster casts of 10 patients were randomly selected and 5 titanium markers were glued to the upper and lower plaster cast. The plaster models were scanned, impressions were taken from the plaster models and the impressions were also scanned. Linear measurements were performed on all three models, to assess accuracy and reproducibility. Besides that, matching of the scanned plaster models and scanned impressions was done, to assess the accuracy of the matching procedure. Results show that all measurement errors are smaller than 0.2 mm, and that 81% is smaller than 0.1 mm. Matching of the scanned plaster casts and scanned impressions show a mean error between the two surfaces of the upper arch of 0.14 mm and for the lower arch of 0.18 mm. The time needed for reconstructing the CBCT scans to a digital patient, where the impressions are integrated into the CBCT scan of the patient takes about 15 minutes, with little variance between patients. In conclusion, we can state that this new method is a reliable method to integrate digital dental casts into CBCT scans. As far as radiation exposure, soft tissue deformation and digital handling processes are concerned, it is a significant improvement compared to the previously published methods. PMID:23527111

  1. METHOD FOR OBSERVATION OF DEEMBEDDED SECTIONS OF FISH GONAD BY SCANNING ELECTRON MICROSCOPY

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This article reports a method for examining the intracellular structure of fish gonads using a scanning electron microscope(SEM). The specimen preparation procedure is similar to that for transmission electron microscopy wherein samples cut into semi-thin sections are fixed and embedded in plastic. The embedment matrix was removed by solvents. Risen-free specimens could be observed by SEM. The morphology of matured sperms in the gonad was very clear, and the oocyte internal structures appeared in three-dimensional images. Spheroidal nucleoli and yolk vesicles and several bundles of filaments adhered on the nucleoli could be viewed by SEM for the first time.

  2. Cancer cell imaging by stable wet near-field scanning optical microscope with resonance tracking method

    International Nuclear Information System (INIS)

    Park, Kyoung-Duck; Park, Doo-Jae; Jeong, Mun-Seok; Choi, Geun-Chang; Lee, Seung-Gol; Byeon, Clare-Chisu; Choi, Soo-Bong

    2014-01-01

    We report on a successful topographical and optical imaging of various cancer cells in liquid and in air by using a stable wet near-field scanning optical microscope that utilizes a resonance tracking method. We observed a clear dehydration which gives rise to a decrease in the cell volume down to 51%. In addition, a micro-ball lens effect due to the round-shaped young cancer cells was observed from near-field imaging, where the refractive index of young cancer cells was deduced.

  3. The development of an automatic scanning method for CR-39 neutron dosimeter

    International Nuclear Information System (INIS)

    Tawara, Hiroko; Miyajima, Mitsuhiro; Sasaki, Shin-ichi; Hozumi, Ken-ichi

    1989-01-01

    A method of measuring low level neutron dose has been developed with CR-39 track detectors using an automatic scanning system. It is composed of the optical microscope with a video camera, an image processor and a personal computer. The focus point of the microscope and the X-Y stage are controlled from the computer. The minimum detectable neutron dose is estimated at 4.6 mrem in the uniform field of neutron with equivalent energy spectrum to Am-Be source from the results of automatic measurements. (author)

  4. Analytical examination of a spiral beam scanning method for uniform irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Mitsuhiro; Okumura, Susumu; Arakawa, Kazuo [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment

    1997-03-01

    A new circular beam scanning method for uniform irradiation of high-energy, intense ion beams over a large area has been developed. A sweeping speed and a trajectory density in a radial direction are kept constant to obtain uniform fluence distribution. A radial position of a beam spot on a target and an angular frequency of the circular motion are expressed by an irrational function of time. The beam is swept continuously, and a beam trajectory becomes spiral. More than 90 % uniformity of the fluence distribution can been achieved over a large area. (author)

  5. Cancer cell imaging by stable wet near-field scanning optical microscope with resonance tracking method

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kyoung-Duck [Sungkyunkwan University, Suwon (Korea, Republic of); Inha University, Incheon (Korea, Republic of); Park, Doo-Jae; Jeong, Mun-Seok [Sungkyunkwan University, Suwon (Korea, Republic of); Choi, Geun-Chang [Seoul National University, Seoul (Korea, Republic of); Lee, Seung-Gol [Inha University, Incheon (Korea, Republic of); Byeon, Clare-Chisu [Kyungpook National University, Daegu (Korea, Republic of); Choi, Soo-Bong [Incheon National University, Incheon (Korea, Republic of)

    2014-05-15

    We report on a successful topographical and optical imaging of various cancer cells in liquid and in air by using a stable wet near-field scanning optical microscope that utilizes a resonance tracking method. We observed a clear dehydration which gives rise to a decrease in the cell volume down to 51%. In addition, a micro-ball lens effect due to the round-shaped young cancer cells was observed from near-field imaging, where the refractive index of young cancer cells was deduced.

  6. A method to select aperture margin in collimated spot scanning proton therapy

    International Nuclear Information System (INIS)

    Wang, Dongxu; Smith, Blake R; Gelover, Edgar; Flynn, Ryan T; Hyer, Daniel E

    2015-01-01

    The use of collimator or aperture may sharpen the lateral dose gradient for spot scanning proton therapy. However, to date, there has not been a standard method to determine the aperture margin for a single field in collimated spot scanning proton therapy. This study describes a theoretical framework to select the optimal aperture margin for a single field, and also presents the spot spacing limit required such that the optimal aperture margin exists. Since, for a proton pencil beam partially intercepted by collimator, the maximum point dose (spot center) shifts away from the original pencil beam central axis, we propose that the optimal margin should be equal to the maximum pencil beam center shift under the condition that spot spacing is small with respect to the maximum pencil beam center shift, which can be numerically determined based on beam modeling data. A test case is presented which demonstrates agreement with the prediction made based on the proposed methods. When apertures are applied in a commercial treatment planning system this method may be implemented. (note)

  7. Enhanced oil recovery methods studied by gamma tracer scanning at simulated reservoir conditions

    International Nuclear Information System (INIS)

    Eriksen, D.O.; Haugen, O.B.; Bjornstad, T.

    2009-01-01

    During recovery (production) of hydrocarbons pressure is maintained by injecting prepared sea water and recycled gas (lean gas) into dedicated injection wells. In one well at the Snorre field in the North Sea the injected gas was recycled too fast to enable support of pressure and squeezing of oil. To plug this high-permeable area the operator wanted to inject foam as a test of its possibilities to decrease gas permeability. As part of the project laboratory tests were included. In these tests we could for the first time map the foam inside the sandstone sample at simulated reservoir conditions. The tracers used were 22 Na + for the γ-scanning of the aqueous brine, tritiated water for permeability measurements, and 35 S-labeled organic sulfonic acid of the same compound as the surfactant. This method resulted in a 'negative' mapping of the foam, i.e. measurements of the absence or exclusion of the aqueous phase by the foam. This method was new and showed that radiotracer-based γ-scanning could give much more accurate measurements of the position of the foam than the standard method using measurements of pressure drops over parts of the core. (author)

  8. A Differential Scanning Calorimetry Method for Construction of Continuous Cooling Transformation Diagram of Blast Furnace Slag

    Science.gov (United States)

    Gan, Lei; Zhang, Chunxia; Shangguan, Fangqin; Li, Xiuping

    2012-06-01

    The continuous cooling crystallization of a blast furnace slag was studied by the application of the differential scanning calorimetry (DSC) method. A kinetic model describing the correlation between the evolution of the degree of crystallization with time was obtained. Bulk cooling experiments of the molten slag coupled with numerical simulation of heat transfer were conducted to validate the results of the DSC methods. The degrees of crystallization of the samples from the bulk cooling experiments were estimated by means of the X-ray diffraction (XRD) and the DSC method. It was found that the results from the DSC cooling and bulk cooling experiments are in good agreement. The continuous cooling transformation (CCT) diagram of the blast furnace slag was constructed according to crystallization kinetic model and experimental data. The obtained CCT diagram characterizes with two crystallization noses at different temperature ranges.

  9. A License Plate Locating Method Based on Tophat-bothat Changing and Line Scanning

    International Nuclear Information System (INIS)

    Hou, P G; Zhao, J; Liu, M

    2006-01-01

    The automatic license plate recognition is an important technique to obtain traffic information, it mixes computer vision, image processing techniques and pattern recognition techniques, it is an important technique in intelligent traffic system. In a vehicle license plate recognition system, plate region detection is the key step before the final recognition. This article introduces the whole process of plate region detection. Top - hat and bot - hat transformation are used for enhancing the image contrast in this paper, and wavelet threshold method is used as image filter, and a improved line scanning is used for plate region detection at last. This method has strong practicability. The experimental results demonstrate that the method introduced in this paper is effective

  10. Weld quality inspection using laser-EMAT ultrasonic system and C-scan method

    Science.gov (United States)

    Yang, Lei; Ume, I. Charles

    2014-02-01

    Laser/EMAT ultrasonic technique has attracted more and more interests in weld quality inspection because of its non-destructive and non-contact characteristics. When ultrasonic techniques are used to detect welds joining relative thin plates, the dominant ultrasonic waves present in the plates are Lamb waves, which propagate all through the thickness. Traditional Time of Flight(ToF) method loses its power. The broadband nature of laser excited ultrasound plus dispersive and multi-modal characteristic of Lamb waves make the EMAT acquired signals very complicated in this situation. Challenge rises in interpreting the received signals and establishing relationship between signal feature and weld quality. In this paper, the laser/EMAT ultrasonic technique was applied in a C-scan manner to record full wave propagation field over an area close to the weld. Then the effect of weld defect on the propagation field of Lamb waves was studied visually by watching an movie resulted from the recorded signals. This method was proved to be effective to detect the presence of hidden defect in the weld. Discrete wavelet transform(DWT) was applied to characterize the acquired ultrasonic signals and ideal band-pass filter was used to isolate wave components most sensitive to the weld defect. Different interactions with the weld defect were observed for different wave components. Thus this C-Scan method, combined with DWT and ideal band-pass filter, proved to be an effective methodology to experimentally study interactions of various laser excited Lamb Wave components with weld defect. In this work, the method was demonstrated by inspecting a hidden local incomplete penetration in weld. In fact, this method can be applied to study Lamb Wave interactions with any type of structural inconsistency. This work also proposed a ideal filtered based method to effectively reduce the total experimental time.

  11. Novel edge treatment method for improving the transmission reconstruction quality in Tomographic Gamma Scanning.

    Science.gov (United States)

    Han, Miaomiao; Guo, Zhirong; Liu, Haifeng; Li, Qinghua

    2018-05-01

    Tomographic Gamma Scanning (TGS) is a method used for the nondestructive assay of radioactive wastes. In TGS, the actual irregular edge voxels are regarded as regular cubic voxels in the traditional treatment method. In this study, in order to improve the performance of TGS, a novel edge treatment method is proposed that considers the actual shapes of these voxels. The two different edge voxel treatment methods were compared by computing the pixel-level relative errors and normalized mean square errors (NMSEs) between the reconstructed transmission images and the ideal images. Both methods were coupled with two different interative algorithms comprising Algebraic Reconstruction Technique (ART) with a non-negativity constraint and Maximum Likelihood Expectation Maximization (MLEM). The results demonstrated that the traditional method for edge voxel treatment can introduce significant error and that the real irregular edge voxel treatment method can improve the performance of TGS by obtaining better transmission reconstruction images. With the real irregular edge voxel treatment method, MLEM algorithm and ART algorithm can be comparable when assaying homogenous matrices, but MLEM algorithm is superior to ART algorithm when assaying heterogeneous matrices. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Differential scanning calorimetry method for purity determination: A case study on polycyclic aromatic hydrocarbons and chloramphenicol

    International Nuclear Information System (INIS)

    Kestens, V.; Zeleny, R.; Auclair, G.; Held, A.; Roebben, G.; Linsinger, T.P.J.

    2011-01-01

    Highlights: → Purity assessment of polycyclic aromatic hydrocarbons and chloramphenicol by DSC. → DSC results compared with traditional purity methods. → Different methods give different results, multiple method approach recommended. → DSC sensitive to impurities that have similar structures as main component. - Abstract: In this study the validity and suitability of differential scanning calorimetry (DSC) to determine the purity of selected polycyclic aromatic hydrocarbons and chloramphenicol has been investigated. The study materials were two candidate certified reference materials (CRMs), 6-methylchrysene and benzo[a]pyrene, and two different batches of commercially available highly pure chloramphenicol. The DSC results were compared with those obtained by other methods, namely gas and liquid chromatography with mass spectrometric detection, liquid chromatography with diode array detection, and quantitative nuclear magnetic resonance. The purity results obtained by these different analytical methods confirm the well-known challenges of comparing results of different method-defined measurands. In comparison with other methods, DSC has a much narrower working range. This limits the applicability of DSC as purity determination method, for instance during the assignment of the purity value of a CRM. Nevertheless, this study showed that DSC can be a powerful technique to detect impurities that are structurally very similar to the main purity component. From this point of view, and because of its good repeatability, DSC can be considered as a valuable technique to investigate the homogeneity and stability of candidate purity CRMs.

  13. Accuracy of multi-trait genomic selection using different methods

    NARCIS (Netherlands)

    Calus, M.P.L.; Veerkamp, R.F.

    2011-01-01

    Background Genomic selection has become a very important tool in animal genetics and is rapidly emerging in plant genetics. It holds the promise to be particularly beneficial to select for traits that are difficult or expensive to measure, such as traits that are measured in one environment and

  14. Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC.

    Science.gov (United States)

    Kim, Eui-Soo; Sonstegard, Tad S; da Silva, Marcos V G B; Gasbarre, Louis C; Van Tassell, Curtis P

    2015-01-01

    Genetic markers associated with parasite indicator traits are ideal targets for study of marker assisted selection aimed at controlling infections that reduce herd use of anthelminthics. For this study, we collected gastrointestinal (GI) nematode fecal egg count (FEC) data from post-weaning animals of an Angus resource population challenged to a 26 week natural exposure on pasture. In all, data from 487 animals was collected over a 16 year period between 1992 and 2007, most of which were selected for a specific DRB1 allele to reduce the influence of potential allelic variant effects of the MHC locus. A genome-wide association study (GWAS) based on BovineSNP50 genotypes revealed six genomic regions located on bovine Chromosomes 3, 5, 8, 15 and 27; which were significantly associated (-log10 p=4.3) with Box-Cox transformed mean FEC (BC-MFEC). DAVID analysis of the genes within the significant genomic regions suggested a correlation between our results and annotation for genes involved in inflammatory response to infection. Furthermore, ROH and selection signature analyses provided strong evidence that the genomic regions associated BC-MFEC have not been affected by local autozygosity or recent experimental selection. These findings provide useful information for parasite resistance prediction for young grazing cattle and suggest new candidate gene targets for development of disease-modifying therapies or future studies of host response to GI parasite infection.

  15. Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC.

    Directory of Open Access Journals (Sweden)

    Eui-Soo Kim

    Full Text Available Genetic markers associated with parasite indicator traits are ideal targets for study of marker assisted selection aimed at controlling infections that reduce herd use of anthelminthics. For this study, we collected gastrointestinal (GI nematode fecal egg count (FEC data from post-weaning animals of an Angus resource population challenged to a 26 week natural exposure on pasture. In all, data from 487 animals was collected over a 16 year period between 1992 and 2007, most of which were selected for a specific DRB1 allele to reduce the influence of potential allelic variant effects of the MHC locus. A genome-wide association study (GWAS based on BovineSNP50 genotypes revealed six genomic regions located on bovine Chromosomes 3, 5, 8, 15 and 27; which were significantly associated (-log10 p=4.3 with Box-Cox transformed mean FEC (BC-MFEC. DAVID analysis of the genes within the significant genomic regions suggested a correlation between our results and annotation for genes involved in inflammatory response to infection. Furthermore, ROH and selection signature analyses provided strong evidence that the genomic regions associated BC-MFEC have not been affected by local autozygosity or recent experimental selection. These findings provide useful information for parasite resistance prediction for young grazing cattle and suggest new candidate gene targets for development of disease-modifying therapies or future studies of host response to GI parasite infection.

  16. Reducing charging effects in scanning electron microscope images by Rayleigh contrast stretching method (RCS).

    Science.gov (United States)

    Wan Ismail, W Z; Sim, K S; Tso, C P; Ting, H Y

    2011-01-01

    To reduce undesirable charging effects in scanning electron microscope images, Rayleigh contrast stretching is developed and employed. First, re-scaling is performed on the input image histograms with Rayleigh algorithm. Then, contrast stretching or contrast adjustment is implemented to improve the images while reducing the contrast charging artifacts. This technique has been compared to some existing histogram equalization (HE) extension techniques: recursive sub-image HE, contrast stretching dynamic HE, multipeak HE and recursive mean separate HE. Other post processing methods, such as wavelet approach, spatial filtering, and exponential contrast stretching, are compared as well. Overall, the proposed method produces better image compensation in reducing charging artifacts. Copyright © 2011 Wiley Periodicals, Inc.

  17. Evaluation of methods for selecting the midventilation bin in 4DCT scans of lung cancer patients

    DEFF Research Database (Denmark)

    Nygaard, Ditte Eklund; Persson, Gitte Fredberg; Brink, Carsten

    2013-01-01

    based on: 1) visual evaluation of tumour displacement; 2) rigid registration of tumour position; 3) diaphragm displacement in the CC direction; and 4) carina displacement in the CC direction. Determination of the MidV bin based on the displacement of the manually delineated gross tumour volume (GTV.......4-5.4) mm, 1.9 (0.5-6.9) mm, 2.0 (0.5-12.3) mm and 1.1 (0.4-5.4) mm for the visual, rigid registration, diaphragm, carina, and reference method. Median (range) absolute difference between geometric MidV error for the evaluated methods and the reference method was 0.0 (0.0-1.2) mm, 0.0 (0.0-1.7) mm, 0.7 (0.......0-3.9) mm and 1.0 (0.0-6.9) mm for the visual, rigid registration, diaphragm and carina method. Conclusion. The visual and semi-automatic rigid registration methods were equivalent in accuracy for selecting the MidV bin of a 4DCT scan. The methods based on diaphragm and carina displacement cannot...

  18. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

    DEFF Research Database (Denmark)

    Bohlin, J; Skjerve, E; Ussery, David

    2008-01-01

    with here are mainly used to examine similarities between archaeal and bacterial DNA from different genomes. These methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, which can be determined by genomic nucleotide content, smaller oligonucleotide frequencies......, or be based on specific statistical distributions. Advantages with these statistical methods include measurements of phylogenetic relationship with relatively small pieces of DNA sampled from almost anywhere within genomes, detection of foreign/conserved DNA, and homology searches. Our aim was to explore...... the reliability and best suited applications for some popular methods, which include relative oligonucleotide frequencies (ROF), di- to hexanucleotide zero'th order Markov methods (ZOM) and 2.order Markov chain Method (MCM). Tests were performed on distant homology searches with large DNA sequences, detection...

  19. Laser Scanning in Engineering Surveying: Methods of Measurement and Modeling of Structures

    Directory of Open Access Journals (Sweden)

    Lenda Grzegorz

    2016-06-01

    Full Text Available The study is devoted to the uses of laser scanning in the field of engineering surveying. It is currently one of the main trends of research which is developed at the Department of Engineering Surveying and Civil Engineering at the Faculty of Mining Surveying and Environmental Engineering of AGH University of Science and Technology in Krakow. They mainly relate to the issues associated with tower and shell structures, infrastructure of rail routes, or development of digital elevation models for a wide range of applications. These issues often require the use of a variety of scanning techniques (stationary, mobile, but the differences also regard the planning of measurement stations and methods of merging point clouds. Significant differences appear during the analysis of point clouds, especially when modeling objects. Analysis of the selected parameters is already possible basing on ad hoc measurements carried out on a point cloud. However, only the construction of three-dimensional models provides complete information about the shape of structures, allows to perform the analysis in any place and reduces the amount of the stored data. Some structures can be modeled in the form of simple axes, sections, or solids, for others it becomes necessary to create sophisticated models of surfaces, depicting local deformations. The examples selected for the study allow to assess the scope of measurement and office work for a variety of uses related to the issue set forth in the title of this study. Additionally, the latest, forward-looking technology was presented - laser scanning performed from Unmanned Aerial Vehicles (drones. Currently, it is basically in the prototype phase, but it might be expected to make a significant progress in numerous applications in the field of engineering surveying.

  20. Genomes correction and assembling: present methods and tools

    Science.gov (United States)

    Wojcieszek, Michał; Pawełkowicz, Magdalena; Nowak, Robert; Przybecki, Zbigniew

    2014-11-01

    Recent rapid development of next generation sequencing (NGS) technologies provided significant impact into genomics field of study enabling implementation of many de novo sequencing projects of new species which was previously confined by technological costs. Along with advancement of NGS there was need for adjustment in assembly programs. New algorithms must cope with massive amounts of data computation in reasonable time limits and processing power and hardware is also an important factor. In this paper, we address the issue of assembly pipeline for de novo genome assembly provided by programs presently available for scientist both as commercial and as open - source software. The implementation of four different approaches - Greedy, Overlap - Layout - Consensus (OLC), De Bruijn and Integrated resulting in variation of performance is the main focus of our discussion with additional insight into issue of short and long reads correction.

  1. Comparison of methods for genomic localization of gene trap sequences

    Directory of Open Access Journals (Sweden)

    Ferrin Thomas E

    2006-09-01

    Full Text Available Abstract Background Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event poses a challenging annotation problem because gene trap sequence tags, which represent sequence near the vector insertion site of a trapped gene, are typically short and often contain unresolved residues. To understand better the localization of these sequences on the mouse genome, we compared stand-alone versions of the alignment programs BLAT, SSAHA, and MegaBLAST. A set of 3,369 sequence tags was aligned to build 34 of the mouse genome using default parameters for each algorithm. Known genome coordinates for the cognate set of full-length genes (1,659 sequences were used to evaluate localization results. Results In general, all three programs performed well in terms of localizing sequences to a general region of the genome, with only relatively subtle errors identified for a small proportion of the sequence tags. However, large differences in performance were noted with regard to correctly identifying exon boundaries. BLAT correctly identified the vast majority of exon boundaries, while SSAHA and MegaBLAST missed the majority of exon boundaries. SSAHA consistently reported the fewest false positives and is the fastest algorithm. MegaBLAST was comparable to BLAT in speed, but was the most susceptible to localizing sequence tags incorrectly to pseudogenes. Conclusion The differences in performance for sequence tags and full-length reference sequences were surprisingly small. Characteristic variations in localization results for each program were noted that affect the localization of sequence at exon boundaries, in particular.

  2. Genome-wide prediction of cis-regulatory regions using supervised deep learning methods.

    Science.gov (United States)

    Li, Yifeng; Shi, Wenqiang; Wasserman, Wyeth W

    2018-05-31

    In the human genome, 98% of DNA sequences are non-protein-coding regions that were previously disregarded as junk DNA. In fact, non-coding regions host a variety of cis-regulatory regions which precisely control the expression of genes. Thus, Identifying active cis-regulatory regions in the human genome is critical for understanding gene regulation and assessing the impact of genetic variation on phenotype. The developments of high-throughput sequencing and machine learning technologies make it possible to predict cis-regulatory regions genome wide. Based on rich data resources such as the Encyclopedia of DNA Elements (ENCODE) and the Functional Annotation of the Mammalian Genome (FANTOM) projects, we introduce DECRES based on supervised deep learning approaches for the identification of enhancer and promoter regions in the human genome. Due to their ability to discover patterns in large and complex data, the introduction of deep learning methods enables a significant advance in our knowledge of the genomic locations of cis-regulatory regions. Using models for well-characterized cell lines, we identify key experimental features that contribute to the predictive performance. Applying DECRES, we delineate locations of 300,000 candidate enhancers genome wide (6.8% of the genome, of which 40,000 are supported by bidirectional transcription data), and 26,000 candidate promoters (0.6% of the genome). The predicted annotations of cis-regulatory regions will provide broad utility for genome interpretation from functional genomics to clinical applications. The DECRES model demonstrates potentials of deep learning technologies when combined with high-throughput sequencing data, and inspires the development of other advanced neural network models for further improvement of genome annotations.

  3. Decommissioning and dismantling: Qualification of gamma scanning method for decontrolling measurement of radioactive wastes. Final report

    International Nuclear Information System (INIS)

    Genrich, V.; Sattler, P.

    1998-01-01

    At the time being measurements for the release of buildings and parts of buildings are mainly performed with contamination monitors, free release equipment, wipe test a. s. o. The technical application of in-situ gamma-scanning systems for release measurement should be demonstrated with this research project. This method presents considerable advantages in comparison with standard procedures, as f. ex. reduction of radioactive waste or area covering investigation of the inspected building. A system with a NaI(Tl) and a HPGe-detector was applied. With the high-resolving system it can be shown that also low limit values can be kept with short measurement time. With the NaI(Tl)-detector system it was demonstrated that with limit values lower than 1 Bq/m 3 there may be problems observing the limit values. The investigation showed that especially the high-resolving system for the release measurement of buildings (f. ex. floors, walls, complete rooms) is well-suited. The in-situ gamma-scanning shows big advantages in its economy as f. ex. no sampling and only short measurement times are required. The sharp limitation of the existing contamination and the reduction of radioactive waste involved herewith are further advantages which justify the application of this measurement technique. (orig.)

  4. Feasibility of Machine Learning Methods for Separating Wood and Leaf Points from Terrestrial Laser Scanning Data

    Science.gov (United States)

    Wang, D.; Hollaus, M.; Pfeifer, N.

    2017-09-01

    Classification of wood and leaf components of trees is an essential prerequisite for deriving vital tree attributes, such as wood mass, leaf area index (LAI) and woody-to-total area. Laser scanning emerges to be a promising solution for such a request. Intensity based approaches are widely proposed, as different components of a tree can feature discriminatory optical properties at the operating wavelengths of a sensor system. For geometry based methods, machine learning algorithms are often used to separate wood and leaf points, by providing proper training samples. However, it remains unclear how the chosen machine learning classifier and features used would influence classification results. To this purpose, we compare four popular machine learning classifiers, namely Support Vector Machine (SVM), Na¨ıve Bayes (NB), Random Forest (RF), and Gaussian Mixture Model (GMM), for separating wood and leaf points from terrestrial laser scanning (TLS) data. Two trees, an Erytrophleum fordii and a Betula pendula (silver birch) are used to test the impacts from classifier, feature set, and training samples. Our results showed that RF is the best model in terms of accuracy, and local density related features are important. Experimental results confirmed the feasibility of machine learning algorithms for the reliable classification of wood and leaf points. It is also noted that our studies are based on isolated trees. Further tests should be performed on more tree species and data from more complex environments.

  5. FEASIBILITY OF MACHINE LEARNING METHODS FOR SEPARATING WOOD AND LEAF POINTS FROM TERRESTRIAL LASER SCANNING DATA

    Directory of Open Access Journals (Sweden)

    D. Wang

    2017-09-01

    Full Text Available Classification of wood and leaf components of trees is an essential prerequisite for deriving vital tree attributes, such as wood mass, leaf area index (LAI and woody-to-total area. Laser scanning emerges to be a promising solution for such a request. Intensity based approaches are widely proposed, as different components of a tree can feature discriminatory optical properties at the operating wavelengths of a sensor system. For geometry based methods, machine learning algorithms are often used to separate wood and leaf points, by providing proper training samples. However, it remains unclear how the chosen machine learning classifier and features used would influence classification results. To this purpose, we compare four popular machine learning classifiers, namely Support Vector Machine (SVM, Na¨ıve Bayes (NB, Random Forest (RF, and Gaussian Mixture Model (GMM, for separating wood and leaf points from terrestrial laser scanning (TLS data. Two trees, an Erytrophleum fordii and a Betula pendula (silver birch are used to test the impacts from classifier, feature set, and training samples. Our results showed that RF is the best model in terms of accuracy, and local density related features are important. Experimental results confirmed the feasibility of machine learning algorithms for the reliable classification of wood and leaf points. It is also noted that our studies are based on isolated trees. Further tests should be performed on more tree species and data from more complex environments.

  6. A storage and display method for radioisotope imaging using scan conversion memory

    International Nuclear Information System (INIS)

    Takizawa, Masaomi; Kobayashi, Toshio; Nakanishi, Fumiko; Suzuki, Shigeo; Miyabayashi, Hiroyasu

    1975-01-01

    The scan conversion memory (SCM) has been applied to a method for the storage and display of radioisotope images. Scan data were fed into SCM as pulse signals with X and Y axis from the scinti-scanner or the scinti-camera. The electric charge on the SCM target is directly proportional to the pulse density. A TV display was executed immediately after the recording of a radioisotope image. If necessary, a seven additive color display to the image density could be obtained by a simple color slicer, and the image could be hard-copied by a video hard-copy printer. Characteristics of the SCM were experimentally clarified as follows: the practical resolution was 700 line/TV; ten levels gray scale were discriminated on the video monitor, the uniformity, measured by an oscilloscope was less than 20%, and dead time of the pulse interval at full scale signal was 5 μ sec. In their representation, the SCM scintigrams were observed as closely resembling conventional film scintigrams. Superimposed imaging of an X-ray picture and a radioisotope image can be realized by using the SCM, for an increase in anatomical localization on reading images. The SCM scintigram can be applied rapidly and can be the viewer of radioisotope imaging. (auth.)

  7. Method for calibration-free scanned-wavelength modulation spectroscopy for gas sensing

    Science.gov (United States)

    Hanson, Ronald K.; Jeffries, Jay B.; Sun, Kai; Sur, Ritobrata; Chao, Xing

    2018-04-10

    A method of calibration-free scanned-wavelength modulation spectroscopy (WMS) absorption sensing is provided by obtaining absorption lineshape measurements of a gas sample on a sensor using 1f-normalized WMS-2f where an injection current to an injection current-tunable diode laser (TDL) is modulated at a frequency f, where a wavelength modulation and an intensity modulation of the TDL are simultaneously generated, extracting using a numerical lock-in program and a low-pass filter appropriate band-width WMS-nf (n=1, 2, . . . ) signals, where the WMS-nf signals are harmonics of the f, determining a physical property of the gas sample according to ratios of the WMS-nf signals, determining the zero-absorption background using scanned-wavelength WMS, and determining non-absorption losses using at least two of the harmonics, where a need for a non-absorption baseline measurement is removed from measurements in environments where collision broadening has blended transition linewidths, where calibration free WMS measurements without knowledge of the transition linewidth is enabled.

  8. A Review on Migration Methods in B-Scan Ground Penetrating Radar Imaging

    Directory of Open Access Journals (Sweden)

    Caner Özdemir

    2014-01-01

    Full Text Available Even though ground penetrating radar has been well studied and applied by many researchers for the last couple of decades, the focusing problem in the measured GPR images is still a challenging task. Although there are many methods offered by different scientists, there is not any complete migration/focusing method that works perfectly for all scenarios. This paper reviews the popular migration methods of the B-scan GPR imaging that have been widely accepted and applied by various researchers. The brief formulation and the algorithm steps for the hyperbolic summation, the Kirchhoff migration, the back-projection focusing, the phase-shift migration, and the ω-k migration are presented. The main aim of the paper is to evaluate and compare the migration algorithms over different focusing methods such that the reader can decide which algorithm to use for a particular application of GPR. Both the simulated and the measured examples that are used for the performance comparison of the presented algorithms are provided. Other emerging migration methods are also pointed out.

  9. Genome-wide linkage scan for primary open angle glaucoma: influences of ancestry and age at diagnosis.

    Directory of Open Access Journals (Sweden)

    Kristy R Crooks

    Full Text Available Primary open-angle glaucoma (POAG is the most common form of glaucoma and one of the leading causes of vision loss worldwide. The genetic etiology of POAG is complex and poorly understood. The purpose of this work is to identify genomic regions of interest linked to POAG. This study is the largest genetic linkage study of POAG performed to date: genomic DNA samples from 786 subjects (538 Caucasian ancestry, 248 African ancestry were genotyped using either the Illumina GoldenGate Linkage 4 Panel or the Illumina Infinium Human Linkage-12 Panel. A total of 5233 SNPs was analyzed in 134 multiplex POAG families (89 Caucasian ancestry, 45 African ancestry. Parametric and non-parametric linkage analyses were performed on the overall dataset and within race-specific datasets (Caucasian ancestry and African ancestry. Ordered subset analysis was used to stratify the data on the basis of age of glaucoma diagnosis. Novel linkage regions were identified on chromosomes 1 and 20, and two previously described loci-GLC1D on chromosome 8 and GLC1I on chromosome 15--were replicated. These data will prove valuable in the context of interpreting results from genome-wide association studies for POAG.

  10. A simple method for the parallel deep sequencing of full influenza A genomes

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise; Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen

    2011-01-01

    Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool....... This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus...

  11. A report on ultrafast scanning methods of cerebral computed angiotomography, 2

    International Nuclear Information System (INIS)

    Fukui, Keiji; Sadamoto, Kazuhiko; Ohue, Shiro; Nakamura, Hisashi; Yamamoto, Yuji; Asari, Syoji; Kimura, Hideki; Sakaki, Saburo.

    1986-01-01

    Forty milliliters of meglumine iothalamate 282 mg iodine/ml (60 % Conray) were injected into the basilic vein at the rate of 2 ml/second through an 18 G JELCO needle. Just before the completion of the injection, dynamic scanning with table increments was performed. Three to eight scans were taken 16 - 47 seconds after the single-bolus injection of the contrast medium, while the CT number at the circle of Willis was kept high. The three following different scanning techniques were newly developed and investigated as to their clinical application: 1) Overlapping scanning: 10 mm-slice-thickness scans with 5-mm table increments can be useful for the detection of lesions in a relatively limited range, such as unruptured cerebral aneurysms. For this purpose, the overlapping axial CT scans are centered at 25, 30, and 35 mm above the canthomeatal line (CML), and the overlapping modified coronal CT scans are centered at 35, 40, and 45 mm in front of the external auditory meatus (EAM) at an approximately 60 deg angle to the CML from the occipital side. 2) Sequential scanning: 10 mm-slice-thickness scans with 10-mm table increments are applied to the diagnosis of lesions over a wide range, such as brain tumors, AVMs, and isodense chronic subdural hematomas, because this procedure can scan over a wider range with a single injection than can overlapping scanning. Thin-section sequential scanning, such as 2 mm-slice-thickness scans with 2-mm table increments, is useful for minute examinations in order to ascertain the relationship between the cerebral vessels and the surrounding structures. 3) Two-step contrast-enhanced scanning: double overlapping or sequential scannings with a contrast injection at a certain interval can be used to examine the relationship between the tumor and the abnormal vascularity in surrounding areas which have different maximum timings of enhancement. (J.P.N.)

  12. An inverse method for determining the interaction force between the probe and sample using scanning near-field optical microscopy

    International Nuclear Information System (INIS)

    Chang, Win-Jin; Fang, Te-Hua

    2006-01-01

    This study proposes a means for calculating the interaction force during the scanning process using a scanning near-field optical microscope (SNOM) probe. The determination of the interaction force in the scanning system is regarded as an inverse vibration problem. The conjugate gradient method is applied to treat the inverse problem using available displacement measurements. The results show that the conjugate gradient method is less sensitive to measurement errors and prior information on the functional form of quality was not required. Furthermore, the initial guesses for the interaction force can be arbitrarily chosen for the iteration process

  13. Method for updating pipelined, single port Z-buffer by segments on a scan line

    International Nuclear Information System (INIS)

    Hannah, M.R.

    1990-01-01

    This patent describes, in a raster scan, computer controlled video display system for presenting an image to an observer. Having Z-buffer for storing Z values and a frame buffer for storing pixel values, a method for updating the Z-buffer with new Z values to replace old Z values. It comprises: calculating a new pixel value and a new Z value for each pixel location in pixel locations, performing a Z comparison for each new Z value by comparing the old Z value with the new Z value for each pixel location, the Z comparison being performed sequentially in one direction through the plurality of pixel locations, and updating the Z-buffer only after the Z comparison produces a combination of a fail condition for a current pixel location subsequent to producing a pass condition for a pixel location immediately preceding the current pixel location

  14. Investigation of nonlinear optical properties of various organic materials by the Z-scan method

    Science.gov (United States)

    Ganeev, R. A.; Boltaev, G. S.; Tugushev, R. I.; Usmanov, T.

    2012-06-01

    We have studied the nonlinear optical properties of various organic materials (vegetable oil, juice, wine, cognac, Coca-Cola and Fanta drinks, Nescafé coffee, tea, gasoline, clock oil, glycerol, and polyphenyl ether) that are used in everyday life. Their nonlinearities have been studied by the Z-scan method in the near-IR and visible spectral ranges. We have shown that the majority of samples possess a nonlinear absorption; however, some of the studied materials show a strong saturated absorption and nonlinear refraction. Red wine and glycerol proved to be the most interesting materials. For these samples, we have observed a change in the sign of the nonlinear absorption with increasing laser intensity, which was attributed to the competition between two-photon absorption and saturated absorption.

  15. SINGLE TREE DETECTION FROM AIRBORNE LASER SCANNING DATA USING A MARKED POINT PROCESS BASED METHOD

    Directory of Open Access Journals (Sweden)

    J. Zhang

    2013-05-01

    Full Text Available Tree detection and reconstruction is of great interest in large-scale city modelling. In this paper, we present a marked point process model to detect single trees from airborne laser scanning (ALS data. We consider single trees in ALS recovered canopy height model (CHM as a realization of point process of circles. Unlike traditional marked point process, we sample the model in a constraint configuration space by making use of image process techniques. A Gibbs energy is defined on the model, containing a data term which judge the fitness of the model with respect to the data, and prior term which incorporate the prior knowledge of object layouts. We search the optimal configuration through a steepest gradient descent algorithm. The presented hybrid framework was test on three forest plots and experiments show the effectiveness of the proposed method.

  16. Graph Structure-Based Simultaneous Localization and Mapping Using a Hybrid Method of 2D Laser Scan and Monocular Camera Image in Environments with Laser Scan Ambiguity

    Directory of Open Access Journals (Sweden)

    Taekjun Oh

    2015-07-01

    Full Text Available Localization is an essential issue for robot navigation, allowing the robot to perform tasks autonomously. However, in environments with laser scan ambiguity, such as long corridors, the conventional SLAM (simultaneous localization and mapping algorithms exploiting a laser scanner may not estimate the robot pose robustly. To resolve this problem, we propose a novel localization approach based on a hybrid method incorporating a 2D laser scanner and a monocular camera in the framework of a graph structure-based SLAM. 3D coordinates of image feature points are acquired through the hybrid method, with the assumption that the wall is normal to the ground and vertically flat. However, this assumption can be relieved, because the subsequent feature matching process rejects the outliers on an inclined or non-flat wall. Through graph optimization with constraints generated by the hybrid method, the final robot pose is estimated. To verify the effectiveness of the proposed method, real experiments were conducted in an indoor environment with a long corridor. The experimental results were compared with those of the conventional GMappingapproach. The results demonstrate that it is possible to localize the robot in environments with laser scan ambiguity in real time, and the performance of the proposed method is superior to that of the conventional approach.

  17. A novel bioinformatics method for efficient knowledge discovery by BLSOM from big genomic sequence data.

    Science.gov (United States)

    Bai, Yu; Iwasaki, Yuki; Kanaya, Shigehiko; Zhao, Yue; Ikemura, Toshimichi

    2014-01-01

    With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a "genome signature," and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).

  18. A scanning electron microscope method for automated, quantitative analysis of mineral matter in coal

    Energy Technology Data Exchange (ETDEWEB)

    Creelman, R.A.; Ward, C.R. [R.A. Creelman and Associates, Epping, NSW (Australia)

    1996-07-01

    Quantitative mineralogical analysis has been carried out in a series of nine coal samples from Australia, South Africa and China using a newly-developed automated image analysis system coupled to a scanning electron microscopy. The image analysis system (QEM{asterisk}SEM) gathers X-ray spectra and backscattered electron data from a number of points on a conventional grain-mount polished section under the SEM, and interprets the data from each point in mineralogical terms. The cumulative data in each case was integrated to provide a volumetric modal analysis of the species present in the coal samples, expressed as percentages of the respective coals` mineral matter. Comparison was made of the QEM{asterisk}SEM results to data obtained from the same samples using other methods of quantitative mineralogical analysis, namely X-ray diffraction of the low-temperature oxygen-plasma ash and normative calculation from the (high-temperature) ash analysis and carbonate CO{sub 2} data. Good agreement was obtained from all three methods for quartz in the coals, and also for most of the iron-bearing minerals. The correlation between results from the different methods was less strong, however, for individual clay minerals, or for minerals such as calcite, dolomite and phosphate species that made up only relatively small proportions of the mineral matter. The image analysis approach, using the electron microscope for mineralogical studies, has significant potential as a supplement to optical microscopy in quantitative coal characterisation. 36 refs., 3 figs., 4 tabs.

  19. Standard test method for nondestructive assay of radioactive material by tomographic gamma scanning

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2010-01-01

    1.1 This test method describes the nondestructive assay (NDA) of gamma ray emitting radionuclides inside containers using tomographic gamma scanning (TGS). High resolution gamma ray spectroscopy is used to detect and quantify the radionuclides of interest. The attenuation of an external gamma ray transmission source is used to correct the measurement of the emission gamma rays from radionuclides to arrive at a quantitative determination of the radionuclides present in the item. 1.2 The TGS technique covered by the test method may be used to assay scrap or waste material in cans or drums in the 1 to 500 litre volume range. Other items may be assayed as well. 1.3 The test method will cover two implementations of the TGS procedure: (1) Isotope Specific Calibration that uses standards of known radionuclide masses (or activities) to determine system response in a mass (or activity) versus corrected count rate calibration, that applies to only those specific radionuclides for which it is calibrated, and (2) Respo...

  20. Accuracy and reliability of a novel method for fusion of digital dental casts and cone beam computed tomography scans

    NARCIS (Netherlands)

    Rangel, F.A.; Maal, T.J.J.; Bronkhorst, E.M.; Breuning, K.H.; Schols, J.G.J.H.; Berge, S.J.; Kuijpers-Jagtman, A.M.

    2013-01-01

    Several methods have been proposed to integrate digital models into Cone Beam Computed Tomography scans. Since all these methods have some drawbacks such as radiation exposure, soft tissue deformation and time-consuming digital handling processes, we propose a new method to integrate digital dental

  1. Development of techniques and methods for evaluation of quality of scanned image in mammography

    International Nuclear Information System (INIS)

    Carmo Santana, P. do; Nogueira, M.S.

    2008-01-01

    Cancer is the second cause of death in the Brazilian female population and breast cancer is the most frequent neoplasm amongst women. Mammography is an essential tool for diagnosis and early detection of this disease. In order to be effective, the mammography must be of good quality. The Brazilian College of Radiology (CBR), the National Agency for Health Surveillance (ANVISA) and international bodies recommend standards of practice for mammography. Due to the risk of ionizing radiation, techniques that minimize dose and optimize image quality are essential to ensure that all women are submitted to mammography procedures of high quality for the detection of breast cancer. In this research were analyzed components of the image treatment via digital and developed methods and techniques of analysis aiming the detection of structures for medical diagnosis, decreasing variations due to subjectivity. It used free software Image J, to make the evaluations of the information contained in the scanned images. We use the scanned images of calibration of a simulated breast to calibrate the program Image J. Thus, it was able to correctly convert the values of the scale of shades of gray in optical density values of presenting the standard deviation for each measure held. Applying the test t-student noticed that the values obtained with the digital system to the level of contrast and spatial resolution are consistent with the results obtained so subjective, since there was no significant difference (p <0.05) for all comparisons evaluated. Since then, this methodology is recommended in routine evaluations of services of mammography. (author)

  2. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

    Science.gov (United States)

    Wang, Harris H; Church, George M

    2011-01-01

    Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm.

    Directory of Open Access Journals (Sweden)

    Daniel M de Brito

    Full Text Available Genomic Islands (GIs are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP--Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me.

  4. An inverse method for crack characterization from ultrasonic B-Scan images

    International Nuclear Information System (INIS)

    Faur, M.; Roy, O.; Benoist, PH.; Morisseau, PH.

    1996-01-01

    Concern has been expressed about the capabilities of performing non destructive evaluation (NDE) of flaws located near to the outer surface in nuclear pressurized water reactor (PWR) vessels. The ultrasonic examination of PWR is accomplished from the inside with ultrasonic focused transducers working in the pulse echo mode. By recording the echoes as a function of time, the Ascan representation may be obtained. Many ultrasonic flaw detectors used for NDE are based on the simple Ascan concept involving measuring a time interval called 'time of flight'. By combining the Ascan concept synchronized transducer scanning, one can produce Bscan images that are two dimensional descriptions of the flaw interaction with the ultrasonic field. In the following, the flaw is assumed to be an axially oriented crack (the most serious flaw to be found in a pressurized component). In the case of the outer surface cracks (OSC's), analyzing and interpreting ultrasonic Ascan images become difficult because of the various reflections of the ultrasonic beam on the crack and on the outer surface (the so-called corner effect). Methods for automatic interpretation of ultrasonic experimental data are currently under investigation. In this paper, we present an inverse method for determining the geometrical characteristics of OSC's from ultrasonic Bscan images. The direct model used for the inversion procedure predicts synthetic Bscan images of ultrasonic examination of blocks containing planar defects interrogated by focused probes. (authors)

  5. Method and apparatus to debug an integrated circuit chip via synchronous clock stop and scan

    Science.gov (United States)

    Bellofatto, Ralph E [Ridgefield, CT; Ellavsky, Matthew R [Rochester, MN; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Gooding, Thomas M [Rochester, MN; Haring, Rudolf A [Cortlandt Manor, NY; Hehenberger, Lance G [Leander, TX; Ohmacht, Martin [Yorktown Heights, NY

    2012-03-20

    An apparatus and method for evaluating a state of an electronic or integrated circuit (IC), each IC including one or more processor elements for controlling operations of IC sub-units, and each the IC supporting multiple frequency clock domains. The method comprises: generating a synchronized set of enable signals in correspondence with one or more IC sub-units for starting operation of one or more IC sub-units according to a determined timing configuration; counting, in response to one signal of the synchronized set of enable signals, a number of main processor IC clock cycles; and, upon attaining a desired clock cycle number, generating a stop signal for each unique frequency clock domain to synchronously stop a functional clock for each respective frequency clock domain; and, upon synchronously stopping all on-chip functional clocks on all frequency clock domains in a deterministic fashion, scanning out data values at a desired IC chip state. The apparatus and methodology enables construction of a cycle-by-cycle view of any part of the state of a running IC chip, using a combination of on-chip circuitry and software.

  6. A systematic study of genome context methods: calibration, normalization and combination

    Directory of Open Access Journals (Sweden)

    Dale Joseph M

    2010-10-01

    Full Text Available Abstract Background Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use. Results We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the four methods. A thorough exploration of the parameter space for each method is performed and results across different target organisms are presented. We propose the use of normalization procedures as those used on microarray data for the genome context scores. We show that substantial gains can be achieved from the use of a simple normalization technique. In particular, the sensitivity of the phylogenetic profile method is improved by around 25% after normalization, resulting, to our knowledge, on the best-performing phylogenetic profile system in the literature. Finally, we show results from combining the various genome context methods into a single score. When using a cross-validation procedure to train the combiners, with both original and normalized scores as input, a decision tree combiner results in gains of up to 20% with respect to the gene neighbor method. Overall, this represents a gain of around 15% over what can be considered the state of the art in this area: the four original genome context methods combined using a

  7. The validity of ultrasonographic scanning as screening method for abdominal aortic aneurysm

    DEFF Research Database (Denmark)

    Lindholt, Jes Sanddal; Vammen, Sten; Juul, Søren

    1999-01-01

    the sensitivity and specificity of screening for abdominal aortic aneurysms (AAAs) with ultrasonographic scanning (US) is unknown. The aim of the study was to validate US as screening test for AAAs.......the sensitivity and specificity of screening for abdominal aortic aneurysms (AAAs) with ultrasonographic scanning (US) is unknown. The aim of the study was to validate US as screening test for AAAs....

  8. Decommissioning and dismantling: Qualification of the gamma scanning method as a certified method for radiological decontrolling measurement. Final report; Stillegung und Rueckbau: Qualifizierung des Gamma-Scanning zur Freimessung. Genehmigungspraxis. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Kirchhoff, J.; Stasch, W.P.

    1998-10-01

    Prior to release from the radiological supervision and control regime of the AtG (German Atomic Energy Act), nuclear facilities have to be scanned using licensed radioactivity measuring methods for providing evidence that the remaining radioactive contamination is below the legally defined limits and excludes hazards to the population, material goods, or the environment. The manually performed {alpha}/{beta} measuring methods applied so far for radiological decontrolling measurement are surface scanning methods measuring the contamination of very thin surface layers of the structures, while radioactivity in deeper layers is not necessarily detected. The gamma scanning method presented in this document is capable of scanning the structures and materials of nuclear facilities from the surface down to much deeper layers in just one measuring run. The automated scanning process at the same time offers the advantage of preventing the uncertainties possibly contributed through human factors. (orig./CB) [Deutsch] Vor der Entlassung von kerntechnischen Anlagen aus dem Geltungsbereich des AtG ist sicherzustellen, dass von der Anlage nach Freigabe aus der atomrechtlichen Ueberwachung keine Gefahren fuer Personen, Sachgueter und die Umwelt ausgehen koennen. Hierzu sind die Anlagen freizumessen, d.h. es ist durch qualifizierte Messverfahren sicherzustellen, dass festgelegte radiologische Grenzwerte unterschritten werden. Die bisherigen auf {alpha}/{beta}-Messung beruhenden Freimessverfahren (Kontaminationsmonitore) erfassen nur die Radioaktivitaet in duennsten Oberflaechenschichten. Radioaktivitaet in darunter liegenden Schichten wird nicht zwangslaeufig erfasst. Zudem erfolgen diese Messungen ausschliesslich manuell. Das Gamma-Scanning-Freimessverfahren erfasst neben der Oberflaechenschicht gleichzeitig auch tiefere Schichten. Der Nachweis der Grenzwertunterschreitung kann somit in nur einem Arbeitsgang erbracht werden. Durch automatisiertes Scannen koennte darueber hinaus

  9. Adapted methods for scanning electron microscopy (SEM in assessment of human sperm morphology

    Directory of Open Access Journals (Sweden)

    Petra Nussdorfer

    2018-02-01

    Full Text Available Infertility is a widespread problem, and in some cases, the routine basic semen analysis is not sufficient to detect the cause of male infertility. The use of the scanning electron microscope (SEM could provide a detailed insight into spermatozoa morphology, but it requires specific sample preparation techniques. The purpose of this study was to select, adjust, and optimize a method for the preparation of spermatozoa samples prior to SEM analysis, and to establish the protocol required for its use in clinical practice. We examined sperm samples of 50 men. The samples were fixed with modified iso-osmolar aldehyde solution followed by osmium post-fixation. In the first method, dehydration of the cells and subsequent critical point drying (CPD were performed on a coverslip. In the second method, the samples were dehydrated in centrifuge tubes; hexamethyldisilazane (HMDS was used as a drying agent instead of CPD, and the samples were air-dried. The third procedure was based on a membrane filter. The samples were dehydrated and dried with HMDS in a Gooch crucible, continuously, without centrifugation or redispersion of the sample. Our results showed that the fixation with modified iso-osmolar aldehyde solution followed by osmium post-fixation, and combined with dehydration and CPD on a coverslip, is the most convenient procedure for SEM sample preparation. In the case of small-size samples or low sperm concentration, dehydration and drying with HMDS on the membrane filter enabled the best reliability, repeatability, and comparability of the results. The presented procedures are suitable for routine use, and they can be applied to confirm as well as to correct a diagnosis.

  10. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries).

    Science.gov (United States)

    Li, M-H; Tiirikka, T; Kantanen, J

    2014-02-01

    In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.

  11. Bayesian methods for jointly estimating genomic breeding values of one continuous and one threshold trait.

    Directory of Open Access Journals (Sweden)

    Chonglong Wang

    Full Text Available Genomic selection has become a useful tool for animal and plant breeding. Currently, genomic evaluation is usually carried out using a single-trait model. However, a multi-trait model has the advantage of using information on the correlated traits, leading to more accurate genomic prediction. To date, joint genomic prediction for a continuous and a threshold trait using a multi-trait model is scarce and needs more attention. Based on the previously proposed methods BayesCπ for single continuous trait and BayesTCπ for single threshold trait, we developed a novel method based on a linear-threshold model, i.e., LT-BayesCπ, for joint genomic prediction of a continuous trait and a threshold trait. Computing procedures of LT-BayesCπ using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the advantages of LT-BayesCπ over BayesCπ and BayesTCπ with regard to the accuracy of genomic prediction on both traits. Factors affecting the performance of LT-BayesCπ were addressed. The results showed that, in all scenarios, the accuracy of genomic prediction obtained from LT-BayesCπ was significantly increased for the threshold trait compared to that from single trait prediction using BayesTCπ, while the accuracy for the continuous trait was comparable with that from single trait prediction using BayesCπ. The proposed LT-BayesCπ could be a method of choice for joint genomic prediction of one continuous and one threshold trait.

  12. Elimination Voltammetry with Linear Scan as a New Detection Method for DNA Sensors

    Directory of Open Access Journals (Sweden)

    Rene Kizek

    2005-11-01

    Full Text Available The paper describes successful coupling of adsorptive transfer stripping (AdTS andelimination voltammetry with linear scan (EVLS for the resolution of reduction signals of cytosine (Cand adenine (A residues in hetero-oligodeoxynucleotides (ODNs. Short ODNs (9-mers and 20-merswere adsorbed from a small volume on a hanging mercury drop electrode (HMDE. After washing ofthe ODN-modified electrode by water and its transferring to an electrochemical cell, voltammetric curves were measured. The AdTS EVLS was able to determine of C/A ratio of ODNs through theelimination function conserving the diffusion current component and eliminating kinetic and chargingcurrent components. This function, which provides the elimination signal in a peak-counterpeak form,increased the current sensitivity for A and C resolution, and for the recognition of bases sequences inODN chains. Optimal conditions of elimination experiments such as pH, time of adsorption, and scanrate were found. The combination of EVLS with AdTS procedure can be considered as a newdetection method in a DNA sensor.

  13. Challenges of the Usual Graphical Methods Used to Characterize Phase Change Materials by Differential Scanning Calorimetry

    Directory of Open Access Journals (Sweden)

    Stéphane Gibout

    2018-01-01

    Full Text Available Modeling the thermal behavior of a plant or devices using Phase Change Materials (PCM requires to know their thermophysical properties. The Differential Scanning Calorimetry (DSC is a technic largely used to investigate them. However, under the pretext to experiment with small samples, some authors consider the DSC curves as directly representing the properties of the materials without realizing that this interpretation is very often incompatible with the thermodynamics laws: as an example, although a pure substance melts at a fixed temperature T F , it is proposed a melting through a temperature range higher than T F and depending on the experiments (heating rates, sample masses..., for solutions the suggested characteristic temperatures are incompatible with the phase diagram, and also a hysteresis phenomenon is invented... In this paper, we demonstrate by a model coupling thermodynamics and conduction heat transfers, that the DSC curves are exactly compatible with the thermodynamics of phase changes (melting at fixed temperature for pure substances, in conformity with phase diagrams for solutions.... The cases of pure substances, saline solutions, substances with impurities or solid solutions are detailed. We indicate which information can, however, be given by the curves. We also propose a more sophisticated method by inverse calculations to determine the specific enthalpy whose all the thermodynamical properties can be deduced. Finally, we give some indications to understand and use the results indicating supercooling.

  14. Ionic liquids: differential scanning calorimetry as a new indirect method for determination of vaporization enthalpies.

    Science.gov (United States)

    Verevkin, Sergey P; Emel'yanenko, Vladimir N; Zaitsau, Dzmitry H; Ralys, Ricardas V; Schick, Christoph

    2012-04-12

    Differential scanning calorimetry (DSC) has been used to measure enthalpies of synthesis reactions of the 1-alkyl-3-methylimidazolium bromide [C(n)mim][Br] ionic liquids from 1-methylimidazole and n-alkyl bromides (with n = 4, 5, 6, 7, and 8). The optimal experimental conditions have been elaborated. Enthalpies of formation of these ionic liquids in the liquid state have been determined using the DSC results according to the Hess Law. The ideal-gas enthalpies of formation of [C(n)mim][Br] were calculated using the methods of quantum chemistry. They were used together with the DSC results to derive indirectly the enthalpies of vaporization of the ionic liquids under study. In order to validate the indirect determination, the experimental vaporization enthalpy of [C(4)mim][Br] was measured by using a quartz crystal microbalance (QCM). The combination of reaction enthalpy measurements by DSC with modern high-level first-principles calculations opens valuable indirect thermochemical options to obtain values of vaporization enthalpies of ionic liquids.

  15. Method to characterize inorganic particulates in lung tissue biopsies using field emission scanning electron microscopy

    Science.gov (United States)

    Lowers, Heather; Breit, George N.; Strand, Matthew; Pillers, Renee M.; Meeker, Gregory P.; Todorov, Todor I.; Plumlee, Geoffrey S.; Wolf, Ruth E.; Robinson, Maura; Parr, Jane; Miller, Robert J.; Groshong, Steve; Green, Francis; Rose, Cecile

    2018-01-01

    Humans accumulate large numbers of inorganic particles in their lungs over a lifetime. Whether this causes or contributes to debilitating disease over a normal lifespan depends on the type and concentration of the particles. We developed and tested a protocol for in situ characterization of the types and distribution of inorganic particles in biopsied lung tissue from three human groups using field emission scanning electron microscopy (FE-SEM) combined with energy dispersive spectroscopy (EDS). Many distinct particle types were recognized among the 13 000 particles analyzed. Silica, feldspars, clays, titanium dioxides, iron oxides and phosphates were the most common constituents in all samples. Particles were classified into three general groups: endogenous, which form naturally in the body; exogenic particles, natural earth materials; and anthropogenic particles, attributed to industrial sources. These in situ results were compared with those using conventional sodium hypochlorite tissue digestion and particle filtration. With the exception of clays and phosphates, the relative abundances of most common particle types were similar in both approaches. Nonetheless, the digestion/filtration method was determined to alter the texture and relative abundances of some particle types. SEM/EDS analysis of digestion filters could be automated in contrast to the more time intensive in situ analyses.

  16. Development of a method of testing irradiation devices by gamma scanning inside a research nuclear reactor

    International Nuclear Information System (INIS)

    Michel, Francois.

    1975-01-01

    A tridimensional experiment of spectrometry of an irradiation device located inside the reactor Siloe at a place shielded against spurious radiations, is exposed. The automatic scanning system that was developed, makes it possible to fully analyze in about 24 hours, the irradiation device (fuel pin, coolant and structures). The process combined with a 'pre-processing' program allows first partial results to be simultaneously obtained, more refined results being achieved during the next week, using the 'heavy processing'. The irradiation of the device is only interrupted during the compelling duty shutdown of the reactor, the evolution of the device during the successive irradiation cycles being thus followed up without pertubing said evolution. The reproducibility was studied at a local stage for testing the collimation of the detection unit (1% accuracy) and for testing the whole set 'processing measurement and computation' (5% accuracy). The sensitivity has been illustrated by detecting and measuring local singularities inside fuel (pellets), determining the detection efficiency dependence on the radial distribution of fission products and measuring nucleides inside the coolant flow (limiting value 10 -7 ). The accuracy of the method is evaluated at 5% for relative measurement of an experimental device during its in-pile lifetime and as 10% for quantitative absolute measurements [fr

  17. An overview of recent developments in genomics and associated statistical methods.

    Science.gov (United States)

    Bickel, Peter J; Brown, James B; Huang, Haiyan; Li, Qunhua

    2009-11-13

    The landscape of genomics has changed drastically in the last two decades. Increasingly inexpensive sequencing has shifted the primary focus from the acquisition of biological sequences to the study of biological function. Assays have been developed to study many intricacies of biological systems, and publicly available databases have given rise to integrative analyses that combine information from many sources to draw complex conclusions. Such research was the focus of the recent workshop at the Isaac Newton Institute, 'High dimensional statistics in biology'. Many computational methods from modern genomics and related disciplines were presented and discussed. Using, as much as possible, the material from these talks, we give an overview of modern genomics: from the essential assays that make data-generation possible, to the statistical methods that yield meaningful inference. We point to current analytical challenges, where novel methods, or novel applications of extant methods, are presently needed.

  18. Measuring the quality of infection control in Dutch nursing homes using a standardized method; the Infection prevention RIsk Scan (IRIS)

    NARCIS (Netherlands)

    Willemsen, I.; Nelson-Melching, J.; Hendriks, Y.; Mulders, A.; Verhoeff, S.; Kluytmans-Vandenbergh, M.; Kluytmans, J.

    2014-01-01

    BACKGROUND: We developed a standardised method to assess the quality of infection control in Dutch Nursing Home (NH), based on a cross-sectional survey that visualises the results. The method was called the Infection control RIsk Infection Scan (IRIS). We tested the applicability of this new tool in

  19. Automated bone removal in CT angiography: Comparison of methods based on single energy and dual energy scans

    International Nuclear Information System (INIS)

    Straten, Marcel van; Schaap, Michiel; Dijkshoorn, Marcel L.; Greuter, Marcel J.; Lugt, Aad van der; Krestin, Gabriel P.; Niessen, Wiro J.

    2011-01-01

    Purpose: To evaluate dual energy based methods for bone removal in computed tomography angiography (CTA) images and compare these with single energy based methods that use an additional, nonenhanced, CT scan. Methods: Four different bone removal methods were applied to CT scans of an anthropomorphic thorax phantom, acquired with a second generation dual source CT scanner. The methods differed by the way information on the presence of bone was obtained (either by using an additional, nonenhanced scan or by scanning with two tube voltages at the same time) and by the way the bone was removed from the CTA images (either by masking or subtracting the bone). The phantom contained parts which mimic vessels of various diameters in direct contact with bone. Both a quantitative and qualitative analysis of image quality after bone removal was performed. Image quality was quantified by the contrast-to-noise ratio (CNR) normalized to the square root of the dose (CNRD). At locations where vessels touch bone, the quality of the bone removal and the vessel preservation were visually assessed. The dual energy based methods were assessed with and without the addition of a 0.4 mm tin filter to the high voltage x-ray tube filtration. For each bone removal method, the dose required to obtain a certain CNR after bone removal was compared with the dose of a reference scan with the same CNR but without automated bone removal. The CNRD value of the reference scan was maximized by choosing the lowest tube voltage available. Results: All methods removed the bone completely. CNRD values were higher for the masking based methods than for the subtraction based methods. Single energy based methods had a higher CNRD value than the corresponding dual energy based methods. For the subtraction based dual energy method, tin filtration improved the CNRD value with approximately 50%. For the masking based dual energy method, it was easier to differentiate between iodine and bone when tin filtration

  20. Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.

    Directory of Open Access Journals (Sweden)

    Nicole Soranzo

    2009-04-01

    Full Text Available Recent genome-wide (GW scans have identified several independent loci affecting human stature, but their contribution through the different skeletal components of height is still poorly understood. We carried out a genome-wide scan in 12,611 participants, followed by replication in an additional 7,187 individuals, and identified 17 genomic regions with GW-significant association with height. Of these, two are entirely novel (rs11809207 in CATSPER4, combined P-value = 6.1x10(-8 and rs910316 in TMED10, P-value = 1.4x10(-7 and two had previously been described with weak statistical support (rs10472828 in NPR3, P-value = 3x10(-7 and rs849141 in JAZF1, P-value = 3.2x10(-11. One locus (rs1182188 at GNA12 identifies the first height eQTL. We also assessed the contribution of height loci to the upper- (trunk and lower-body (hip axis and femur skeletal components of height. We find evidence for several loci associated with trunk length (including rs6570507 in GPR126, P-value = 4x10(-5 and rs6817306 in LCORL, P-value = 4x10(-4, hip axis length (including rs6830062 at LCORL, P-value = 4.8x10(-4 and rs4911494 at UQCC, P-value = 1.9x10(-4, and femur length (including rs710841 at PRKG2, P-value = 2.4x10(-5 and rs10946808 at HIST1H1D, P-value = 6.4x10(-6. Finally, we used conditional analyses to explore a possible differential contribution of the height loci to these different skeletal size measurements. In addition to validating four novel loci controlling adult stature, our study represents the first effort to assess the contribution of genetic loci to three skeletal components of height. Further statistical tests in larger numbers of individuals will be required to verify if the height loci affect height preferentially through these subcomponents of height.

  1. Genome-wide comparison of ultraviolet and ethyl methanesulphonate mutagenesis methods for the brown alga Ectocarpus.

    Science.gov (United States)

    Godfroy, Olivier; Peters, Akira F; Coelho, Susana M; Cock, J Mark

    2015-12-01

    Ectocarpus has emerged as a model organism for the brown algae and a broad range of genetic and genomic resources are being generated for this species. The aim of the work presented here was to evaluate two mutagenesis protocols based on ultraviolet irradiation and ethyl methanesulphonate treatment using genome resequencing to measure the number, type and distribution of mutations generated by the two methods. Ultraviolet irradiation generated a greater number of genetic lesions than ethyl methanesulphonate treatment, with more than 400 mutations being detected in the genome of the mutagenised individual. This study therefore confirms that the ultraviolet mutagenesis protocol is suitable for approaches that require a high density of mutations, such as saturation mutagenesis or Targeting Induced Local Lesions in Genomes (TILLING). Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Innovative method for optimizing Side-Scan Sonar mapping: The blind band unveiled

    Science.gov (United States)

    Pergent, Gérard; Monnier, Briac; Clabaut, Philippe; Gascon, Gilles; Pergent-Martini, Christine; Valette-Sansevin, Audrey

    2017-07-01

    Over the past few years, the mapping of Mediterranean marine habitats has become a priority for scientists, environment managers and stakeholders, in particular in order to comply with European directives (Water Framework Directive and Marine Strategy Framework Directive) and to implement legislation to ensure their conservation. Side-scan sonar (SSS) is recognised as one of the most effective tool for underwater mapping. However, interpretation of acoustic data (sonograms) requires extensive field calibration and the ground-truthing process remains essential. Several techniques are commonly used, with sampling methods involving grabs, scuba diving observations or Remotely Operated Vehicle (ROV) underwater video recordings. All these techniques are time consuming, expensive and only provide sporadic informations. In the present study, the possibility of coupling a camera with a SSS and acquiring underwater videos in a continuous way has been tested. During the 'PosidCorse' oceanographic survey carried out along the eastern coast of Corsica, optical and acoustic data were respectively obtained using a GoPro™ camera and a Klein 3000™ SSS. Thereby, five profiles were performed between 10 and 50 m depth, corresponding to more than 20 km of data acquisition. The vertical images recorded with the camera fixed under the SSS and positioned facing downwards provided photo mosaics of very good quality corresponding to the entire sonograms's blind band. From the photo mosaics, 94% of the different bottom types and main habitats have been identified; specific structures linked to hydrodynamics conditions, anthropic and biological activities have also been observed as well as the substrate on which the Posidonia oceanica meadow grows. The association between acoustic data and underwater videos has proved to be a non-destructive and cost-effective method for ground-truthing in marine habitats mapping. Nevertheless, in order to optimize the results over the next surveys

  3. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

    NARCIS (Netherlands)

    Heidaritabar, M.; Vereijken, A.; Muir, W.M.; Meuwissen, T.H.E.; Cheng, H.; Megens, H.J.W.C.; Groenen, M.; Bastiaansen, J.W.M.

    2014-01-01

    Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60¿K SNP chip with markers spaced throughout the

  4. Molecular recognition of DNA-protein complexes: A straightforward method combining scanning force and fluorescence microscopy

    NARCIS (Netherlands)

    H. Sanchez (Humberto); R. Kanaar (Roland); C. Wyman (Claire)

    2010-01-01

    textabstractCombining scanning force and fluorescent microscopy allows simultaneous identification of labeled biomolecules and analysis of their nanometer level architectural arrangement. Fluorescent polystyrene nano-spheres were used as reliable objects for alignment of optical and topographic

  5. Evaluation of Enterococcus faecalis adhesion, penetration, and method to prevent the penetration of Enterococcus faecalis into root cementum: Confocal laser scanning microscope and scanning electron microscope analysis.

    Science.gov (United States)

    Halkai, Rahul S; Hegde, Mithra N; Halkai, Kiran R

    2016-01-01

    To ascertain the role of Enterococcus faecalis in persistent infection and a possible method to prevent the penetration of E. faecalis into root cementum. One hundred and twenty human single-rooted extracted teeth divided into five groups. Group I (control): intact teeth, Group II: no apical treatment done, Group III divided into two subgroups. In Groups IIIa and IIIb, root apex treated with lactic acid of acidic and neutral pH, respectively. Group IV: apical root cementum exposed to lactic acid and roughened to mimic the apical resorption. Group V: apical treatment done same as Group IV and root-end filling done using mineral trioxide aggregate (MTA). Apical one-third of all samples immersed in E. faecalis broth for 8 weeks followed by bone morphogenetic protein and obturation and again immersed into broth for 8 weeks. Teeth split into two halves and observed under confocal laser scanning microscope and scanning electron microscope, organism identified by culture and polymerase chain reaction techniques. Adhesion and penetration was observed in Group IIIa and Group IV. Only adhesion in Group II and IIIB and no adhesion and penetration in Group I and V. Adhesion and penetration of E. faecalis into root cementum providing a long-term nidus for subsequent infection are the possible reason for persistent infection and root-end filling with MTA prevents the adhesion and penetration.

  6. Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding

    Science.gov (United States)

    de los Campos, Gustavo; Hickey, John M.; Pong-Wong, Ricardo; Daetwyler, Hans D.; Calus, Mario P. L.

    2013-01-01

    Genomic-enabled prediction is becoming increasingly important in animal and plant breeding and is also receiving attention in human genetics. Deriving accurate predictions of complex traits requires implementing whole-genome regression (WGR) models where phenotypes are regressed on thousands of markers concurrently. Methods exist that allow implementing these large-p with small-n regressions, and genome-enabled selection (GS) is being implemented in several plant and animal breeding programs. The list of available methods is long, and the relationships between them have not been fully addressed. In this article we provide an overview of available methods for implementing parametric WGR models, discuss selected topics that emerge in applications, and present a general discussion of lessons learned from simulation and empirical data analysis in the last decade. PMID:22745228

  7. A genomic background based method for association analysis in related individuals.

    Directory of Open Access Journals (Sweden)

    Najaf Amin

    Full Text Available BACKGROUND: Feasibility of genotyping of hundreds and thousands of single nucleotide polymorphisms (SNPs in thousands of study subjects have triggered the need for fast, powerful, and reliable methods for genome-wide association analysis. Here we consider a situation when study participants are genetically related (e.g. due to systematic sampling of families or because a study was performed in a genetically isolated population. Of the available methods that account for relatedness, the Measured Genotype (MG approach is considered the 'gold standard'. However, MG is not efficient with respect to time taken for the analysis of genome-wide data. In this context we proposed a fast two-step method called Genome-wide Association using Mixed Model and Regression (GRAMMAR for the analysis of pedigree-based quantitative traits. This method certainly overcomes the drawback of time limitation of the measured genotype (MG approach, but pays in power. One of the major drawbacks of both MG and GRAMMAR, is that they crucially depend on the availability of complete and correct pedigree data, which is rarely available. METHODOLOGY: In this study we first explore type 1 error and relative power of MG, GRAMMAR, and Genomic Control (GC approaches for genetic association analysis. Secondly, we propose an extension to GRAMMAR i.e. GRAMMAR-GC. Finally, we propose application of GRAMMAR-GC using the kinship matrix estimated through genomic marker data, instead of (possibly missing and/or incorrect genealogy. CONCLUSION: Through simulations we show that MG approach maintains high power across a range of heritabilities and possible pedigree structures, and always outperforms other contemporary methods. We also show that the power of our proposed GRAMMAR-GC approaches to that of the 'gold standard' MG for all models and pedigrees studied. We show that this method is both feasible and powerful and has correct type 1 error in the context of genome-wide association analysis

  8. Method for visualization and presentation of priceless old prints based on precise 3D scan

    Science.gov (United States)

    Bunsch, Eryk; Sitnik, Robert

    2014-02-01

    Graphic prints and manuscripts constitute main part of the cultural heritage objects created by the most of the known civilizations. Their presentation was always a problem due to their high sensitivity to light and changes of external conditions (temperature, humidity). Today it is possible to use an advanced digitalization techniques for documentation and visualization of mentioned objects. In the situation when presentation of the original heritage object is impossible, there is a need to develop a method allowing documentation and then presentation to the audience of all the aesthetical features of the object. During the course of the project scans of several pages of one of the most valuable books in collection of Museum of Warsaw Archdiocese were performed. The book known as "Great Dürer Trilogy" consists of three series of woodcuts by the Albrecht Dürer. The measurement system used consists of a custom designed, structured light-based, high-resolution measurement head with automated digitization system mounted on the industrial robot. This device was custom built to meet conservators' requirements, especially the lack of ultraviolet or infrared radiation emission in the direction of measured object. Documentation of one page from the book requires about 380 directional measurements which constitute about 3 billion sample points. The distance between the points in the cloud is 20 μm. Provided that the measurement with MSD (measurement sampling density) of 2500 points makes it possible to show to the publicity the spatial structure of this graphics print. An important aspect is the complexity of the software environment created for data processing, in which massive data sets can be automatically processed and visualized. Very important advantage of the software which is using directly clouds of points is the possibility to manipulate freely virtual light source.

  9. Inverse PCR-based method for isolating novel SINEs from genome.

    Science.gov (United States)

    Han, Yawei; Chen, Liping; Guan, Lihong; He, Shunping

    2014-04-01

    Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.

  10. Application of 3D documentation and geometric reconstruction methods in traffic accident analysis: with high resolution surface scanning, radiological MSCT/MRI scanning and real data based animation.

    Science.gov (United States)

    Buck, Ursula; Naether, Silvio; Braun, Marcel; Bolliger, Stephan; Friederich, Hans; Jackowski, Christian; Aghayev, Emin; Christe, Andreas; Vock, Peter; Dirnhofer, Richard; Thali, Michael J

    2007-07-20

    The examination of traffic accidents is daily routine in forensic medicine. An important question in the analysis of the victims of traffic accidents, for example in collisions between motor vehicles and pedestrians or cyclists, is the situation of the impact. Apart from forensic medical examinations (external examination and autopsy), three-dimensional technologies and methods are gaining importance in forensic investigations. Besides the post-mortem multi-slice computed tomography (MSCT) and magnetic resonance imaging (MRI) for the documentation and analysis of internal findings, highly precise 3D surface scanning is employed for the documentation of the external body findings and of injury-inflicting instruments. The correlation of injuries of the body to the injury-inflicting object and the accident mechanism are of great importance. The applied methods include documentation of the external and internal body and the involved vehicles and inflicting tools as well as the analysis of the acquired data. The body surface and the accident vehicles with their damages were digitized by 3D surface scanning. For the internal findings of the body, post-mortem MSCT and MRI were used. The analysis included the processing of the obtained data to 3D models, determination of the driving direction of the vehicle, correlation of injuries to the vehicle damages, geometric determination of the impact situation and evaluation of further findings of the accident. In the following article, the benefits of the 3D documentation and computer-assisted, drawn-to-scale 3D comparisons of the relevant injuries with the damages to the vehicle in the analysis of the course of accidents, especially with regard to the impact situation, are shown on two examined cases.

  11. Performance comparison of two efficient genomic selection methods (gsbay & MixP) applied in aquacultural organisms

    Science.gov (United States)

    Su, Hailin; Li, Hengde; Wang, Shi; Wang, Yangfan; Bao, Zhenmin

    2017-02-01

    Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools MixP and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop ( Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction (GBLUP) method which has been applied widely. Our results showed that both MixP and gsbay could accurately estimate single-nucleotide polymorphism (SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values (GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by MixP; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by MixP and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with MixP the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by MixP and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

  12. Impact of the method of registering Terrestrial Laser Scanning data on the quality of documenting cultural heritage structures

    Directory of Open Access Journals (Sweden)

    M. Kedzierski

    2015-08-01

    Full Text Available When documenting historical structures and objects, especially delicate artefacts such as pieces of sacred art, only techniques that allow remote, non-contact methods that enable the most precise measurements should be used to obtain data. TLS can be considered as such a technique however in order to obtain complete information for the entire structure, there is usually a need to acquire data from more than one measuring station. In this case, the most important and essential step of processing TLS data is the registration of scans. The paper contains a description of research and analyses concerning the registration of point clouds using three methods: manual, automatic and a combination of the two. The research was carried on measurement data from a historical synagogue. The structure was divided into three parts – three scans. The accuracy with which these scans were registered was assessed and a 3D model of the interior was created.

  13. Genomic DNA extraction method from pearl millet ( Pennisetum ...

    African Journals Online (AJOL)

    DNA extraction is difficult in a variety of plants because of the presence of metabolites that interfere with DNA isolation procedures and downstream applications such as DNA restriction, amplification, and cloning. Here we describe a modified procedure based on the hexadecyltrimethylammonium bromide (CTAB) method to ...

  14. Genomic DNA extraction method from Annona senegalensis Pers ...

    African Journals Online (AJOL)

    Extraction of DNA in many plants is difficult because of the presence of metabolites that interfere with DNA isolation procedures and downstream applications such as DNA restriction, replications, amplification, as well as cloning. Modified procedure based on the hexadecyltrimethyl ammoniumbromide (CTAB) method is ...

  15. The Study on Radioactive Nuclide Distributions within a Fuel Rod by Tomographic Gamma Scanning Method

    International Nuclear Information System (INIS)

    Quanhu, Zhang; Lee, H. K.; Hong, K. P.; Choo, Y. S.; Kim, D. S.

    2005-06-01

    Based on the specified need of the IMEF, the feasibility of Tomographic Gamma Scanning (TGS) technique has been investigated for its potential for non-destructive gamma scanning measurements of irradiated fuel rods. TGS technique has been developed for determining some radioactive isotopes' distributions of a fuel rod in hot cell. The results obtained from the simulation model extracting from real gamma scanning experimental condition in this work by new developed computer simulation codes confirmed that the gamma emission TGS technique has potential for determination of radioactive isotopes' distributions of a fuel rod. In order to verify the simulation codes, we have designed several computation schemes for both 3 by 3 and 10 by 10 fuel rod model under present situation at M1 hot cell in IMEF. The results which relative errors are less than 10% show that we have simulated and implemented determination of radioactive isotopes' distributions on simulated fuel rod by TGS technique successfully

  16. Method and apparatus for a high-resolution three dimensional confocal scanning transmission electron microscope

    Science.gov (United States)

    de Jonge, Niels [Oak Ridge, TN

    2010-08-17

    A confocal scanning transmission electron microscope which includes an electron illumination device providing an incident electron beam propagating in a direction defining a propagation axis, and a precision specimen scanning stage positioned along the propagation axis and movable in at least one direction transverse to the propagation axis. The precision specimen scanning stage is configured for positioning a specimen relative to the incident electron beam. A projector lens receives a transmitted electron beam transmitted through at least part of the specimen and focuses this transmitted beam onto an image plane, where the transmitted beam results from the specimen being illuminated by the incident electron beam. A detection system is placed approximately in the image plane.

  17. The role of model-based methods in the development of single scan techniques

    International Nuclear Information System (INIS)

    Laruelle, Marc

    2000-01-01

    Single scan techniques are highly desirable for clinical trials involving radiotracers because they increase logistical feasibility, improve patient compliance, and decrease the cost associated with the study. However, the information derived from single scans usually are biased by factors unrelated to the process of interest. Therefore, identification of these factors and evaluation of their impact on the proposed outcome measure is important. In this paper, the impact of confounding factors on single scan measurements is illustrated by discussing the effect of between-subject or between-condition differences in radiotracer plasma clearance on normalized activity ratios (specific to nonspecific ratios) in the tissue of interest. Computer simulation based on kinetic analyses are presented to demonstrate this effect. It is proposed that the presence of this and other confounding factors should not necessarily preclude clinical trials based on single scan techniques. First, knowledge of the distribution of plasma clearance values in a sample of the investigated population allows researchers to assign limits to this potential bias. This information can be integrated in the power analysis. Second, the impact of this problem will vary according to the characteristic of the radiotracer, and this information can be used in the development and selection of the radiotracer. Third, simple modification of the experimental design (such as administration of the radiotracer as a bolus, followed by constant infusion, rather than as a single bolus) might remove this potential confounding factor and allow appropriate quantification within the limits of a single scanning session. In conclusion, model-based kinetic characterization of radiotracer distribution and uptake is critical to the design and interpretation of clinical trials based on single scan techniques

  18. Line scan analysis of the component of Ru porcelain by SRXRF method

    International Nuclear Information System (INIS)

    Zhu Jian; Mao Zhenwei; Yang Yimin; Feng Min; Wang Changsui; Sun Xinmin; Guo Musen; Huang Yuying; He Wei

    2002-01-01

    The technique of the SRXRF line scan analysis was used to measure contents of 11 elements at the broken plane of the Ru porcelain from porcelain glaze to body. It is found that there exists a great different layer of contents of elements between the porcelain glaze and body. The mechanism may be that in the process of firing the porcelain, materials of glass-glaze of porcelain glaze infiltrate into the surface of porcelain body, that could fit the phenomenon of observation by different microscopes (stereomicroscope, polarizing microscope and scanning electron microscope)

  19. A genome-wide linkage scan for dietary energy and nutrient intakes: the Health, Risk Factors, Exercise Training, and Genetics (HERITAGE) Family Study.

    Science.gov (United States)

    Collaku, Agron; Rankinen, Tuomo; Rice, Treva; Leon, Arthur S; Rao, D C; Skinner, James S; Wilmore, Jack H; Bouchard, Claude

    2004-05-01

    A poor diet is a risk factor for chronic diseases such as obesity, cardiovascular disease, hypertension, and some cancers. Twin and family studies suggest that genetic factors potentially influence energy and nutrient intakes. We sought to identify genomic regions harboring genes affecting total energy, carbohydrate, protein, and fat intakes. We performed a genomic scan in 347 white sibling pairs and 99 black sibling pairs. Dietary energy and nutrient intakes were assessed by using Willett's food-frequency questionnaire. Single-point and multipoint Haseman-Elston regression techniques were used to test for linkage. These subjects were part of the Health, Risk Factors, Exercise Training, and Genetics (HERITAGE) Family Study, a multicenter project undertaken by 5 laboratories. In the whites, the strongest evidence of linkage appeared for dietary energy and nutrient intakes on chromosomes 1p21.2 (P = 0.0002) and 20q13.13 (P = 0.00007), and that for fat intake appeared on chromosome 12q14.1 (P = 0.0013). The linkage evidence on chromosomes 1 and 20 related to total energy intake rather than to the intake of specific macronutrients. In the blacks, promising linkages for macronutrient intakes occurred on chromosomes 12q23-q24.21, 1q32.1, and 7q11.1. Several potential candidate genes are encoded in and around the linkage regions on chromosomes 1p21.2, 12q14.1, and 20q13.13. These are the first reported human quantitative trait loci for dietary energy and macronutrient intakes. Further study may refine these quantitative trait loci to identify potential candidate genes for energy and specific macronutrient intakes that would be amenable to more detailed molecular studies.

  20. Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...the Plant DB link list in simple search page) Genome analysis methods Presence or... absence of Genome analysis methods information in this DB (link to the Genome analysis methods information ...base Site Policy | Contact Us Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  1. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

    DEFF Research Database (Denmark)

    Hou, Yong; Wu, Kui; Shi, Xulian

    2015-01-01

    methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly...... performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level....

  2. A 4D dose computation method to investigate motion interplay effects in scanned ion beam prostate therapy

    International Nuclear Information System (INIS)

    Ammazzalorso, F; Jelen, U

    2014-01-01

    In particle therapy, the interplay between beam scanning and target motion during treatment delivery may result in dose deterioration. Interplay effects have been studied for targets exhibiting periodic respiratory motion, however, they are not well understood for irregular motion patterns, such as those exhibited by the prostate. In this note, we propose and validate a 4D dose computation method, which enables estimation of effective dose delivered to the prostate by scanning ion beams in presence of intrafraction motion, as well as facilitates investigation of various motion interplay countermeasures. (note)

  3. Initial radioiodine remnant ablation success rates compared by diagnostic scan methods: I123 versus I131

    International Nuclear Information System (INIS)

    Choi, W.; Choi, E.; Yoo, I.; Kim, S.; Han, E.; Lee, S.; Lee, W.

    2015-01-01

    Full text of publication follows. Objective: to see if diagnostic whole body scan (DxWBS) performed with I-131 prior diminishes the success rate of initial radioiodine remnant ablation (RRA) compared to I-123 DxWBS in differentiated thyroid cancer patients. Material and methods: consecutive thyroid cancer patients who received total thyroidectomy for differentiated thyroid cancer and then high dose RRA (either 100 mCi or 150 mCi) within 6 months were included. DxWBSs were performed with I-123 or with I-131. Prior to the DxWBSs, all patients followed strict low iodine diet for 2 weeks and withdrew hormone to stimulate TSH above 30 mIU/l. Patients with extra-thyroidal extension of tumor, lymph node metastasis, or distant metastasis were excluded. The initial RRA was defined as successful if the next DxWBS done 6 months to 1 year later was negative and stimulated thyroglobulin level was below 2 ng/ml. Results: of 71 patients who had I-123 DxWBSs, 31 patients went on to receive RRA with 100 mCi and 40 patients received 150 mCi. Of 73 patients who had I-131 DxWBSs, 66 received 100 mCi and 7 patients received 150 mCi. The overall success rate was 79% for patients who had I-123 DxWBS prior to RRA (68% for 100 mCi and 86% for 150 mCi), and 68% for patient who had I-131 DxWBSs (68% for 100 mCi and 71% for 150 mCi). Conclusion: for patients who received 100 mCi, the RRA success rate was the same for I-123 DxWBS and I-131 DxWBS. For patients treated with 150 mCi, the success rate may be lower in patients who receive RRA following DxWBS with I-131 compared to DxWBS with I-123. (authors)

  4. Is TrichoScan a new diagnostic method for diffuse hair loss?

    Science.gov (United States)

    Uce Özkol, Hatice; Çalka, Ömer; Akdeniz, Necmettin

    2014-01-01

    In this study, we investigated the sensitivity of TrichoScan, a computer-based phototrichogram, in the evaluation of diffuse hair loss in women and the relationship between iron deficiency anemia and hair loss. We recruited 100 female patients with diffuse hair loss. In all of the patients, a 1-cm2 area of hair located in a temporoparietal region was shortened to 0.5 mm. The shaved scalp regions were stained with black dye. The subject then waited for 12 min. Subsequently, pictures of these regions were taken with a videodermoscope and analyzed with the TrichoScan software program. The ferritin levels were markedly low in these groups. The ratio of anagen was highest in the telogen effluvium (TE) mild group, followed by the TE severe group, and was lowest in the androgenetic alopecia (AGA) group (P hair analysis results with the TrichoScan software were satisfactory and the results were consistent with the clinical diagnosis. In particular, the use of TrichoScan was very successful in the differentiation between AGA and TE.

  5. Scanning Lidar Spatial Calibration and Alignment Method for Wind Turbine Wake Characterization

    DEFF Research Database (Denmark)

    Herges, Thomas; Maniaci, David; Naughton, Brian

    2017-01-01

    Sandia National Laboratories and the National Renewable Energy Laboratory conducted a field campaign at the Scaled Wind Farm Technology (SWiFT) Facility using a customized scanning lidar from the Technical University of Denmark. The results from this field campaign will support the validation...

  6. A review of patient dose and optimisation methods in adult and paediatric CT scanning

    International Nuclear Information System (INIS)

    Dougeni, E.; Faulkner, K.; Panayiotakis, G.

    2012-01-01

    Highlights: ► CT scanning frequency has grown with the development of new clinical applications. ► Up to 32-fold dose variation was observed for similar type of procedures. ► Scanning parameters should be optimised for patient size and clinical indication. ► Cancer risks knowledge amongst physicians of certain specialties was poor. ► A significant number of non-indicated CT scans could be eliminated. - Abstract: An increasing number of publications and international reports on computed tomography (CT) have addressed important issues on optimised imaging practice and patient dose. This is partially due to recent technological developments as well as to the striking rise in the number of CT scans being requested. CT imaging has extended its role to newer applications, such as cardiac CT, CT colonography, angiography and urology. The proportion of paediatric patients undergoing CT scans has also increased. The published scientific literature was reviewed to collect information regarding effective dose levels during the most common CT examinations in adults and paediatrics. Large dose variations were observed (up to 32-fold) with some individual sites exceeding the recommended dose reference levels, indicating a large potential to reduce dose. Current estimates on radiation-related cancer risks are alarming. CT doses account for about 70% of collective dose in the UK and are amongst the highest in diagnostic radiology, however the majority of physicians underestimate the risk, demonstrating a decreased level of awareness. Exposure parameters are not always adjusted appropriately to the clinical question or to patient size, especially for children. Dose reduction techniques, such as tube-current modulation, low-tube voltage protocols, prospective echocardiography-triggered coronary angiography and iterative reconstruction algorithms can substantially decrease doses. An overview of optimisation studies is provided. The justification principle is discussed along

  7. A Classification-oriented Method of Feature Image Generation for Vehicle-borne Laser Scanning Point Clouds

    Directory of Open Access Journals (Sweden)

    YANG Bisheng

    2016-02-01

    Full Text Available An efficient method of feature image generation of point clouds to automatically classify dense point clouds into different categories is proposed, such as terrain points, building points. The method first uses planar projection to sort points into different grids, then calculates the weights and feature values of grids according to the distribution of laser scanning points, and finally generates the feature image of point clouds. Thus, the proposed method adopts contour extraction and tracing means to extract the boundaries and point clouds of man-made objects (e.g. buildings and trees in 3D based on the image generated. Experiments show that the proposed method provides a promising solution for classifying and extracting man-made objects from vehicle-borne laser scanning point clouds.

  8. Determination of solid surface composition by the X-ray fluorescence method under total external reflection with angular scanning

    International Nuclear Information System (INIS)

    Krasnolutskij, V.P.

    2000-01-01

    Possibilities of determination of composition of surface layers by X-ray fluorescence analysis under total reflection of incident radiation with angular scanning of a target are investigated. For the case of the GaAs target it is shown that the sensibility of this method is sufficient for a control of element composition in layer of thickness 1 nm. A simple method for solution of inverse task of analysis of a two component medium is considered [ru

  9. Experimental Quasi-Microwave Whole-Body Averaged SAR Estimation Method Using Cylindrical-External Field Scanning

    OpenAIRE

    Kawamura, Yoshifumi; Hikage, Takashi; Nojima, Toshio

    2010-01-01

    The aim of this study is to develop a new whole-body averaged specific absorption rate (SAR) estimation method based on the external-cylindrical field scanning technique. This technique is adopted with the goal of simplifying the dosimetry estimation of human phantoms that have different postures or sizes. An experimental scaled model system is constructed. In order to examine the validity of the proposed method for realistic human models, we discuss the pros and cons of measurements and nume...

  10. Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

    Science.gov (United States)

    Lee, Patrick K H; Men, Yujie; Wang, Shanquan; He, Jianzhong; Alvarez-Cohen, Lisa

    2015-02-03

    Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

  11. Comparison of two different segmentation methods on planar lung perfusion scan with reference to quantitative value on SPECT/CT

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Min Seok; Kang, Yeon Koo; Ha, Seung Gyun [Dept. of Nuclear Medicine, Seoul National University Hospital, Seoul (Korea, Republic of); and others

    2017-06-15

    Until now, there was no single standardized regional segmentation method of planar lung perfusion scan. We compared planar scan based two segmentation methods, which are frequently used in the Society of Nuclear Medicine, with reference to the lung perfusion single photon emission computed tomography (SPECT)/computed tomography (CT) derived values in lung cancer patients. Fifty-five lung cancer patients (male:female, 37:18; age, 67.8 ± 10.7 years) were evaluated. The patients underwent planar scan and SPECT/CT after injection of technetium-99 m macroaggregated albumin (Tc-99 m-MAA). The % uptake and predicted postoperative percentage forced expiratory volume in 1 s (ppoFEV1%) derived from both posterior oblique (PO) and anterior posterior (AP) methods were compared with SPECT/CT derived parameters. Concordance analysis, paired comparison, reproducibility analysis and spearman correlation analysis were conducted. The % uptake derived from PO method showed higher concordance with SPECT/CT derived % uptake in every lobe compared to AP method. Both methods showed significantly different lobar distribution of % uptake compared to SPECT/CT. For the target region, ppoFEV1% measured from PO method showed higher concordance with SPECT/CT, but lower reproducibility compared to AP method. Preliminary data revealed that every method significantly correlated with actual postoperative FEV1%, with SPECT/CT showing the best correlation. The PO method derived values showed better concordance with SPECT/CT compared to the AP method. Both PO and AP methods showed significantly different lobar distribution compared to SPECT/CT. In clinical practice such difference according to different methods and lobes should be considered for more accurate postoperative lung function prediction.

  12. Method of mechanical holding of cantilever chip for tip-scan high-speed atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Shingo [Department of Physics, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); Uchihashi, Takayuki; Ando, Toshio [Department of Physics, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); Bio-AFM Frontier Research Center, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 (Japan); Core Research for Evolutional Science and Technology of the Japan Science and Technology Agency, 7 Goban-cho, Chiyoda-ku, Tokyo 102-0076 (Japan)

    2015-06-15

    In tip-scan atomic force microscopy (AFM) that scans a cantilever chip in the three dimensions, the chip body is held on the Z-scanner with a holder. However, this holding is not easy for high-speed (HS) AFM because the holder that should have a small mass has to be able to clamp the cantilever chip firmly without deteriorating the Z-scanner’s fast performance, and because repeated exchange of cantilever chips should not damage the Z-scanner. This is one of the reasons that tip-scan HS-AFM has not been established, despite its advantages over sample stage-scan HS-AFM. Here, we present a novel method of cantilever chip holding which meets all conditions required for tip-scan HS-AFM. The superior performance of this novel chip holding mechanism is demonstrated by imaging of the α{sub 3}β{sub 3} subcomplex of F{sub 1}-ATPase in dynamic action at ∼7 frames/s.

  13. Rapid methods for the extraction and archiving of molecular grade fungal genomic DNA.

    Science.gov (United States)

    Borman, Andrew M; Palmer, Michael; Johnson, Elizabeth M

    2013-01-01

    The rapid and inexpensive extraction of fungal genomic DNA that is of sufficient quality for molecular approaches is central to the molecular identification, epidemiological analysis, taxonomy, and strain typing of pathogenic fungi. Although many commercially available and in-house extraction procedures do eliminate the majority of contaminants that commonly inhibit molecular approaches, the inherent difficulties in breaking fungal cell walls lead to protocols that are labor intensive and that routinely take several hours to complete. Here we describe several methods that we have developed in our laboratory that allow the extremely rapid and inexpensive preparation of fungal genomic DNA.

  14. Methods to improve genomic prediction and GWAS using combined Holstein populations

    DEFF Research Database (Denmark)

    Li, Xiujin

    The thesis focuses on methods to improve GWAS and genomic prediction using combined Holstein populations and investigations G by E interaction. The conclusions are: 1) Prediction reliabilities for Brazilian Holsteins can be increased by adding Nordic and Frensh genotyped bulls and a large G by E...... interaction exists between populations. 2) Combining data from Chinese and Danish Holstein populations increases the power of GWAS and detects new QTL regions for milk fatty acid traits. 3) The novel multi-trait Bayesian model efficiently estimates region-specific genomic variances, covariances...

  15. The reality of virtual anthropology: Comparing digitizer and laser scan data collection methods for the quantitative assessment of the cranium.

    Science.gov (United States)

    Algee-Hewitt, Bridget F B; Wheat, Amber D

    2016-05-01

    The use of geometric morphometry to study cranial variation has steadily grown in appeal over the past decade in biological anthropology. Publication trends suggest that the most popular methods for three-dimensional data acquisition involve landmark-based coordinate data collection using a digitizer. Newer laser scan approaches are seeing increasing use, owing to the benefits that densely sampled data offer. While both of these methods have their utility, research that investigates their compatibility is lacking. The purpose of this project is to compare, quantitatively, craniometrics collected with a digitizer against data extracted from laser scans using the same individuals and laboratory conditions. Three-dimensional (x,y,z) coordinates and traditional inter-landmark distances (ILDs) were obtained with a Microscribe digitizer and 360° color models produced from NextEngine laser scans for 38 adult crania representing five cemeteries from the ADBOU skeletal collection in Denmark. Variance-based tests were performed to evaluate the disagreement between data collected with a digitizer and from laser scan models. Consideration was given to differences among landmarks by type, between ILDs calculated from landmark coordinates, and in morphology for the cemetery populations. Further, the reliability of laser scan data collection was assessed by intra-observer error tests. Researchers should be aware of the potential error associated with the use of Types II and III landmarks and the limitations on reliability imposed by object-to-scanner placement. This project reveals how laser scans can provide a valuable digital archive of cranial material that can be reasonably exploited for the "virtual" collection of coordinates and the calculation of ILDs. © 2015 Wiley Periodicals, Inc.

  16. Genome scan of clot lysis time and its association with thrombosis in a protein C deficient kindred

    Science.gov (United States)

    Meltzer, M.E.; Hasstedt, S.J.; Vossen, C.Y.; Callas, P.W.; de Groot, Ph.G.; Rosendaal, F.R.; Lisman, T.; Bovill, E.G.

    2011-01-01

    Summary Background Previously we found increased clot lysis time (CLT), as measured with a plasma-based assay, to increase the risk of venous thrombosis in two population-based case-control studies. Genes influencing CLT are yet unknown. Objectives and Patients/Methods We tested CLT as risk factor for venous thrombosis in Kindred Vermont II (n=346), a pedigree suffering from a high thrombosis risk, partially attributable to a type I protein C deficiency. Furthermore we tested for quantitative trait loci (QTL) for CLT using variance component linkage analysis. Results Protein C deficient family members had shorter CLT than non-deficient members (median CLT 67 versus 75 minutes). One standard deviation increase in CLT increased risk of venous thrombosis 2.4-fold in non-deficient family members. Protein C deficiency without elevated CLT increased risk 6.9-fold. Combining both risk factors yielded a 27.8-fold increased risk. Heritability of CLT was 42-52%. We found suggestive evidence of linkage on chromosome 11 (62 cM), partly explained by the prothrombin 20210A mutation, and on chromosome 13 (52 cM). Thrombin Activatable Fibrinolysis Inhibitor genotypes did not explain the variation in CLT. Conclusion Hypofibrinolysis appears to increase thrombosis risk in this family especially in combination with protein C deficiency. Protein C deficiency is associated with short CLT. CLT is partly genetically regulated. Suggestive QTL were found on chromosome 11 and 13. PMID:21575129

  17. Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations.

    Science.gov (United States)

    Schaid, Daniel J

    2010-01-01

    Measures of genomic similarity are the basis of many statistical analytic methods. We review the mathematical and statistical basis of similarity methods, particularly based on kernel methods. A kernel function converts information for a pair of subjects to a quantitative value representing either similarity (larger values meaning more similar) or distance (smaller values meaning more similar), with the requirement that it must create a positive semidefinite matrix when applied to all pairs of subjects. This review emphasizes the wide range of statistical methods and software that can be used when similarity is based on kernel methods, such as nonparametric regression, linear mixed models and generalized linear mixed models, hierarchical models, score statistics, and support vector machines. The mathematical rigor for these methods is summarized, as is the mathematical framework for making kernels. This review provides a framework to move from intuitive and heuristic approaches to define genomic similarities to more rigorous methods that can take advantage of powerful statistical modeling and existing software. A companion paper reviews novel approaches to creating kernels that might be useful for genomic analyses, providing insights with examples [1]. Copyright © 2010 S. Karger AG, Basel.

  18. Radiation Scanning Methods for Ship-to-Rail Intermodal Cargo Containers

    International Nuclear Information System (INIS)

    Reichmuth, Barbara A.; Stansbury, Paul S.; Taira, Randal Y.; Sanquist, Thomas F.; Collins, Robert

    2009-01-01

    The Department of Homeland Security's (DHS) Domestic Nuclear Detection Office (DNDO) runs the Rail Test Center (RTC) at the Port of Tacoma (POT). The RTC affords DNDO with the opportunity to test radiological and nuclear threat detection systems associated with the unique on-dock rail environment while in an operational seaport. DNDO selected the Pacific Northwest National Laboratory (PNNL) to manage the RTC. The RTC is conducting various evaluation studies to assess scanning opportunities in terms of their affects on the number of container moves required and the affect that the scanning opportunity has on the time it takes to move a container through the on-dock transfer process from ship to rail. The velocity and the number of container moves are directly associated with incremental costs to the terminal operators; increases in either of these parameters help in-form the potential for incremental costs that would result from the implementation of the opportunity.

  19. Line scanning analysis of Dilingtou Yue porcelain in Southern Song Dynasty by SRXRF method

    International Nuclear Information System (INIS)

    Zhu Shoumei; Mao Zhenwei; Feng Min; Zhu Jian; Ling Xue; Sheng Yueming; Huang Yuying; He Wei

    2004-01-01

    The SRXRF line scanning analysis technique was used to measure the elements' content in the Dilingtou Yue porcelain sherd of Southern Song Dynasty from glaze to body. It is found that there exists a middle layer between the porcelain glaze and body. And a line scanning analysis comparison was made with the Ru porcelain in Northern Song Dynasty. There are some differences between them and the middle layer of Dilingtou Yue sherd is a little thinner than the Ru sherd's. And elements' content distributions in glaze are different from Ru porcelain's and the changes of contents from the surface to the inner side of glaze are undulatory. The results indicate that the differences may result from the different materials of body and the different kilns. (authors)

  20. Nodule detection methods using autocorrelation features on 3D chest CT scans

    International Nuclear Information System (INIS)

    Hara, T.; Zhou, X.; Okura, S.; Fujita, H.; Kiryu, T.; Hoshi, H.

    2007-01-01

    Lung cancer screening using low dose X-ray CT scan has been an acceptable examination to detect cancers at early stage. We have been developing an automated detection scheme for lung nodules on CT scan by using second-order autocorrelation features and the initial performance for small nodules (< 10 mm) shows a high true-positive rate with less than four false-positive marks per case. In this study, an open database of lung images, LIDC (Lung Image Database Consortium), was employed to evaluate our detection scheme as an consistency test. The detection performance for solid and solitary nodules in LIDC, included in the first data set opened by the consortium, was 83% (10/12) true-positive rate with 3.3 false-positive marks per case. (orig.)

  1. New calibration method for I-scan sensors to enable the precise measurement of pressures delivered by 'pressure garments'.

    Science.gov (United States)

    Macintyre, Lisa

    2011-11-01

    Accurate measurement of the pressure delivered by medical compression products is highly desirable both in monitoring treatment and in developing new pressure inducing garments or products. There are several complications in measuring pressure at the garment/body interface and at present no ideal pressure measurement tool exists for this purpose. This paper summarises a thorough evaluation of the accuracy and reproducibility of measurements taken following both of Tekscan Inc.'s recommended calibration procedures for I-scan sensors; and presents an improved method for calibrating and using I-scan pressure sensors. The proposed calibration method enables accurate (±2.1 mmHg) measurement of pressures delivered by pressure garments to body parts with a circumference ≥30 cm. This method is too cumbersome for routine clinical use but is very useful, accurate and reproducible for product development or clinical evaluation purposes. Copyright © 2011 Elsevier Ltd and ISBI. All rights reserved.

  2. Multi-Channel Electronically Scanned Cryogenic Pressure Sensor And Method For Making Same

    Science.gov (United States)

    Chapman, John J. (Inventor); Hopson, Purnell, Jr. (Inventor); Holloway, Nancy M. (Inventor)

    2001-01-01

    A miniature, multi-channel, electronically scanned pressure measuring device uses electrostatically bonded silicon dies in a multi-element array. These dies are bonded at specific sites on a glass, pre-patterned substrate. Thermal data is multiplexed and recorded on each individual pressure measuring diaphragm. The device functions in a cryogenic environment without the need of heaters to keep the sensor at constant temperatures.

  3. A cost-effective laser scanning method for mapping stream channel geometry and roughness

    Science.gov (United States)

    Lam, Norris; Nathanson, Marcus; Lundgren, Niclas; Rehnström, Robin; Lyon, Steve

    2015-04-01

    In this pilot project, we combine an Arduino Uno and SICK LMS111 outdoor laser ranging camera to acquire high resolution topographic area scans for a stream channel. The microprocessor and imaging system was installed in a custom gondola and suspended from a wire cable system. To demonstrate the systems capabilities for capturing stream channel topography, a small stream (< 2m wide) in the Krycklan Catchment Study was temporarily diverted and scanned. Area scans along the stream channel resulted in a point spacing of 4mm and a point cloud density of 5600 points/m2 for the 5m by 2m area. A grain size distribution of the streambed material was extracted from the point cloud using a moving window, local maxima search algorithm. The median, 84th and 90th percentiles (common metrics to describe channel roughness) of this distribution were found to be within the range of measured values while the largest modelled element was approximately 35% smaller than its measured counterpart. The laser scanning system captured grain sizes between 30mm and 255mm (coarse gravel/pebbles and boulders based on the Wentworth (1922) scale). This demonstrates that our system was capable of resolving both large-scale geometry (e.g. bed slope and stream channel width) and small-scale channel roughness elements (e.g. coarse gravel/pebbles and boulders) for the study area. We further show that the point cloud resolution is suitable for estimating ecohydraulic parameters such as Manning's n and hydraulic radius. Although more work is needed to fine-tune our system's design, these preliminary results are encouraging, specifically for those with a limited operational budget.

  4. A new method using Scanning Electron Microscopy (SEM) for preparation of anisopterous odonates.

    Science.gov (United States)

    Del Palacio, Alejandro; Sarmiento, Patricia Laura; Javier, Muzón

    2017-10-01

    Anisopterous odonate male's secondary genitalia is a complex of several structures, among them the vesica spermalis is the most informative with important specific characters. The observation of those characters, mostly of membranous nature, is difficult in the Scanning Electron Microscope due to dehydration and metallization processes. In this contribution, we discuss a new and low cost procedure for the observation of these characters in the SEM, compatible with the most common agents used for preserving specimens. © 2017 Wiley Periodicals, Inc.

  5. Sample preparation methods for scanning electron microscopy of homogenized Al-Mg-Si billets: A comparative study

    International Nuclear Information System (INIS)

    Österreicher, Johannes Albert; Kumar, Manoj; Schiffl, Andreas; Schwarz, Sabine; Hillebrand, Daniel; Bourret, Gilles Remi

    2016-01-01

    Characterization of Mg-Si precipitates is crucial for optimizing the homogenization heat treatment of Al-Mg-Si alloys. Although sample preparation is key for high quality scanning electron microscopy imaging, most common methods lead to dealloying of Mg-Si precipitates. In this article we systematically evaluate different sample preparation methods: mechanical polishing, etching with various reagents, and electropolishing using different electrolytes. We demonstrate that the use of a nitric acid and methanol electrolyte for electropolishing a homogenized Al-Mg-Si alloy prevents the dissolution of Mg-Si precipitates, resulting in micrographs of higher quality. This preparation method is investigated in depth and the obtained scanning electron microscopy images are compared with transmission electron micrographs: the shape and size of Mg-Si precipitates appear very similar in either method. The scanning electron micrographs allow proper identification and measurement of the Mg-Si phases including needles with lengths of roughly 200 nm. These needles are β″ precipitates as confirmed by high resolution transmission electron microscopy. - Highlights: •Secondary precipitation in homogenized 6xxx Al alloys is crucial for extrudability. •Existing sample preparation methods for SEM are improvable. •Electropolishing with nitric acid/methanol yields superior quality in SEM. •The obtained micrographs are compared to TEM micrographs.

  6. Sample preparation methods for scanning electron microscopy of homogenized Al-Mg-Si billets: A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Österreicher, Johannes Albert; Kumar, Manoj [LKR Light Metals Technologies Ranshofen, Austrian Institute of Technology, Postfach 26, 5282 Ranshofen (Austria); Schiffl, Andreas [Hammerer Aluminium Industries Extrusion GmbH, Lamprechtshausener Straße 69, 5282 Ranshofen (Austria); Schwarz, Sabine [University Service Centre for Transmission Electron Microscopy, Vienna University of Technology, Wiedner Hauptstr. 8-10, 1040 Wien (Austria); Hillebrand, Daniel [Hammerer Aluminium Industries Extrusion GmbH, Lamprechtshausener Straße 69, 5282 Ranshofen (Austria); Bourret, Gilles Remi, E-mail: gilles.bourret@sbg.ac.at [Department of Materials Science and Physics, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg (Austria)

    2016-12-15

    Characterization of Mg-Si precipitates is crucial for optimizing the homogenization heat treatment of Al-Mg-Si alloys. Although sample preparation is key for high quality scanning electron microscopy imaging, most common methods lead to dealloying of Mg-Si precipitates. In this article we systematically evaluate different sample preparation methods: mechanical polishing, etching with various reagents, and electropolishing using different electrolytes. We demonstrate that the use of a nitric acid and methanol electrolyte for electropolishing a homogenized Al-Mg-Si alloy prevents the dissolution of Mg-Si precipitates, resulting in micrographs of higher quality. This preparation method is investigated in depth and the obtained scanning electron microscopy images are compared with transmission electron micrographs: the shape and size of Mg-Si precipitates appear very similar in either method. The scanning electron micrographs allow proper identification and measurement of the Mg-Si phases including needles with lengths of roughly 200 nm. These needles are β″ precipitates as confirmed by high resolution transmission electron microscopy. - Highlights: •Secondary precipitation in homogenized 6xxx Al alloys is crucial for extrudability. •Existing sample preparation methods for SEM are improvable. •Electropolishing with nitric acid/methanol yields superior quality in SEM. •The obtained micrographs are compared to TEM micrographs.

  7. Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.).

    Science.gov (United States)

    Kwong, Qi Bin; Teh, Chee Keng; Ong, Ai Ling; Chew, Fook Tim; Mayes, Sean; Kulaveerasingam, Harikrishna; Tammi, Martti; Yeoh, Suat Hui; Appleton, David Ross; Harikrishna, Jennifer Ann

    2017-12-11

    Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals. This family is an important breeding source for developing new mother palms for superior oil yield and bunch characters. The traits of interest selected for this study were fruit-to-bunch (F/B), shell-to-fruit (S/F), kernel-to-fruit (K/F), mesocarp-to-fruit (M/F), oil per palm (O/P) and oil-to-dry mesocarp (O/DM). The marker systems evaluated were simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). RR-BLUP, Bayesian A, B, Cπ, LASSO, Ridge Regression and two machine learning methods (SVM and Random Forest) were used to evaluate GS accuracy of the traits. The kinship coefficient between individuals in this family ranged from 0.35 to 0.62. S/F and O/DM had the highest genomic heritability, whereas F/B and O/P had the lowest. The accuracies using 135 SSRs were low, with accuracies of the traits around 0.20. The average accuracy of machine learning methods was 0.24, as compared to 0.20 achieved by other methods. The trait with the highest mean accuracy was F/B (0.28), while the lowest were both M/F and O/P (0.18). By using whole genomic SNPs, the accuracies for all traits, especially for O/DM (0.43), S/F (0.39) and M/F (0.30) were improved. The average accuracy of machine learning methods was 0.32, compared to 0.31 achieved by other methods. Due to high genomic resolution, the use of whole-genome SNPs improved the efficiency of GS dramatically for oil palm and is recommended for dura breeding programs. Machine learning slightly

  8. The possibility to determine a constant of spin-orbit interaction by scanning tunneling microscopy method

    International Nuclear Information System (INIS)

    Khotkevich, N.V.; Kolesnichenko, Yu.A.; Vovk, N.P.

    2016-01-01

    The electron tunneling from the quasi-two-dimensional (surface) states with the spin-orbit interaction into bulk-mode states is studied in the framework of a model of an infinitely thin inhomogeneous tunnel magnetic barrier. The influence of the scattering of quasi-two-dimensional electrons by a single magnetic defect on the tunnel current is analyzed. Analytic formulas for the conductance of a tunnel point-contact as a function of its distance from the defect are obtained. It is shown that the analysis of the local magnetization density around the defect by means of spin-polarized scanning tunneling microscopy allows finding the constant of spin orbit interaction.

  9. Comparative Analysis of the Genomic DNA Isolation Methods on Inula sp. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Emre SEVİNDİK

    2016-12-01

    Full Text Available Simple, fast, low-cost and high throughput protocols are required for DNA isolation of plant species. In this study, phenol chloroform isoamyl alcohol and commercial (Sigma DNA isolation kit methods were applied on some Inula species that belong to Asteraceae family. Genomic DNA amounts, A260, A280, A260/A230 and purity degrees (A260/A280 that were obtained through both methods were measured through electrophoresis and spectrophotometer. Additionally, PCR amplification was realized by primer pairs specific to nrDNA ITS, cpDNA ndhF (972F-1603R and trnL-F regions. Results showed that maximum genomic DNA in nanograms obtained by phenol chloroform isoamyl alcohol method. The study also revealed that I. macrocephala had the maximum DNA and I. heterolepis had the minimum DNA amount. A260/A280 purity degrees showed that the highest and lowest purity in gDNAs obtained through phenol-choloform isoamyl alcohol method were in I.aucheriana and I. salicina, respectively. The highest and lowest purity degrees of gDNAs obtained through commercial kit was observed in I. fragilis and I. macrocephala samples, respectively. PCR amplification results showed that while band profiles of each three regions (ITS, trnL-F and ndhF did not yield positive results in PCR amplifications using phenol-choloform isoamyl alcohol method; PCR band profiles obtained through commercial kit yielded positive results. As a result, it is fair to say that the relation of genomic DNA with PCR was found to be more efficient although the maximum amount of genomic DNA was obtained through phenol chloroform isoamyl alcohol method.

  10. A simple but precise method for quantitative measurement of the quality of the laser focus in a scanning optical microscope.

    Science.gov (United States)

    Trägårdh, J; Macrae, K; Travis, C; Amor, R; Norris, G; Wilson, S H; Oppo, G-L; McConnell, G

    2015-07-01

    We report a method for characterizing the focussing laser beam exiting the objective in a laser scanning microscope. This method provides the size of the optical focus, the divergence of the beam, the ellipticity and the astigmatism. We use a microscopic-scale knife edge in the form of a simple transmission electron microscopy grid attached to a glass microscope slide, and a light-collecting optical fibre and photodiode underneath the specimen. By scanning the laser spot from a reflective to a transmitting part of the grid, a beam profile in the form of an error function can be obtained and by repeating this with the knife edge at different axial positions relative to the beam waist, the divergence and astigmatism of the postobjective laser beam can be obtained. The measured divergence can be used to quantify how much of the full numerical aperture of the lens is used in practice. We present data of the beam radius, beam divergence, ellipticity and astigmatism obtained with low (0.15, 0.7) and high (1.3) numerical aperture lenses and lasers commonly used in confocal and multiphoton laser scanning microscopy. Our knife-edge method has several advantages over alternative knife-edge methods used in microscopy including that the knife edge is easy to prepare, that the beam can be characterized also directly under a cover slip, as necessary to reduce spherical aberrations for objectives designed to be used with a cover slip, and it is suitable for use with commercial laser scanning microscopes where access to the laser beam can be limited. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  11. Scan Statistics

    CERN Document Server

    Glaz, Joseph

    2009-01-01

    Suitable for graduate students and researchers in applied probability and statistics, as well as for scientists in biology, computer science, pharmaceutical science and medicine, this title brings together a collection of chapters illustrating the depth and diversity of theory, methods and applications in the area of scan statistics.

  12. High-definition, single-scan 2D MRI in inhomogeneous fields using spatial encoding methods.

    Science.gov (United States)

    Ben-Eliezer, Noam; Shrot, Yoav; Frydman, Lucio

    2010-01-01

    An approach has been recently introduced for acquiring two-dimensional (2D) nuclear magnetic resonance images in a single scan, based on the spatial encoding of the spin interactions. This article explores the potential of integrating this spatial encoding together with conventional temporal encoding principles, to produce 2D single-shot images with moderate field of views. The resulting "hybrid" imaging scheme is shown to be superior to traditional schemes in non-homogeneous magnetic field environments. An enhancement of previously discussed pulse sequences is also proposed, whereby distortions affecting the image along the spatially encoded axis are eliminated. This new variant is also characterized by a refocusing of T(2)(*) effects, leading to a restoration of high-definition images for regions which would otherwise be highly dephased and thus not visible. These single-scan 2D images are characterized by improved signal-to-noise ratios and a genuine T(2) contrast, albeit not free from inhomogeneity distortions. Simple postprocessing algorithms relying on inhomogeneity phase maps of the imaged object can successfully remove most of these residual distortions. Initial results suggest that this acquisition scheme has the potential to overcome strong field inhomogeneities acting over extended acquisition durations, exceeding 100 ms for a single-shot image.

  13. Validation of a new noniterative method for accurate position determination of a scanning laser vibrometer

    Science.gov (United States)

    Pauwels, Steven; Boucart, Nick; Dierckx, Benoit; Van Vlierberghe, Pieter

    2000-05-01

    The use of a scanning laser Doppler vibrometer for vibration testing is becoming a popular instrument. The scanning laser Doppler vibrometer is a non-contacting transducer that can measure many points at a high spatial resolution in a short time. Manually aiming the laser beam at the points that need to be measured is very time consuming. In order to use it effectively, the position of the laser Doppler vibrometer needs to be determined relative to the structure. If the position of the laser Doppler vibrometer is known, any visible point on the structure can be hit and measured automatically. A new algorithm for this position determination is developed, based on a geometry model of the structure. After manually aiming the laser beam at 4 or more known points, the laser position and orientation relative to the structure is determined. Using this calculated position and orientation a list with the mirror angles for every measurement point is generated, which is used during the measurement. The algorithm is validated using 3 practical cases. In the first case a plate is used of which the points are measured very accurately, so the geometry model is assumed to be perfect. The second case is a brake disc. Here the geometry points are measured with a ruler, thus not so accurate. The final validation is done on a body in white of a car. A reduced finite element model is used as geometry model. This calibration shows that the new algorithm is very effective and practically usable.

  14. A method for accurate detection of genomic microdeletions using real-time quantitative PCR

    Directory of Open Access Journals (Sweden)

    Bassett Anne S

    2005-12-01

    Full Text Available Abstract Background Quantitative Polymerase Chain Reaction (qPCR is a well-established method for quantifying levels of gene expression, but has not been routinely applied to the detection of constitutional copy number alterations of human genomic DNA. Microdeletions or microduplications of the human genome are associated with a variety of genetic disorders. Although, clinical laboratories routinely use fluorescence in situ hybridization (FISH to identify such cryptic genomic alterations, there remains a significant number of individuals in which constitutional genomic imbalance is suspected, based on clinical parameters, but cannot be readily detected using current cytogenetic techniques. Results In this study, a novel application for real-time qPCR is presented that can be used to reproducibly detect chromosomal microdeletions and microduplications. This approach was applied to DNA from a series of patient samples and controls to validate genomic copy number alteration at cytoband 22q11. The study group comprised 12 patients with clinical symptoms of chromosome 22q11 deletion syndrome (22q11DS, 1 patient trisomic for 22q11 and 4 normal controls. 6 of the patients (group 1 had known hemizygous deletions, as detected by standard diagnostic FISH, whilst the remaining 6 patients (group 2 were classified as 22q11DS negative using the clinical FISH assay. Screening of the patients and controls with a set of 10 real time qPCR primers, spanning the 22q11.2-deleted region and flanking sequence, confirmed the FISH assay results for all patients with 100% concordance. Moreover, this qPCR enabled a refinement of the region of deletion at 22q11. Analysis of DNA from chromosome 22 trisomic sample demonstrated genomic duplication within 22q11. Conclusion In this paper we present a qPCR approach for the detection of chromosomal microdeletions and microduplications. The strategic use of in silico modelling for qPCR primer design to avoid regions of repetitive

  15. A quantitative comparison of single-cell whole genome amplification methods.

    Directory of Open Access Journals (Sweden)

    Charles F A de Bourcy

    Full Text Available Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA, Multiple Annealing and Looping Based Amplification Cycles (MALBAC, and the PicoPLEX single-cell WGA kit (NEB-WGA. We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.

  16. Characterization of electro-oxidation catalysts using scanning electrochemical and mass spectral methods

    Science.gov (United States)

    Jambunathan, Krishnakumar

    Low temperature fuel cells have many potential benefits, including high efficiency, high energy density and environmental friendliness. However, logistically appealing fuels for this system, such as reformed hydrocarbons or alcohols, exhibit poor performance because of catalyst poisoning that occurs during oxidation at the anode. This research focuses on the analysis of several model fuels and catalyst materials to understand the impact of catalyst poisoning on reactivity. Two novel experimental tools were developed based upon the local measurement of catalyst performance using scanning, reactivity mapping probes. The Scanning Electrochemical Microscope (SECM) was used to directly measure the rate constant for hydrogen oxidation in the presence and absence of dissolved CO. The Scanning Differential Electrochemical Mass Spectrometer (SDEMS) was exploited to measure the partial and complete oxidation products of methanol and ethanol oxidation. The reactivity of Pt and Pt/Ru catalysts towards the hydrogen oxidation reaction in the absence and presence of adsorbed CO was elucidated using the SECM. Steady state rate constant measurements in the absence of CO showed that the rate of hydrogen oxidation reaction exceeded 1 cms-1 . Steady state rate constant measurements in the presence of CO indicated that the platinum surface is completely inactive due to adsorbed CO. Addition of as little as 6% Ru to the Pt electrode was found to significantly improve the activity of the electrode towards CO removal. SDEMS was used to study the electro-oxidation of methanol on Pt xRuy electrodes at different electrode potentials and temperatures. Screening measurements performed with the SDEMS showed that PtxRu y electrodes containing 6--40% Ru had the highest activity for methanol oxidation. Current efficiencies for CO2 were also calculated under different conditions. SDEMS was also used to study the electro-oxidation of ethanol on Pt xRuy electrodes. The reaction was found to occur

  17. Comparison of 2 root surface area measurement methods: 3-dimensional laser scanning and cone-beam computed tomography

    International Nuclear Information System (INIS)

    Tasanapanont, Jintana; Apisariyakul, Janya; Wattanachai, Tanapan; Jotikasthira, Dhirawat; Sriwilas, Patiyut; Midtboe, Marit

    2017-01-01

    The aim of this study was to compare the use of 3-dimensional (3D) laser scanning and cone-beam computed tomography (CBCT) as methods of root surface measurement. Thirty teeth (15 maxillary first premolars and 15 mandibular first premolars) from 8 patients who required extractions for orthodontic treatment were selected. Before extraction, pre-treatment CBCT images of all the patients were recorded. First, a CBCT image was imported into simulation software (Mimics version 15.01; Materialise, Leuven, Belgium) and the root surface area of each tooth was calculated using 3-Matic (version 7.01, Materialise, Leuven, Belgium). After extraction, all the teeth were scanned and the root surface area of each extracted tooth was calculated. The root surface areas calculated using these 2 measurement methods were analyzed using the paired t-test (P<.05). Correlations between the 2 methods were determined by calculating the Pearson correlation coefficient. The intraclass correlation coefficient (ICC) was used to assess intraobserver reliability. The root surface area measurements (230.11±41.97 mm"2) obtained using CBCT were slightly greater than those (229.31±42.46 mm2) obtained using 3D laser scanning, but not significantly (P=.425). A high Pearson correlation coefficient was found between the CBCT and the 3D laser scanner measurements. The intraobserver ICC was 1.000 for 3D laser scanning and 0.990 for CBCT. This study presents a novel CBCT approach for measuring the root surface area; this technique can be used for estimating the root surface area of non-extracted teeth

  18. Comparison of 2 root surface area measurement methods: 3-dimensional laser scanning and cone-beam computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Tasanapanont, Jintana; Apisariyakul, Janya; Wattanachai, Tanapan; Jotikasthira, Dhirawat [Dept. of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai (Thailand); Sriwilas, Patiyut [Dept. of Radiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Midtboe, Marit [Dept. of Clinical Dentistry - Orthodontics, Faculty of Medicine and Dentistry, University of Bergen, Bergen (Norway)

    2017-06-15

    The aim of this study was to compare the use of 3-dimensional (3D) laser scanning and cone-beam computed tomography (CBCT) as methods of root surface measurement. Thirty teeth (15 maxillary first premolars and 15 mandibular first premolars) from 8 patients who required extractions for orthodontic treatment were selected. Before extraction, pre-treatment CBCT images of all the patients were recorded. First, a CBCT image was imported into simulation software (Mimics version 15.01; Materialise, Leuven, Belgium) and the root surface area of each tooth was calculated using 3-Matic (version 7.01, Materialise, Leuven, Belgium). After extraction, all the teeth were scanned and the root surface area of each extracted tooth was calculated. The root surface areas calculated using these 2 measurement methods were analyzed using the paired t-test (P<.05). Correlations between the 2 methods were determined by calculating the Pearson correlation coefficient. The intraclass correlation coefficient (ICC) was used to assess intraobserver reliability. The root surface area measurements (230.11±41.97 mm{sup 2}) obtained using CBCT were slightly greater than those (229.31±42.46 mm2) obtained using 3D laser scanning, but not significantly (P=.425). A high Pearson correlation coefficient was found between the CBCT and the 3D laser scanner measurements. The intraobserver ICC was 1.000 for 3D laser scanning and 0.990 for CBCT. This study presents a novel CBCT approach for measuring the root surface area; this technique can be used for estimating the root surface area of non-extracted teeth.

  19. A new method of CT scanning for the diagnosis of mandibular fractures; A preliminary report: diagnosis of condyle fractures

    Energy Technology Data Exchange (ETDEWEB)

    Tsukagoshi, Taku; Satoh, Kaneshige; Onizuka, Takuya (Showa Univ., Tokyo (Japan). School of Medicine)

    1990-08-01

    The condylar neck of the mandible is one of the most common fracture sites in the facial skeleton. Such a fracture is routinely diagnosed by A-P, lateral oblique, and Towne projection roentgenography or orthopantomography. Despite the combination of these films, fracture of the neck of the mandible is still difficult to diagnose definitely. Therefore, a new CT scanning method was developed for diagnosing fractures of the neck of the condylar mandible. The CT axis is projected along the length of the mandible, extending from the condyle to the symphysis. This projection visualizes both the condyle and the mandibular symphysis in the same plane. The patient is placed in a supine position with the head fully extended. The base line, a line extending from the midpoint of the glenoid fossa to the menton, is determined with a lateral facial cephalogram. CT scanning with a 5 mm window is performed in parallel with and 2 cm anterior to and 2 cm posterior to the base line. When CT scanning was performed in a healthy volunteer, the condition of the condyle and the condylar neck of the mandible was clearly shown, and the view extended from the condyle to the symphysis. For automobile accident patients in whom fracture of the neck of the mandible was associated with fracture of the symphysis, two fractures were found in the same plane. A newly developed CT scanning technique is useful in the diagnosis of fractures of the condylar neck of the mandible and in the identification of fractures at other mandibular sites. It also allows scanning of patients in a supine position, which may aid in managing patients with multiple traumas. (N.K.).

  20. Thermal conductivity profile determination in proton-irradiated ZrC by spatial and frequency scanning thermal wave methods

    International Nuclear Information System (INIS)

    Jensen, C.; Chirtoc, M.; Horny, N.; Antoniow, J. S.; Pron, H.; Ban, H.

    2013-01-01

    Using complementary thermal wave methods, the irradiation damaged region of zirconium carbide (ZrC) is characterized by quantifiably profiling the thermophysical property degradation. The ZrC sample was irradiated by a 2.6 MeV proton beam at 600 °C to a dose of 1.75 displacements per atom. Spatial scanning techniques including scanning thermal microscopy (SThM), lock-in infrared thermography (lock-in IRT), and photothermal radiometry (PTR) were used to directly map the in-depth profile of thermal conductivity on a cross section of the ZrC sample. The advantages and limitations of each system are discussed and compared, finding consistent results from all techniques. SThM provides the best resolution finding a very uniform thermal conductivity envelope in the damaged region measuring ∼52 ± 2 μm deep. Frequency-based scanning PTR provides quantification of the thermal parameters of the sample using the SThM measured profile to provide validation of a heating model. Measured irradiated and virgin thermal conductivities are found to be 11.9 ± 0.5 W m −1 K −1 and 26.7 ±1 W m −1 K −1 , respectively. A thermal resistance evidenced in the frequency spectra of the PTR results was calculated to be (1.58 ± 0.1) × 10 −6 m 2 K W −1 . The measured thermal conductivity values compare well with the thermal conductivity extracted from the SThM calibrated signal and the spatially scanned PTR. Combined spatial and frequency scanning techniques are shown to provide a valuable, complementary combination for thermal property characterization of proton-irradiated ZrC. Such methodology could be useful for other studies of ion-irradiated materials

  1. The memory effect of nanoscale memristors investigated by conducting scanning probe microscopy methods

    Directory of Open Access Journals (Sweden)

    César Moreno

    2012-11-01

    Full Text Available We report on the use of scanning force microscopy as a versatile tool for the electrical characterization of nanoscale memristors fabricated on ultrathin La0.7Sr0.3MnO3 (LSMO films. Combining conventional conductive imaging and nanoscale lithography, reversible switching between low-resistive (ON and high-resistive (OFF states was locally achieved by applying voltages within the range of a few volts. Retention times of several months were tested for both ON and OFF states. Spectroscopy modes were used to investigate the I–V characteristics of the different resistive states. This permitted the correlation of device rectification (reset with the voltage employed to induce each particular state. Analytical simulations by using a nonlinear dopant drift within a memristor device explain the experimental I–V bipolar cycles.

  2. Systematic differences in the response of genetic variation to pedigree and genome-based selection methods.

    Science.gov (United States)

    Heidaritabar, M; Vereijken, A; Muir, W M; Meuwissen, T; Cheng, H; Megens, H-J; Groenen, M A M; Bastiaansen, J W M

    2014-12-01

    Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P selected regions were identified. Empirical thresholds for local allele frequency changes were determined from gene dropping, and differed considerably between GS (0.167-0.198) and BLUP (0.105-0.126). Between lines, the genomic regions with large changes in allele frequencies showed limited overlap. Our results show that GS applies selection pressure much more locally than BLUP, resulting in larger allele frequency changes. With these results, novel insights into the nature of selection on quantitative traits have been gained and important questions regarding the long-term impact of GS are raised. The rapid changes to a part of the genetic architecture, while another part may not be selected, at least in the short term, require careful consideration, especially when selection occurs before phenotypes are observed.

  3. Constructs and methods for genome editing and genetic engineering of fungi and protists

    Science.gov (United States)

    Hittinger, Christopher Todd; Alexander, William Gerald

    2018-01-30

    Provided herein are constructs for genome editing or genetic engineering in fungi or protists, methods of using the constructs and media for use in selecting cells. The construct include a polynucleotide encoding a thymidine kinase operably connected to a promoter, suitably a constitutive promoter; a polynucleotide encoding an endonuclease operably connected to an inducible promoter; and a recognition site for the endonuclease. The constructs may also include selectable markers for use in selecting recombinations.

  4. TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile.

    Science.gov (United States)

    Huang, Yen-Tsung; Hsu, Thomas; Christiani, David C

    2014-01-01

    The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X (2) distributions that can be obtained using permutation with scaled X (2) approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (number data, and causal mechanisms of the five pathways require further study.

  5. Detection of Ground Clutter from Weather Radar Using a Dual-Polarization and Dual-Scan Method

    Directory of Open Access Journals (Sweden)

    Mohammad-Hossein Golbon-Haghighi

    2016-06-01

    Full Text Available A novel dual-polarization and dual-scan (DPDS classification algorithm is developed for clutter detection in weather radar observations. Two consecutive scans of dual-polarization radar echoes are jointly processed to estimate auto- and cross-correlation functions. Discriminants are then defined and estimated in order to separate clutter from weather based on their physical and statistical properties. An optimal Bayesian classifier is used to make a decision on clutter presence from the estimated discriminant functions. The DPDS algorithm is applied to the data collected with the KOUN polarimetric radar and compared with the existing detection methods. It is shown that the DPDS algorithm yields a higher probability of detection and lower false alarm rate in clutter detection.

  6. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

    Directory of Open Access Journals (Sweden)

    Tetreau Guillaume

    2008-10-01

    Full Text Available Abstract Background For most organisms, developing hundreds of genetic markers spanning the whole genome still requires excessive if not unrealistic efforts. In this context, there is an obvious need for methodologies allowing the low-cost, fast and high-throughput genotyping of virtually any species, such as the Diversity Arrays Technology (DArT. One of the crucial steps of the DArT technique is the genome complexity reduction, which allows obtaining a genomic representation characteristic of the studied DNA sample and necessary for subsequent genotyping. In this article, using the mosquito Aedes aegypti as a study model, we describe a new genome complexity reduction method taking advantage of the abundance of miniature inverted repeat transposable elements (MITEs in the genome of this species. Results Ae. aegypti genomic representations were produced following a two-step procedure: (1 restriction digestion of the genomic DNA and simultaneous ligation of a specific adaptor to compatible ends, and (2 amplification of restriction fragments containing a particular MITE element called Pony using two primers, one annealing to the adaptor sequence and one annealing to a conserved sequence motif of the Pony element. Using this protocol, we constructed a library comprising more than 6,000 DArT clones, of which at least 5.70% were highly reliable polymorphic markers for two closely related mosquito strains separated by only a few generations of artificial selection. Within this dataset, linkage disequilibrium was low, and marker redundancy was evaluated at 2.86% only. Most of the detected genetic variability was observed between the two studied mosquito strains, but individuals of the same strain could still be clearly distinguished. Conclusion The new complexity reduction method was particularly efficient to reveal genetic polymorphisms in Ae. egypti. Overall, our results testify of the flexibility of the DArT genotyping technique and open new

  7. A Review of Study Designs and Statistical Methods for Genomic Epidemiology Studies using Next Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Qian eWang

    2015-04-01

    Full Text Available Results from numerous linkage and association studies have greatly deepened scientists’ understanding of the genetic basis of many human diseases, yet some important questions remain unanswered. For example, although a large number of disease-associated loci have been identified from genome-wide association studies (GWAS in the past 10 years, it is challenging to interpret these results as most disease-associated markers have no clear functional roles in disease etiology, and all the identified genomic factors only explain a small portion of disease heritability. With the help of next-generation sequencing (NGS, diverse types of genomic and epigenetic variations can be detected with high accuracy. More importantly, instead of using linkage disequilibrium to detect association signals based on a set of pre-set probes, NGS allows researchers to directly study all the variants in each individual, therefore promises opportunities for identifying functional variants and a more comprehensive dissection of disease heritability. Although the current scale of NGS studies is still limited due to the high cost, the success of several recent studies suggests the great potential for applying NGS in genomic epidemiology, especially as the cost of sequencing continues to drop. In this review, we discuss several pioneer applications of NGS, summarize scientific discoveries for rare and complex diseases, and compare various study designs including targeted sequencing and whole-genome sequencing using population-based and family-based cohorts. Finally, we highlight recent advancements in statistical methods proposed for sequencing analysis, including group-based association tests, meta-analysis techniques, and annotation tools for variant prioritization.

  8. A Lightweight Surface Reconstruction Method for Online 3D Scanning Point Cloud Data Oriented toward 3D Printing

    Directory of Open Access Journals (Sweden)

    Buyun Sheng

    2018-01-01

    Full Text Available The existing surface reconstruction algorithms currently reconstruct large amounts of mesh data. Consequently, many of these algorithms cannot meet the efficiency requirements of real-time data transmission in a web environment. This paper proposes a lightweight surface reconstruction method for online 3D scanned point cloud data oriented toward 3D printing. The proposed online lightweight surface reconstruction algorithm is composed of a point cloud update algorithm (PCU, a rapid iterative closest point algorithm (RICP, and an improved Poisson surface reconstruction algorithm (IPSR. The generated lightweight point cloud data are pretreated using an updating and rapid registration method. The Poisson surface reconstruction is also accomplished by a pretreatment to recompute the point cloud normal vectors; this approach is based on a least squares method, and the postprocessing of the PDE patch generation was based on biharmonic-like fourth-order PDEs, which effectively reduces the amount of reconstructed mesh data and improves the efficiency of the algorithm. This method was verified using an online personalized customization system that was developed with WebGL and oriented toward 3D printing. The experimental results indicate that this method can generate a lightweight 3D scanning mesh rapidly and efficiently in a web environment.

  9. A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains.

    Science.gov (United States)

    Zhang, Y J; Zhang, S; Liu, X Z; Wen, H A; Wang, M

    2010-07-01

    A simple and rapid method (designated thermolysis) for extracting genomic DNA from bulk fungal strains was described. In the thermolysis method, a few mycelia or yeast cells were first rinsed with pure water to remove potential PCR inhibitors and then incubated in a lysis buffer at 85 degrees C to break down cell walls and membranes. This method was used to extract genomic DNA from large numbers of fungal strains (more than 92 species, 35 genera of three phyla) isolated from different sections of natural Ophiocordyceps sinensis specimens. Regions of interest from high as well as single-copy number genes were successfully amplified from the extracted DNA samples. The DNA samples obtained by this method can be stored at -20 degrees C for over 1 year. The method was effective, easy and fast and allowed batch DNA extraction from multiple fungal isolates. Use of the thermolysis method will allow researchers to obtain DNA from fungi quickly for use in molecular assays. This method requires only minute quantities of starting material and is suitable for diverse fungal species.

  10. 3D And 4D Cloud Lifecycle Investigations Using Innovative Scanning Radar Analysis Methods. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Kollias, Pavlos [Stony Brook Univ., NY (United States)

    2017-04-23

    With the vast upgrades to the ARM program radar measurement capabilities in 2010 and beyond, our ability to probe the 3D structure of clouds and associated precipitation has increased dramatically. This project build on the PI's and co-I's expertisein the analysis of radar observations. The first research thrust aims to document the 3D morphological (as depicted by the radar reflectivity structure) and 3D dynamical (cloud$-$scale eddies) structure of boundary layer clouds. Unraveling the 3D dynamical structure of stratocumulus and shallow cumulus clouds requires decomposition of the environmental wind contribution and particle sedimentation velocity from the observed radial Doppler velocity. The second thrust proposes to unravel the mechanism of cumulus entrainment (location, scales) and its impact on microphysics utilizing radar measurements from the vertically pointing and new scanning radars at the ARM sites. The third research thrust requires the development of a cloud$-$tracking algorithm that monitors the properties of cloud.

  11. Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis

    Directory of Open Access Journals (Sweden)

    Ueki Masao

    2012-05-01

    Full Text Available Abstract Background Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Individual hypothesis testing for SNP-SNP pairs as in common genome-wide association study (GWAS however involves difficulty in setting overall p-value due to complicated correlation structure, namely, the multiple testing problem that causes unacceptable false negative results. A large number of SNP-SNP pairs than sample size, so-called the large p small n problem, precludes simultaneous analysis using multiple regression. The method that overcomes above issues is thus needed. Results We adopt an up-to-date method for ultrahigh-dimensional variable selection termed the sure independence screening (SIS for appropriate handling of numerous number of SNP-SNP interactions by including them as predictor variables in logistic regression. We propose ranking strategy using promising dummy coding methods and following variable selection procedure in the SIS method suitably modified for gene-gene interaction analysis. We also implemented the procedures in a software program, EPISIS, using the cost-effective GPGPU (General-purpose computing on graphics processing units technology. EPISIS can complete exhaustive search for SNP-SNP interactions in standard GWAS dataset within several hours. The proposed method works successfully in simulation experiments and in application to real WTCCC (Wellcome Trust Case–control Consortium data. Conclusions Based on the machine-learning principle, the proposed method gives powerful and flexible genome-wide search for various patterns of gene-gene interaction.

  12. Experimental Quasi-Microwave Whole-Body Averaged SAR Estimation Method Using Cylindrical-External Field Scanning

    Science.gov (United States)

    Kawamura, Yoshifumi; Hikage, Takashi; Nojima, Toshio

    The aim of this study is to develop a new whole-body averaged specific absorption rate (SAR) estimation method based on the external-cylindrical field scanning technique. This technique is adopted with the goal of simplifying the dosimetry estimation of human phantoms that have different postures or sizes. An experimental scaled model system is constructed. In order to examine the validity of the proposed method for realistic human models, we discuss the pros and cons of measurements and numerical analyses based on the finite-difference time-domain (FDTD) method. We consider the anatomical European human phantoms and plane-wave in the 2GHz mobile phone frequency band. The measured whole-body averaged SAR results obtained by the proposed method are compared with the results of the FDTD analyses.

  13. Box-scan: A novel 3DXRD method for studies of recrystallization and grain growth

    DEFF Research Database (Denmark)

    Lyckegaard, Allan; Poulsen, Henning Friis; Ludwig, Wolfgang

    2012-01-01

    Within the last decade a number of x-ray diffraction methods have been presented for non-destructive 3D characterization of polycrystalline materials. 3DXRD [1] and Diffraction Contrast Tomography [2,3,4] are examples of such methods providing full spatial and crystallographic information...... of the individual grains. Both methods rely on specially designed high-resolution near-field detectors for acquire the shape of the illuminated grains, and therefore the spatial resolution is for both methods limited by the resolution of the detector, currently ~2 micrometers. Applying these methods using...... for dynamic studies requiring high temporal resolution and set-ups involving bulky sample environments (e.g. furnaces, stress-rigs etc.)...

  14. RESEARCH ON COORDINATE TRANSFORMATION METHOD OF GB-SAR IMAGE SUPPORTED BY 3D LASER SCANNING TECHNOLOGY

    Directory of Open Access Journals (Sweden)

    P. Wang

    2018-04-01

    Full Text Available In the image plane of GB-SAR, identification of deformation distribution is usually carried out by artificial interpretation. This method requires analysts to have adequate experience of radar imaging and target recognition, otherwise it can easily cause false recognition of deformation target or region. Therefore, it is very meaningful to connect two-dimensional (2D plane coordinate system with the common three-dimensional (3D terrain coordinate system. To improve the global accuracy and reliability of the transformation from 2D coordinates of GB-SAR images to local 3D coordinates, and overcome the limitation of traditional similarity transformation parameter estimation method, 3D laser scanning data is used to assist the transformation of GB-SAR image coordinates. A straight line fitting method for calculating horizontal angle was proposed in this paper. After projection into a consistent imaging plane, we can calculate horizontal rotation angle by using the linear characteristics of the structure in radar image and the 3D coordinate system. Aided by external elevation information by 3D laser scanning technology, we completed the matching of point clouds and pixels on the projection plane according to the geometric projection principle of GB-SAR imaging realizing the transformation calculation of GB-SAR image coordinates to local 3D coordinates. Finally, the effectiveness of the method is verified by the GB-SAR deformation monitoring experiment on the high slope of Geheyan dam.

  15. Research on Coordinate Transformation Method of Gb-Sar Image Supported by 3d Laser Scanning Technology

    Science.gov (United States)

    Wang, P.; Xing, C.

    2018-04-01

    In the image plane of GB-SAR, identification of deformation distribution is usually carried out by artificial interpretation. This method requires analysts to have adequate experience of radar imaging and target recognition, otherwise it can easily cause false recognition of deformation target or region. Therefore, it is very meaningful to connect two-dimensional (2D) plane coordinate system with the common three-dimensional (3D) terrain coordinate system. To improve the global accuracy and reliability of the transformation from 2D coordinates of GB-SAR images to local 3D coordinates, and overcome the limitation of traditional similarity transformation parameter estimation method, 3D laser scanning data is used to assist the transformation of GB-SAR image coordinates. A straight line fitting method for calculating horizontal angle was proposed in this paper. After projection into a consistent imaging plane, we can calculate horizontal rotation angle by using the linear characteristics of the structure in radar image and the 3D coordinate system. Aided by external elevation information by 3D laser scanning technology, we completed the matching of point clouds and pixels on the projection plane according to the geometric projection principle of GB-SAR imaging realizing the transformation calculation of GB-SAR image coordinates to local 3D coordinates. Finally, the effectiveness of the method is verified by the GB-SAR deformation monitoring experiment on the high slope of Geheyan dam.

  16. Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

    Science.gov (United States)

    Borrayo, Ernesto; Mendizabal-Ruiz, E Gerardo; Vélez-Pérez, Hugo; Romo-Vázquez, Rebeca; Mendizabal, Adriana P; Morales, J Alejandro

    2014-01-01

    Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

  17. Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t_db_link_en.zip (36.3 KB) - 6 Genome analysis methods pgdbj_dna_marker_linkage_map_genome_analysis_methods_... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  18. Update History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

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    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...B link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods is opened. About This...ate History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  19. Determination of the oxidizing property: proposal of an alternative method based on differential scanning calorimetry

    International Nuclear Information System (INIS)

    Gigante, L.; Dellavedova, M.; Pasturenzi, C.; Lunghi, A.; Mattarella, M.; Cardillo, P.

    2008-01-01

    Determination of chemical-physical and hazardous properties of substances is a very important matter in the chemical industry, considering the growing attention of public opinion regarding safety and eco-compatibility aspects of products. In the present work, attention was focused on characterization of oxidizing properties. In case of solid compounds, the current method (Dir 84/449/CEE 6) compares the maximum combustion rate of the examined substance to the maximum combustion rate of a reference mixture. This method shows a lot of disvantages and does not provide a quantitative result. In the following work an alternative method, based on DSC measurements, is proposed for the determination of oxidizing properties. [it

  20. Model Robust Calibration: Method and Application to Electronically-Scanned Pressure Transducers

    Science.gov (United States)

    Walker, Eric L.; Starnes, B. Alden; Birch, Jeffery B.; Mays, James E.

    2010-01-01

    This article presents the application of a recently developed statistical regression method to the controlled instrument calibration problem. The statistical method of Model Robust Regression (MRR), developed by Mays, Birch, and Starnes, is shown to improve instrument calibration by reducing the reliance of the calibration on a predetermined parametric (e.g. polynomial, exponential, logarithmic) model. This is accomplished by allowing fits from the predetermined parametric model to be augmented by a certain portion of a fit to the residuals from the initial regression using a nonparametric (locally parametric) regression technique. The method is demonstrated for the absolute scale calibration of silicon-based pressure transducers.

  1. Applications of asynoptic space - Time Fourier transform methods to scanning satellite measurements

    Science.gov (United States)

    Lait, Leslie R.; Stanford, John L.

    1988-01-01

    A method proposed by Salby (1982) for computing the zonal space-time Fourier transform of asynoptically acquired satellite data is discussed. The method and its relationship to other techniques are briefly described, and possible problems in applying it to real data are outlined. Examples of results obtained using this technique are given which demonstrate its sensitivity to small-amplitude signals. A number of waves are found which have previously been observed as well as two not heretofore reported. A possible extension of the method which could increase temporal and longitudinal resolution is described.

  2. Automated lesion detection on MRI scans using combined unsupervised and supervised methods

    International Nuclear Information System (INIS)

    Guo, Dazhou; Fridriksson, Julius; Fillmore, Paul; Rorden, Christopher; Yu, Hongkai; Zheng, Kang; Wang, Song

    2015-01-01

    Accurate and precise detection of brain lesions on MR images (MRI) is paramount for accurately relating lesion location to impaired behavior. In this paper, we present a novel method to automatically detect brain lesions from a T1-weighted 3D MRI. The proposed method combines the advantages of both unsupervised and supervised methods. First, unsupervised methods perform a unified segmentation normalization to warp images from the native space into a standard space and to generate probability maps for different tissue types, e.g., gray matter, white matter and fluid. This allows us to construct an initial lesion probability map by comparing the normalized MRI to healthy control subjects. Then, we perform non-rigid and reversible atlas-based registration to refine the probability maps of gray matter, white matter, external CSF, ventricle, and lesions. These probability maps are combined with the normalized MRI to construct three types of features, with which we use supervised methods to train three support vector machine (SVM) classifiers for a combined classifier. Finally, the combined classifier is used to accomplish lesion detection. We tested this method using T1-weighted MRIs from 60 in-house stroke patients. Using leave-one-out cross validation, the proposed method can achieve an average Dice coefficient of 73.1 % when compared to lesion maps hand-delineated by trained neurologists. Furthermore, we tested the proposed method on the T1-weighted MRIs in the MICCAI BRATS 2012 dataset. The proposed method can achieve an average Dice coefficient of 66.5 % in comparison to the expert annotated tumor maps provided in MICCAI BRATS 2012 dataset. In addition, on these two test datasets, the proposed method shows competitive performance to three state-of-the-art methods, including Stamatakis et al., Seghier et al., and Sanjuan et al. In this paper, we introduced a novel automated procedure for lesion detection from T1-weighted MRIs by combining both an unsupervised and a

  3. [Molecular beacon based PNA-FISH method combined with fluorescence scanning for rapid detection of Listeria monocytogenes].

    Science.gov (United States)

    Wu, Shan; Zhang, Xiaofeng; Shuai, Jiangbing; Li, Ke; Yu, Huizhen; Jin, Chenchen

    2016-07-04

    To simplify the PNA-FISH (Peptide nucleic acid-fluorescence in situ hybridization) test, molecular beacon based PNA probe combined with fluorescence scanning detection technology was applied to replace the original microscope observation to detect Listeria monocytogenes The 5′ end and 3′ end of the L. monocytogenes specific PNA probes were labeled with the fluorescent group and the quenching group respectively, to form a molecular beacon based PNA probe. When PNA probe used for fluorescence scanning and N1 treatment as the control, the false positive rate was 11.4%, and the false negative rate was 0; when N2 treatment as the control, the false positive rate decreased to 4.3%, but the false negative rate rose to 18.6%. When beacon based PNA probe used for fluorescence scanning, taken N1 treatment as blank control, the false positive rate was 8.6%, and the false negative rate was 1.4%; taken N2 treatment as blank control, the false positive rate was 5.7%, and the false negative rate was 1.4%. Compared with PNA probe, molecular beacon based PNA probe can effectively reduce false positives and false negatives. The success rates of hybridization of the two PNA probes were 83.3% and 95.2% respectively; and the rates of the two beacon based PNA probes were 91.7% and 90.5% respectively, which indicated that labeling the both ends of the PNA probe dose not decrease the hybridization rate with the target bacteria. The combination of liquid phase PNA-FISH and fluorescence scanning method, can significantly improve the detection efficiency.

  4. Manipulations of Wavefront Propagation: Useful Methods and Applications for Interferometric Measurements and Scanning

    Directory of Open Access Journals (Sweden)

    Avi Karsenty

    2017-01-01

    Full Text Available Phase measurements obtained by high-coherence interferometry are restricted by the 2π ambiguity, to height differences smaller than λ/2. A further restriction in most interferometric systems is for focusing the system on the measured object. We present two methods that overcome these restrictions. In the first method, different segments of a measured wavefront are digitally propagated and focused locally after measurement. The divergent distances, by which the diverse segments of the wavefront are propagated in order to achieve a focused image, provide enough information so as to resolve the 2π ambiguity. The second method employs an interferogram obtained by a spectrum constituting a small number of wavelengths. The magnitude of the interferogram’s modulations is utilized to resolve the 2π ambiguity. Such methods of wavefront propagation enable several applications such as focusing and resolving the 2π ambiguity, as described in the article.

  5. Continuous-Scan Phased Array Measurement Methods for Turbofan Engine Acoustic Testing, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — ATA Engineering, Inc., (ATA) proposes an SBIR project to advance the technology readiness level (TRL) of a method for measuring phased array acoustic data for...

  6. Simply scan--optical methods for elemental carbon measurement in diesel exhaust particulate.

    Science.gov (United States)

    Forder, James A

    2014-08-01

    This article describes a performance assessment of three optical methods, a Magee Scientific OT21 Transmissometer, a Hach-Lange Microcolor II difference gloss meter, and a combination of an office scanner with Adobe Photoshop software. The optical methods measure filter staining as a proxy for elemental carbon in diesel exhaust particulate (DEP) exposure assessment and the suitability of each as a replacement for the existing Bosch meter optical method. Filters loaded with DEP were produced from air in a non-coal mine and the exhaust gases from a mobile crane. These were measured with each apparatus and then by combustion to obtain a reference elemental carbon value. The results from each apparatus were then plotted against both the Bosch number and reference elemental carbon values. The equations of the best fit lines for these plots were derived, and these gave functions for elemental carbon and Bosch number from the output of each new optical method. For each optical method, the range of DEP loadings which can be measured has been determined, and conversion equations for elemental carbon and Bosch number have been obtained. All three optical methods studied will effectively quantify blackness as a measure of elemental carbon. Of these the Magee Scientific OT21 transmissometer has the best performance. The Microcolor II and scanner/photoshop methods will in addition allow conversion to Bosch number which may be useful if historical Bosch data are available and functions for this are described. The scanner/photoshop method demonstrates a technique to obtain measurements of DEP exposure without the need to purchase specialized instrumentation. © The Author 2014. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

  7. Two efficient methods for isolation of high-quality genomic DNA from entomopathogenic fungi.

    Science.gov (United States)

    Serna-Domínguez, María G; Andrade-Michel, Gilda Y; Arredondo-Bernal, Hugo C; Gallou, Adrien

    2018-03-27

    Conventional and commercial methods for isolation of nucleic acids are available for fungal samples including entomopathogenic fungi (EPF). However, there is not a unique optimal method for all organisms. The cell wall structure and the wide range of secondary metabolites of EPF can broadly interfere with the efficiency of the DNA extraction protocol. This study compares three commercial protocols: DNeasy® Plant Mini Kit (Qiagen), Wizard® Genomic DNA Purification Kit (Promega), and Axygen™ Multisource Genomic DNA Miniprep Kit (Axygen) and three conventional methods based on different buffers: SDS, CTAB/PVPP, and CTAB/β-mercaptoethanol versus three cell lysis procedures: liquid nitrogen homogenization and two bead-beating materials (i.e., tungsten-carbide and stainless-steel) for four representative species of EPF (i.e., Beauveria bassiana, Hirsutella citriformis, Isaria javanica, and Metarhizium anisopliae). Liquid nitrogen homogenization combined with DNeasy® Plant Mini Kit (i.e., QN) or SDS buffer (i.e., SN) significantly improved the yield with a good purity (~1.8) and high integrity (>20,000 bp) of genomic DNA in contrast with other methods, also, these results were better when compared with the two bead-beating materials. The purified DNA was evaluated by PCR-based techniques: amplification of translation elongation factor 1-α (TEF) and two highly sensitive molecular markers (i.e., ISSR and AFLP) with reliable and reproducible results. Despite a variation in yield, purity, and integrity of extracted DNA across the four species of EPF with the different DNA extraction methods, the SN and QN protocols maintained a high-quality of DNA which is required for downstream molecular applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

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    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t list, Marker list, QTL list, Plant DB link & Genome analysis methods © Satoshi ... Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  9. Quantitative Method to Measure Thermal Conductivity of One-Dimensional Nanostructures Based on Scanning Thermal Wave Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kyung Bae; Chung, Jae Hun; Hwang, Gwang Seok; Jung, Eui Han; Kwon, Oh Myoung [Korea University, Seoul (Korea, Republic of)

    2014-12-15

    We present a method to quantitatively measure the thermal conductivity of one-dimensional nanostructures by utilizing scanning thermal wave microscopy (STWM) at a nanoscale spatial resolution. In this paper, we explain the principle for measuring the thermal diffusivity of one-dimensional nanostructures using STWM and the theoretical analysis procedure for quantifying the thermal diffusivity. The SWTM measurement method obtains the thermal conductivity by measuring the thermal diffusivity, which has only a phase lag relative to the distance corresponding to the transferred thermal wave. It is not affected by the thermal contact resistances between the heat source and nanostructure and between the nanostructure and probe. Thus, the heat flux applied to the nanostructure is accurately obtained. The proposed method provides a very simple and quantitative measurement relative to conventional measurement techniques.

  10. A continuous OSL scanning method for analysis of radiation depth-dose profiles in bricks

    DEFF Research Database (Denmark)

    Bøtter-Jensen, L.; Jungner, H.; Poolton, N.R.J.

    1995-01-01

    This article describes the development of a method for directly measuring radiation depth-dose profiles from brick, tile and porcelain cores, without the need for sample separation techniques. For the brick cores, examples are shown of the profiles generated by artificial irradiation using...... the different photon energies from Cs-137 and Co-60 gamma sources; comparison is drawn with both the theoretical calculations derived from Monte Carlo simulations, as well as experimental measurements made using more conventional optically stimulated luminescence methods of analysis....

  11. Thermal Scanning Conductometry (TSC) as a General Method for Studying and Controlling the Phase Behavior of Conductive Physical Gels.

    Science.gov (United States)

    Bielejewski, Michal

    2018-01-23

    The thermal scanning conductometry protocol is a new approach in studying ionic gels based on low molecular weight gelators. The method is designed to follow the dynamically changing state of the ionogels, and to deliver more information and details about the subtle change of conductive properties with an increase or decrease in the temperature. Moreover, the method allows the performance of long term (i.e. days, weeks) measurements at a constant temperature to investigate the stability and durability of the system and the aging effects. The main advantage of the TSC method over classical conductometry is the ability to perform measurements during the gelation process, which was impossible with the classical method due to temperature stabilization, which usually takes a long time before the individual measurement. It is a well-known fact that to obtain the physical gel phase, the cooling stage must be fast; moreover, depending on the cooling rate, different microstructures can be achieved. The TSC method can be performed with any cooling/heating rate that can be assured by the external temperature system. In our case, we can achieve linear temperature change rates between 0.1 and approximately 10 °C/min. The thermal scanning conductometry is designed to work in cycles, continuously changing between heating and cooling stages. Such an approach allows study of the reproducibility of the thermally reversible gel-sol phase transition. Moreover, it allows the performance of different experimental protocols on the same sample, which can be refreshed to initial state (if necessary) without removal from the measuring cell. Therefore, the measurements can be performed faster, in a more efficient way, and with much higher reproducibility and accuracy. Additionally, the TSC method can be also used as a tool to manufacture the ionogels with targeted properties, like microstructure, with an instant characterization of conductive properties.

  12. Inverse method for effects characterization from ultrasonic b-scan images

    International Nuclear Information System (INIS)

    Faur, M.

    1999-02-01

    In service inspections of French nuclear pressure water reactor vessels are carried out automatically in complete immersion from the inside by means of ultrasonic focused probes working in the pulse echo mode. Concern has been expressed about the capabilities of performing non destructive evaluation of the Outer Surface Defects (OSD), i.e. defects located in the vicinity of the outer surface of the inspected components. OSD are insonified by both a direct field that passes through the inner surface (water/steel) of the component containing the defect and a secondary field reflected from the outer surface. Consequently, the Bscan images, containing the signatures of such defects, are complicated and their interpretation is a difficult task. This work deals with extraction of the maximum available information for characterizing OSD from ultrasonic Bscan images. Our main objectives are to obtain the type of OSD and their geometric parameters by means of two specific inverse methods. The first method is used for the identification of the geometrical parameters of the equivalent planar OSD from segmented Bscan images. Ultrasonic equivalent defect sizing model-based methods may be used to size a defect in a material by obtaining a best-fit simple equivalent shape that matches the ultrasonic observed data. We illustrate the application of such an equivalent sizing OSD method that is based on a simplified direct model. The major drawback of this identification method, as used to date, is that only a part of the useful information contained into original Bscan image, i.e. segmented Bscan image, is used for defect characterization. Moreover, it requires the availability of defect classification information (i.e. if the defect is volumetric or planer, e. g. a crack or a lack of fusion), which, generally, may be as difficult to obtain as the defect parameters themselves. Therefore, we propose a parameter estimation method for extracting complementary information on the defect

  13. New method for characterizing paper coating structures using argon ion beam milling and field emission scanning electron microscopy.

    Science.gov (United States)

    Dahlström, C; Allem, R; Uesaka, T

    2011-02-01

    We have developed a new method for characterizing microstructures of paper coating using argon ion beam milling technique and field emission scanning electron microscopy. The combination of these two techniques produces extremely high-quality images with very few artefacts, which are particularly suited for quantitative analyses of coating structures. A new evaluation method has been developed by using marker-controlled watershed segmentation technique of the secondary electron images. The high-quality secondary electron images with well-defined pores makes it possible to use this semi-automatic segmentation method. One advantage of using secondary electron images instead of backscattered electron images is being able to avoid possible overestimation of the porosity because of the signal depth. A comparison was made between the new method and the conventional method using greyscale histogram thresholding of backscattered electron images. The results showed that the conventional method overestimated the pore area by 20% and detected around 5% more pores than the new method. As examples of the application of the new method, we have investigated the distributions of coating binders, and the relationship between local coating porosity and base sheet structures. The technique revealed, for the first time with direct evidence, the long-suspected coating non-uniformity, i.e. binder migration, and the correlation between coating porosity versus base sheet mass density, in a straightforward way. © 2010 The Authors Journal compilation © 2010 The Royal Microscopical Society.

  14. Comparison of conventional full spine radiographs and fluoroscopic scanning method in young patients with idiopathic scoliosis; Vergleich von konventioneller Wirbelsaeulenganzaufnahme und fluoroskopischer Scan-Methode bei jungen Patienten mit idiopathischer Skoliose

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, J.; Kottke, R.; Claussen, C. [Abt. fuer Radiologische Diagnostik, Universitaetsklinikum Tuebingen (Germany); Kluba, T.; Niemeyer, T.; Hahnfeldt, T. [Klinik und Poliklinik fuer Orthopaedie, Universitaetsklinikum Tuebingen (Germany); Vonthein, R. [Inst. fuer Medizinische Biometrie, Universitaetsklinikum Tuebingen (Germany); Kamm, K.F. [Philips Medizin Systeme GmbH, Hamburg (Germany)

    2005-08-01

    Purpose: evaluation of low-dose full spine radiographs using fluoroscopic images for the assessment of the Cobb angle measurement in patients with scoliosis. Material and methods: twenty-one consecutive patients (aged 10-27 years, mean age 14 years) with a conventional full spine examination (film speed class 800) underwent a follow-up exam using digital pulsed fluoroscopy (Multi Diagnost 4, Philips Medical Systems, Eindhoven, The Netherlands). The mean follow-up was 9 months. During a synchronized scan with a C-arm speed of 4 cm/sec fluoroscopic images were stored with a pulsed frequency of 3 images per second. The single images were merged and reconstructed to one image with the software easy spine (Philips medical Systems, Eindhoven, The Netherlands). The corresponding dose-area product values (DAP) of both methods were compared. Three independent observers assessed Cobb angles and image quality for each technique. Results: the mean DAP values for conventional imaging was 94.9 cGy x cm{sup 2} and for fluoroscopy 7.8 cGy x cm{sup 2}, respectively. A significant dose reduction of 91.8% (CI 91% to 95%) was calculated. The average absolute angle difference between the observers was found to be 2.7 for conventional imaging and 2.4 for the fluoroscopic method. Interobserver standard deviation of 2.9 was lower than the 5.3 for conventional images. Image quality was better in the conventional images. Conclusion: using the scanning method, we could achieve a mean reduction of the radiation dose of 92%, while the accuracy of the Cobb angle measurements was comparable for both techniques despite of reduced image quality of digital fluoroscopy. (orig.)

  15. BIOETHICS METHODS IN THE ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS OF THE HUMAN GENOME PROJECT LITERATURE

    Science.gov (United States)

    Walker, Rebecca; Morrissey, Clair

    2013-01-01

    While bioethics as a field has concerned itself with methodological issues since the early years, there has been no systematic examination of how ethics is incorporated into research on the Ethical, Legal and Social Implications (ELSI) of the Human Genome Project. Yet ELSI research may bear a particular burden of investigating and substantiating its methods given public funding, an explicitly cross-disciplinary approach, and the perceived significance of adequate responsiveness to advances in genomics. We undertook a qualitative content analysis of a sample of ELSI publications appearing between 2003-2008 with the aim of better understanding the methods, aims, and approaches to ethics that ELSI researchers employ. We found that the aims of ethics within ELSI are largely prescriptive and address multiple groups. We also found that the bioethics methods used in the ELSI literature are both diverse between publications and multiple within publications, but are usually not themselves discussed or employed as suggested by bioethics method proponents. Ethics in ELSI is also sometimes undistinguished from related inquiries (such as social, legal, or political investigations). PMID:23796275

  16. Ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping for high-intensity focused ultrasound.

    Science.gov (United States)

    Ding, Ting; Zhang, Siyuan; Fu, Quanyou; Xu, Zhian; Wan, Mingxi

    2014-01-01

    This paper presented an ultrasound line-by-line scanning method of spatial-temporal active cavitation mapping applicable in a liquid or liquid filled tissue cavities exposed by high-intensity focused ultrasound (HIFU). Scattered signals from cavitation bubbles were obtained in a scan line immediately after one HIFU exposure, and then there was a waiting time of 2 s long enough to make the liquid back to the original state. As this pattern extended, an image was built up by sequentially measuring a series of such lines. The acquisition of the beamformed radiofrequency (RF) signals for a scan line was synchronized with HIFU exposure. The duration of HIFU exposure, as well as the delay of the interrogating pulse relative to the moment while HIFU was turned off, could vary from microseconds to seconds. The feasibility of this method was demonstrated in tap-water and a tap-water filled cavity in the tissue-mimicking gelatin-agar phantom as capable of observing temporal evolutions of cavitation bubble cloud with temporal resolution of several microseconds, lateral and axial resolution of 0.50 mm and 0.29 mm respectively. The dissolution process of cavitation bubble cloud and spatial distribution affected by cavitation previously generated were also investigated. Although the application is limited by the requirement for a gassy fluid (e.g. tap water, etc.) that allows replenishment of nuclei between HIFU exposures, the technique may be a useful tool in spatial-temporal cavitation mapping for HIFU with high precision and resolution, providing a reference for clinical therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Functional regression method for whole genome eQTL epistasis analysis with sequencing data.

    Science.gov (United States)

    Xu, Kelin; Jin, Li; Xiong, Momiao

    2017-05-18

    Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves. A single number for measuring gene expression which is widely used for microarray measured gene expression analysis is highly unlikely to sufficiently account for large expression variation across the gene. Simultaneously analyzing epistatic architecture using the RNA-seq and whole genome sequencing (WGS) data poses enormous challenges. We develop a nonlinear functional regression model (FRGM) with functional responses where the position-level read counts within a gene are taken as a function of genomic position, and functional predictors where genotype profiles are viewed as a function of genomic position, for epistasis analysis with RNA-seq data. Instead of testing the interaction of all possible pair-wises SNPs, the FRGM takes a gene as a basic unit for epistasis analysis, which tests for the interaction of all possible pairs of genes and use all the information that can be accessed to collectively test interaction between all possible pairs of SNPs within two genome regions. By large-scale simulations, we demonstrate that the proposed FRGM for epistasis analysis can achieve the correct type 1 error and has higher power to detect the interactions between genes than the existing methods. The proposed methods are applied to the RNA-seq and WGS data from the 1000 Genome Project. The numbers of pairs of significantly interacting genes after Bonferroni correction

  18. A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits

    Directory of Open Access Journals (Sweden)

    Hayashi Takeshi

    2013-01-01

    Full Text Available Abstract Background Genomic selection is an effective tool for animal and plant breeding, allowing effective individual selection without phenotypic records through the prediction of genomic breeding value (GBV. To date, genomic selection has focused on a single trait. However, actual breeding often targets multiple correlated traits, and, therefore, joint analysis taking into consideration the correlation between traits, which might result in more accurate GBV prediction than analyzing each trait separately, is suitable for multi-trait genomic selection. This would require an extension of the prediction model for single-trait GBV to multi-trait case. As the computational burden of multi-trait analysis is even higher than that of single-trait analysis, an effective computational method for constructing a multi-trait prediction model is also needed. Results We described a Bayesian regression model incorporating variable selection for jointly predicting GBVs of multiple traits and devised both an MCMC iteration and variational approximation for Bayesian estimation of parameters in this multi-trait model. The proposed Bayesian procedures with MCMC iteration and variational approximation were referred to as MCBayes and varBayes, respectively. Using simulated datasets of SNP genotypes and phenotypes for three traits with high and low heritabilities, we compared the accuracy in predicting GBVs between multi-trait and single-trait analyses as well as between MCBayes and varBayes. The results showed that, compared to single-trait analysis, multi-trait analysis enabled much more accurate GBV prediction for low-heritability traits correlated with high-heritability traits, by utilizing the correlation structure between traits, while the prediction accuracy for uncorrelated low-heritability traits was comparable or less with multi-trait analysis in comparison with single-trait analysis depending on the setting for prior probability that a SNP has zero

  19. Classical Measurement Methods and Laser Scanning Usage in Shaft Hoist Assembly Inventory

    Science.gov (United States)

    Jaśkowski, Wojciech; Lipecki, Tomasz; Matwij, Wojciech; Jabłoński, Mateusz

    2018-03-01

    The shaft hoist assembly is the base of underground mining plant. Its efficiency and correct operation is subject to restrictive legal regulations and is controlled on a daily visual assessment by shaft crew and energomechanics. In addition, in the regular interval, the shaft hoist assembly is subject to a thorough inventory, which includes the determination of the geometrical relationships between the hoisting machine, the headframe and the shaft with its housing. Inventory measurements for shaft and headframe are used for years of conventional geodetic methods including mechanical or laser plumbing and tachymetric surveys. Additional precision levelling is also used for measuring shafts of hoisting machines and rope pulleys. Continuous modernization of measuring technology makes it possible to implement the further methods to the above mentioned purposes. The comparison of the accuracy and the economics of performing measurements based on many years of experience with comprehensive inventory of shaft hoist assembly using various research techniques was made and detailed in the article.

  20. STEM VQ Method, Using Scanning Transmission Electron Microscopy (STEM) for Accurate Virus Quantification

    Science.gov (United States)

    2017-02-02

    WEEV in Ontario, Canada in 194126. This virus has a passage history including both animals and cell culture. Biosafety level (BSL-)-3 laboratory...Agarose-Based Plaque Assay Each virus stock was quantitated by standard agarose-based plaque assay23...samples used here were well prepared and the standard macro was used. As we have developed this method we have observed that while inferior

  1. Scanning method as an unbiased simulation technique and its application to the study of self-attracting random walks

    Science.gov (United States)

    Meirovitch, Hagai

    1985-12-01

    The scanning method proposed by us [J. Phys. A 15, L735 (1982); Macromolecules 18, 563 (1985)] for simulation of polymer chains is further developed and applied, for the first time, to a model with finite interactions. In addition to ``importance sampling,'' we remove the bias introduced by the scanning method with a procedure suggested recently by Schmidt [Phys. Rev. Lett. 51, 2175 (1983)]; this procedure has the advantage of enabling one to estimate the statistical error. We find these two procedures to be equally efficient. The model studied is an N-step random walk on a lattice, in which a random walk i has a statistical weight &, where p∞ for any dimension d by Donsker and Varadhan (DV) and by others. and lnφ, where φ is the survival probability in the trapping problem, diverge like Nα with α=d/(d+2). Most numerical studies, however, have failed to reach the DV regime in which d/(d+2) becomes a good approximation for α. On the other hand, our results for α (obtained for Nzero, and that the probability of a walk returning to the origin behaves approximately as N-1/3 for both d=2 and 3.

  2. A laboratory measurement method for pressure sensitive adhesives in agglomeration deinking of mixed office waste paper: The high-low scanning contrast method

    OpenAIRE

    Guolin Tong; Shuang Sun; Cuixia Wang; Kecheng Fu; Yungchang F. Chin

    2012-01-01

    A simple measurement method for pressure sensitive adhesives (PSA) in an agglomeration deinking system of mixed office waste paper was studied. This method was based on the different scanning performance of ink and PSA specks in hot-pressed and oven-dried handsheets with the change of contrast values that had been selected and set in the image analysis software. The numbers of ink specks per square meter (NPM) were well recognized at both low and high contrast values and exhibited a very good...

  3. Classical Measurement Methods and Laser Scanning Usage in Shaft Hoist Assembly Inventory

    Directory of Open Access Journals (Sweden)

    Jaśkowski Wojciech

    2018-01-01

    Full Text Available The shaft hoist assembly is the base of underground mining plant. Its efficiency and correct operation is subject to restrictive legal regulations and is controlled on a daily visual assessment by shaft crew and energomechanics. In addition, in the regular interval, the shaft hoist assembly is subject to a thorough inventory, which includes the determination of the geometrical relationships between the hoisting machine, the headframe and the shaft with its housing. Inventory measurements for shaft and headframe are used for years of conventional geodetic methods including mechanical or laser plumbing and tachymetric surveys. Additional precision levelling is also used for measuring shafts of hoisting machines and rope pulleys. Continuous modernization of measuring technology makes it possible to implement the further methods to the above mentioned purposes. The comparison of the accuracy and the economics of performing measurements based on many years of experience with comprehensive inventory of shaft hoist assembly using various research techniques was made and detailed in the article.

  4. Radiopharmaceutical scanning agents

    International Nuclear Information System (INIS)

    1976-01-01

    This invention is directed to dispersions useful in preparing radiopharmaceutical scanning agents, to technetium labelled dispersions, to methods for preparing such dispersions and to their use as scanning agents

  5. Nuclear Scans

    Science.gov (United States)

    Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...

  6. A Method for Preparing Spaceflight RNAlater-Fixed Arabidopsis thaliana (Brassicaceae Tissue for Scanning Electron Microscopy

    Directory of Open Access Journals (Sweden)

    Eric R. Schultz

    2013-07-01

    Full Text Available Premise of the study: In spaceflight experiments, tissues for morphologic study are fixed in 3% glutaraldehyde, while tissues for molecular study are fixed in RNAlater; thus, an experiment containing both study components requires multiple fixation strategies. The possibility of using RNAlater-fixed materials for standard SEM-based morphometric investigation was explored to expand the library of tissues available for analysis and maximize usage of samples returned from spaceflight, but these technologies have wide application to any situation where recovery of biological resources is limited. Methods and Results: RNAlater-fixed samples were desalinated in distilled water, dehydrated through graded methanol, plunged into liquid ethane, and transferred to cryovials for freeze-substitution. Sample tissues were critical point dried, mounted, sputter-coated, and imaged. Conclusions: The protocol resulted in acceptable SEM images from RNAlater-fixed Arabidopsis thaliana tissue. The majority of the tissues remained intact, including general morphology and finer details such as root hairs and trichomes.

  7. Estimation of debonded area in bearing babbitt metal by C-Scan method

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Gye-jo; Park, Sang-ki [Korea Electric Power Research Inst., Taejeon (Korea); Cha, Seok-ju [Korea South Eastern Power Corp., Seoul (Korea). GEN Sector; Park, Young-woo [Chungnam National Univ., Taejeon (Korea). Mechatronics

    2006-07-01

    The debonding area which had a complex boundary was imaged with a immersion technique, and the acoustic image was compared with the actual area. The amplitude information from focused transducer can discriminate between a defected boundary area and a sound interface of dissimilar metal. The shape of irregular boundary and area was processed by a histogram equalization, after that, through the clustering and labelling, it makes the defect area cleared. Each pixel has ultrasonic intensity rate and represents a position data. The estimation error in measuring debonding area was within 4% by image processing technique. The validity of this immersion method and image equalizing technique has been done for the inspection of power plant turbine's thrust bearings. (orig.)

  8. Empirical Performance of Cross-Validation With Oracle Methods in a Genomics Context.

    Science.gov (United States)

    Martinez, Josue G; Carroll, Raymond J; Müller, Samuel; Sampson, Joshua N; Chatterjee, Nilanjan

    2011-11-01

    When employing model selection methods with oracle properties such as the smoothly clipped absolute deviation (SCAD) and the Adaptive Lasso, it is typical to estimate the smoothing parameter by m-fold cross-validation, for example, m = 10. In problems where the true regression function is sparse and the signals large, such cross-validation typically works well. However, in regression modeling of genomic studies involving Single Nucleotide Polymorphisms (SNP), the true regression functions, while thought to be sparse, do not have large signals. We demonstrate empirically that in such problems, the number of selected variables using SCAD and the Adaptive Lasso, with 10-fold cross-validation, is a random variable that has considerable and surprising variation. Similar remarks apply to non-oracle methods such as the Lasso. Our study strongly questions the suitability of performing only a single run of m-fold cross-validation with any oracle method, and not just the SCAD and Adaptive Lasso.

  9. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)

    OpenAIRE

    Li, M-H; Tiirikka, T; Kantanen, J

    2013-01-01

    In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three kno...

  10. An automated annotation tool for genomic DNA sequences using

    Indian Academy of Sciences (India)

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated ...

  11. Comparison of statistical sampling methods with ScannerBit, the GAMBIT scanning module

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, Gregory D. [University of California, Physics and Astronomy Department, Los Angeles, CA (United States); McKay, James; Scott, Pat [Imperial College London, Department of Physics, Blackett Laboratory, London (United Kingdom); Farmer, Ben; Conrad, Jan [AlbaNova University Centre, Oskar Klein Centre for Cosmoparticle Physics, Stockholm (Sweden); Stockholm University, Department of Physics, Stockholm (Sweden); Roebber, Elinore [McGill University, Department of Physics, Montreal, QC (Canada); Putze, Antje [LAPTh, Universite de Savoie, CNRS, Annecy-le-Vieux (France); Collaboration: The GAMBIT Scanner Workgroup

    2017-11-15

    We introduce ScannerBit, the statistics and sampling module of the public, open-source global fitting framework GAMBIT. ScannerBit provides a standardised interface to different sampling algorithms, enabling the use and comparison of multiple computational methods for inferring profile likelihoods, Bayesian posteriors, and other statistical quantities. The current version offers random, grid, raster, nested sampling, differential evolution, Markov Chain Monte Carlo (MCMC) and ensemble Monte Carlo samplers. We also announce the release of a new standalone differential evolution sampler, Diver, and describe its design, usage and interface to ScannerBit. We subject Diver and three other samplers (the nested sampler MultiNest, the MCMC GreAT, and the native ScannerBit implementation of the ensemble Monte Carlo algorithm T-Walk) to a battery of statistical tests. For this we use a realistic physical likelihood function, based on the scalar singlet model of dark matter. We examine the performance of each sampler as a function of its adjustable settings, and the dimensionality of the sampling problem. We evaluate performance on four metrics: optimality of the best fit found, completeness in exploring the best-fit region, number of likelihood evaluations, and total runtime. For Bayesian posterior estimation at high resolution, T-Walk provides the most accurate and timely mapping of the full parameter space. For profile likelihood analysis in less than about ten dimensions, we find that Diver and MultiNest score similarly in terms of best fit and speed, outperforming GreAT and T-Walk; in ten or more dimensions, Diver substantially outperforms the other three samplers on all metrics. (orig.)

  12. Alternative Method of On-Orbit Response-Versus-Scan-Angle Characterization for MODIS Reflective Solar Bands

    Science.gov (United States)

    Chen, Hongda; Xiong, Xiaoxiong; Angal, Amit; Geng, Xu; Wu, Aisheng

    2016-01-01

    The moderate resolution imaging spectroradiometer (MODIS) has 20 reflective solar bands (RSB), covering a spectral range from 0.41 to 2.2 microns, which are calibrated on-orbit using its onboard calibrators, which include a solar diffuser, a solar diffuser stability monitor, and a spectroradiometric calibration assembly. A space view (SV) port is used to provide a background reference and also facilitates near-monthly lunar observations through a spacecraft roll. In every scan, the Earth's surface, SV, and onboard calibrators are viewed via a two-sided scan mirror, the reflectance of which depends on the angle of incidence (AOI) as well as the wavelength of the incident light. Response-versus-scan-angle (RVS) is defined as a dependence function of the scan mirror's reflectance over AOI. An initial RVS for each RSB was measured prelaunch for both Terra and Aqua MODIS. Algorithms have been developed to track the on-orbit RVS variation using the measurements from the onboard calibrators, supplemented with the earth view (EV) trends from pseudoinvariant desert targets obtained at different AOI. Since the mission beginning, the MODIS characterization support team (MCST) has dedicated efforts in evaluating approaches of characterizing the on-orbit RVS. A majority of the approaches focused on fitting the data at each AOI over time and then deriving the relative change at different AOI. The current version of the on-orbit RVS algorithm, as implemented in the collection 6 (C6) level-1B (L1B), is also based on the above rationale. It utilizes the EV response trends from the pseudoinvariant Libyan desert targets to supplement the gain derived from the onboard calibrators. The primary limitation of this approach is the assumption of the temporal stability of these desert sites. Consequently, MCST developed an approach that derives the on-orbit RVS change using measurements from a single desert site, combined with the on-orbit lunar measurements. In addition, the EV and onboard

  13. A novel method of estimating dose responses for polymer gels using texture analysis of scanning electron microscopy images.

    Directory of Open Access Journals (Sweden)

    Cheng-Ting Shih

    Full Text Available Polymer gels are regarded as a potential dosimeter for independent validation of absorbed doses in clinical radiotherapy. Several imaging modalities have been used to convert radiation-induced polymerization to absorbed doses from a macro-scale viewpoint. This study developed a novel dose conversion mechanism by texture analysis of scanning electron microscopy (SEM images. The modified N-isopropyl-acrylamide (NIPAM gels were prepared under normoxic conditions, and were administered radiation doses from 5 to 20 Gy. After freeze drying, the gel samples were sliced for SEM scanning with 50×, 500×, and 3500× magnifications. Four texture indices were calculated based on the gray level co-occurrence matrix (GLCM. The results showed that entropy and homogeneity were more suitable than contrast and energy as dose indices for higher linearity and sensitivity of the dose response curves. After parameter optimization, an R (2 value of 0.993 can be achieved for homogeneity using 500× magnified SEM images with 27 pixel offsets and no outlier exclusion. For dose verification, the percentage errors between the prescribed dose and the measured dose for 5, 10, 15, and 20 Gy were -7.60%, 5.80%, 2.53%, and -0.95%, respectively. We conclude that texture analysis can be applied to the SEM images of gel dosimeters to accurately convert micro-scale structural features to absorbed doses. The proposed method may extend the feasibility of applying gel dosimeters in the fields of diagnostic radiology and radiation protection.

  14. Fundamental study of microelectronic chip response under laser ultrasonic-interferometric inspection using C-scan method

    Science.gov (United States)

    Yang, Lei; Gong, Jie; Ume, I. Charles

    2014-02-01

    In modern surface mount packaging technologies, such as flip chips, chip scale packages, and ball grid arrays(BGA), chips are attached to the substrates/printed wiring board (PWB) using solder bump interconnections. The quality of solder bumps between the chips and the substrate/board is difficult to inspect. Laser ultrasonic-interferometric technique was proved to be a promising approach for solder bump inspection because of its noncontact and nondestructive characteristics. Different indicators extracted from received signals have been used to predict the potential defects, such as correlation coefficient, error ratio, frequency shifting, etc. However, the fundamental understanding of the chip behavior under laser ultrasonic inspection is still missing. Specifically, it is not sure whether the laser interferometer detected out-of-plane displacements were due to wave propagation or structural vibration when the chip was excited by pulsed laser. Plus, it is found that the received signals are chip dependent. Both challenges impede the interpretation of acquired signals. In this paper, a C-scan method was proposed to study the underlying phenomenon during laser ultrasonic inspection. The full chip was inspected. The response of the chip under laser excitation was visualized in a movie resulted from acquired signals. Specifically, a BGA chip was investigated to demonstrate the effectiveness of this method. By characterizing signals using discrete wavelet transform(DWT), both ultrasonic wave propagation and vibration were observed. Separation of them was successfully achieved using ideal band-pass filter and visualized in resultant movies, too. The observed ultrasonic waves were characterized and their respective speeds were measured by applying 2-D FFT. The C-scan method, combined with different digital signal processing techniques, was proved to be an very effective methodology to learn the behavior of chips under laser excitation. This general procedure can be

  15. A simple and efficient total genomic DNA extraction method for individual zooplankton.

    Science.gov (United States)

    Fazhan, Hanafiah; Waiho, Khor; Shahreza, Md Sheriff

    2016-01-01

    Molecular approaches are widely applied in species identification and taxonomic studies of minute zooplankton. One of the most focused zooplankton nowadays is from Subclass Copepoda. Accurate species identification of all life stages of the generally small sized copepods through molecular analysis is important, especially in taxonomic and systematic assessment of harpacticoid copepod populations and to understand their dynamics within the marine community. However, total genomic DNA (TGDNA) extraction from individual harpacticoid copepods can be problematic due to their small size and epibenthic behavior. In this research, six TGDNA extraction methods done on individual harpacticoid copepods were compared. The first new simple, feasible, efficient and consistent TGDNA extraction method was designed and compared with the commercial kit and modified available TGDNA extraction methods. The newly described TGDNA extraction method, "Incubation in PCR buffer" method, yielded good and consistent results based on the high success rate of PCR amplification (82%) compared to other methods. Coupled with its relatively consistent and economical method the "Incubation in PCR buffer" method is highly recommended in the TGDNA extraction of other minute zooplankton species.

  16. Stabilized alcohol solution of reducing salt formulations for use in preparing radioisotope labelled scanning agents: liver scanning technetium-99m colloid and method of preparation

    International Nuclear Information System (INIS)

    1980-01-01

    The preparation of a radiolabelled scanning agent for imaging reticuloendothelial organs, including the liver and spleen, is described. It consists of a sup(99m)Tc labelled colloid of a metal ion salt reductant, such as SnCl 2 , TiCl 3 , CrCl 2 or FeCl 2 , and an anhydrous non-oxidising organic solvent, such as diethyl ether, ethanol or another aliphatic alcohol. Examples are given of the effects of varying the pH, the metal ion salt reductant concentration, the eluate and solvent volumes and the temperature of the radiopharmaceutical on the tagging efficiency and organ distribution in mice and rabbits. (U.K.)

  17. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.

    Science.gov (United States)

    Jorjani, Hadi; Zavolan, Mihaela

    2014-04-01

    Accurate identification of transcription start sites (TSSs) is an essential step in the analysis of transcription regulatory networks. In higher eukaryotes, the capped analysis of gene expression technology enabled comprehensive annotation of TSSs in genomes such as those of mice and humans. In bacteria, an equivalent approach, termed differential RNA sequencing (dRNA-seq), has recently been proposed, but the application of this approach to a large number of genomes is hindered by the paucity of computational analysis methods. With few exceptions, when the method has been used, annotation of TSSs has been largely done manually. In this work, we present a computational method called 'TSSer' that enables the automatic inference of TSSs from dRNA-seq data. The method rests on a probabilistic framework for identifying both genomic positions that are preferentially enriched in the dRNA-seq data as well as preferentially captured relative to neighboring genomic regions. Evaluating our approach for TSS calling on several publicly available datasets, we find that TSSer achieves high consistency with the curated lists of annotated TSSs, but identifies many additional TSSs. Therefore, TSSer can accelerate genome-wide identification of TSSs in bacterial genomes and can aid in further characterization of bacterial transcription regulatory networks. TSSer is freely available under GPL license at http://www.clipz.unibas.ch/TSSer/index.php

  18. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures

    OpenAIRE

    Thomson, John P.; Fawkes, Angie; Ottaviano, Raffaele; Hunter, Jennifer M.; Shukla, Ruchi; Mjoseng, Heidi K.; Clark, Richard; Coutts, Audrey; Murphy, Lee; Meehan, Richard R.

    2015-01-01

    Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially ...

  19. A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

    Science.gov (United States)

    Tsirigos, Aristotelis; Rigoutsos, Isidore

    2005-01-01

    In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the alpha-, beta- and gamma-herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.

  20. Comparison of Single and Multi-Scale Method for Leaf and Wood Points Classification from Terrestrial Laser Scanning Data

    Science.gov (United States)

    Wei, Hongqiang; Zhou, Guiyun; Zhou, Junjie

    2018-04-01

    The classification of leaf and wood points is an essential preprocessing step for extracting inventory measurements and canopy characterization of trees from the terrestrial laser scanning (TLS) data. The geometry-based approach is one of the widely used classification method. In the geometry-based method, it is common practice to extract salient features at one single scale before the features are used for classification. It remains unclear how different scale(s) used affect the classification accuracy and efficiency. To assess the scale effect on the classification accuracy and efficiency, we extracted the single-scale and multi-scale salient features from the point clouds of two oak trees of different sizes and conducted the classification on leaf and wood. Our experimental results show that the balanced accuracy of the multi-scale method is higher than the average balanced accuracy of the single-scale method by about 10 % for both trees. The average speed-up ratio of single scale classifiers over multi-scale classifier for each tree is higher than 30.

  1. Development of a Novel Scanning Thermal Microscopy (SThM) Method to Measure the Thermal Conductivity of Biological Cells.

    Science.gov (United States)

    Nakanishi, Kouichi; Kogure, Akinori; Kuwana, Ritsuko; Takamatsu, Hiromu; Ito, Kiyoshi

    2017-01-01

     Differences in the physical properties of individual cells cannot be evaluated with conventional experimental methods that are used to study groups of cells obtained from pure cultures. To examine the differences in the thermal tolerance of individual cells that are genetically identical, a method is needed to measure the thermal energy required to kill single cells. We developed a scanning thermal microscopy (SThM) system and measured the thermal conductivity of various bacterial cells, for example, spore formeing Bacillus genus and non spore-forming bacteria such as Escherichia coli. The thermal conductivity of vegetative cells (0.61 to 0.75 W/m・K) was found to be higher than that of spores (0.29 to 0.45 W/m・K). Furthermore the newly developed method enables us to estimate the thermal energy needed to kill individual cells or spores. We believe that this method can estimate the thermal energy required to achieve the cell for sterilization by heating.

  2. A new method for the recovery and evidential comparison of footwear impressions using 3D structured light scanning.

    Science.gov (United States)

    Thompson, T J U; Norris, P

    2018-05-01

    Footwear impressions are one of the most common forms of evidence to be found at a crime scene, and can potentially offer the investigator a wealth of intelligence. Our aim is to highlight a new and improved technique for the recovery of footwear impressions, using three-dimensional structured light scanning. Results from this preliminary study demonstrate that this new approach is non-destructive, safe to use and is fast, reliable and accurate. Further, since this is a digital method, there is also the option of digital comparison between items of footwear and footwear impressions, and an increased ability to share recovered footwear impressions between forensic staff thus speeding up the investigation. Copyright © 2018 The Chartered Society of Forensic Sciences. Published by Elsevier B.V. All rights reserved.

  3. Characterization of phase change materials for thermal control of photovoltaics using Differential Scanning Calorimetry and Temperature History Method

    International Nuclear Information System (INIS)

    Hasan, A.; McCormack, S.J.; Huang, M.J.; Norton, B.

    2014-01-01

    Highlights: • Five PCM are characterized using tow techniques for PV temperature regulation. • Thermophysical properties of interest are determined and compared with literature. • Determined PCM properties are discussed as criteria for PV temperature regulation. • One PCM identified as potential candidate for PV temperature regulation. - Abstract: Five solid–liquid phase change materials comprising three basic classes, paraffin waxes, salt hydrates and mixtures of fatty acids were thermophysically characterized for thermal regulation applications in photovoltaics. The PCM were investigated using Differential Scanning Calorimetry and Temperature History Method to find their thermophysical properties of interest. The relationship between thermophysical properties of the PCM and their choice as temperature regulators in photovoltaics is discussed in relation to the ambient conditions under which PV systems operate

  4. A method for separation of the terrain and non-terrain from Vehicle-borne Laser Scanning Data

    International Nuclear Information System (INIS)

    Wei, Jiangxia; Zhong, Ruofei

    2014-01-01

    Half the points from vehicle-borne laser scanning data are terrain data. If you want to extract features such as trees, street lights and buildings, terrain points must be removed. Nowadays, either airborne or vehicle-borne laser data, are mostly used to set an elevation threshold based on the scanning line or POS data to determine whether the point is a terrain point or not, but the disadvantage is part of low buildings or other feature objects will be lost. If the study area has high differences in the horizontal or the forward direction, this method is not applicable. This paper investigates a new methodology to extract the terrain points, which has great significance for data reduction and classification. The procedure includes the following steps: 1)Pre-processing: to remove discrete points and abnormal points. 2) Divided all the points into grid, calculating the average value of the XY and the minimum value of the Z of all the points in the same grid as the central point of the grid.3) Choose nearest six points which are close to the centre point to fitting the quadratic surface.4)Compare the normal vector of the fitting surface of the grid to the normal vector of the 8-neighborhood, if the difference is too big, it will be smoothed.5) Determine whether the point in the grid is on the surface, if the point belongs to the surface, it will be classified as terrain point. The results and evaluation have shown the effectiveness of the method and its potential in separation of the terrain of various areas

  5. SU-E-T-561: Development of Depth Dose Measurement Technique Using the Multilayer Ionization Chamber for Spot Scanning Method

    International Nuclear Information System (INIS)

    Takayanagi, T; Fujitaka, S; Umezawa, M; Ito, Y; Nakashima, C; Matsuda, K

    2014-01-01

    Purpose: To develop a measurement technique which suppresses the difference between profiles obtained with a multilayer ionization chamber (MLIC) and with a water phantom. Methods: The developed technique multiplies the raw MLIC data by a correction factor that depends on the initial beam range and water equivalent depth. The correction factor is derived based on a Bragg curve calculation formula considering range straggling and fluence loss caused by nuclear reactions. Furthermore, the correction factor is adjusted based on several integrated depth doses measured with a water phantom and the MLIC. The measured depth dose profiles along the central axis of the proton field with a nominal field size of 10 by 10 cm were compared between the MLIC using the new technique and the water phantom. The spread out Bragg peak was 20 cm for fields with a range of 30.6 cm and 6.9 cm. Raw MLIC data were obtained with each energy layer, and integrated after multiplying by the correction factor. The measurements were performed by a spot scanning nozzle at Nagoya Proton Therapy Center, Japan. Results: The profile measured with the MLIC using the new technique is consistent with that of the water phantom. Moreover, 97% of the points passed the 1% dose /1mm distance agreement criterion of the gamma index. Conclusion: We have demonstrated that the new technique suppresses the difference between profiles obtained with the MLIC and with the water phantom. It was concluded that this technique is useful for depth dose measurement in proton spot scanning method

  6. A New Recursive Filtering Method of Terrestrial Laser Scanning Data to Preserve Ground Surface Information in Steep-Slope Areas

    Directory of Open Access Journals (Sweden)

    Mi-Kyeong Kim

    2017-11-01

    Full Text Available Landslides are one of the critical natural hazards that cause human, infrastructure, and economic losses. Risk of catastrophic losses due to landslides is significant given sprawled urban development near steep slopes and the increasing proximity of large populations to hilly areas. For reducing these losses, a high-resolution digital terrain model (DTM is an essential piece of data for a qualitative or a quantitative investigation of slopes that may lead to landslides. Data acquired by a terrestrial laser scanning (TLS, called a point cloud, has been widely used to generate a DTM, since a TLS is appropriate for detecting small- to large-scale ground features on steep slopes. For an accurate DTM, TLS data should be filtered to remove non-ground points, but most current algorithms for extracting ground points from a point cloud have been developed for airborne laser scanning (ALS data and not TLS data. Moreover, it is a challenging task to generate an accurate DTM from a steep-slope area by using existing algorithms. For these reasons, we developed an algorithm to automatically extract only ground points from the point clouds of steep terrains. Our methodology is focused on TLS datasets and utilizes the adaptive principal component analysis–triangular irregular network (PCA-TIN approach. Our method was applied to two test areas and the results showed that the algorithm can cope well with steep slopes, giving an accurate surface model compared to conventional algorithms. Total accuracy values of the generated DTMs in the form of root mean squared errors are 1.84 cm and 2.13 cm over the areas of 5252 m2 and 1378 m2, respectively. The slope-based adaptive PCA-TIN method demonstrates great potential for TLS-derived DTM construction in steep-slope landscapes.

  7. On-Line Multi-Damage Scanning Spatial-Wavenumber Filter Based Imaging Method for Aircraft Composite Structure

    Directory of Open Access Journals (Sweden)

    Yuanqiang Ren

    2017-05-01

    Full Text Available Structural health monitoring (SHM of aircraft composite structure is helpful to increase reliability and reduce maintenance costs. Due to the great effectiveness in distinguishing particular guided wave modes and identifying the propagation direction, the spatial-wavenumber filter technique has emerged as an interesting SHM topic. In this paper, a new scanning spatial-wavenumber filter (SSWF based imaging method for multiple damages is proposed to conduct on-line monitoring of aircraft composite structures. Firstly, an on-line multi-damage SSWF is established, including the fundamental principle of SSWF for multiple damages based on a linear piezoelectric (PZT sensor array, and a corresponding wavenumber-time imaging mechanism by using the multi-damage scattering signal. Secondly, through combining the on-line multi-damage SSWF and a PZT 2D cross-shaped array, an image-mapping method is proposed to conduct wavenumber synthesis and convert the two wavenumber-time images obtained by the PZT 2D cross-shaped array to an angle-distance image, from which the multiple damages can be directly recognized and located. In the experimental validation, both simulated multi-damage and real multi-damage introduced by repeated impacts are performed on a composite plate structure. The maximum localization error is less than 2 cm, which shows good performance of the multi-damage imaging method. Compared with the existing spatial-wavenumber filter based damage evaluation methods, the proposed method requires no more than the multi-damage scattering signal and can be performed without depending on any wavenumber modeling or measuring. Besides, this method locates multiple damages by imaging instead of the geometric method, which helps to improve the signal-to-noise ratio. Thus, it can be easily applied to on-line multi-damage monitoring of aircraft composite structures.

  8. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

    Science.gov (United States)

    Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

    2013-04-10

    Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Correcting for cryptic relatedness by a regression-based genomic control method

    Directory of Open Access Journals (Sweden)

    Yang Yaning

    2009-12-01

    Full Text Available Abstract Background Genomic control (GC method is a useful tool to correct for the cryptic relatedness in population-based association studies. It was originally proposed for correcting for the variance inflation of Cochran-Armitage's additive trend test by using information from unlinked null markers, and was later generalized to be applicable to other tests with the additional requirement that the null markers are matched with the candidate marker in allele frequencies. However, matching allele frequencies limits the number of available null markers and thus limits the applicability of the GC method. On the other hand, errors in genotype/allele frequencies may cause further bias and variance inflation and thereby aggravate the effect of GC correction. Results In this paper, we propose a regression-based GC method using null markers that are not necessarily matched in allele frequencies with the candidate marker. Variation of allele frequencies of the null markers is adjusted by a regression method. Conclusion The proposed method can be readily applied to the Cochran-Armitage's trend tests other than the additive trend test, the Pearson's chi-square test and other robust efficiency tests. Simulation results show that the proposed method is effective in controlling type I error in the presence of population substructure.

  10. Benchmarking Relatedness Inference Methods with Genome-Wide Data from Thousands of Relatives.

    Science.gov (United States)

    Ramstetter, Monica D; Dyer, Thomas D; Lehman, Donna M; Curran, Joanne E; Duggirala, Ravindranath; Blangero, John; Mezey, Jason G; Williams, Amy L

    2017-09-01

    Inferring relatedness from genomic data is an essential component of genetic association studies, population genetics, forensics, and genealogy. While numerous methods exist for inferring relatedness, thorough evaluation of these approaches in real data has been lacking. Here, we report an assessment of 12 state-of-the-art pairwise relatedness inference methods using a data set with 2485 individuals contained in several large pedigrees that span up to six generations. We find that all methods have high accuracy (92-99%) when detecting first- and second-degree relationships, but their accuracy dwindles to 76% of relative pairs. Overall, the most accurate methods are Estimation of Recent Shared Ancestry (ERSA) and approaches that compute total IBD sharing using the output from GERMLINE and Refined IBD to infer relatedness. Combining information from the most accurate methods provides little accuracy improvement, indicating that novel approaches, such as new methods that leverage relatedness signals from multiple samples, are needed to achieve a sizeable jump in performance. Copyright © 2017 Ramstetter et al.

  11. Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules.

    Science.gov (United States)

    Kersten, Roland D; Ziemert, Nadine; Gonzalez, David J; Duggan, Brendan M; Nizet, Victor; Dorrestein, Pieter C; Moore, Bradley S

    2013-11-19

    Glycosyl groups are an essential mediator of molecular interactions in cells and on cellular surfaces. There are very few methods that directly relate sugar-containing molecules to their biosynthetic machineries. Here, we introduce glycogenomics as an experiment-guided genome-mining approach for fast characterization of glycosylated natural products (GNPs) and their biosynthetic pathways from genome-sequenced microbes by targeting glycosyl groups in microbial metabolomes. Microbial GNPs consist of aglycone and glycosyl structure groups in which the sugar unit(s) are often critical for the GNP's bioactivity, e.g., by promoting binding to a target biomolecule. GNPs are a structurally diverse class of molecules with important pharmaceutical and agrochemical applications. Herein, O- and N-glycosyl groups are characterized in their sugar monomers by tandem mass spectrometry (MS) and matched to corresponding glycosylation genes in secondary metabolic pathways by a MS-glycogenetic code. The associated aglycone biosynthetic genes of the GNP genotype then classify the natural product to further guide structure elucidation. We highlight the glycogenomic strategy by the characterization of several bioactive glycosylated molecules and their gene clusters, including the anticancer agent cinerubin B from Streptomyces sp. SPB74 and an antibiotic, arenimycin B, from Salinispora arenicola CNB-527.

  12. Comparison of methods used to identify superior individuals in genomic selection in plant breeding.

    Science.gov (United States)

    Bhering, L L; Junqueira, V S; Peixoto, L A; Cruz, C D; Laviola, B G

    2015-09-10

    The aim of this study was to evaluate different methods used in genomic selection, and to verify those that select a higher proportion of individuals with superior genotypes. Thus, F2 populations of different sizes were simulated (100, 200, 500, and 1000 individuals) with 10 replications each. These consisted of 10 linkage groups (LG) of 100 cM each, containing 100 equally spaced markers per linkage group, of which 200 controlled the characteristics, defined as the 20 initials of each LG. Genetic and phenotypic values were simulated assuming binomial distribution of effects for each LG, and the absence of dominance. For phenotypic values, heritabilities of 20, 50, and 80% were considered. To compare methodologies, the analysis processing time, coefficient of coincidence (selection of 5, 10, and 20% of superior individuals), and Spearman correlation between true genetic values, and the genomic values predicted by each methodology were determined. Considering the processing time, the three methodologies were statistically different, rrBLUP was the fastest, and Bayesian LASSO was the slowest. Spearman correlation revealed that the rrBLUP and GBLUP methodologies were equivalent, and Bayesian LASSO provided the lowest correlation values. Similar results were obtained in coincidence variables among the individuals selected, in which Bayesian LASSO differed statistically and presented a lower value than the other methodologies. Therefore, for the scenarios evaluated, rrBLUP is the best methodology for the selection of genetically superior individuals.

  13. Three-dimensional analysis of micro- and nanostructure of biomaterials and cells by method of scanning probe nanotomography

    Directory of Open Access Journals (Sweden)

    A. E. Efimov

    2017-01-01

    Full Text Available Aim: to perform a three-dimensional analysis of micro- and nanosctucture and quantitative morphological parameters of alginate spherical microcarriers and porous regenerated silk macrocarriers modifi ed by microparticles of decellularized rat liver matrix and human hepatoma HepG2 cells adhered to micro- and macro carriers. Materials and methods. Three-dimensional porous matrices made from regenerated silk by salt leaching technique and alginate spherical microcarriers fabricated by encapsulation were vitalized by human hepatome HepG2 cells. Study of three-dimensional structure of cells and micro- and macro carriers was carried out at –120 °С by scanning probe cryonanotomography technique with use of experimental setup combining cryoultramicrotome and scanning probe microscope.Results. Three-dimensional nanotomographical reconstructions of HepG2 cells adhered to macropore wall of regenerated silk macrocarrier and to spherical alginate microcarrier are obtained. Morphological parameters (mean roughness, effective surface area and autocorrelation length are determined for surfaces of macro and microcarriers and adhered cells. The determined mean roughness of alginate microcarrier surface is 76.4 ± 7.5 nm, while that of surface of macropore wall of regenerated silk macrocarrier is 133.8 ± 16.2 nm. At the same time mean roughness of cells adhered to micro- and macrocarriers are 118.5 ± 9.0 и 158.8 ± 21.6 nm correspondingly. Three-dimensional reconstructions of intracellular compartments with dimensions from 140 to 500 nm are also obtained.Conclusion. Obtained as a result of study quantitative morphology characteristics of surfaces of cell carriers and adhered cells show signifi cant degree of correlation of morphological parameters of cells and their carriers. Use of scanning probe cryonanotomography technique for three-dimensional analysis of structure and characteristics of biomaterials, cells and bio-artifi cial cellular systems

  14. Database Description - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ... QTL list, Plant DB link & Genome analysis methods Alternative name - DOI 10.18908/lsdba.nbdc01194-01-000 Cr...ers and QTLs are curated manually from the published literature. The marker information includes marker sequences, genotyping methods... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  15. A comparison of statistical methods for genomic selection in a mice population

    Directory of Open Access Journals (Sweden)

    Neves Haroldo HR

    2012-11-01

    Full Text Available Abstract Background The availability of high-density panels of SNP markers has opened new perspectives for marker-assisted selection strategies, such that genotypes for these markers are used to predict the genetic merit of selection candidates. Because the number of markers is often much larger than the number of phenotypes, marker effect estimation is not a trivial task. The objective of this research was to compare the predictive performance of ten different statistical methods employed in genomic selection, by analyzing data from a heterogeneous stock mice population. Results For the five traits analyzed (W6W: weight at six weeks, WGS: growth slope, BL: body length, %CD8+: percentage of CD8+ cells, CD4+/ CD8+: ratio between CD4+ and CD8+ cells, within-family predictions were more accurate than across-family predictions, although this superiority in accuracy varied markedly across traits. For within-family prediction, two kernel methods, Reproducing Kernel Hilbert Spaces Regression (RKHS and Support Vector Regression (SVR, were the most accurate for W6W, while a polygenic model also had comparable performance. A form of ridge regression assuming that all markers contribute to the additive variance (RR_GBLUP figured among the most accurate for WGS and BL, while two variable selection methods ( LASSO and Random Forest, RF had the greatest predictive abilities for %CD8+ and CD4+/ CD8+. RF, RKHS, SVR and RR_GBLUP outperformed the remainder methods in terms of bias and inflation of predictions. Conclusions Methods with large conceptual differences reached very similar predictive abilities and a clear re-ranking of methods was observed in function of the trait analyzed. Variable selection methods were more accurate than the remainder in the case of %CD8+ and CD4+/CD8+ and these traits are likely to be influenced by a smaller number of QTL than the remainder. Judged by their overall performance across traits and computational requirements, RR

  16. A fully automatic end-to-end method for content-based image retrieval of CT scans with similar liver lesion annotations.

    Science.gov (United States)

    Spanier, A B; Caplan, N; Sosna, J; Acar, B; Joskowicz, L

    2018-01-01

    The goal of medical content-based image retrieval (M-CBIR) is to assist radiologists in the decision-making process by retrieving medical cases similar to a given image. One of the key interests of radiologists is lesions and their annotations, since the patient treatment depends on the lesion diagnosis. Therefore, a key feature of M-CBIR systems is the retrieval of scans with the most similar lesion annotations. To be of value, M-CBIR systems should be fully automatic to handle large case databases. We present a fully automatic end-to-end method for the retrieval of CT scans with similar liver lesion annotations. The input is a database of abdominal CT scans labeled with liver lesions, a query CT scan, and optionally one radiologist-specified lesion annotation of interest. The output is an ordered list of the database CT scans with the most similar liver lesion annotations. The method starts by automatically segmenting the liver in the scan. It then extracts a histogram-based features vector from the segmented region, learns the features' relative importance, and ranks the database scans according to the relative importance measure. The main advantages of our method are that it fully automates the end-to-end querying process, that it uses simple and efficient techniques that are scalable to large datasets, and that it produces quality retrieval results using an unannotated CT scan. Our experimental results on 9 CT queries on a dataset of 41 volumetric CT scans from the 2014 Image CLEF Liver Annotation Task yield an average retrieval accuracy (Normalized Discounted Cumulative Gain index) of 0.77 and 0.84 without/with annotation, respectively. Fully automatic end-to-end retrieval of similar cases based on image information alone, rather that on disease diagnosis, may help radiologists to better diagnose liver lesions.

  17. In silico method for modelling metabolism and gene product expression at genome scale

    Energy Technology Data Exchange (ETDEWEB)

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  18. G-MAPSEQ – a new method for mapping reads to a reference genome

    Directory of Open Access Journals (Sweden)

    Wojciechowski Pawel

    2016-06-01

    Full Text Available The problem of reads mapping to a reference genome is one of the most essential problems in modern computational biology. The most popular algorithms used to solve this problem are based on the Burrows-Wheeler transform and the FM-index. However, this causes some issues with highly mutated sequences due to a limited number of mutations allowed. G-MAPSEQ is a novel, hybrid algorithm combining two interesting methods: alignment-free sequence comparison and an ultra fast sequence alignment. The former is a fast heuristic algorithm which uses k-mer characteristics of nucleotide sequences to find potential mapping places. The latter is a very fast GPU implementation of sequence alignment used to verify the correctness of these mapping positions. The source code of G-MAPSEQ along with other bioinformatic software is available at: http://gpualign.cs.put.poznan.pl.

  19. Comparative investigation of the gel chromatography column scanning method for quality control of /sup 99/sup(m)Tc-methylenediphosphonate

    Energy Technology Data Exchange (ETDEWEB)

    Darte, L

    1981-04-01

    Gel chromatography column scanning (GCS) is the method of choice for quality control of sup(99m)Tc-MDP preparations. Using this method all the labelled components are obtained rapidly in one simple test procedure. The influence of various parameters such as gel type, column size, prehistory of column, equilibration, eluent, elution volume and flow rate upon the results have been investigated. Test results for sup(99 m)Tc-MDP have been compared for several different GCS systems, a few TLC systems and column chromatography with fraction collection. The GCS technique, optimized for testing sup(99m)Tc-MDP preparations has been applied in a few experiments in which very good reproducibility is required: Labelling kinetics and stability when stored at room temperature or in a refrigerator and influence of the sup(99m)Te/(sup(99m)Tc + /sup 99/Tc) atomic ratio and of the amount of radioactivity on the sup(99m)Tc-MDP labelling yield, covering parameter ranges of clinical interest, have been studied.

  20. AUTOMATIC EXTRACTION OF ROCK JOINTS FROM LASER SCANNED DATA BY MOVING LEAST SQUARES METHOD AND FUZZY K-MEANS CLUSTERING

    Directory of Open Access Journals (Sweden)

    S. Oh

    2012-09-01

    Full Text Available Recent development of laser scanning device increased the capability of representing rock outcrop in a very high resolution. Accurate 3D point cloud model with rock joint information can help geologist to estimate stability of rock slope on-site or off-site. An automatic plane extraction method was developed by computing normal directions and grouping them in similar direction. Point normal was calculated by moving least squares (MLS method considering every point within a given distance to minimize error to the fitting plane. Normal directions were classified into a number of dominating clusters by fuzzy K-means clustering. Region growing approach was exploited to discriminate joints in a point cloud. Overall procedure was applied to point cloud with about 120,000 points, and successfully extracted joints with joint information. The extraction procedure was implemented to minimize number of input parameters and to construct plane information into the existing point cloud for less redundancy and high usability of the point cloud itself.

  1. Identification of genomic insertion and flanking sequence of G2-EPSPS and GAT transgenes in soybean using whole genome sequencing method

    Directory of Open Access Journals (Sweden)

    Bingfu Guo

    2016-07-01

    Full Text Available Molecular characterization of sequences flanking exogenous fragment insertions is essential for safety assessment and labeling of genetically modified organisms (GMO. In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS method. About 21 Gb sequence data (~21× coverage for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundary of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of the genomic insertion site of the G2-EPSPS and GAT transgenes will facilitate the use of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS is a cost-effective and rapid method of identifying sites of T-DNA insertions and flanking sequences in soybean.

  2. A new method to cluster genomes based on cumulative Fourier power spectrum.

    Science.gov (United States)

    Dong, Rui; Zhu, Ziyue; Yin, Changchuan; He, Rong L; Yau, Stephen S-T

    2018-06-20

    Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum). Copyright © 2018. Published by Elsevier B.V.

  3. A Fast and Robust Feature-Based Scan-Matching Method in 3D SLAM and the Effect of Sampling Strategies

    Directory of Open Access Journals (Sweden)

    Cihan Ulas

    2013-11-01

    Full Text Available Simultaneous localization and mapping (SLAM plays an important role in fully autonomous systems when a GNSS (global navigation satellite system is not available. Studies in both 2D indoor and 3D outdoor SLAM are based on the appearance of environments and utilize scan-matching methods to find rigid body transformation parameters between two consecutive scans. In this study, a fast and robust scan-matching method based on feature extraction is introduced. Since the method is based on the matching of certain geometric structures, like plane segments, the outliers and noise in the point cloud are considerably eliminated. Therefore, the proposed scan-matching algorithm is more robust than conventional methods. Besides, the registration time and the number of iterations are significantly reduced, since the number of matching points is efficiently decreased. As a scan-matching framework, an improved version of the normal distribution transform (NDT is used. The probability density functions (PDFs of the reference scan are generated as in the traditional NDT, and the feature extraction - based on stochastic plane detection - is applied to the only input scan. By using experimental dataset belongs to an outdoor environment like a university campus, we obtained satisfactory performance results. Moreover, the feature extraction part of the algorithm is considered as a special sampling strategy for scan-matching and compared to other sampling strategies, such as random sampling and grid-based sampling, the latter of which is first used in the NDT. Thus, this study also shows the effect of the subsampling on the performance of the NDT.

  4. Renal scan

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003790.htm Renal scan To use the sharing features on this ... anaphylaxis . Alternative Names Renogram; Kidney scan Images Kidney anatomy Kidney - blood and urine flow References Chernecky CC, ...

  5. CT Scan

    Science.gov (United States)

    ... disease, lung nodules and liver masses Monitor the effectiveness of certain treatments, such as cancer treatment Detect ... scan done in a hospital or an outpatient facility. CT scans are painless and, with newer machines, ...

  6. The use of real time ultrasound scanning as a teaching method of anatomy in an undergraduate sonography and medical imaging degree in an Australian university

    International Nuclear Information System (INIS)

    Bowman, A.; Lawson, C.; McKillup, S.

    2016-01-01

    Background: Real-time ultrasound scanning is increasing in popularity as a teaching tool for human anatomy because it is non-invasive, offers real-time 3-D anatomy and is cheaper than dissections. Aim: To assess real-time ultrasound scanning as a teaching method of human anatomy, and to determine what teaching methods medical imaging and sonography students consider effective for understanding human anatomy. Method: Surveys were distributed to two consecutive cohorts of first year medical imaging and medical sonography students at CQUniversity. Participation was voluntary. Comparisons among teaching methods were made using repeated measures ANOVA. Results: Real-time ultrasound scanning was the most preferred method of delivery for anatomy classes overall especially compared to computer programs, videos, 3-D radiological images and dissection. Specifically, students indicated that ultrasound scanning was the preferred method to encourage learning from experience (F 7,231  = 2.942, p = 0.006), to develop team skills (F 7,231  = 4.550, p < 0.006), to follow complex instructions (F 7,231  = 4.656 p < 0.001) and to appreciate anatomical variation (F 7,231  = 2.067, p = 0.048). Dissection was the least favoured teaching method. Conclusion: Real-time ultrasound scanning is a useful tool for teaching anatomy, and animal dissections are a poor substitute for the use of human cadavers. - Highlights: • Real-time ultrasound scanning is a valid teaching tool for human anatomy. • Real-time ultrasound is preferred by students compared to other teaching methods. • Dissection is the least favoured method to learn anatomy. • Ultrasound encourages learning from experience and develops team skills.

  7. Hydroxyapatite, fluor-hydroxyapatite and fluorapatite produced via the sol-gel method: bonding to titanium and scanning electron microscopy.

    Science.gov (United States)

    Tredwin, Christopher J; Georgiou, George; Kim, Hae-Won; Knowles, Jonathan C

    2013-05-01

    Hydroxyapatite (HA), fluor-hydroxyapatite (FHA) with varying levels of fluoride ion substitution and fluorapatite (FA) production has been characterised and optimised by the sol-gel method and the dissolution and biological properties of these materials were investigated. It was the objective of this study to investigate the potential bond strength and interaction of these materials with titanium. HA, FHA and FA were synthesised by a sol-gel method. Calcium nitrate and triethyl phosphite were used as precursors under an ethanol-water based solution. Different amounts of ammonium fluoride (NH4F) were incorporated for the preparation of the FHA and FA sol-gels. Using a spin coating technique the sol-gels were coated onto commercially pure titanium disks and crystallised at various temperatures. Using scanning electron microscopy (SEM) and elemental analysis, the surface characteristics, coating thickness and interaction of the Ti substrate and coating were investigated. The bond strengths of the coating to the Ti were investigated using an Instron Universal Load Testing Machine. Statistical analysis was performed with a two-way analysis of variance and post hoc testing with a Bonferroni correction. (1) Coating speed inversely influenced the coating thickness. (2) Increasing fluoride ion substitution and heating temperature significantly increased bond strength and (3) increasing fluoride ion substitution increased the coating thickness. FHA and FA synthesised using the sol-gel technique may offer a superior alternative to coating titanium implants with HA and plasma spraying. HA, FHA and FA materials synthesised by the sol-gel method may also have a use as bone grafting materials. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  8. Evaluation of early changes induced by diuron in the rat urinary bladder using different processing methods for scanning electron microscopy.

    Science.gov (United States)

    Fava, Rafaela Marono; Ferragut Cardoso, Ana Paula; da Rocha, Mitscheli Sanches; Nascimento E Pontes, Merielen Garcia; de Camargo, João Lauro Viana; de Oliveira, Maria Luiza Cotrim Sartor

    2015-07-03

    Diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] is a substituted urea herbicide carcinogenic to the rat urinary bladder at high dietary levels. The suggested non-genotoxic mode of action (MOA) of diuron encompasses cytotoxicity and necrosis followed by regenerative hyperplasia. Prenecrotic swollen cells as observed under scanning electron microscopy (SEM) have been reported as early morphological alterations, putatively related to diuron cytotoxicity. However, these changes were not observed in a previous SEM study conducted in this laboratory. This study evaluated whether these early alterations are actually due to diuron cytotoxicity or artifacts related to different processing methods used for SEM analysis. Male Wistar rats were fed ad libitum with basal diet, 7.1% sodium saccharin (NaS) or 2.500ppm diuron for seven days or 15 weeks. The urinary bladders were processed for histological and labeling indices examinations and for SEM using two different processing methods. The incidence of simple hyperplasia after 15 weeks of exposure to diuron or to NaS was significantly increased. By SEM, the incidences and severity of lesions were significantly increased in the diuron group independently of exposure time. The different SEM processing methods used allowed for visualization of swollen superficial cells after seven days of diuron exposure. Probably the absence these cells in a previous study was due to the use very few animals. Our results support the hypothesis that the swollen cell is an early key event due to diuron-induced cytotoxicity and is the result of a degenerative process involved in the non-genotoxic carcinogenic mode of action of high doses of diuron. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  9. Evaluation of early changes induced by diuron in the rat urinary bladder using different processing methods for scanning electron microscopy

    International Nuclear Information System (INIS)

    Fava, Rafaela Marono; Ferragut Cardoso, Ana Paula; Sanches da Rocha, Mitscheli; Nascimento e Pontes, Merielen Garcia; Viana de Camargo, João Lauro; Cotrim Sartor de Oliveira, Maria Luiza

    2015-01-01

    Diuron [3-(3,4-dichlorophenyl)-1,1-dimethylurea] is a substituted urea herbicide carcinogenic to the rat urinary bladder at high dietary levels. The suggested non-genotoxic mode of action (MOA) of diuron encompasses cytotoxicity and necrosis followed by regenerative hyperplasia. Prenecrotic swollen cells as observed under scanning electron microscopy (SEM) have been reported as early morphological alterations, putatively related to diuron cytotoxicity. However, these changes were not observed in a previous SEM study conducted in this laboratory. This study evaluated whether these early alterations are actually due to diuron cytotoxicity or artifacts related to different processing methods used for SEM analysis. Male Wistar rats were fed ad libitum with basal diet, 7.1% sodium saccharin (NaS) or 2.500 ppm diuron for seven days or 15 weeks. The urinary bladders were processed for histological and labeling indices examinations and for SEM using two different processing methods. The incidence of simple hyperplasia after 15 weeks of exposure to diuron or to NaS was significantly increased. By SEM, the incidences and severity of lesions were significantly increased in the diuron group independently of exposure time. The different SEM processing methods used allowed for visualization of swollen superficial cells after seven days of diuron exposure. Probably the absence these cells in a previous study was due to the use very few animals. Our results support the hypothesis that the swollen cell is an early key event due to diuron-induced cytotoxicity and is the result of a degenerative process involved in the non-genotoxic carcinogenic mode of action of high doses of diuron

  10. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

    Science.gov (United States)

    Raviram, Ramya; Rocha, Pedro P; Müller, Christian L; Miraldi, Emily R; Badri, Sana; Fu, Yi; Swanzey, Emily; Proudhon, Charlotte; Snetkova, Valentina; Bonneau, Richard; Skok, Jane A

    2016-03-01

    4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait") that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.

  11. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  12. Comparison on genomic predictions using GBLUP models and two single-step blending methods with different relationship matrices in the Nordic Holstein population

    DEFF Research Database (Denmark)

    Gao, Hongding; Christensen, Ole Fredslund; Madsen, Per

    2012-01-01

    Background A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a single-step method may need to be adjusted because marker-based and pedigree-based relationship matrices may...... not be on the same scale. The same may apply when a GBLUP model includes both genomic breeding values and residual polygenic effects. The objective of this study was to compare single-step blending methods and GBLUP methods with and without adjustment of the genomic relationship matrix for genomic prediction of 16......) a simple GBLUP method, 2) a GBLUP method with a polygenic effect, 3) an adjusted GBLUP method with a polygenic effect, 4) a single-step blending method, and 5) an adjusted single-step blending method. In the adjusted GBLUP and single-step methods, the genomic relationship matrix was adjusted...

  13. Development of a method of absorbed dose on-line monitoring at product processing by scanned electron beam

    International Nuclear Information System (INIS)

    Pomatsalyuk, R.I.; Shevchenko, V.A.; Tenishev, A.Eh.; Titov, D.V.; Uvarov, V.L.

    2016-01-01

    The conditions of the contact-free absorbed dose monitoring at industrial product processing by electron beam are investigated. The method is based on analysing the collected charge in a stack monitor (SM) mounted down-stream of irradiated object. Using computer simulation on the basis of a modified transport code PENELOPE-2008, it is shown that by placing a filter of low-energy electrons before SM it is possible to obtain the one-to-one correlation dependence between the monitor charge and absorbed energy of radiation in the processed object. At a certain surface density of the filter, this dependence takes on the form similar to linear. The possibility to use an air gap between the object and SM as such a filter has been demonstrated. For the conditions of radiation plant with an electron accelerator LU-10 of NSC KIPT, the optimum distance of the SM location has been established. For the practical range of the electron energy, beam scan width and surface density of the irradiated product, the constants of ''product absorbed energy-to- SM charge '' linear dependence have been determined. The capability to establish the average absorbed dose in the object moving trough the irradiation zone on the SM current is shown. The calculation data are in satisfactory agreement with the results of measurements.

  14. Genome analysis methods: Arabidopsis lyrata [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

    Lifescience Database Archive (English)

    Full Text Available (http://genome.imim.es/software/geneid/) applying dicot and A. thaliana specific matrices 32,670 (v1.0) JGI; http://www.phytozome.net/alyrata v1.0 v1.0 10.1038/ng.807 21478890 ... ...8.3x Arachne 1,309 ... Fgenesh package of ab initio and homology-based gene predictors, EuGene12, and GeneID13

  15. Genome analysis methods: Lotus japonicus [PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive

    Lifescience Database Archive (English)

    Full Text Available Lotus japonicus Draft 2n=12 472 Mb 2008 Sanger (Clone-based) ... 315.1 Mb 3-5x Parace...l Genome Assembler 954 110,940 Kazusa Annotation PipelinE for Lotus japonicus (KAPSEL) 37,971 (v2.5) KDRI; http://www.kazusa.or.jp/lotus/ v2.5 v2.5 10.1093/dnares/dsn008 18511435 ...

  16. Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

    Directory of Open Access Journals (Sweden)

    Dan Dou

    2017-07-01

    Full Text Available Genome delivery to the proper cellular compartment for transcription and replication is a primary goal of viruses. However, methods for analyzing viral genome localization and differentiating genomes with high identity are lacking, making it difficult to investigate entry-related processes and co-examine heterogeneous RNA viral populations. Here, we present an RNA labeling approach for single-cell analysis of RNA viral replication and co-infection dynamics in situ, which uses the versatility of padlock probes. We applied this method to identify influenza A virus (IAV infections in cells and lung tissue with single-nucleotide specificity and to classify entry and replication stages by gene segment localization. Extending the classification strategy to co-infections of IAVs with single-nucleotide variations, we found that the dependence on intracellular trafficking places a time restriction on secondary co-infections necessary for genome reassortment. Altogether, these data demonstrate how RNA viral genome labeling can help dissect entry and co-infections.

  17. Whole-genome regression and prediction methods applied to plant and animal breeding

    NARCIS (Netherlands)

    Los Campos, De G.; Hickey, J.M.; Pong-Wong, R.; Daetwyler, H.D.; Calus, M.P.L.

    2013-01-01

    Genomic-enabled prediction is becoming increasingly important in animal and plant breeding, and is also receiving attention in human genetics. Deriving accurate predictions of complex traits requires implementing whole-genome regression (WGR) models where phenotypes are regressed on thousands of

  18. A simple, rapid and efficient method for the extraction of genomic ...

    African Journals Online (AJOL)

    The isolation of intact, high-molecular-mass genomic DNA is essential for many molecular biology applications including long range PCR, endonuclease restriction digestion, southern blot analysis, and genomic library construction. Many protocols are available for the extraction of DNA from plant material, but obtain it is ...

  19. Noninvasive computerized scanning method for the correlation between the facial soft and hard tissues for an integrated three-dimensional anthropometry and cephalometry.

    Science.gov (United States)

    Galantucci, Luigi Maria; Percoco, Gianluca; Lavecchia, Fulvio; Di Gioia, Eliana

    2013-05-01

    The article describes a new methodology to scan and integrate facial soft tissue surface with dental hard tissue models in a three-dimensional (3D) virtual environment, for a novel diagnostic approach.The facial and the dental scans can be acquired using any optical scanning systems: the models are then aligned and integrated to obtain a full virtual navigable representation of the head of the patient. In this article, we report in detail and further implemented a method for integrating 3D digital cast models into a 3D facial image, to visualize the anatomic position of the dentition. This system uses several 3D technologies to scan and digitize, integrating them with traditional dentistry records. The acquisitions were mainly performed using photogrammetric scanners, suitable for clinics or hospitals, able to obtain high mesh resolution and optimal surface texture for the photorealistic rendering of the face. To increase the quality and the resolution of the photogrammetric scanning of the dental elements, the authors propose a new technique to enhance the texture of the dental surface. Three examples of the application of the proposed procedure are reported in this article, using first laser scanning and photogrammetry and then only photogrammetry. Using cheek retractors, it is possible to scan directly a great number of dental elements. The final results are good navigable 3D models that integrate facial soft tissue and dental hard tissues. The method is characterized by the complete absence of ionizing radiation, portability and simplicity, fast acquisition, easy alignment of the 3D models, and wide angle of view of the scanner. This method is completely noninvasive and can be repeated any time the physician needs new clinical records. The 3D virtual model is a precise representation both of the soft and the hard tissue scanned, and it is possible to make any dimensional measure directly in the virtual space, for a full integrated 3D anthropometry and

  20. Genome-wide linkage scan for maximum and length-dependent knee muscle strength in young men: significant evidence for linkage at chromosome 14q24.3.

    Science.gov (United States)

    De Mars, G; Windelinckx, A; Huygens, W; Peeters, M W; Beunen, G P; Aerssens, J; Vlietinck, R; Thomis, M A I

    2008-05-01

    Maintenance of high muscular fitness is positively related to bone health, functionality in daily life and increasing insulin sensitivity, and negatively related to falls and fractures, morbidity and mortality. Heritability of muscle strength phenotypes ranges between 31% and 95%, but little is known about the identity of the genes underlying this complex trait. As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to muscle and bone cross-sectional area, isometric knee flexion and extension torque, and torque-length relationship for knee flexors and extensors. In total, 283 informative male siblings (17-36 years old), belonging to 105 families, were used to conduct a genome-wide SNP-based multipoint linkage analysis. The strongest evidence for linkage was found for the torque-length relationship of the knee flexors at 14q24.3 (LOD = 4.09; p<10(-5)). Suggestive evidence for linkage was found at 14q32.2 (LOD = 3.00; P = 0.005) for muscle and bone cross-sectional area, at 2p24.2 (LOD = 2.57; p = 0.01) for isometric knee torque at 30 degrees flexion, at 1q21.3, 2p23.3 and 18q11.2 (LOD = 2.33, 2.69 and 2.21; p<10(-4) for all) for the torque-length relationship of the knee extensors and at 18p11.31 (LOD = 2.39; p = 0.0004) for muscle-mass adjusted isometric knee extension torque. We conclude that many small contributing genes rather than a few important genes are involved in causing variation in different underlying phenotypes of muscle strength. Furthermore, some overlap in promising genomic regions were identified among different strength phenotypes.

  1. COMPARATIVE EVALUATION OF CONVENTIONAL VERSUS RAPID METHODS FOR AMPLIFIABLE GENOMIC DNA ISOLATION OF CULTURED Azospirillum sp. JG3

    Directory of Open Access Journals (Sweden)

    Stalis Norma Ethica

    2013-12-01

    Full Text Available As an initial attempt to reveal genetic information of Azospirillum sp. JG3 strain, which is still absence despite of the strains' ability in producing valued enzymes, two groups of conventional methods: lysis-enzyme and column-kit; and two rapid methods: thermal disruption and intact colony were evaluated. The aim is to determine the most practical method for obtaining high-grade PCR product using degenerate primers as part of routine-basis protocols for studying the molecular genetics of the Azospirillal bacteria. The evaluation includes the assessment of electrophoresis gel visualization, pellet appearance, preparation time, and PCR result of extracted genomic DNA from each method. Our results confirmed that the conventional methods were more superior to the rapid methods in generating genomic DNA isolates visible on electrophoresis gel. However, modification made in the previously developed DNA isolation protocol giving the simplest and most rapid method of all methods used in this study for extracting PCR-amplifiable DNA of Azospirillum sp. JG3. Intact bacterial cells (intact colony loaded on electrophoresis gel could present genomic DNA band, but could not be completely amplified by PCR without thermal treatment. It can also be inferred from our result that the 3 to 5-min heating in dH2O step is critical for the pre-treatment of colony PCR of Azospirillal cells.

  2. Cytogenetic method of determining effect of threshold values of anthropogenic factors on the plant and animal genome

    International Nuclear Information System (INIS)

    Arkhipchuk, V.V.; Romanenko, V.D.; Arkhipchuk, M.V.; Kipnis, L.S.

    1993-01-01

    The use of nucleolar characteristics to access the action of physical and chemical factors on living objects is a promising trend in the creation of new and highly sensitive biological tests. The advantages of this process are that the effect of the threshold values of the anthropogenic factors is recorded as a change in functional activity of the cell genome and not as the restructuring of the karyotype. The aim of this research was to test a cytogenetic method of determining the modifying action of various factors on the plant and animal genome, based on analysis of quantitative characteristics of the nucleoli and to extend its use to different groups of organisms

  3. Genome-wide association scan identifies a risk locus for preeclampsia on 2q14, near the inhibin, beta B gene.

    Directory of Open Access Journals (Sweden)

    Matthew P Johnson

    Full Text Available Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p = 3.58×10(-7, OR = 1.57; rs12711941, p = 4.26×10(-7, OR = 1.56 satisfied our genome-wide significance threshold (modified Bonferroni p0.92. We attempted to provide evidence of a putative regulatory role for these SNPs using bioinformatic analyses and found that they all reside within regions of low sequence conservation and/or low complexity, suggesting functional importance is low. We also explored the mRNA expression in decidua of genes ±500 kb of INHBB and found a nominally significant correlation between a transcript encoded by the EPB41L5 gene, ∼250 kb centromeric to INHBB, and preeclampsia (p = 0.03. We were unable to replicate the associations shown by the significant GWAS SNPs in case-control cohorts from Norway and Finland, leading us to conclude that it is more likely that these SNPs are in LD with as yet unidentified causal variant(s.

  4. A new method to detect and correct sample tilt in scanning transmission electron microscopy bright-field imaging

    Energy Technology Data Exchange (ETDEWEB)

    Brown, H.G. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Ishikawa, R.; Sánchez-Santolino, G. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Lugg, N.R., E-mail: shibata@sigma.t.u-tokyo.ac.jp [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Ikuhara, Y. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan); Allen, L.J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Shibata, N. [Institute of Engineering Innovation, School of Engineering, University of Tokyo, Tokyo 113-8656 (Japan)

    2017-02-15

    Important properties of functional materials, such as ferroelectric shifts and octahedral distortions, are associated with displacements of the positions of lighter atoms in the unit cell. Annular bright-field scanning transmission electron microscopy is a good experimental method for investigating such phenomena due to its ability to image light and heavy atoms simultaneously. To map atomic positions at the required accuracy precise angular alignment of the sample with the microscope optical axis is necessary, since misalignment (tilt) of the specimen contributes to errors in position measurements of lighter elements in annular bright-field imaging. In this paper it is shown that it is possible to detect tilt with the aid of images recorded using a central bright-field detector placed within the inner radius of the annular bright-field detector. For a probe focus near the middle of the specimen the central bright-field image becomes especially sensitive to tilt and we demonstrate experimentally that misalignment can be detected with a precision of less than a milliradian, as we also confirm in simulation. Coma in the probe, an aberration that can be misidentified as tilt of the specimen, is also investigated and it is shown how the effects of coma and tilt can be differentiated. The effects of tilt may be offset to a large extent by shifting the diffraction plane detector an amount equivalent to the specimen tilt and we provide an experimental proof of principle of this using a segmented detector system. - Highlights: • Octahedral distortions are associated with displacements of lighter atoms. • Annular bright-field imaging is sensitive to light and heavy atoms simultaneously. • Mistilt of the specimen leads to errors in position measurements of lighter elements. • It is possible to detect tilt using images taken by a central bright-field detector. • Tilt may be offset by shifting the diffraction plane detector by an equivalent amount.

  5. A Rapid and Efficient Method for Purifying High Quality Total RNA from Peaches (Prunus persica for Functional Genomics Analyses

    Directory of Open Access Journals (Sweden)

    LEE MEISEL

    2005-01-01

    Full Text Available Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica. Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

  6. Partial digestion with restriction enzymes of ultraviolet-irradiated human genomic DNA: a method for identifying restriction site polymorphisms

    International Nuclear Information System (INIS)

    Nobile, C.; Romeo, G.

    1988-01-01

    A method for partial digestion of total human DNA with restriction enzymes has been developed on the basis of a principle already utilized by P.A. Whittaker and E. Southern for the analysis of phage lambda recombinants. Total human DNA irradiated with uv light of 254 nm is partially digested by restriction enzymes that recognize sequences containing adjacent thymidines because of TT dimer formation. The products resulting from partial digestion of specific genomic regions are detected in Southern blots by genomic-unique DNA probes with high reproducibility. This procedure is rapid and simple to perform because the same conditions of uv irradiation are used for different enzymes and probes. It is shown that restriction site polymorphisms occurring in the genomic regions analyzed are recognized by the allelic partial digest patterns they determine

  7. A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.

    Directory of Open Access Journals (Sweden)

    Qiling Li

    Full Text Available The use of DNA from archival formalin and paraffin embedded (FFPE tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue.Ovarian tissues, which were obtained and formalin-fixed and paraffin-embedded in either 1999 or 2011, were sectioned and stained with hematoxylin-eosin (H&E.Epithelial cells were captured by laser micro dissection, and their DNA subjected to whole genomic bisulfite conversion, whole genomic polymerase chain reaction (PCR amplification, and purification. Sequencing and software analyses were performed to identify the extent of genomic methylation. We observed that 31.7% of sequence reads from the DNA in the 1999 archival FFPE tissue, and 70.6% of the reads from the 2011 sample, could be matched with the genome. Methylation rates of CpG on the Watson and Crick strands were 32.2% and 45.5%, respectively, in the 1999 sample, and 65.1% and 42.7% in the 2011 sample.We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples.

  8. Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements.

    Science.gov (United States)

    Kumazawa, Yoshinori; Endo, Hideki

    2004-04-30

    The mitochondrial genome of the Komodo dragon (Varanus komodoensis) was nearly completely sequenced, except for two highly repetitive noncoding regions. An efficient sequencing method for squamate mitochondrial genomes was established by combining the long polymerase chain reaction (PCR) technology and a set of reptile-oriented primers designed for nested PCR amplifications. It was found that the mitochondrial genome had novel gene arrangements in which genes from NADH dehydrogenase subunit 6 to proline tRNA were extensively shuffled with duplicate control regions. These control regions had 99% sequence similarity over 700 bp. Although snake mitochondrial genomes are also known to possess duplicate control regions with nearly identical sequences, the location of the second control region suggested independent occurrence of the duplication on lineages leading to snakes and the Komodo dragon. Another feature of the mitochondrial genome of the Komodo dragon was the considerable number of tandem repeats, including sequences with a strong secondary structure, as a possible site for the slipped-strand mispairing in replication. These observations are consistent with hypotheses that tandem duplications via the slipped-strand mispairing may induce mitochondrial gene rearrangements and may serve to maintain similar copies of the control region.

  9. Technical Note: Reliability of Suchey-Brooks and Buckberry-Chamberlain methods on 3D visualizations from CT and laser scans

    DEFF Research Database (Denmark)

    Villa, Chiara; Buckberry, Jo; Cattaneo, Cristina

    2013-01-01

    Previous studies have reported that the ageing method of Suchey-Brooks (pubic bone) and some of the features applied by Lovejoy et al. and Buckberry-Chamberlain (auricular surface) can be confidently performed on 3D visualizations from CT-scans. In this study, seven observers applied the Suchey......-Brooks and the Buckberry-Chamberlain methods on 3D visualizations based on CT-scans and, for the first time, on 3D visualizations from laser scans. We examined how the bone features can be evaluated on 3D visualizations and whether the different modalities (direct observations of bones, 3D visualization from CT......-observer agreement was obtained in the evaluation of the pubic bone in all modalities. In 3D visualizations of the auricular surfaces, transverse organization and apical changes could be evaluated, although with high inter-observer variability; micro-, macroporosity and surface texture were very difficult to score...

  10. Concept and development of measurement method of time sensitivity profile (TSP) in X-ray CT. Comparison of non-helical, single-slice helical, and multi-slice helical scans

    International Nuclear Information System (INIS)

    Tsujioka, Katsumi; Ida, Yoshihiro; Ohtsubo, Hironori; Takahashi, Yasukata; Niwa, Masayoshi

    2000-01-01

    We focused on the time element contained in a single CT image, and devised the concept of a time-sensitivity profile (TSP) describing how the time element is translated into an image. We calculated the data collection time range when the helical pitch is changed in non helical scans, single slice helical scans, and multi slice helical scans. We then calculated the time sensitivity profile (TSP) from the weighting applied when the data collection time range is translated into an image. TSP was also measured for each scanning method using our self-made moving phantom. TSPs obtained from the calculation and the experiments were very close. TSP showed interesting characteristics with each scanning method, especially in the case of multi slice helical scanning, in which TSP became shorter as helical pitch increased. We referred to the TSP's FWHM as the effective scanning time. When we conducted multi slice helical scanning at helical pitch 3, the effective scanning time increased to about 24% longer than that of a non helical scan. When we conducted multi slice helical scanning at helical pitch 5 or 6, the effective scanning time was about half that of a non helical scan. The time sensitivity profile (TSP) is a totally new concept that we consider an important element in discussing the time resolution of a CT scanner. The results of this review will provide significant data in determining the scanning parameters when scanning a moving object. (author)

  11. Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni.

    Directory of Open Access Journals (Sweden)

    Jacob A Tennessen

    Full Text Available New strategies to combat the global scourge of schistosomiasis may be revealed by increased understanding of the mechanisms by which the obligate snail host can resist the schistosome parasite. However, few molecular markers linked to resistance have been identified and characterized in snails.Here we test six independent genetic loci for their influence on resistance to Schistosoma mansoni strain PR1 in the 13-16-R1 strain of the snail Biomphalaria glabrata. We first identify a genomic region, RADres, showing the highest differentiation between susceptible and resistant inbred lines among 1611 informative restriction-site associated DNA (RAD markers, and show that it significantly influences resistance in an independent set of 439 outbred snails. The additive effect of each RADres resistance allele is 2-fold, similar to that of the previously identified resistance gene sod1. The data fit a model in which both loci contribute independently and additively to resistance, such that the odds of infection in homozygotes for the resistance alleles at both loci (13% infected is 16-fold lower than the odds of infection in snails without any resistance alleles (70% infected. Genome-wide linkage disequilibrium is high, with both sod1 and RADres residing on haplotype blocks >2 Mb, and with other markers in each block also showing significant effects on resistance; thus the causal genes within these blocks remain to be demonstrated. Other candidate loci had no effect on resistance, including the Guadeloupe Resistance Complex and three genes (aif, infPhox, and prx1 with immunological roles and expression patterns tied to resistance, which must therefore be trans-regulated.The loci RADres and sod1 both have strong effects on resistance to S. mansoni. Future approaches to control schistosomiasis may benefit from further efforts to characterize and harness this natural genetic variation.

  12. Cooperative scans

    NARCIS (Netherlands)

    M. Zukowski (Marcin); P.A. Boncz (Peter); M.L. Kersten (Martin)

    2004-01-01

    textabstractData mining, information retrieval and other application areas exhibit a query load with multiple concurrent queries touching a large fraction of a relation. This leads to individual query plans based on a table scan or large index scan. The implementation of this access path in most

  13. Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...Database Site Policy | Contact Us Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  14. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  15. Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...e Site Policy | Contact Us Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  16. Capturing the target genes of BldD in Saccharopolyspora erythraea using improved genomic SELEX method.

    Science.gov (United States)

    Wu, Hang; Mao, Yongrong; Chen, Meng; Pan, Hui; Huang, Xunduan; Ren, Min; Wu, Hao; Li, Jiali; Xu, Zhongdong; Yuan, Hualing; Geng, Ming; Weaver, David T; Zhang, Lixin; Zhang, Buchang

    2015-03-01

    BldD (SACE_2077), a key developmental regulator in actinomycetes, is the first identified transcriptional factor in Saccharopolyspora erythraea positively regulating erythromycin production and morphological differentiation. Although the BldD of S. erythraea binds to the promoters of erythromycin biosynthetic genes, the interaction affinities are relatively low, implying the existence of its other target genes in S. erythraea. Through the genomic systematic evolution of ligands by exponential enrichment (SELEX) method that we herein improved, four DNA sequences of S. erythraea A226, corresponding to the promoter regions of SACE_0306 (beta-galactosidase), SACE_0811 (50S ribosomal protein L25), SACE_3410 (fumarylacetoacetate hydrolase), and SACE_6014 (aldehyde dehydrogenase), were captured with all three BldD concentrations of 0.5, 1, and 2 μM, while the previously identified intergenic regions of eryBIV-eryAI and ermE-eryCI plus the promoter region of SACE_7115, the amfC homolog for aerial mycelium formation, could be captured only when the BldD's concentration reached 2 μM. Electrophoretic mobility shift assay (EMSA) analysis indicated that BldD specifically bound to above seven DNA sequences, and quantitative real-time PCR (qRT-PCR) assay showed that the transcriptional levels of the abovementioned target genes decreased when bldD was disrupted in A226. Furthermore, SACE_7115 and SACE_0306 in A226 were individually inactivated, showing that SACE_7115 was predominantly involved in aerial mycelium formation, while SACE_0306 mainly controlled erythromycin production. This study provides valuable information for better understanding of the pleiotropic regulator BldD in S. erythraea, and the improved method may be useful for uncovering regulatory networks of other transcriptional factors.

  17. Scanning thermal microscopy based on a quartz tuning fork and a micro-thermocouple in active mode (2ω method)

    International Nuclear Information System (INIS)

    Bontempi, Alexia; Nguyen, Tran Phong; Salut, Roland; Thiery, Laurent; Teyssieux, Damien; Vairac, Pascal

    2016-01-01

    A novel probe for scanning thermal microscope using a micro-thermocouple probe placed on a Quartz Tuning Fork (QTF) is presented. Instead of using an external deflection with a cantilever beam for contact detection, an original combination of piezoelectric resonator and thermal probe is employed. Due to a non-contact photothermal excitation principle, the high quality factor of the QTF allows the probe-to-surface contact detection. Topographic and thermal scanning images obtained on a specific sample points out the interest of our system as an alternative to cantilevered resistive probe systems which are the most spread.

  18. Scanning thermal microscopy based on a quartz tuning fork and a micro-thermocouple in active mode (2ω method).

    Science.gov (United States)

    Bontempi, Alexia; Nguyen, Tran Phong; Salut, Roland; Thiery, Laurent; Teyssieux, Damien; Vairac, Pascal

    2016-06-01

    A novel probe for scanning thermal microscope using a micro-thermocouple probe placed on a Quartz Tuning Fork (QTF) is presented. Instead of using an external deflection with a cantilever beam for contact detection, an original combination of piezoelectric resonator and thermal probe is employed. Due to a non-contact photothermal excitation principle, the high quality factor of the QTF allows the probe-to-surface contact detection. Topographic and thermal scanning images obtained on a specific sample points out the interest of our system as an alternative to cantilevered resistive probe systems which are the most spread.

  19. Scanning thermal microscopy based on a quartz tuning fork and a micro-thermocouple in active mode (2ω method)

    Energy Technology Data Exchange (ETDEWEB)

    Bontempi, Alexia; Nguyen, Tran Phong; Salut, Roland; Thiery, Laurent; Teyssieux, Damien; Vairac, Pascal [FEMTO-ST Institute UMR 6174, Université de Franche-Comté, CNRS, ENSMM, UTBM, 15B Avenue des Montboucons, F-25030 Besançon (France)

    2016-06-15

    A novel probe for scanning thermal microscope using a micro-thermocouple probe placed on a Quartz Tuning Fork (QTF) is presented. Instead of using an external deflection with a cantilever beam for contact detection, an original combination of piezoelectric resonator and thermal probe is employed. Due to a non-contact photothermal excitation principle, the high quality factor of the QTF allows the probe-to-surface contact detection. Topographic and thermal scanning images obtained on a specific sample points out the interest of our system as an alternative to cantilevered resistive probe systems which are the most spread.

  20. Methods for Motion Correction Evaluation Using 18F-FDG Human Brain Scans on a High-Resolution PET Scanner

    DEFF Research Database (Denmark)

    Keller, Sune H.; Sibomana, Merence; Olesen, Oline Vinter

    2012-01-01

    Many authors have reported the importance of motion correction (MC) for PET. Patient motion during scanning disturbs kinetic analysis and degrades resolution. In addition, using misaligned transmission for attenuation and scatter correction may produce regional quantification bias in the reconstr......Many authors have reported the importance of motion correction (MC) for PET. Patient motion during scanning disturbs kinetic analysis and degrades resolution. In addition, using misaligned transmission for attenuation and scatter correction may produce regional quantification bias...... in the reconstructed emission images. The purpose of this work was the development of quality control (QC) methods for MC procedures based on external motion tracking (EMT) for human scanning using an optical motion tracking system. Methods: Two scans with minor motion and 5 with major motion (as reported...... (automated image registration) software. The following 3 QC methods were used to evaluate the EMT and AIR MC: a method using the ratio between 2 regions of interest with gray matter voxels (GM) and white matter voxels (WM), called GM/WM; mutual information; and cross correlation. Results: The results...

  1. [Application of precursor ion scanning method in rapid screening of illegally added phosphodiesterase-5 inhibitors and their unknown derivatives in Chinese traditional patent medicines and health foods].

    Science.gov (United States)

    Sun, Jing; Cao, Ling; Feng, Youlong; Tan, Li

    2014-11-01

    The compounds with similar structure often have similar pharmacological activities. So it is a trend for illegal addition that new derivatives of effective drugs are synthesized to avoid the statutory test. This bring challenges to crack down on illegal addition behavior, however, modified derivatives usually have similar product ions, which allow for precursor ion scanning. In this work, precursor ion scanning mode of a triple quadrupole mass spectrometer was first applied to screen illegally added drugs in complex matrix such as Chinese traditional patent medicines and healthy foods. Phosphodiesterase-5 inhibitors were used as experimental examples. Through the analysis of the structure and mass spectrum characteristics of the compounds, phosphodiesterase-5 inhibitors were classified, and their common product ions were screened by full scan of product ions of typical compounds. Then high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method with precursor ion scanning mode was established based on the optimization of MS parameters. The effect of mass parameters and the choice of fragment ions were also studied. The method was applied to determine actual samples and further refined. The results demonstrated that this method can meet the need of rapid screening of unknown derivatives of phosphodiesterase-5 inhibitors in complex matrix, and prevent unknown derivatives undetected. This method shows advantages in sensitivity, specificity and efficiency, and is worth to be further investigated.

  2. Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

    Science.gov (United States)

    Jia, Yi; Jannink, Jean-Luc

    2012-01-01

    Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored. PMID:23086217

  3. A novel data mining method to identify assay-specific signatures in functional genomic studies

    Directory of Open Access Journals (Sweden)

    Guidarelli Jack W

    2006-08-01

    Full Text Available Abstract Background: The highly dimensional data produced by functional genomic (FG studies makes it difficult to visualize relationships between gene products and experimental conditions (i.e., assays. Although dimensionality reduction methods such as principal component analysis (PCA have been very useful, their application to identify assay-specific signatures has been limited by the lack of appropriate methodologies. This article proposes a new and powerful PCA-based method for the identification of assay-specific gene signatures in FG studies. Results: The proposed method (PM is unique for several reasons. First, it is the only one, to our knowledge, that uses gene contribution, a product of the loading and expression level, to obtain assay signatures. The PM develops and exploits two types of assay-specific contribution plots, which are new to the application of PCA in the FG area. The first type plots the assay-specific gene contribution against the given order of the genes and reveals variations in distribution between assay-specific gene signatures as well as outliers within assay groups indicating the degree of importance of the most dominant genes. The second type plots the contribution of each gene in ascending or descending order against a constantly increasing index. This type of plots reveals assay-specific gene signatures defined by the inflection points in the curve. In addition, sharp regions within the signature define the genes that contribute the most to the signature. We proposed and used the curvature as an appropriate metric to characterize these sharp regions, thus identifying the subset of genes contributing the most to the signature. Finally, the PM uses the full dataset to determine the final gene signature, thus eliminating the chance of gene exclusion by poor screening in earlier steps. The strengths of the PM are demonstrated using a simulation study, and two studies of real DNA microarray data – a study of

  4. Determination of some elements along the length of pine needles by means of the scanning energy dispersive x-ray fluorescence (EDXRF) method

    International Nuclear Information System (INIS)

    Viksna, A.; Katkevics, J.; Nulle, S.

    1998-01-01

    The scanning energy dispersive X-ray fluorescence (EDXDF) is used to measure the distribution of trace elements along the length of single pine needles. The current set up allows simultaneous determination up to 15 trace elements. The pilot experiments showed that the distribution of some elements varied along length of the pine needle. Concentration variations of trace elements with the needle age and needle position within the foliage crown were also observed. This could be one way of studying the annual physiological cycle of needles. The scanning EDXRF method was compared with graphite furnace atomic absorption spectrometry (GFAAS). (authors)

  5. Genome-wide linkage scan to identify loci associated with type 2 diabetes and blood lipid phenotypes in the Sikh Diabetes Study.

    Directory of Open Access Journals (Sweden)

    Dharambir K Sanghera

    Full Text Available In this investigation, we have carried out an autosomal genome-wide linkage analysis to map genes associated with type 2 diabetes (T2D and five quantitative traits of blood lipids including total cholesterol, high-density lipoprotein (HDL cholesterol, low-density lipoprotein (LDL cholesterol, very low-density lipoprotein (VLDL cholesterol, and triglycerides in a unique family-based cohort from the Sikh Diabetes Study (SDS. A total of 870 individuals (526 male/344 female from 321 families were successfully genotyped using 398 polymorphic microsatellite markers with an average spacing of 9.26 cM on the autosomes. Results of non-parametric multipoint linkage analysis using S(all statistics (implemented in Merlin did not reveal any chromosomal region to be significantly associated with T2D in this Sikh cohort. However, linkage analysis for lipid traits using QTL-ALL analysis revealed promising linkage signals with p≤0.005 for total cholesterol, LDL cholesterol, and HDL cholesterol at chromosomes 5p15, 9q21, 10p11, 10q21, and 22q13. The most significant signal (p = 0.0011 occurred at 10q21.2 for HDL cholesterol. We also observed linkage signals for total cholesterol at 22q13.32 (p = 0.0016 and 5p15.33 (p = 0.0031 and for LDL cholesterol at 10p11.23 (p = 0.0045. Interestingly, some of linkage regions identified in this Sikh population coincide with plausible candidate genes reported in recent genome-wide association and meta-analysis studies for lipid traits. Our study provides the first evidence of linkage for loci associated with quantitative lipid traits at four chromosomal regions in this Asian Indian population from Punjab. More detailed examination of these regions with more informative genotyping, sequencing, and functional studies should lead to rapid detection of novel targets of therapeutic importance.

  6. Radionuclide scanning

    International Nuclear Information System (INIS)

    Shapiro, B.

    1986-01-01

    Radionuclide scanning is the production of images of normal and diseased tissues and organs by means of the gamma-ray emissions from radiopharmaceutical agents having specific distributions in the body. The gamma rays are detected at the body surface by a variety of instruments that convert the invisible rays into visible patterns representing the distribution of the radionuclide in the body. The patterns, or images, obtained can be interpreted to provide or to aid diagnoses, to follow the course of disease, and to monitor the management of various illnesses. Scanning is a sensitive technique, but its specificity may be low when interpreted alone. To be used most successfully, radionuclide scanning must be interpreted in conjunction with other techniques, such as bone radiographs with bone scans, chest radiographs with lung scans, and ultrasonic studies with thyroid scans. Interpretation is also enhanced by providing pertinent clinical information because the distribution of radiopharmaceutical agents can be altered by drugs and by various procedures besides physiologic and pathologic conditions. Discussion of the patient with the radionuclide scanning specialist prior to the study and review of the results with that specialist after the study are beneficial

  7. Sizing up arthropod genomes: an evaluation of the impact of environmental variation on genome size estimates by flow cytometry and the use of qPCR as a method of estimation.

    Science.gov (United States)

    Gregory, T Ryan; Nathwani, Paula; Bonnett, Tiffany R; Huber, Dezene P W

    2013-09-01

    A study was undertaken to evaluate both a pre-existing method and a newly proposed approach for the estimation of nuclear genome sizes in arthropods. First, concerns regarding the reliability of the well-established method of flow cytometry relating to impacts of rearing conditions on genome size estimates were examined. Contrary to previous reports, a more carefully controlled test found negligible environmental effects on genome size estimates in the fly Drosophila melanogaster. Second, a more recently touted method based on quantitative real-time PCR (qPCR) was examined in terms of ease of use, efficiency, and (most importantly) accuracy using four test species: the flies Drosophila melanogaster and Musca domestica and the beetles Tribolium castaneum and Dendroctonus ponderosa. The results of this analysis demonstrated that qPCR has the tendency to produce substantially different genome size estimates from other established techniques while also being far less efficient than existing methods.

  8. Long-term response to genomic selection: effects of estimation method and reference population structure for different genetic architectures.

    Science.gov (United States)

    Bastiaansen, John W M; Coster, Albart; Calus, Mario P L; van Arendonk, Johan A M; Bovenhuis, Henk

    2012-01-24

    Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects. Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations. Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure. The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was

  9. Surface topography acquisition method for double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry.

    Science.gov (United States)

    Zhang, Tao; Gao, Feng; Jiang, Xiangqian

    2017-10-02

    This paper proposes an approach to measure double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry (DPWSI). The principle and mathematical model is discussed and the measurement system is calibrated with a combination of standard step-height samples for both probes vertical calibrations and a specially designed calibration artefact for building up the space coordinate relationship of the dual-probe measurement system. The topography of the specially designed artefact is acquired by combining the measurement results with white light scanning interferometer (WLSI) and scanning electron microscope (SEM) for reference. The relative location of the two probes is then determined with 3D registration algorithm. Experimental validation of the approach is provided and the results show that the method is able to measure double-sided near-right-angle structured surfaces with nanometer vertical resolution and micrometer lateral resolution.

  10. An Audit of Second-Trimester Fetal Anomaly Scans Based on a Novel Image-Scoring Method in the Southwest Region of the Netherlands.

    Science.gov (United States)

    Ursem, Nicolette T C; Peters, Ingrid A; Kraan-van der Est, Mieke N; Reijerink-Verheij, Jacqueline C I Y; Knapen, Maarten F C M; Cohen-Overbeek, Titia E

    2017-06-01

    Since 2007 the second-trimester fetal anomaly scan is offered to all pregnant women as part of the national prenatal screening program in the Netherlands. Dutch population-based screening programs generally have a well-described system to achieve quality assurance. Because of the absence of a uniform system to monitor the actual performance of the fetal anomaly scan in 2012, we developed a standardized image-scoring method. The aim of this study was to evaluate the scanning performance of all sonographers in the southwestern region of the Netherlands using this image-scoring method. Each sonographer was requested to set up a digital portfolio. A portfolio consists of five logbooks from five different pregnant women, each containing 25 fetal anatomical structures and six biometric measures of randomly selected fetal anomaly scans. During the study period, 425 logbooks of 85 sonographers were assessed as part of the audit process. Seventy-three out of 85 sonographers (86%) met the criteria in the primary audit, and 12 sonographers required individual hands-on training. A successful assessment was achieved for 11 sonographers in the re-audit and one sonographer ceased her contract. Moreover, 2.1% of the required images were not digitally stored and therefore could not be reviewed. Quality assessment using the image-scoring method demonstrated that most of the sonographers met the expectations of the audit process, but those who had subpar performance met the expectations after retraining. © 2017 by the American Institute of Ultrasound in Medicine.

  11. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  12. Optimization of transmission-scan time for the FixER method: a MR-based PET attenuation correction with a weak fixed-position external radiation source

    Energy Technology Data Exchange (ETDEWEB)

    Kawaguchi, Hiroshi; Hirano, Yoshiyuki; Kershaw, Jeff; Yoshida, Eiji [Molecular Imaging Center, National Institute of Radiological Sciences, Chiba (Japan); Shiraishi, Takahiro [Molecular Imaging Center, National Institute of Radiological Sciences, Chiba (Japan); Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba (Japan); Suga, Mikio [Molecular Imaging Center, National Institute of Radiological Sciences, Chiba (Japan); Center for Frontier Medical Engineering, Chiba University (Japan); Obata, Takayuki [Molecular Imaging Center, National Institute of Radiological Sciences, Chiba (Japan); Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Chiba (Japan); Ito, Hiroshi; Yamaya, Taiga [Molecular Imaging Center, National Institute of Radiological Sciences, Chiba (Japan)

    2014-07-29

    In recent work, we proposed an MRI-based attenuation-coefficient (μ-value) estimation method that uses a weak fixed-position external radiation source to construct an attenuation map for PET/MRI. In this presentation we refer to this method as FixER, and perform a series of simulations to investigate the duration of the transmission scan required to accurately estimate μ-values.

  13. Optimization of transmission-scan time for the FixER method: a MR-based PET attenuation correction with a weak fixed-position external radiation source

    International Nuclear Information System (INIS)

    Kawaguchi, Hiroshi; Hirano, Yoshiyuki; Kershaw, Jeff; Yoshida, Eiji; Shiraishi, Takahiro; Suga, Mikio; Obata, Takayuki; Ito, Hiroshi; Yamaya, Taiga

    2014-01-01

    In recent work, we proposed an MRI-based attenuation-coefficient (μ-value) estimation method that uses a weak fixed-position external radiation source to construct an attenuation map for PET/MRI. In this presentation we refer to this method as FixER, and perform a series of simulations to investigate the duration of the transmission scan required to accurately estimate μ-values.

  14. A genome-wide scan reveals important roles of DNA methylation in human longevity by regulating age-related disease genes.

    Directory of Open Access Journals (Sweden)

    Fu-Hui Xiao

    Full Text Available It is recognized that genetic factors contribute to human longevity. Besides the hypothesis of existence of longevity genes, another suggests that a lower frequency of risk alleles decreases the incidence of age-related diseases in the long-lived people. However, the latter finds no support from recent genetic studies. Considering the crucial role of epigenetic modification in gene regulation, we then hypothesize that suppressing disease-related genes in longevity individuals is likely achieved by epigenetic modification, e.g. DNA methylation. To test this hypothesis, we investigated the genome-wide methylation profile in 4 Chinese female centenarians and 4 middle-aged controls using methyl-DNA immunoprecipitation sequencing. 626 differentially methylated regions (DMRs were observed between both groups. Interestingly, genes with these DMRs were enriched in age-related diseases, including type-2 diabetes, cardiovascular disease, stroke and Alzheimer's disease. This pattern remains rather stable after including methylomes of two white individuals. Further analyses suggest that the observed DMRs likely have functional roles in regulating disease-associated gene expressions, with some genes [e.g. caspase 3 (CASP3] being down-regulated whereas the others [i.e. interleukin 1 receptor, type 2 (IL1R2] up-regulated. Therefore, our study suggests that suppressing the disease-related genes via epigenetic modification is an important contributor to human longevity.

  15. A genome-wide scan for autoimmune thyroiditis in the Old Order Amish: replication of genetic linkage on chromosome 5q11.2-q14.3.

    Science.gov (United States)

    Allen, Elsie M; Hsueh, Wen-Chi; Sabra, Mona M; Pollin, Toni I; Ladenson, Paul W; Silver, Kristi D; Mitchell, Braxton D; Shuldiner, Alan R

    2003-03-01

    Autoimmune thyroiditis (AITD) is a common disorder characterized by circulating antibodies to epitopes of thyroid tissue and hypothyroidism (Hashimoto's thyroiditis or AITD-hypothyroidism), although many subjects with AITD are euthyroid. Current evidence suggests that AITD is familial and polygenic. We studied AITD in a homogeneous founder Caucasian population, the Old Order Amish of Lancaster County, Pennsylvania. We found autoimmune thyroiditis, defined by the presence of circulating antimicrosomal antibodies, to be relatively common in the Amish, with a prevalence of 22.7%. The prevalence of AITD-hypothyroidism was 9.2%. We performed a genome-wide linkage analysis with 373 short tandem repeat markers in 445 subjects from 29 families. We observed suggestive evidence of linkage of AITD to a locus on chromosome 5q11.2-q14.3 (LOD, 2.30; P = 0.0006 at 94 cM; closest marker, D5S428), a region that was previously reported to be linked to AITD-hypothyroidism in a Japanese study. AITD-hypothyroidism showed a more modest linkage peak to the same region (LOD, 1.46; P = 0.005). Possible linkage (nominal P Amish.

  16. Genome-wide scan identifies variant in TNFSF13 associated with serum IgM in a healthy Chinese male population.

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    Ming Yang

    Full Text Available IgM provides a first line of defense during microbial infections. Serum IgM levels are detected routinely in clinical practice. And IgM is a genetically complex trait. We conducted a two-stage genome-wide association study (GWAS to identify genetic variants affecting serum IgM levels in a Chinese population of 3495, including 1999 unrelated subjects in the first stage and 1496 independent individuals in the second stage. Our data show that a common single nucleotide polymorphism (SNP, rs11552708 located in the TNFSF13 gene was significantly associated with IgM levels (p = 5.00×10(-7 in first stage, p = 1.34×10(-3 in second stage, and p = 4.22×10(-9 when combined. Besides, smoking was identified to be associated with IgM levels in both stages (P0.05. It is suggested that TNFSF13 may be a susceptibility gene affecting serum IgM levels in Chinese male population.

  17. Accuracy of full-arch scans using intraoral and extraoral scanners: an in vitro study using a new method of evaluation.

    Science.gov (United States)

    Muallah, Jonas; Wesemann, Christian; Nowak, Roxana; Robben, Jan; Mah, James; Pospiech, Peter; Bumann, Axel

    The aim of this study was to compare the accuracy of six intraoral scanners as regards clinically relevant distances using a new method of evaluation. An additional objective was to compare intraoral scanners with the indirect digitization of model scanners. A resin master model was created by 3D printing and drilled in five places to reflect the following distances: intermolar width (IMW), intercanine width (ICW), and arch length (AL). To determine a gold standard, the distances were measured with a coordinate measuring instrument (Zeiss O-Inspect 422). The master model was scanned 37 times with the following intraoral scanners: Apollo DI (Sirona), CS 3500 (Carestream Dental), iTero (Cadent), PlanScan (Planmeca), Trios (3Shape), and True Definition (3M Espe), and indirectly digitized with the OrthoX Scan (Dentaurum). The digital models were then measured, and deviations from the gold standard calculated. Significant differences were found between the devices. Among the intraoral scanners, Trios and iTero showed the most accurate results, although CS 3500, True Definition, and Apollo DI achieved comparable results. PlanScan demonstrated the highest deviations from the gold standard, and presented a high standard deviation (SD). Direct digitization revealed comparable (and, in fact, slightly higher) accuracy than indirect digitization. Both indirect digitization and most of the intraoral scanners were therefore demonstrated to be suitable for use in the orthodontic office, with the exception of PlanScan, which did not meet the demands of individual orthodontic treatment.

  18. RS-SNP: a random-set method for genome-wide association studies

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    Mukherjee Sayan

    2011-03-01

    Full Text Available Abstract Background The typical objective of Genome-wide association (GWA studies is to identify single-nucleotide polymorphisms (SNPs and corresponding genes with the strongest evidence of association (the 'most-significant SNPs/genes' approach. Borrowing ideas from micro-array data analysis, we propose a new method, named RS-SNP, for detecting sets of genes enriched in SNPs moderately associated to the phenotype. RS-SNP assesses whether the number of significant SNPs, with p-value P ≤ α, belonging to a given SNP set is statistically significant. The rationale of proposed method is that two kinds of null hypotheses are taken into account simultaneously. In the first null model the genotype and the phenotype are assumed to be independent random variables and the null distribution is the probability of the number of significant SNPs in greater than observed by chance. The second null model assumes the number of significant SNPs in depends on the size of and not on the identity of the SNPs in . Statistical significance is assessed using non-parametric permutation tests. Results We applied RS-SNP to the Crohn's disease (CD data set collected by the Wellcome Trust Case Control Consortium (WTCCC and compared the results with GENGEN, an approach recently proposed in literature. The enrichment analysis using RS-SNP and the set of pathways contained in the MSigDB C2 CP pathway collection highlighted 86 pathways rich in SNPs weakly associated to CD. Of these, 47 were also indicated to be significant by GENGEN. Similar results were obtained using the MSigDB C5 pathway collection. Many of the pathways found to be enriched by RS-SNP have a well-known connection to CD and often with inflammatory diseases. Conclusions The proposed method is a valuable alternative to other techniques for enrichment analysis of SNP sets. It is well founded from a theoretical and statistical perspective. Moreover, the experimental comparison with GENGEN highlights that it is

  19. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

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    Ramya Raviram

    2016-03-01

    Full Text Available 4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait" that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.

  20. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification.

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    Saharnaz Bigdeli

    Full Text Available Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides. This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated

  1. An efficient genotyping method for genome-modified animals and human cells generated with CRISPR/Cas9 system.

    Science.gov (United States)

    Zhu, Xiaoxiao; Xu, Yajie; Yu, Shanshan; Lu, Lu; Ding, Mingqin; Cheng, Jing; Song, Guoxu; Gao, Xing; Yao, Liangming; Fan, Dongdong; Meng, Shu; Zhang, Xuewen; Hu, Shengdi; Tian, Yong

    2014-09-19

    The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system, and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.

  2. Method for determining scan timing based on analysis of formation process of the time-density curve

    International Nuclear Information System (INIS)

    Yamaguchi, Isao; Ishida, Tomokazu; Kidoya, Eiji; Higashimura, Kyoji; Suzuki, Masayuki

    2005-01-01

    A strict determination of scan timing is needed for dynamic multi-phase scanning and 3D-CT angiography (3D-CTA) by multi-detector row CT (MDCT). In the present study, contrast media arrival time (T AR ) was measured in the abdominal aorta at the bifurcation of the celiac artery for confirmation of circulatory differences in patients. In addition, we analyzed the process of formation of the time-density curve (TDC) and examined factors that affect the time to peak aortic enhancement (T PA ). Mean T AR was 15.57±3.75 s. TDCs were plotted for each duration of injection. The rising portions of TDCs were superimposed on one another. TDCs with longer injection durations were piled up upon one another. Rise angle was approximately constant in response to each flow rate. Rise time (T R ) showed a good correlation with injection duration (T ID ). T R was 1.01 T ID (R 2 =0.994) in the phantom study and 0.94 T lD -0.60 (R 2 =0.988) in the clinical study. In conclusion, for the selection of optimal scan timing it is useful to determine T R at a given point and to determine the time from T AR . (author)

  3. A Visualization Method for Corrosion Damage on Aluminum Plates Using an Nd:YAG Pulsed Laser Scanning System.

    Science.gov (United States)

    Lee, Inbok; Zhang, Aoqi; Lee, Changgil; Park, Seunghee

    2016-12-16

    This paper proposes a non-contact nondestructive evaluation (NDE) technique that uses laser-induced ultrasonic waves to visualize corrosion damage in aluminum alloy plate structures. The non-contact, pulsed-laser ultrasonic measurement system generates ultrasonic waves using a galvanometer-based Q-switched Nd:YAG laser and measures the ultrasonic waves using a piezoelectric (PZT) sensor. During scanning, a wavefield can be acquired by changing the excitation location of the laser point and measuring waves using the PZT sensor. The corrosion damage can be detected in the wavefield snapshots using the scattering characteristics of the waves that encounter corrosion. The structural damage is visualized by calculating the logarithmic values of the root mean square (RMS), with a weighting parameter to compensate for the attenuation caused by geometrical spreading and dispersion of the waves. An intact specimen is used to conduct a comparison with corrosion at different depths and sizes in other specimens. Both sides of the plate are scanned with the same scanning area to observe the effect of the location where corrosion has formed. The results show that the damage can be successfully visualized for almost all cases using the RMS-based functions, whether it formed on the front or back side. Also, the system is confirmed to have distinguished corroded areas at different depths.

  4. Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans

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    Alizé Lacoste Jeanson

    2017-05-01

    Full Text Available Background Estimating volumes and masses of total body components is important for the study and treatment monitoring of nutrition and nutrition-related disorders, cancer, joint replacement, energy-expenditure and exercise physiology. While several equations have been offered for estimating total body components from MRI slices, no reliable and tested method exists for CT scans. For the first time, body composition data was derived from 41 high-resolution whole-body CT scans. From these data, we defined equations for estimating volumes and masses of total body AT and LT from corresponding tissue areas measured in selected CT scan slices. Methods We present a new semi-automatic approach to defining the density cutoff between adipose tissue (AT and lean tissue (LT in such material. An intra-class correlation coefficient (ICC was used to validate the method. The equations for estimating the whole-body composition volume and mass from areas measured in selected slices were modeled with ordinary least squares (OLS linear regressions and support vector machine regression (SVMR. Results and Discussion The best predictive equation for total body AT volume was based on the AT area of a single slice located between the 4th and 5th lumbar vertebrae (L4-L5 and produced lower prediction errors (|PE| = 1.86 liters, %PE = 8.77 than previous equations also based on CT scans. The LT area of the mid-thigh provided the lowest prediction errors (|PE| = 2.52 liters, %PE = 7.08 for estimating whole-body LT volume. We also present equations to predict total body AT and LT masses from a slice located at L4-L5 that resulted in reduced error compared with the previously published equations based on CT scans. The multislice SVMR predictor gave the theoretical upper limit for prediction precision of volumes and cross-validated the results.

  5. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  6. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

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    Jiabing Ji

    Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to