WorldWideScience

Sample records for genome scanning method

  1. AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome

    Directory of Open Access Journals (Sweden)

    Mei Lingling

    2011-11-01

    Full Text Available Abstract Background To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. Results Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA. Conclusions AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and

  2. The relative power of genome scans to detect local adaptation depends on sampling design and statistical method.

    Science.gov (United States)

    Lotterhos, Katie E; Whitlock, Michael C

    2015-03-01

    Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in 'pair' and 'transect' sampling strategies. We compared F(ST) outlier and genetic-environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (F(ST) or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and F(ST) had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data. © 2015 John Wiley & Sons Ltd.

  3. 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.

  4. 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.

  5. Footwear scanning systems and methods

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. A genome-wide scan for preeclampsia in the Netherlands

    NARCIS (Netherlands)

    Lachmeijer, AMA; Arngrimsson, R; Bastiaans, EJ; Frigge, ML; Pals, G; Sigurdardottir, S; Stefansson, H; Palsson, B; Nicolae, D; Kong, A; Aarnoudse, JG; Gulcher, [No Value; Dekker, GA; ten Kate, LP; Stefansson, K

    2001-01-01

    Preeclampsia, hallmarked by de novo hypertension and proteinuria in pregnancy, has a familial tendency. Recently, a large Icelandic genome-wide scan provided evidence for a maternal susceptibility locus for preeclampsia on chromosome 2p13 which was confirmed by a genome scan from Australia and New

  7. A Laser Scanning Tracking Method

    Science.gov (United States)

    Xu, Gaoyue; Hu, Baoli; Wang, Jiangping

    1988-04-01

    In this paper, a new tracking approach, a laser scanning tracking method (LSTM) is proposed. The LSTM has been designed to track a cylindrical retroreflective target mounted on the object, which makes plane motion. The retroreflector pasted by scotchlite reflective sheeting (mad. in 3M ,0.) i s located by scanning a laser beam in holizontal. When the retroreflector is struck, its position that is azimuth is read by microcomputer and the aiming device is servocontrolled by microcomputer according to this azimuth immediately. This is a step-by-step tracking method. The time of servo-reponse is less than one millisecona in actual tests. The angular accuracy is less than 0.5 milliradian. The track angular velocity is greater than one radian/second.

  8. An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

    Indian Academy of Sciences (India)

    Andrew M. Lynn; Chakresh Kumar Jain; K. Kosalai; Pranjan Barman; Nupur Thakur; Harish Batra; Alok Bhattacharya

    2001-04-01

    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 annotation of genome DNA sequences.

  9. 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

  10. A new approach for using genome scans to detect recent positive selection in the human genome.

    Directory of Open Access Journals (Sweden)

    Kun Tang

    2007-07-01

    Full Text Available Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP data of both the International HapMap Project and Perlegen Sciences, and detected widespread signals of recent local selection across the genome, consisting of both complete and partial sweeps. A challenging problem of genomic scans of recent positive selection is to clearly distinguish selection from neutral effects, given the high sensitivity of the test statistics to departures from neutral demographic assumptions and the lack of a single, accurate neutral model of human history. We therefore developed a new procedure that is robust across a wide range of demographic and ascertainment models, one that indicates that certain portions of the genome clearly depart from neutrality. Simulations of positive selection showed that our tests have high power towards strong selection sweeps that have undergone fixation. Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits.

  11. Asthma and atopy - a total genome scan for susceptibility genes

    DEFF Research Database (Denmark)

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

    2002-01-01

    . Investigation of different populations will further clarify the topic. We therefore evaluated allergic asthma and increased total and specific IgE in 39, 45 and 57 sib-pairs from 100 Danish allergy families. METHODS: Affected sib-pairs meeting a narrow phenotype definition were selected for the three phenotypes...... atopy, allergic asthma and increased total IgE. We performed a total genome scan using 446 microsatellite markers and obtained nonparametric linkage results from the MAPMAKER/SIBS computer program. RESULTS: Our study revealed four candidate regions (MLS > 2) on chromosome 1p36, 3q21-q22, 5q31 and 6p24-p...

  12. Statistical Methods in Integrative Genomics

    OpenAIRE

    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 f...

  13. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    Science.gov (United States)

    ... Q R S T U V W X Y Z We want to hear from you You are here: News & Events 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 Spotlight on Research 2012 July 2012 (historical) Genome-Wide Scan Reveals Mutation Associated with Melanoma A team of ...

  14. Asthma and atopy - a total genome scan for susceptibility genes

    DEFF Research Database (Denmark)

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

    2002-01-01

    atopy, allergic asthma and increased total IgE. We performed a total genome scan using 446 microsatellite markers and obtained nonparametric linkage results from the MAPMAKER/SIBS computer program. RESULTS: Our study revealed four candidate regions (MLS > 2) on chromosome 1p36, 3q21-q22, 5q31 and 6p24-p...

  15. In silico whole genome association scan for murine prepulse inhibition.

    Directory of Open Access Journals (Sweden)

    Bradley Todd Webb

    Full Text Available BACKGROUND: The complex trait of prepulse inhibition (PPI is a sensory gating measure related to schizophrenia and can be measured in mice. Large-scale public repositories of inbred mouse strain genotypes and phenotypes such as PPI can be used to detect Quantitative Trait Loci (QTLs in silico. However, the method has been criticized for issues including insufficient number of strains, not controlling for false discoveries, the complex haplotype structure of inbred mice, and failing to account for genotypic and phenotypic subgroups. METHODOLOGY/PRINCIPAL FINDINGS: We have implemented a method that addresses these issues by incorporating phylogenetic analyses, multilevel regression with mixed effects, and false discovery rate (FDR control. A genome-wide scan for PPI was conducted using over 17,000 single nucleotide polymorphisms (SNPs in 37 strains phenotyped. Eighty-nine SNPs were significant at a false discovery rate (FDR of 5%. After accounting for long-range linkage disequilibrium, we found 3 independent QTLs located on murine chromosomes 1 and 13. One of the PPI positives corresponds to a region of human chromosome 6p which includes DTNBP1, a gene implicated in schizophrenia. Another region includes the gene Tsn which alters PPI when knocked out. These genes also appear to have correlated expression with PPI. CONCLUSIONS/SIGNIFICANCE: These results support the usefulness of using an improved in silico mapping method to identify QTLs for complex traits such as PPI which can be then be used for to help identify loci influencing schizophrenia in humans.

  16. Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER

    Indian Academy of Sciences (India)

    Gautam Aggarwal; Ramakrishna Ramaswamy

    2002-02-01

    We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.

  17. 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.

  18. 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

    2017-04-10

    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 behavior 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 genome-wide analyses such as GWAS. This article is protected by copyright. All rights reserved.

  19. Scanning probe methods applied to molecular electronics

    OpenAIRE

    Pavliček, Niko

    2013-01-01

    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. A scanning tunneling microscopy (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 individ...

  20. Autofocus method for scanning remote sensing cameras.

    Science.gov (United States)

    Lv, Hengyi; Han, Chengshan; Xue, Xucheng; Hu, Changhong; Yao, Cheng

    2015-07-10

    Autofocus methods are conventionally based on capturing the same scene from a series of positions of the focal plane. As a result, it has been difficult to apply this technique to scanning remote sensing cameras where the scenes change continuously. In order to realize autofocus in scanning remote sensing cameras, a novel autofocus method is investigated in this paper. Instead of introducing additional mechanisms or optics, the overlapped pixels of the adjacent CCD sensors on the focal plane are employed. Two images, corresponding to the same scene on the ground, can be captured at different times. Further, one step of focusing is done during the time interval, so that the two images can be obtained at different focal plane positions. Subsequently, the direction of the next step of focusing is calculated based on the two images. The analysis shows that the method investigated operates without restriction of the time consumption of the algorithm and realizes a total projection for general focus measures and algorithms from digital still cameras to scanning remote sensing cameras. The experiment results show that the proposed method is applicable to the entire focus measure family, and the error ratio is, on average, no more than 0.2% and drops to 0% by reliability improvement, which is lower than that of prevalent approaches (12%). The proposed method is demonstrated to be effective and has potential in other scanning imaging applications.

  1. Genome scan for meat quality traits in Nelore beef cattle.

    Science.gov (United States)

    Tizioto, P C; Decker, J E; Taylor, J F; Schnabel, R D; Mudadu, M A; Silva, F L; Mourão, G B; Coutinho, L L; Tholon, P; Sonstegard, T S; Rosa, A N; Alencar, M M; Tullio, R R; Medeiros, S R; Nassu, R T; Feijó, G L D; Silva, L O C; Torres, R A; Siqueira, F; Higa, R H; Regitano, L C A

    2013-11-01

    Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

  2. Genome-Wide Scan for Methylation Profiles in Keloids

    Directory of Open Access Journals (Sweden)

    Lamont R. Jones

    2015-01-01

    Full Text Available Keloids are benign fibroproliferative tumors of the skin which commonly occur after injury mainly in darker skinned patients. Medical treatment is fraught with high recurrence rates mainly because of an incomplete understanding of the biological mechanisms that lead to keloids. The purpose of this project was to examine keloid pathogenesis from the epigenome perspective of DNA methylation. Genome-wide profiling used the Infinium HumanMethylation450 BeadChip to interrogate DNA from 6 fresh keloid and 6 normal skin samples from 12 anonymous donors. A 3-tiered approach was used to call out genes most differentially methylated between keloid and normal. When compared to normal, of the 685 differentially methylated CpGs at Tier 3, 510 were hypomethylated and 175 were hypermethylated with 190 CpGs in promoter and 495 in nonpromoter regions. The 190 promoter region CpGs corresponded to 152 genes: 96 (63% were hypomethylated and 56 (37% hypermethylated. This exploratory genome-wide scan of the keloid methylome highlights a predominance of hypomethylated genomic landscapes, favoring nonpromoter regions. DNA methylation, as an additional mechanism for gene regulation in keloid pathogenesis, holds potential for novel treatments that reverse deleterious epigenetic changes. As an alternative mechanism for regulating genes, epigenetics may explain why gene mutations alone do not provide definitive mechanisms for keloid formation.

  3. A novel scan statistics approach for clustering identification and comparison in binary genomic data.

    Science.gov (United States)

    Pellin, Danilo; Di Serio, Clelia

    2016-09-22

    In biomedical research a relevant issue is to identify time intervals or portions of a n-dimensional support where a particular event of interest is more likely to occur than expected. Algorithms that require to specify a-priori number/dimension/length of clusters assumed for the data suffer from a high degree of arbitrariness whenever no precise information are available, and this may strongly affect final estimation on parameters. Within this framework, spatial scan-statistics have been proposed in the literature, representing a valid non-parametric alternative. We adapt the so called Bernoulli-model scan statistic to the genomic field and we propose a multivariate extension, named Relative Scan Statistics, for the comparison of two series of Bernoulli r.v. defined over a common support, with the final goal of highlighting unshared event rate variations. Using a probabilistic approach based on success probability estimates and comparison (likelihood based), we can exploit an hypothesis testing procedure to identify clusters and relative clusters. Both the univariate and the novel multivariate extension of the scan statistic confirm previously published findings. The method described in the paper represents a challenging application of scan statistics framework to problem related to genomic data. From a biological perspective, these tools offer the possibility to clinicians and researcher to improve their knowledge on viral vectors integrations process, allowing to focus their attention to restricted over-targeted portion of the genome.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Jingjing Gu

    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

  6. Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 complex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

  7. Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis. WGPScanning analysis showed that all primer pairs yielded PCR products of the expected sizes in all four strains tested. The nucleotide sequences of all the detected virulence factor genes are identical in the four strains and MLST results showed that the four isolates studied and reference strain all belonged to the ST1 com-plex. No new genetic changes were found in the genome structure of the isolates from this Sichuan outbreak.

  8. A dynamic scanning method based on signal-statistics for scanning electron microscopy.

    Science.gov (United States)

    Timischl, F

    2014-01-01

    A novel dynamic scanning method for noise reduction in scanning electron microscopy and related applications is presented. The scanning method dynamically adjusts the scanning speed of the electron beam depending on the statistical behavior of the detector signal and gives SEM images with uniform and predefined standard deviation, independent of the signal value itself. In the case of partially saturated images, the proposed method decreases image acquisition time without sacrificing image quality. The effectiveness of the proposed method is shown and compared to the conventional scanning method and median filtering using numerical simulations.

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

    Science.gov (United States)

    Stein, Catherine M; Zalwango, Sarah; Malone, LaShaunda L; Won, Sungho; Mayanja-Kizza, Harriet; Mugerwa, Roy D; Leontiev, Dmitry V; Thompson, Cheryl L; Cartier, Kevin C; Elston, Robert C; Iyengar, Sudha K; Boom, W Henry; Whalen, Christopher C

    2008-01-01

    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 not

  10. 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

  11. Selection of Acquisition Scan Methods in Intersatellite Optical Communications

    Institute of Scientific and Technical Information of China (English)

    于思源; 高惠德; 马晶; 董蕴华; 马祖光

    2002-01-01

    In this paper, a theoretical model of the acquisition in intersatellite optical communications (IOC) is founded with the assumption that beacon pointing errors could be modeled as Gaussian random variables. An optimal scan method should be chosen according to the average acquisition time under a certain acquisition probability. With analysis of the most common scan methods during the establishment of IOC, the raster-spiral scanning can substitute the spiral scanning is found. The raster scanning and raster-spiral scanning are simulated using Monte Carlo method and the result shows the first one is optimal for acquisition in IOC.

  12. 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.inra.fr/CBGP/software/baypass/.

  13. System and Method for Scan Range Gating

    Science.gov (United States)

    Zuk, David M. (Inventor); Lindemann, Scott (Inventor)

    2017-01-01

    A system for scanning light to define a range gated signal includes a pulsed coherent light source that directs light into the atmosphere, a light gathering instrument that receives the light modified by atmospheric backscatter and transfers the light onto an image plane, a scanner that scans collimated light from the image plane to form a range gated signal from the light modified by atmospheric backscatter, a control circuit that coordinates timing of a scan rate of the scanner and a pulse rate of the pulsed coherent light source so that the range gated signal is formed according to a desired range gate, an optical device onto which an image of the range gated signal is scanned, and an interferometer to which the image of the range gated signal is directed by the optical device. The interferometer is configured to modify the image according to a desired analysis.

  14. Meta analysis of whole-genome linkage scans with data uncertainty: an application to Parkinson's disease

    Directory of Open Access Journals (Sweden)

    Gasser Thomas

    2007-07-01

    Full Text Available Abstract Background Genome wide linkage scans have often been successful in the identification of genetic regions containing susceptibility genes for a disease. Meta analysis is used to synthesize information and can even deliver evidence for findings missed by original studies. If researchers are not contributing their data, extracting valid information from publications is technically challenging, but worth the effort. We propose an approach to include data extracted from published figures of genome wide linkage scans. The validity of the extraction was examined on the basis of those 25 markers, for which sufficient information was reported. Monte Carlo simulations were used to take into account the uncertainty in marker position and in linkage test statistic. For the final meta analysis we compared the Genome Search Meta Analysis method (GSMA and the Corrected p-value Meta analysis Method (CPMM. An application to Parkinson's disease is given. Because we had to use secondary data a meta analysis based on original summary values would be desirable. Results Data uncertainty by replicated extraction of marker position is shown to be much smaller than 30 cM, a distance up to which a maximum LOD score may usually be found away from the true locus. The main findings are not impaired by data uncertainty. Conclusion Applying the proposed method a novel linked region for Parkinson's disease was identified on chromosome 14 (p = 0.036. Comparing the two meta analysis methods we found in this analysis more regions of interest being identified by GSMA, whereas CPMM provides stronger evidence for linkage. For further validation of the extraction method comparisons with raw data would be required.

  15. Meta analysis of whole-genome linkage scans with data uncertainty: an application to Parkinson's disease

    Science.gov (United States)

    Rosenberger, Albert; Sharma, Manu; Müller-Myhsok, Bertram; Gasser, Thomas; Bickeböller, Heike

    2007-01-01

    Background Genome wide linkage scans have often been successful in the identification of genetic regions containing susceptibility genes for a disease. Meta analysis is used to synthesize information and can even deliver evidence for findings missed by original studies. If researchers are not contributing their data, extracting valid information from publications is technically challenging, but worth the effort. We propose an approach to include data extracted from published figures of genome wide linkage scans. The validity of the extraction was examined on the basis of those 25 markers, for which sufficient information was reported. Monte Carlo simulations were used to take into account the uncertainty in marker position and in linkage test statistic. For the final meta analysis we compared the Genome Search Meta Analysis method (GSMA) and the Corrected p-value Meta analysis Method (CPMM). An application to Parkinson's disease is given. Because we had to use secondary data a meta analysis based on original summary values would be desirable. Results Data uncertainty by replicated extraction of marker position is shown to be much smaller than 30 cM, a distance up to which a maximum LOD score may usually be found away from the true locus. The main findings are not impaired by data uncertainty. Conclusion Applying the proposed method a novel linked region for Parkinson's disease was identified on chromosome 14 (p = 0.036). Comparing the two meta analysis methods we found in this analysis more regions of interest being identified by GSMA, whereas CPMM provides stronger evidence for linkage. For further validation of the extraction method comparisons with raw data would be required. PMID:17605797

  16. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    NARCIS (Netherlands)

    Imumorin, I.G.; Kim, B.; Li, Y.; Koning, de D.J.; Arendonk, van J.A.M.; Donato, S.

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We

  17. Whole Genome PCR Scanning (WGPS) of C. burnetii strains from ruminants

    NARCIS (Netherlands)

    Sidi-Boumedine, Karim; Adam, Gilbert; Angen, Oysten; Aspán, A.; Bossers, A.; Roest, H.I.J.; Prigent, Myriam; Thiéry, R.; Rousset, Elodie

    2015-01-01

    Coxiella burnetii is the causative agent of Q fever, a zoonosis that spreads from ruminants to humans via the inhalation of aerosols contaminated by livestock's birth products. This study aimed to compare the genomes of strains isolated from ruminants by “Whole Genome PCR Scanning (WGPS)” in order t

  18. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    NARCIS (Netherlands)

    Imumorin, I.G.; Kim, B.; Li, Y.; Koning, de D.J.; Arendonk, van J.A.M.; Donato, S.

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We ident

  19. A Successive Scans Method of Adjusting Scan-Time for Injection Electroluminescent Display Panels

    Institute of Scientific and Technical Information of China (English)

    OU Peng; YANG Gang; JIANG Quan; WANG Jun; HU Jian-Hua; WU Qi-Peng; LUO Kai-Jun

    2011-01-01

    @@ Aiming at the problem of luminance uniformity for injection electroluminescent display panels, we present a new scan method for display panels according to successive scans theory.First, on the basis of the number of pixels requiring light emitting in one frame period, we adjust the scan time for each row.Secondly, for ensuring image transmission synchronization, the frame period must to be a constant.We adopt a 64 × 32 LED display panel as an example to expound the new scan method and we obtain the good result that the reduce amplitude of luminance non-uniformity is 31.34% and the increase amplitude of the average luminance value is 7.8258%.%Aiming at the problem of luminance uniformity for injection electroluminescent display panels,we present a new scan method for display panets according to successive scans theory.First,on the basis of the number of pixels requiring light emitting in one frame period,we adjust the scan time for each row.Secondly,for ensuring image transmission synchronization,the frame period must to be a constant.We adopt a 64×32 LED display panel as an example to expound the new scan method and we odtain the good result that the reduce amplitude of luminance non-uniformity is 31.34% and the increase amplitude of the average luminance value is 7.8258%.

  20. 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...... of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs....

  1. 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.

  2. Recovery of known T-cell epitopes by computational scanning of a viral genome

    Science.gov (United States)

    Logean, Antoine; Rognan, Didier

    2002-04-01

    A new computational method (EpiDock) is proposed for predicting peptide binding to class I MHC proteins, from the amino acid sequence of any protein of immunological interest. Starting from the primary structure of the target protein, individual three-dimensional structures of all possible MHC-peptide (8-, 9- and 10-mers) complexes are obtained by homology modelling. A free energy scoring function (Fresno) is then used to predict the absolute binding free energy of all possible peptides to the class I MHC restriction protein. Assuming that immunodominant epitopes are usually found among the top MHC binders, the method can thus be applied to predict the location of immunogenic peptides on the sequence of the protein target. When applied to the prediction of HLA-A*0201-restricted T-cell epitopes from the Hepatitis B virus, EpiDock was able to recover 92% of known high affinity binders and 80% of known epitopes within a filtered subset of all possible nonapeptides corresponding to about one tenth of the full theoretical list. The proposed method is fully automated and fast enough to scan a viral genome in less than an hour on a parallel computing architecture. As it requires very few starting experimental data, EpiDock can be used: (i) to predict potential T-cell epitopes from viral genomes (ii) to roughly predict still unknown peptide binding motifs for novel class I MHC alleles.

  3. Scanning for signatures of geographically restricted selection based on population genomics analysis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Natural selection, as the driving force of human evolution, has direct impact on population differentiation. However, it is still unclear to what extent the genetic differentiation has been caused by natural selection. To explore this question, we performed a genome-wide scan with single nucleotide polymorphism (SNP) data from the International HapMap Project. Single locus FST analysis was applied to assess the frequency difference among populations in autosomes. Based on the empirical distribution of FST, we identified 12669 SNPs correlating to population differentiation and 1853 candidate genes subjected to geographic restricted natural selection. Further interpretation of gene ontogeny revealed 121 categories of biological process with the enrichments of candidate genes. Our results suggest that natural selection may play an important role in human population differentiation. In addition, our analysis provides new clues as well as research methods for our understanding of population differentiation and natural selection.

  4. 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.

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

    OpenAIRE

    Gautier, Mathieu

    2015-01-01

    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 (i...

  6. A Genome-wide Pleiotropy Scan for Prostate Cancer Risk

    Science.gov (United States)

    Panagiotou, Orestis A; Travis, Ruth C; Campa, Daniele; Berndt, Sonja I.; Lindstrom, Sara; Kraft, Peter; Schumacher, Fredrick R.; Siddiq, Afshan; Papatheodorou, Stefania I.; Stanford, Janet L.; Albanes, Demetrius; Virtamo, Jarmo; Weinstein, Stephanie J.; Diver, W. Ryan; Gapstur, Susan M.; Stevens, Victoria L.; Boeing, Heiner; Bueno-de-Mesquita, H. Bas; Gurrea, Aurelio Barricarte; Kaaks, Rudolf; Khaw, Kay-Tee; Krogh, Vittorio; Overvad, Kim; Riboli, Elio; Trichopoulos, Dimitrios; Giovannucci, Edward; Stampfer, Meir; Haiman, Christopher; Henderson, Brian; Le Marchand, Loic; Gaziano, J. Michael; Hunter, DavidJ.; Koutros, Stella; Yeager, Meredith; Hoover, Robert N.; Chanock, Stephen J.; Wacholder, Sholom; Key, Timothy J.; Tsilidis, Konstantinos K

    2014-01-01

    Background No single-nucleotide polymorphisms (SNPs) specific for aggressive prostate cancer have been identified in genome-wide association studies (GWAS). Objective To test if SNPs associated with other traits may also affect the risk of aggressive prostate cancer. Design, setting, and participants SNPs implicated in any phenotype other than prostate cancer (p ≤ 10−7) were identified through the catalog of published GWAS and tested in 2891 aggressive prostate cancer cases and 4592 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). The 40 most significant SNPs were followed up in 4872 aggressive prostate cancer cases and 24 534 controls from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium. Outcome measurements and statistical analysis Odds ratios (ORs) and 95% confidence intervals (CIs) for aggressive prostate cancer were estimated. Results and limitations A total of 4666 SNPs were evaluated by the BPC3. Two signals were seen in regions already reported for prostate cancer risk. rs7014346 at 8q24.21 was marginally associated with aggressive prostate cancer in the BPC3 trial (p = 1.6 × 10-6), whereas after meta-analysis by PRACTICAL the summary OR was 1.21 (95%CI 1.16–1.27; p = 3.22 × 10−18). rs9900242 at 17q24.3 was also marginally associated with aggressive disease in the meta-analysis (OR 0.90, 95% CI 0.86–0.94; p = 2.5 × 10−6). Neither of these SNPs remained statistically significant when conditioning on correlated known prostate cancer SNPs. The meta-analysis by BPC3 and PRACTICAL identified a third promising signal, marked by rs16844874 at 2q34, independent of known prostate cancer loci (OR 1.12,95% CI 1.06–1.19; p = 4.67 × 10−5); it has been shown that SNPs correlated with this signal affect glycine concentrations. The main limitation is the heterogeneity in the definition of aggressive prostate cancer between BPC3 and PRACTICAL. Conclusions We did

  7. Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling

    OpenAIRE

    Foster, Joseph M.; Oumie, Assa; Togneri, Fiona S; Vasques, Fabiana Ramos; Hau, Debra; Taylor, Morag; Tinkler-Hundal, Emma; Southward, Katie; Medlow, Paul; McGreeghan-Crosby, Keith; Halfpenny, Iris; McMullan, Dominic J.; Quirke, Phil; Keating, Katherine E; Griffiths, Mike

    2015-01-01

    Background Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations. Methods In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laborat...

  8. 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......-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases...

  9. 3D scan to product design: Methods, techniques, and cases

    NARCIS (Netherlands)

    Lee, W.; Lee, B.; Kim, S.; Jung, H.; Jeon, E.; Choi, T.; You, H.

    2015-01-01

    3D scanning technology has derived great opportunities for ergonomic product designs. This paper is aimed to introduce various research cases and methods based on 3D scanning have conducted by an ergonomics laboratory in South Korea. Sizing systems and representative 3D models developed on anthropom

  10. 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...

  11. Identification of the human chromosomal region containing the iridogoniodysgenesis anomaly locus by genomic-mismatch scanning.

    Science.gov (United States)

    Mirzayans, F; Mears, A J; Guo, S W; Pearce, W G; Walter, M A

    1997-01-01

    Genome-mismatch scanning (GMS) is a new method of linkage analysis that rapidly isolates regions of identity between two genomes. DNA molecules from regions of identity by descent from two relatives are isolated based on their ability to form extended mismatch-free heteroduplexes. We have applied this rapid technology to identify the chromosomal region shared by two fifth-degree cousins with autosomal dominant iridogoniodysgenesis anomaly (IGDA), a rare ocular neurocristopathy. Markers on the short arm of human chromosome 6p were recovered, consistent with the results of conventional linkage analysis conducted in parallel, indicating linkage of IGDA to 6p25. Control markers tested on a second human chromosome were not recovered. A GMS error rate of approximately 11% was observed, well within an acceptable range for a rapid, first screening approach, especially since GMS results would be confirmed by family analysis with selected markers from the putative region of identity by descent. These results demonstrate not only the value of this technique in the rapid mapping of human genetic traits, but the first application of GMS to a multicellular organism. Images Figure 2 PMID:9245991

  12. Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source

    Directory of Open Access Journals (Sweden)

    Børglum Anders D

    2011-07-01

    Full Text Available Abstract Background The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined with clinical information from medical registries, DBS samples could provide a rich source for productive research. However, the amounts of DNA which can be extracted from these precious samples are minute and may be prohibitive for numerous genotypings. Previously, we demonstrated that DBS DNA can be whole-genome amplified and used for reliable genetic analysis on different platforms, including genome-wide scanning arrays. However, it remains unclear whether this approach is workable on a large sample scale. We examined the robustness of using DBS samples for whole-genome amplification following genome-wide scanning, using arrays from Illumina and Affymetrix. Results This study is based on 4,641 DBS samples from the Danish Newborn Screening Biobank, extracted for three separate genome-wide association studies. The amount of amplified DNA was significantly (P Conclusion Our study indicates that archived DBS samples from the Danish Newborn Screening Biobank represent a reliable resource of DNA for whole-genome amplification and subsequent genome-wide association studies. With call-rates equivalent to high quality DNA samples, our results point to new opportunities for using the neonatal biobanks available worldwide in the hunt for genetic components of disease.

  13. A genome scan for quantitative trait loci affecting body conformation traits in Spanish Churra dairy sheep.

    Science.gov (United States)

    Gutiérrez-Gil, B; Alvarez, L; de la Fuente, L F; Sanchez, J P; San Primitivo, F; Arranz, J J

    2011-08-01

    A genome scan for chromosomal regions influencing body conformation traits was conducted for a population of Spanish Churra dairy sheep following a daughter design. A total of 739 ewes from 11 half-sib sire families were included in the study. The ewes were scored for the 5 linear traits used in the breeding scheme of the Churra breed to assess body conformation: stature, rear legs-rear view, foot angle, rump width, and general appearance. All the animals, including the 11 sires, were genotyped for 181 microsatellite markers evenly distributed across the 26 sheep autosomes. Using the yield deviations of the raw scores adjusted for fixed factors as phenotypic measurements, a quantitative trait loci (QTL) analysis was performed on the basis of a multi-marker regression method. Seven suggestive QTL were identified on chromosomes Ovis aries (OAR)2, OAR5, OAR16, OAR23, and OAR26, but none reached a genome-wise significance level. Putative QTL were identified for all of the traits analyzed, except for general appearance score. The suggestive QTL showing the highest test statistic influenced rear legs-rear view and was localized on OAR16, close to the growth hormone receptor coding gene, GHR. Some of the putative linkage associations reported here are consistent with previously reported QTL in cattle for similar traits. To the best of our knowledge, this study provides the first report of QTL for body conformation traits in dairy sheep; further studies will be needed to confirm and redefine the linkage associations reported herein. It is expected that future genome-wide association analyses of larger families will help identify genes underlying these putative genetic effects and provide useful markers for marker-assisted selection of such functional traits.

  14. 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...

  15. Whole genome scan to detect quantitative trait loci for bovine milk protein composition

    NARCIS (Netherlands)

    Schopen, G.C.B.; Koks, P.D.; Arendonk, van J.A.M.; Bovenhuis, H.; Visker, M.H.P.W.

    2009-01-01

    The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein–Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A gen

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

    NARCIS (Netherlands)

    Zhou, Kaixin; Dempfle, Astrid; Arcos-Burgos, Mauricio; Bakker, Steven C; Banaschewski, Tobias; Biederman, Joseph; Buitelaar, Jan; Castellanos, F Xavier; Doyle, Alysa; Ebstein, Richard P; Ekholm, Jenny; Forabosco, Paola; Franke, Barbara; Freitag, Christine; Friedel, Susann; Gill, Michael; Hebebrand, Johannes; Hinney, Anke; Jacob, Christian; Lesch, Klaus Peter; Loo, Sandra K; Lopera, Francisco; McCracken, James T; McGough, James J; Meyer, Jobst; Mick, Eric; Miranda, Ana; Muenke, Maximilian; Mulas, Fernando; Nelson, Stanley F; Nguyen, T Trang; Oades, Robert D; Ogdie, Matthew N; Palacio, Juan David; Pineda, David; Reif, Andreas; Renner, Tobias J; Roeyers, Herbert; Romanos, Marcel; Rothenberger, Aribert; Schäfer, Helmut; Sergeant, Joseph; Sinke, Richard J; Smalley, Susan L; Sonuga-Barke, Edmund; Steinhausen, Hans-Christoph; van der Meulen, Emma; Walitza, Susanne; Warnke, Andreas; Lewis, Cathryn M; Faraone, Stephen V; Asherson, Philip

    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, th

  17. Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan

    Science.gov (United States)

    Aluminum (Al) toxicity is an important limitation to food security in the tropical and subtropical regions. High Al saturation in acid soils limits root development and its ability to uptake water and nutrients. In this study, we present a genome scan for Al tolerance loci with over 50,000 GBS-based...

  18. An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis.

    Science.gov (United States)

    Galindo, J; Grahame, J W; Butlin, R K

    2010-09-01

    Genome scans have been used in the studies of ecological speciation to find genomic regions ('outlier loci') showing reduced gene flow between divergent populations/species. High-throughput sequencing ('454') offers new opportunities in this field via transcriptome sequencing. Divergent ecotypes of the marine gastropod Littorina saxatilis represent a good example of incipient ecological speciation. We performed a 454-based genome scan between H and M ecotypes of L. saxatilis from the British Isles using cDNA of pooled individuals. Allele frequencies were calculated for 2454 single nucleotide polymorphisms (SNPs), within 572 contigs, and 7% of loci were detected as outliers. Functional annotation of the contigs containing outlier SNPs showed that they included shell matrix and muscle proteins (lithostathine, mucin, titin), proteins involved in energetic metabolism (arginine kinase, NADH dehydrogenase) and reverse transcriptases. Follow-up investigations into these proteins and unannotated outliers will be a promising route in the study of ecological speciation in L. saxatilis.

  19. Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar.

    Science.gov (United States)

    Tollenaere, C; Jacquet, S; Ivanova, S; Loiseau, A; Duplantier, J-M; Streiff, R; Brouat, C

    2013-01-01

    Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection. © 2012 Blackwell Publishing Ltd.

  20. Development of Genome-Wide Scan for Selection Signature in Farm Animals

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wen-guang

    2013-01-01

    Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.

  1. Genome-wide scans using archived neonatal dried blood spot samples

    Directory of Open Access Journals (Sweden)

    Wiuf Carsten

    2009-07-01

    Full Text Available Abstract Background Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference. Results Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16, and conflicts with reference DNA in only three per 10,000 genotype calls. Conclusion Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.

  2. A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

    Science.gov (United States)

    Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C.L.L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

    2015-01-01

    We identified 44844 high-quality SNPs by sequencing 92 diverse chickpea accessions belonging to a seed and pod trait-specific association panel using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays. A GWAS (genome-wide association study) in an association panel of 211, including the 92 sequenced accessions, identified 22 major genomic loci showing significant association (explaining 23–47% phenotypic variation) with pod and seed number/plant and 100-seed weight. Eighteen trait-regulatory major genomic loci underlying 13 robust QTLs were validated and mapped on an intra-specific genetic linkage map by QTL mapping. A combinatorial approach of GWAS, QTL mapping and gene haplotype-specific LD mapping and transcript profiling uncovered one superior haplotype and favourable natural allelic variants in the upstream regulatory region of a CesA-type cellulose synthase (Ca_Kabuli_CesA3) gene regulating high pod and seed number/plant (explaining 47% phenotypic variation) in chickpea. The up-regulation of this superior gene haplotype correlated with increased transcript expression of Ca_Kabuli_CesA3 gene in the pollen and pod of high pod/seed number accession, resulting in higher cellulose accumulation for normal pollen and pollen tube growth. A rapid combinatorial genome-wide SNP genotyping-based approach has potential to dissect complex quantitative agronomic traits and delineate trait-regulatory genomic loci (candidate genes) for genetic enhancement in crop plants, including chickpea. PMID:26058368

  3. Application of Ray Scanning Method in Color Measurement

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A new method based on the traditional method of ray scanning has been introduced to resolve the problem of judging the color in the chromaticity diagram by employing the line segments approximate curve-- using polygonal approximate closed curve. Then a vector coordinate could be used to describe the curve instead of curve equations. So it is easy to judge the topology relation between an area and a point or a locus. And any data processing method has been used to save memory, which makes the improved ray scanning method is quite useful in the measurement of color.

  4. Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites

    Science.gov (United States)

    Song, Zhijiao; Zhang, Miaomiao; Li, Fagen; Weng, Qijie; Zhou, Chanpin; Li, Mei; Li, Jie; Huang, Huanhua; Mo, Xiaoyong; Gan, Siming

    2016-01-01

    Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations. PMID:27748400

  5. Viral genome sequencing by random priming methods

    Directory of Open Access Journals (Sweden)

    Zhang Xinsheng

    2008-01-01

    Full Text Available Abstract Background Most emerging health threats are of zoonotic origin. For the overwhelming majority, their causative agents are RNA viruses which include but are not limited to HIV, Influenza, SARS, Ebola, Dengue, and Hantavirus. Of increasing importance therefore is a better understanding of global viral diversity to enable better surveillance and prediction of pandemic threats; this will require rapid and flexible methods for complete viral genome sequencing. Results We have adapted the SISPA methodology 123 to genome sequencing of RNA and DNA viruses. We have demonstrated the utility of the method on various types and sources of viruses, obtaining near complete genome sequence of viruses ranging in size from 3,000–15,000 kb with a median depth of coverage of 14.33. We used this technique to generate full viral genome sequence in the presence of host contaminants, using viral preparations from cell culture supernatant, allantoic fluid and fecal matter. Conclusion The method described is of great utility in generating whole genome assemblies for viruses with little or no available sequence information, viruses from greatly divergent families, previously uncharacterized viruses, or to more fully describe mixed viral infections.

  6. Autosomal genomic scan for loci linked to obesity and energy metabolism in Pima Indians.

    OpenAIRE

    Norman, R. A.; Tataranni, P A; Pratley, R; Thompson, D B; Hanson, R. L.; Prochazka, M; Baier, L; Ehm, M. G.; Sakul, H; Foroud, T; Garvey, W. T.; Burns, D.; Knowler, W. C.; Bennett, P. H.; Bogardus, C

    1998-01-01

    An autosomal genomic scan to search for linkage to obesity and energy metabolism was completed in Pima Indians, a population prone to obesity. Obesity was assessed by percent body fat (by hydrodensitometry) and fat distribution (the ratio of waist circumference to thigh circumference). Energy metabolism was measured in a respiratory chamber as 24-h metabolic rate, sleeping metabolic rate, and 24-h respiratory quotient (24RQ), an indicator of the ratio of carbohydrate oxidation to fat oxidatio...

  7. 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.

  8. Non-random mate choice in humans: insights from a genome scan.

    Science.gov (United States)

    Laurent, R; Toupance, B; Chaix, R

    2012-02-01

    Little is known about the genetic factors influencing mate choice in humans. Still, there is evidence for non-random mate choice with respect to physical traits. In addition, some studies suggest that the Major Histocompatibility Complex may affect pair formation. Nowadays, the availability of high density genomic data sets gives the opportunity to scan the genome for signatures of non-random mate choice without prior assumptions on which genes may be involved, while taking into account socio-demographic factors. Here, we performed a genome scan to detect extreme patterns of similarity or dissimilarity among spouses throughout the genome in three populations of African, European American, and Mexican origins from the HapMap 3 database. Our analyses identified genes and biological functions that may affect pair formation in humans, including genes involved in skin appearance, morphogenesis, immunity and behaviour. We found little overlap between the three populations, suggesting that the biological functions potentially influencing mate choice are population specific, in other words are culturally driven. Moreover, whenever the same functional category of genes showed a significant signal in two populations, different genes were actually involved, which suggests the possibility of evolutionary convergences.

  9. High-throughput DNA Stretching in Continuous Elongational Flow for Genome Sequence Scanning

    Science.gov (United States)

    Meltzer, Robert; Griffis, Joshua; Safranovitch, Mikhail; Malkin, Gene; Cameron, Douglas

    2014-03-01

    Genome Sequence Scanning (GSS) identifies and compares bacterial genomes by stretching long (60 - 300 kb) genomic DNA restriction fragments and scanning for site-selective fluorescent probes. Practical application of GSS requires: 1) high throughput data acquisition, 2) efficient DNA stretching, 3) reproducible DNA elasticity in the presence of intercalating fluorescent dyes. GSS utilizes a pseudo-two-dimensional micron-scale funnel with convergent sheathing flows to stretch one molecule at a time in continuous elongational flow and center the DNA stream over diffraction-limited confocal laser excitation spots. Funnel geometry has been optimized to maximize throughput of DNA within the desired length range (>10 million nucleobases per second). A constant-strain detection channel maximizes stretching efficiency by applying a constant parabolic tension profile to each molecule, minimizing relaxation and flow-induced tumbling. The effect of intercalator on DNA elasticity is experimentally controlled by reacting one molecule of DNA at a time in convergent sheathing flows of the dye. Derivations of accelerating flow and non-linear tension distribution permit alignment of detected fluorescence traces to theoretical templates derived from whole-genome sequence data.

  10. Autosomal genomic scan for loci linked to obesity and energy metabolism in Pima Indians.

    Science.gov (United States)

    Norman, R A; Tataranni, P A; Pratley, R; Thompson, D B; Hanson, R L; Prochazka, M; Baier, L; Ehm, M G; Sakul, H; Foroud, T; Garvey, W T; Burns, D; Knowler, W C; Bennett, P H; Bogardus, C; Ravussin, E

    1998-01-01

    An autosomal genomic scan to search for linkage to obesity and energy metabolism was completed in Pima Indians, a population prone to obesity. Obesity was assessed by percent body fat (by hydrodensitometry) and fat distribution (the ratio of waist circumference to thigh circumference). Energy metabolism was measured in a respiratory chamber as 24-h metabolic rate, sleeping metabolic rate, and 24-h respiratory quotient (24RQ), an indicator of the ratio of carbohydrate oxidation to fat oxidation. Five hundred sixteen microsatellite markers with a median spacing of 6.4 cM were analyzed, in 362 siblings who had measurements of body composition and in 220 siblings who had measurements of energy metabolism. These comprised 451 sib pairs in 127 nuclear families, for linkage analysis to obesity, and 236 sib pairs in 82 nuclear families, for linkage analysis to energy metabolism. Pointwise and multipoint methods for regression of sib-pair differences in identity by descent, as well as a sibling-based variance-components method, were used to detect linkage. LOD scores >=2 were found at 11q21-q22, for percent body fat (LOD=2.1; P=.001), at 11q23-q24, for 24-h energy expenditure (LOD=2.0; P=.001), and at 1p31-p21 (LOD=2.0) and 20q11.2 (LOD=3.0; P=.0001), for 24RQ, by pointwise and multipoint analyses. With the variance-components method, the highest LOD score (LOD=2.3 P=.0006) was found at 18q21, for percent body fat, and at 1p31-p21 (LOD=2.8; P=.0003), for 24RQ. Possible candidate genes include LEPR (leptin receptor), at 1p31, and ASIP (agouti-signaling protein), at 20q11.2. PMID:9497255

  11. Band excitation method applicable to scanning probe microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Jesse, Stephen; Kalinin, Sergei V.

    2017-01-03

    Scanning probe microscopy may include a method for generating a band excitation (BE) signal and simultaneously exciting a probe at a plurality of frequencies within a predetermined frequency band based on the excitation signal. A response of the probe is measured across a subset of frequencies of the predetermined frequency band and the excitation signal is adjusted based on the measured response.

  12. 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......, and are adapted to use neighbourhood information in 2D and 3D. Articial Poisson noise is added to the provided dataset to determine how well each of the methods handles noise. Good noise handling will allow lower dose scannings. The investigated methods did not perform better than the reference model in terms...

  13. 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.

  14. Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model

    Science.gov (United States)

    Duforet-Frebourg, Nicolas; Bazin, Eric; Blum, Michael G.B.

    2014-01-01

    There is a considerable impetus in population genomics to pinpoint loci involved in local adaptation. A powerful approach to find genomic regions subject to local adaptation is to genotype numerous molecular markers and look for outlier loci. One of the most common approaches for selection scans is based on statistics that measure population differentiation such as FST. However, there are important caveats with approaches related to FST because they require grouping individuals into populations and they additionally assume a particular model of population structure. Here, we implement a more flexible individual-based approach based on Bayesian factor models. Factor models capture population structure with latent variables called factors, which can describe clustering of individuals into populations or isolation-by-distance patterns. Using hierarchical Bayesian modeling, we both infer population structure and identify outlier loci that are candidates for local adaptation. In order to identify outlier loci, the hierarchical factor model searches for loci that are atypically related to population structure as measured by the latent factors. In a model of population divergence, we show that it can achieve a 2-fold or more reduction of false discovery rate compared with the software BayeScan or with an FST approach. We show that our software can handle large data sets by analyzing the single nucleotide polymorphisms of the Human Genome Diversity Project. The Bayesian factor model is implemented in the open-source PCAdapt software. PMID:24899666

  15. A genome-wide scan for Eysenckian personality dimensions in adolescent twin sibships: psychoticism, extraversion, neuroticism, and lie.

    Science.gov (United States)

    Gillespie, Nathan A; Zhu, Gu; Evans, David M; Medland, Sarah E; Wright, Margie J; Martin, Nick G

    2008-12-01

    We report the first genome-wide scan of adolescent personality. We conducted a genome-wide scan to detect linkage for measures of adolescent Psychoticism, Extraversion, Neuroticism, and Lie from the Junior Eysenck Personality Questionnaire. Data are based on 1,280 genotyped Australian adolescent twins and their siblings. The highest linkage peaks were found on chromosomes 16 and 19 for Neuroticism, on chromosomes 1, 7, 10, 13 m, and 18 for Psychoticism, and on chromosomes 2 and 3 for Extraversion.

  16. Identification of outliers in a genomic scan for selection along environmental gradients in the bamboo locust, Ceracris kiangsu.

    Science.gov (United States)

    Feng, Xiao-Jing; Jiang, Guo-Fang; Fan, Zhou

    2015-09-03

    Identification of loci under divergent selection is a key step in understanding the evolutionary process because those loci are responsible for the genetic variations that affect fitness in different environments. Understanding how environmental forces give rise to adaptive genetic variation is a challenge in pest control. Here, we performed an amplified fragment length polymorphism (AFLP) genome scan in populations of the bamboo locust, Ceracris kiangsu, to search for candidate loci that are influenced by selection along an environmental gradient in southern China. In outlier locus detection, loci that demonstrate significantly higher or lower among-population genetic differentiation than expected under neutrality are identified as outliers. We used several outlier detection methods to study the features of C. kiangsu, including method DFDIST, BayeScan, and logistic regression. A total of 97 outlier loci were detected in the C. kiangsu genome with very high statistical supports. Moreover, the results suggested that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, humidity and sunshine. These findings illustrate that divergent selection and potential local adaptation are prevalent in locusts despite seemingly high levels of gene flow. Thus, we propose that native environments in each population may induce divergent natural selection.

  17. Genome scan for parent-of-origin QTL effects on bovine growth and carcass traits

    Directory of Open Access Journals (Sweden)

    Ikhide G. Imumorin

    2011-07-01

    Full Text Available Parent-of-origin effects (POE such as genomic imprinting influence growth and body composition in livestock, rodents and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL with POE on growth and carcass traits in Angus x Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs of which 6 were significant at 5% genome-wide level and 18 at the 5% chromosome-wide significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 [linkage region of 0 – 9 cM; genomic region of 5.0 – 10.8 Mb], for which only one imprinted orthologue is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4% ~ 5.1% of each trait’s phenotypic variance. Comparative in-silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologues map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only 2 (GNAS and PEG3 have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologues of imprinted genes so as to investigate their effects on quantitative traits.

  18. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits.

    Science.gov (United States)

    Imumorin, Ikhide G; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A; De Donato, Marcos; Taylor, Jeremy F; Kim, Jong-Joo

    2011-01-01

    Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.

  19. Processing Methods for Conical Scan Hopped-Frequency Signal

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-hong; LONG Teng

    2006-01-01

    The new radar system of combination of the hopped-frequency with the conical scanis presented. According to the principle and expression of the conical scan hopped-frequency signal, the angle processing method in which angle information is obtained by taking discrete Fourier transform (DFT) for the conical envelop o f each scattering centre by means of high range resolution profile (HRRP) is presented,and the corresponding formula is derived. The influence of non-ideal factors, such as amplitude fluctuation noise and system noise, leakage of time and frequency domain, unstable rotation of antenna, and missile rotation, on angle-measurement precision and the possible solving methods are also focused on. The simulation results show that the combination of the hopped-frequency and conical scan system could get satisfactory angle information, which could ensure good quality when used in practical tracking radar.

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

    DEFF Research Database (Denmark)

    Perola, Markus; Sammalisto, Sampo; Hiekkalinna, Tero

    2007-01-01

    Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists...... of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locus (QTL) analysis of one of the most heritable human complex traits, adult stature (body height......) using genome-wide scans performed for 3,817 families (8,450 individuals) derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom with an approximate ten-centimorgan microsatellite marker map. The marker maps for different studies differed and they were...

  1. Novel fringe scanning/Fourier transform method of synthetic imaging

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, T.M.; Albano, R.K.

    1993-08-01

    We have developed a one-dimensional theory and a computer model for synthetically imaging scenes using a novel fringe scanning/Fourier transform technique. Our method probes a scene using two interfering beams of slightly different frequency. These beams form a moving fringe pattern which scans the scene and resonates with any spatial frequency components having the same spatial frequency as the scanning fringe pattern. A simple, non-imaging detector above the scene observes any scattered radiation from the scene falling onto it. If a resonance occurs between the scanning fringe pattern and the scene, then the scattered radiation will be modulated at the difference frequency between the two probing beams. By changing the spatial period of the fringe pattern and then measuring the amplitude and phase of the modulated radiation that is scattered from the scene, the Fourier amplitudes and phases of the different spatial frequency components making up the scene can be measured. A synthetic image of the scene being probed can be generated from this Fourier amplitude and phase data by taking the inverse Fourier transform of this information. This technique could be used to image objects using light, ultrasonic, or other electromagnetic or acoustic waves.

  2. Scanning coherent scattering methods for actinic EUV mask inspection

    Science.gov (United States)

    Ekinci, Y.; Helfenstein, P.; Rajeev, R.; Mochi, I.; Mohacsi, I.; Gobrecht, J.; Yoshitake, S.

    2016-10-01

    Actinic mask inspection for EUV lithography with targeted specifications of resolution, sensitivity, and throughput remains a big hurdle for the successful insertion of EUVL into high volume manufacturing and effective solutions are needed to address this. We present a method for actinic mask inspection based on scanning coherent scattering microscopy. In this method, the mask is scanned with an EUV beam of relatively small spot size and the scattered light is recorded with a pixel detector. Customized algorithms reconstruct the aerial image by iteratively solving the phaseproblem using over-determined diffraction data gathered by scanning across the specimen with a finite illumination. This approach provides both phase and amplitude of actinic aerial images of the mask with high resolution without the need to use high NA (numerical aperture) lenses. Futher, we describe a reflective mode EUV mask scanning lensless imaging tool (RESCAN), which was installed at the XIL-II beamline and later at the SIM beamline of the Swiss Light Source and show reconstructed aerial images down to 10 nm (on-wafer) resolution. As a complementary method, the a-priori knowledge of the sample is employed to identify potential defect sites by analyzing the diffraction patterns. In this method, the recorded diffraction patterns are compared with the die or database data (i.e. previously measured or calculated diffraction data from the defect-free mask layout respectively) and their difference is interpreted as the defect signal. Dynamic software filtering helps to suppress the strong diffraction from defect-free structures and allows registration of faint defects with high sensitivity. Here, we discuss the basic principles of these Fourier domain techniques and its potential for actinic mask inspection with high signal-to-noise ratio and high throughput.

  3. 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

    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.......An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399-404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99...

  4. 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

    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.......An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99...

  5. 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

  6. Computational alanine scanning with linear scaling semiempirical quantum mechanical methods.

    Science.gov (United States)

    Diller, David J; Humblet, Christine; Zhang, Xiaohua; Westerhoff, Lance M

    2010-08-01

    Alanine scanning is a powerful experimental tool for understanding the key interactions in protein-protein interfaces. Linear scaling semiempirical quantum mechanical calculations are now sufficiently fast and robust to allow meaningful calculations on large systems such as proteins, RNA and DNA. In particular, they have proven useful in understanding protein-ligand interactions. Here we ask the question: can these linear scaling quantum mechanical methods developed for protein-ligand scoring be useful for computational alanine scanning? To answer this question, we assembled 15 protein-protein complexes with available crystal structures and sufficient alanine scanning data. In all, the data set contains Delta Delta Gs for 400 single point alanine mutations of these 15 complexes. We show that with only one adjusted parameter the quantum mechanics-based methods outperform both buried accessible surface area and a potential of mean force and compare favorably to a variety of published empirical methods. Finally, we closely examined the outliers in the data set and discuss some of the challenges that arise from this examination.

  7. 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...

  8. Benchmarking of methods for genomic taxonomy.

    Science.gov (United States)

    Larsen, Mette V; Cosentino, Salvatore; Lukjancenko, Oksana; Saputra, Dhany; Rasmussen, Simon; Hasman, Henrik; Sicheritz-Pontén, Thomas; Aarestrup, Frank M; Ussery, David W; Lund, Ole

    2014-05-01

    One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. 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; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.

  9. Optoelectronic scanning system upgrade by energy center localization methods

    Science.gov (United States)

    Flores-Fuentes, W.; Sergiyenko, O.; Rodriguez-Quiñonez, J. C.; Rivas-López, M.; Hernández-Balbuena, D.; Básaca-Preciado, L. C.; Lindner, L.; González-Navarro, F. F.

    2016-11-01

    A problem of upgrading an optoelectronic scanning system with digital post-processing of the signal based on adequate methods of energy center localization is considered. An improved dynamic triangulation analysis technique is proposed by an example of industrial infrastructure damage detection. A modification of our previously published method aimed at searching for the energy center of an optoelectronic signal is described. Application of the artificial intelligence algorithm of compensation for the error of determining the angular coordinate in calculating the spatial coordinate through dynamic triangulation is demonstrated. Five energy center localization methods are developed and tested to select the best method. After implementation of these methods, digital compensation for the measurement error, and statistical data analysis, a non-parametric behavior of the data is identified. The Wilcoxon signed rank test is applied to improve the result further. For optical scanning systems, it is necessary to detect a light emitter mounted on the infrastructure being investigated to calculate its spatial coordinate by the energy center localization method.

  10. International genomic evaluation methods for dairy cattle

    Science.gov (United States)

    Background Genomic evaluations are rapidly replacing traditional evaluation systems used for dairy cattle selection. Economies of scale in genomics promote cooperation across country borders. Genomic information can be transferred across countries using simple conversion equations, by modifying mult...

  11. A comparison in association and linkage genome-wide scans for alcoholism susceptibility genes using single-nucleotide polymorphisms.

    Science.gov (United States)

    Chiu, Yen-Feng; Liu, Su-Yun; Tsai, Ya-Yu

    2005-12-30

    We conducted genome-wide linkage scans using both microsatellite and single-nucleotide polymorphism (SNP) markers. Regions showing the strongest evidence of linkage to alcoholism susceptibility genes were identified. Haplotype analyses using a sliding-window approach for SNPs in these regions were performed. In addition, we performed a genome-wide association scan using SNP data. SNPs in these regions with evidence of association (P alcoholism (the most significant SNP had a p-value of 0.030) as those identified from association genomic screening (the most significant SNP had a p-value of 2.0 x 10(-8)).

  12. A method for fast feature extraction in threshold scans

    Science.gov (United States)

    Mertens, Marius C.; Ritman, James

    2014-01-01

    We present a fast, analytical method to calculate the threshold and noise parameters from a threshold scan. This is usually done by fitting a response function to the data which is computationally very intensive. The runtime can be minimized by a hardware implementation, e.g. using an FPGA, which in turn requires to minimize the mathematical complexity of the algorithm in order to fit into the available resources on the FPGA. The systematic errors of the method are analyzed and reasonable choices of the parameters for use in practice are given.

  13. An Improved Peak Sidelobe Reduction Method for Subarrayed Beam Scanning

    Directory of Open Access Journals (Sweden)

    Hang Hu

    2015-01-01

    Full Text Available This paper focused on PSL (peak sidelobe level reduction for subarrayed beam scanning in phased array radars. The desired GSP (Gaussian Subarray Patterns are achieved by creating a subarray weighting network. The GSP-based method could reduce PSL of array pattern; compared with the method based on the desired subarray pattern which is defined by ideal space-domain filter, the PSL reduction performance is improved remarkably. Further, based on the concept adopting superelement patterns to approximately express original subarray patterns, the simplified GSP-based method is proposed. So the dimension of each matrix required for creating the weighting network, which was originally the same as the element number, could be reduced to the same as the subarray number. Consequently, we achieve remarkable reduction of the computation burden; simultaneously, the PSL mitigation performance is degraded slightly. Simulation results demonstrate the validity of the introduced methods.

  14. Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

    Science.gov (United States)

    Steane, Dorothy A; Potts, Brad M; McLean, Elizabeth; Prober, Suzanne M; Stock, William D; Vaillancourt, René E; Byrne, Margaret

    2014-05-01

    Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation. © 2014 John Wiley & Sons Ltd.

  15. Genome-wide linkage scan for loci associated with epilepsy in Belgian shepherd dogs

    Directory of Open Access Journals (Sweden)

    Regan Kelly R

    2010-05-01

    Full Text Available Abstract Background Idiopathic epilepsy in the Belgian shepherd dog is known to have a substantial genetic component. The objective of this study was to identify genomic regions associated with the expression of generalized seizures in the Belgian Tervuren and Sheepdog. Results DNA from 366 dogs, of which 74 were classified as epileptic, representing two extended families were subjected to a genome-wide linkage scan using 410 microsatellite markers yielding informative coverage averaging 5.95 ± 0.21 Mb. Though previous studies based on pedigree analyses proposed a major gene of influence, the present study demonstrated the trait to be highly polygenic. Studies of complex disorders in humans indicate that a liberal composite evaluation of genetic linkage is needed to identify underlying quantitative trait loci (QTLs. Four chromosomes yielded tentative linkage based upon LOD scores in excess of 1.0. Possible QTLs within these regions were supported also by analyses of multipoint linkage, allele frequency, TDT, and transmission of haplotype blocks. Conclusions Taken together the data tentatively indicate six QTLs, three on CFA 2, and one on each of CFA 6, 12, and 37, that support fine mapping for mutations associated with epilepsy in the Belgian shepherd. The study also underscores the complexity of genomic linkage studies for polygenic disorders.

  16. 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.

  17. 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 ...

  18. Identifying genomic regions for fine-mapping using genome scan meta-analysis (GSMA) to identify the minimum regions of maximum significance (MRMS) across populations.

    Science.gov (United States)

    Cooper, Margaret E; Goldstein, Toby H; Maher, Brion S; Marazita, Mary L

    2005-12-30

    In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA). Using the 7-cM microsatellite map, nonparametric multipoint linkage analyses were performed separately on each of the four simulated populations independently to determine p-values. The genome of each population was divided into 20-cM bin regions, and each bin was rank-ordered based on the most significant linkage p-value for that population in that region. The bin ranks were then averaged across all four studies to determine the most significant 20-cM regions over all studies. Statistical significance of the averaged bin ranks was determined from a normal distribution of randomly assigned rank averages. To narrow the region of interest for fine-mapping, the meta-analysis was repeated two additional times, with each of the 20-cM bins offset by 7 cM and 13 cM, respectively, creating regions of overlap with the original method. The 6-7 cM shared regions, where the highest averaged 20-cM bins from each of the three offsets overlap, designated the minimum region of maximum significance (MRMS). Application of the GSMA-MRMS method revealed genome wide significance (p-values refer to the average rank assigned to the bin) at regions including or adjacent to all of the simulated disease loci: chromosome 1 (p value value value < 0.05 for 7-14 cM, the region adjacent to D4). This GSMA analysis approach demonstrates the power of linkage meta-analysis to detect multiple genes simultaneously for a complex disorder. The MRMS method enhances this powerful tool to focus on more localized regions of linkage.

  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-wide Scan for Selective Sweeps in Racing Horses

    Science.gov (United States)

    Moon, Sunjin; Lee, Jin Woo; Shin, Donghyun; Shin, Kwang-Yun; Kim, Jun; Choi, Ik-Young; Kim, Jaemin; Kim, Heebal

    2015-01-01

    Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses. PMID:26333666

  1. A Genome-wide Scan for Selective Sweeps in Racing Horses

    Directory of Open Access Journals (Sweden)

    Sunjin Moon

    2015-11-01

    Full Text Available Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2 that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1, pallid (PLDN, and Ras and Rab interactor 2 (RIN2 genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.

  2. 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.

  3. 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.

  4. Efficient strategies for genome scanning using maximum-likelihood affected-sib-pair analysis

    Energy Technology Data Exchange (ETDEWEB)

    Holmans, P.; Craddock, N. [Univ. of Wales College of Medicine, Cardiff (United Kingdom)

    1997-03-01

    Detection of linkage with a systematic genome scan in nuclear families including an affected sibling pair is an important initial step on the path to cloning susceptibility genes for complex genetic disorders, and it is desirable to optimize the efficiency of such studies. The aim is to maximize power while simultaneously minimizing the total number of genotypings and probability of type I error. One approach to increase efficiency, which has been investigated by other workers, is grid tightening: a sample is initially typed using a coarse grid of markers, and promising results are followed up by use of a finer grid. Another approach, not previously considered in detail in the context of an affected-sib-pair genome scan for linkage, is sample splitting: a portion of the sample is typed in the screening stage, and promising results are followed up in the whole sample. In the current study, we have used computer simulation to investigate the relative efficiency of two-stage strategies involving combinations of both grid tightening and sample splitting and found that the optimal strategy incorporates both approaches. In general, typing half the sample of affected pairs with a coarse grid of markers in the screening stage is an efficient strategy under a variety of conditions. If Hardy-Weinberg equilibrium holds, it is most efficient not to type parents in the screening stage. If Hardy-Weinberg equilibrium does not hold (e.g., because of stratification) failure to type parents in the first stage increases the amount of genotyping required, although the overall probability of type I error is not greatly increased, provided the parents are used in the final analysis. 23 refs., 4 figs., 5 tabs.

  5. Identifying genomic regions for fine-mapping using genome scan meta-analysis (GSMA to identify the minimum regions of maximum significance (MRMS across populations

    Directory of Open Access Journals (Sweden)

    Maher Brion S

    2005-12-01

    Full Text Available Abstract In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA. Using the 7-cM microsatellite map, nonparametric multipoint linkage analyses were performed separately on each of the four simulated populations independently to determine p-values. The genome of each population was divided into 20-cM bin regions, and each bin was rank-ordered based on the most significant linkage p-value for that population in that region. The bin ranks were then averaged across all four studies to determine the most significant 20-cM regions over all studies. Statistical significance of the averaged bin ranks was determined from a normal distribution of randomly assigned rank averages. To narrow the region of interest for fine-mapping, the meta-analysis was repeated two additional times, with each of the 20-cM bins offset by 7 cM and 13 cM, respectively, creating regions of overlap with the original method. The 6–7 cM shared regions, where the highest averaged 20-cM bins from each of the three offsets overlap, designated the minimum region of maximum significance (MRMS. Application of the GSMA-MRMS method revealed genome wide significance (p-values refer to the average rank assigned to the bin at regions including or adjacent to all of the simulated disease loci: chromosome 1 (p p-value p-value p-value

  6. Global Fits of the CKM Matrix with the SCAN Method

    CERN Document Server

    Eigen, G; Hitlin, D G; Porter, F C

    2015-01-01

    We present a Scan Method analysis of the allowed region of the rho bar - eta bar plane using the latest input measurements of the CKM matrix elements, sin 2 beta, B0(s,d) mixing, epsilon(K), alpha and gamma. In this approach, we make no assumptions as to the distribution of theory uncertainties; rather, we scan over the range of plausible theoretical uncertainties and determine confidence level contours in the rho bar eta bar plane. We determine alpha from branching fraction and CP asymmetry measurements of B decays to all light pseudoscalar-pseudoscalar, pesudoscalar-vector, vector-vector and a1-psudoscalar mesons and determine gamma from D(*)K(*), D(*) pi and D rho modes, thereby including correlations between the angles of the unitarity triangle. We parametrize the individual decay amplitudes in terms of color-allowed tree, color-suppressed tree, gluonic penguin, singlet penguin, electroweak penguin, as well as W-exchange and W-annihilation amplitudes. Our procedure accounts for all correlations among the ...

  7. A genome scan for quantitative trait loci affecting resistance to Trichostrongylus colubriformis in sheep.

    Science.gov (United States)

    Beh, K J; Hulme, D J; Callaghan, M J; Leish, Z; Lenane, I; Windon, R G; Maddox, J F

    2002-04-01

    A genome linkage scan was carried out using a resource flock of 1029 sheep in six half-sib families. The families were offspring of sires derived by crossing divergent lines of sheep selected for response to challenge with the intestinal parasitic nematode Trichostrongylus colubriformis. All animals in the resource flock were phenotypically assessed for worm resistance soon after weaning using a vaccination/challenge regime. After correcting for fixed effects using a least squares linear model the faecal egg count data obtained following the first challenge and the faecal egg count data obtained after the second challenge were designated Trait 1 and Trait 2, respectively. A total of 472 lambs drawn from the phenotypic extremes of the Trait 2 faecal egg count distribution were genotyped with a panel of 133 microsatellite markers covering all 26 sheep autosomes. Detection of quantitative trait loci (QTL) for each of the faecal egg count traits was determined using interval analysis with the Animap program with recombination rates between markers derived from an existing marker map. No chromosomal regions attained genome-wide significance for QTL influencing either of the traits. However, one region attained chromosome-wide significance and five other regions attained point-wise significance for the presence of QTL affecting parasite resistance.

  8. Whole genome scan to detect quantitative trait loci for bovine milk protein composition.

    Science.gov (United States)

    Schopen, G C B; Koks, P D; van Arendonk, J A M; Bovenhuis, H; Visker, M H P W

    2009-08-01

    The objective of this study was to perform a whole genome scan to detect quantitative trait loci (QTL) for milk protein composition in 849 Holstein-Friesian cows originating from seven sires. One morning milk sample was analysed for the major milk proteins using capillary zone electrophoresis. A genetic map was constructed with 1341 single nucleotide polymorphisms, covering 2829 centimorgans (cM) and 95% of the cattle genome. The chromosomal regions most significantly related to milk protein composition (P(genome) casein, alpha(S2)-casein, beta-casein and kappa-casein. The QTL on BTA11 was found at 124 cM, and affected beta-lactoglobulin, and the QTL on BTA14 was found at 0 cM, and affected protein percentage. The proportion of phenotypic variance explained by the QTL was 3.6% for beta-casein and 7.9% for kappa-casein on BTA6, 28.3% for beta-lactoglobulin on BTA11, and 8.6% for protein percentage on BTA14. The QTL affecting alpha(S2)-casein on BTA6 and 17 showed a significant interaction. We investigated the extent to which the detected QTL affecting milk protein composition could be explained by known polymorphisms in beta-casein, kappa-casein, beta-lactoglobulin and DGAT1 genes. Correction for these polymorphisms decreased the proportion of phenotypic variance explained by the QTL previously found on BTA6, 11 and 14. Thus, several significant QTL affecting milk protein composition were found, of which some QTL could partially be explained by polymorphisms in milk protein genes.

  9. Parameters affecting genome simulation for evaluating genomic selection method.

    Science.gov (United States)

    Nishio, Motohide; Satoh, Masahiro

    2014-10-01

    The present study investigated the parameter settings for obtaining a simulated genome at steady state of allele frequency (mutation-drift equilibrium) and linkage disequilibrium (LD), and evaluated the impact of whether or not the simulated genome reached steady state of allele frequency and LD on the accuracy of genomic estimated breeding values (GEBVs). After 500 to 50,000 historical generations, the base population and subsequent seven generations were generated as recent populations. The allele frequency distribution of the last generations of the historical population and LD in the base population were calculated when varying the values of five parameters: initial minor allele frequency, mutation rate, effective population size, number of markers and chromosome length. The accuracies of GEBVs in the last generation of the recent population were calculated by genomic best linear unbiased prediction. The number of historical generations required to reach mutation-drift equilibrium depended on the initial allele frequency and mutation rate. Regardless of the parameters, LD reached a steady state before allele frequency distribution reached mutation-drift equilibrium. The accuracies of GEBVs largely reflect the extent of linkage disequilibrium with the exception of varying chromosome length, although there were no associations between the accuracies of GEBVs and allele frequency distribution. © 2014 Japanese Society of Animal Science.

  10. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

    Directory of Open Access Journals (Sweden)

    Carol Chapman

    Full Text Available Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.

  11. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

    Science.gov (United States)

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A; Awosika, Joy; Briska, Adam; Ptashkin, Ryan N; Wagner, Trevor; Rajanna, Chythanya; Tsang, Hsinyi; Johnson, Shannon L; Mokashi, Vishwesh P; Chain, Patrick S G; Sozhamannan, Shanmuga

    2015-01-01

    Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.

  12. 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.

  13. Band excitation method applicable to scanning probe microscopy

    Science.gov (United States)

    Jesse, Stephen; Kalinin, Sergei V

    2013-05-28

    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.

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

    OpenAIRE

    S. Goel; Lohani, B.

    2014-01-01

    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 a...

  15. 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

  16. Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever.

    Science.gov (United States)

    Andersen, Kristian G; Shylakhter, Ilya; Tabrizi, Shervin; Grossman, Sharon R; Happi, Christian T; Sabeti, Pardis C

    2012-03-19

    Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 (IL21), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21. Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit.

  17. Detection of quantitative trait loci affecting haematological traits in swine via genome scanning

    Directory of Open Access Journals (Sweden)

    Niu Xiao-Yan

    2010-06-01

    Full Text Available Abstract Background Haematological traits, which consist of mainly three components: leukocyte traits, erythrocyte traits and platelet traits, play extremely important role in animal immune function and disease resistance. But knowledge of the genetic background controlling variability of these traits is very limited, especially in swine. Results In the present study, 18 haematological traits (7 leukocyte traits, 7 erythrocyte traits and 4 platelet traits were measured in a pig resource population consisting of 368 purebred piglets of three breeds (Landrace, Large White and Songliao Black Pig, after inoculation with the swine fever vaccine when the pigs were 21 days old. A whole-genome scan of QTL for these traits was performed using 206 microsatellite markers covering all 18 autosomes and the X chromosome. Using variance component analysis based on a linear mixed model and the false discovery rate (FDR test, 35 QTL with FDR FDR FDR Conclusions Very few QTL were previously identified for hematological traits of pigs and never in purebred populations. Most of the QTL detected here, in particular the QTL for the platelet traits, have not been reported before. Our results lay important foundation for identifying the causal genes underlying the hematological trait variations in pigs.

  18. 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.

  19. Methods of Genome Engineering: a New Era of Molecular Biology.

    Science.gov (United States)

    Chugunova, A A; Dontsova, O A; Sergiev, P V

    2016-07-01

    Genome sequencing now progressing much faster than our understanding of the majority of gene functions. Studies of physiological functions of various genes would not be possible without the ability to manipulate the genome. Methods of genome engineering can now be used to inactivate a gene to study consequences, introduce heterologous genes into the genome for scientific and biotechnology applications, create genes coding for fusion proteins to study gene expression, protein localization, and molecular interactions, and to develop animal models of human diseases to find appropriate treatment. Finally, genome engineering might present the possibility to cure hereditary diseases. In this review, we discuss and compare the most important methods for gene inactivation and editing, as well as methods for incorporation of heterologous genes into the genome.

  20. 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 [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered...ear Year of genome analysis Sequencing method Sequencing method Read counts Read counts Covered genome region Covered...otation method Number of predicted genes Number of predicted genes Genome database Genome database informati... License Update History of This Database Site Policy | Contact Us Genome analysis... methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  1. 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

    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...... definition of both clinical allergic rhinitis and confirmed specific allergy were chosen. Thirty-three affected sib-pair families qualified for the scan that was undertaken using 446 microsatellite markers. Non-parametric linkage results were obtained from MAPMAKER/SIBS computer program. The study revealed...

  2. Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

    Science.gov (United States)

    Moore, Allan F; Jablonski, Kathleen A; McAteer, Jarred B; Saxena, Richa; Pollin, Toni I; Franks, Paul W; Hanson, Robert L; Shuldiner, Alan R; Knowler, William C; Altshuler, David; Florez, Jose C

    2008-09-01

    Genome-wide association scans (GWASs) have identified novel diabetes-associated genes. We evaluated how these variants impact diabetes incidence, quantitative glycemic traits, and response to preventive interventions in 3,548 subjects at high risk of type 2 diabetes enrolled in the Diabetes Prevention Program (DPP), which examined the effects of lifestyle intervention, metformin, and troglitazone versus placebo. We genotyped selected single nucleotide polymorphisms (SNPs) in or near diabetes-associated loci, including EXT2, CDKAL1, CDKN2A/B, IGF2BP2, HHEX, LOC387761, and SLC30A8 in DPP participants and performed Cox regression analyses using genotype, intervention, and their interactions as predictors of diabetes incidence. We evaluated their effect on insulin resistance and secretion at 1 year. None of the selected SNPs were associated with increased diabetes incidence in this population. After adjustments for ethnicity, baseline insulin secretion was lower in subjects with the risk genotype at HHEX rs1111875 (P = 0.01); there were no significant differences in baseline insulin sensitivity. Both at baseline and at 1 year, subjects with the risk genotype at LOC387761 had paradoxically increased insulin secretion; adjustment for self-reported ethnicity abolished these differences. In ethnicity-adjusted analyses, we noted a nominal differential improvement in beta-cell function for carriers of the protective genotype at CDKN2A/B after 1 year of troglitazone treatment (P = 0.01) and possibly lifestyle modification (P = 0.05). We were unable to replicate the GWAS findings regarding diabetes risk in the DPP. We did observe genotype associations with differences in baseline insulin secretion at the HHEX locus and a possible pharmacogenetic interaction at CDKNA2/B.

  3. A genome scan for QTL affecting resistance to Haemonchus contortus in sheep.

    Science.gov (United States)

    Sallé, G; Jacquiet, P; Gruner, L; Cortet, J; Sauvé, C; Prévot, F; Grisez, C; Bergeaud, J P; Schibler, L; Tircazes, A; François, D; Pery, C; Bouvier, F; Thouly, J C; Brunel, J C; Legarra, A; Elsen, J M; Bouix, J; Rupp, R; Moreno, C R

    2012-12-01

    Gastrointestinal nematodes are one of the main health issues in sheep breeding. To identify loci affecting the resistance to Haemonchus contortus, a genome scan was carried out using 1,275 Romane × Martinik Black Belly backcross lambs. The entire population was challenged with Haemonchus contortus in 2 consecutive experimental infections, and fecal egg counts (FEC) and packed cell volumes were measured. A subgroup of 332 lambs with extreme FEC was necropsied to determine the total worm burden, length of female worms, sex ratio in the worm population, abomasal pH, and serum and mucosal G immunoglobulins (IgG) responses. Pepsinogen concentration was measured in another subset of 229 lambs. For QTL detection, 160 microsatellite markers were used as well as the Illumina OvineSNP50 BeadChip that provided 42,469 SNP markers after quality control. Linkage, association, and joint linkage and association analyses were performed with the QTLMAP software. Linkage disequilibrium (LD) was estimated within each pure breed, and association analyses were carried out either considering or not the breed origin of the haplotypes. Four QTL regions on sheep chromosomes (OAR)5, 12, 13, and 21 were identified as key players among many other QTL with small to moderate effects. A QTL on OAR21 affecting pepsinogen concentration exactly matched the pepsinogen (PGA5) locus. A 10-Mbp region affecting FEC after the 1st and 2nd infections was found on OAR12. The SNP markers outperformed microsatellites in the linkage analysis. Taking advantage of the LD helped to refine the locations of the QTL mapped on OAR5 and 13.

  4. Genome-wide linkage scan for the metabolic syndrome: the GENNID study.

    Science.gov (United States)

    Edwards, Karen L; Hutter, Carolyn M; Wan, Jia Yin; Kim, Helen; Monks, Stephanie A

    2008-07-01

    In the United States, the metabolic syndrome (MetS) constitutes a major public health problem with over 47 million persons meeting clinical criteria for MetS. Numerous studies have suggested genetic susceptibility to MetS. The goals of this study were (i) to identify susceptibility loci for MetS in well-characterized families with type 2 diabetes (T2D) in four ethnic groups and (ii) to determine whether evidence for linkage varies across the four groups. The GENNID study (Genetics of NIDDM) is a multicenter study established by the American Diabetes Association in 1993 and comprises a comprehensive, well-characterized resource of T2D families from four ethnic groups (whites, Mexican Americans, African Americans, and Japanese Americans). Principal component factor analysis (PCFA) was used to define quantitative phenotypes of the MetS. Variance components linkage analysis was conducted using microsatellite markers from a 10-cM genome-wide linkage scan, separately in each of the four ethnic groups. Three quantitative MetS factors were identified by PCFA and used as phenotypes for MetS: (i) a weight/waist factor, (ii) a blood pressure factor, and (iii) a lipid factor. Evidence for linkage to each of these factors was observed. For each ethnic group, our results suggest that several regions harbor susceptibility genes for the MetS. The strongest evidence for linkage for MetS phenotypes was observed on chromosome 2 (2q12.1-2q13) in the white sample and on chromosome 3 (3q26.1-3q29) in the Mexican-American sample. In conclusion, the results suggest that several regions harbor MetS susceptibility genes and that heterogeneity may exist across groups.

  5. Additive and epistatic genome-wide association for growth and ultrasound scan measures of carcass-related traits in Brahman cattle.

    Science.gov (United States)

    Ali, A A; Khatkar, M S; Kadarmideen, H N; Thomson, P C

    2015-04-01

    Genome-wide association studies are routinely used to identify genomic regions associated with traits of interest. However, this ignores an important class of genomic associations, that of epistatic interactions. A genome-wide interaction analysis between single nucleotide polymorphisms (SNPs) using highly dense markers can detect epistatic interactions, but is a difficult task due to multiple testing and computational demand. However, It is important for revealing complex trait heredity. This study considers analytical methods that detect statistical interactions between pairs of loci. We investigated a three-stage modelling procedure: (i) a model without the SNP to estimate the variance components; (ii) a model with the SNP using variance component estimates from (i), thus avoiding iteration; and (iii) using the significant SNPs from (ii) for genome-wide epistasis analysis. We fitted these three-stage models to field data for growth and ultrasound measures for subcutaneous fat thickness in Brahman cattle. The study demonstrated the usefulness of modelling epistasis in the analysis of complex traits as it revealed extra sources of genetic variation and identified potential candidate genes affecting the concentration of insulin-like growth factor-1 and ultrasound scan measure of fat depth traits. Information about epistasis can add to our understanding of the complex genetic networks that form the fundamental basis of biological systems. © 2015 Blackwell Verlag GmbH.

  6. An autosomal genomic scan for loci linked to type II diabetes mellitus and body-mass index in Pima Indians.

    Science.gov (United States)

    Hanson, R L; Ehm, M G; Pettitt, D J; Prochazka, M; Thompson, D B; Timberlake, D; Foroud, T; Kobes, S; Baier, L; Burns, D K; Almasy, L; Blangero, J; Garvey, W T; Bennett, P H; Knowler, W C

    1998-01-01

    Genetic factors influence the development of type II diabetes mellitus, but genetic loci for the most common forms of diabetes have not been identified. A genomic scan was conducted to identify loci linked to diabetes and body-mass index (BMI) in Pima Indians, a Native American population with a high prevalence of type II diabetes. Among 264 nuclear families containing 966 siblings, 516 autosomal markers with a median distance between adjacent markers of 6.4 cM were genotyped. Variance-components methods were used to test for linkage with an age-adjusted diabetes score and with BMI. In multipoint analyses, the strongest evidence for linkage with age-adjusted diabetes (LOD = 1.7) was on chromosome 11q, in the region that was also linked most strongly with BMI (LOD = 3.6). Bivariate linkage analyses strongly rejected both the null hypothesis of no linkage with either trait and the null hypothesis of no contribution of the locus to the covariation among the two traits. Sib-pair analyses suggest additional potential diabetes-susceptibility loci on chromosomes 1q and 7q. PMID:9758619

  7. 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...

  8. Parallax scanning methods for stereoscopic three-dimensional imaging

    Science.gov (United States)

    Mayhew, Christopher A.; Mayhew, Craig M.

    2012-03-01

    Under certain circumstances, conventional stereoscopic imagery is subject to being misinterpreted. Stereo perception created from two static horizontally separated views can create a "cut out" 2D appearance for objects at various planes of depth. The subject volume looks three-dimensional, but the objects themselves appear flat. This is especially true if the images are captured using small disparities. One potential explanation for this effect is that, although three-dimensional perception comes primarily from binocular vision, a human's gaze (the direction and orientation of a person's eyes with respect to their environment) and head motion also contribute additional sub-process information. The absence of this information may be the reason that certain stereoscopic imagery appears "odd" and unrealistic. Another contributing factor may be the absence of vertical disparity information in a traditional stereoscopy display. Recently, Parallax Scanning technologies have been introduced, which provide (1) a scanning methodology, (2) incorporate vertical disparity, and (3) produce stereo images with substantially smaller disparities than the human interocular distances.1 To test whether these three features would improve the realism and reduce the cardboard cutout effect of stereo images, we have applied Parallax Scanning (PS) technologies to commercial stereoscopic digital cinema productions and have tested the results with a panel of stereo experts. These informal experiments show that the addition of PS information into the left and right image capture improves the overall perception of three-dimensionality for most viewers. Parallax scanning significantly increases the set of tools available for 3D storytelling while at the same time presenting imagery that is easy and pleasant to view.

  9. 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

  10. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features.

    Science.gov (United States)

    Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza-Revilla, Javier; Fuentes-Guajardo, Macarena; Chacón-Duque, Juan-Camilo; Al-Saadi, Farah; Johansson, Jeanette A; Quinto-Sanchez, Mirsha; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Gonzalez-José, Rolando; Headon, Denis; López-Otín, Carlos; Tobin, Desmond J; Balding, David; Ruiz-Linares, Andrés

    2016-03-01

    We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10(-8) to 3 × 10(-119)), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair.

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

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    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.

  12. Optimized Adaptor Polymerase Chain Reaction Method for Efficient Genomic Walking

    Institute of Scientific and Technical Information of China (English)

    Peng XU; Rui-Ying HU; Xiao-Yan DING

    2006-01-01

    Genomic walking is one of the most useful approaches in genome-related research. Three kinds of PCR-based methods are available for this purpose. However, none of them has been generally applied because they are either insensitive or inefficient. Here we present an efficient PCR protocol, an optimized adaptor PCR method for genomic walking. Using a combination of a touchdown PCR program and a special adaptor, the optimized adaptor PCR protocol achieves high sensitivity with low background noise. By applying this protocol, the insertion sites of a gene trap mouse line and two gene promoters from the incompletely sequenced Xenopus laevis genome were successfully identified with high efficiency. The general application of this protocol in genomic walking was promising.

  13. 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....

  14. 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.

  15. Family-Based Genome-Wide Association Scan of Attention-Deficit/Hyperactivity Disorder

    Science.gov (United States)

    Mick, Eric; Todorov, Alexandre; Smalley, Susan; Hu, Xiaolan; Loo, Sandra; Todd, Richard D.; Biederman, Joseph; Byrne, Deirdre; Dechairo, Bryan; Guiney, Allan; McCracken, James; McGough, James; Nelson, Stanley F.; Reiersen, Angela M.; Wilens, Timothy E.; Wozniak, Janet; Neale, Benjamin M.; Faraone, Stephen V.

    2010-01-01

    Objective: Genes likely play a substantial role in the etiology of attention-deficit/hyperactivity disorder (ADHD). However, the genetic architecture of the disorder is unknown, and prior genome-wide association studies (GWAS) have not identified a genome-wide significant association. We have conducted a third, independent, multisite GWAS of…

  16. 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.......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....

  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. Genome-wide linkage scan identifies two novel genetic loci for coronary artery disease: in GeneQuest families.

    Science.gov (United States)

    Gao, Hanxiang; Li, Lin; Rao, Shaoqi; Shen, Gongqing; Xi, Quansheng; Chen, Shenghan; Zhang, Zheng; Wang, Kai; Ellis, Stephen G; Chen, Qiuyun; Topol, Eric J; Wang, Qing K

    2014-01-01

    Coronary artery disease (CAD) is the leading cause of death worldwide. Recent genome-wide association studies (GWAS) identified >50 common variants associated with CAD or its complication myocardial infarction (MI), but collectively they account for missing heritability". Rare variants with large effects may account for a large portion of missing heritability. Genome-wide linkage studies of large families and follow-up fine mapping and deep sequencing are particularly effective in identifying rare variants with large effects. Here we show results from a genome-wide linkage scan for CAD in multiplex GeneQuest families with early onset CAD and MI. Whole genome genotyping was carried out with 408 markers that span the human genome by every 10 cM and linkage analyses were performed using the affected relative pair analysis implemented in GENEHUNTER. Affected only nonparametric linkage (NPL) analysis identified two novel CAD loci with highly significant evidence of linkage on chromosome 3p25.1 (peak NPL  = 5.49) and 3q29 (NPL  = 6.84). We also identified four loci with suggestive linkage on 9q22.33, 9q34.11, 17p12, and 21q22.3 (NPL  = 3.18-4.07). These results identify novel loci for CAD and provide a framework for fine mapping and deep sequencing to identify new susceptibility genes and novel variants associated with risk of CAD.

  19. Copy Number Variation of UGT 2B Genes in Indian Families Using Whole Genome Scans

    Directory of Open Access Journals (Sweden)

    Avinash M. Veerappa

    2016-01-01

    Full Text Available Background and Objectives. Uridine diphospho-glucuronosyltransferase 2B (UGT2B is a family of genes involved in metabolizing steroid hormones and several other xenobiotics. These UGT2B genes are highly polymorphic in nature and have distinct polymorphisms associated with specific regions around the globe. Copy number variations (CNVs status of UGT2B17 in Indian population is not known and their disease associations have been inconclusive. It was therefore of interest to investigate the CNV profile of UGT2B genes. Methods. We investigated the presence of CNVs in UGT2B genes in 31 members from eight Indian families using Affymetrix Genome-Wide Human SNP Array 6.0 chip. Results. Our data revealed >50% of the study members carried CNVs in UGT2B genes, of which 76% showed deletion polymorphism. CNVs were observed more in UGT2B17 (76.4% than in UGT2B15 (17.6%. Molecular network and pathway analysis found enrichment related to steroid metabolic process, carboxylesterase activity, and sequence specific DNA binding. Interpretation and Conclusion. We report the presence of UGT2B gene deletion and duplication polymorphisms in Indian families. Network analysis indicates the substitutive role of other possible genes in the UGT activity. The CNVs of UGT2B genes are very common in individuals indicating that the effect is neutral in causing any suspected diseases.

  20. 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.

  1. 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.

  2. Novel Method to measure the gain of UHF directional antennas using distance scan

    NARCIS (Netherlands)

    Witvliet, Ben A.; Maanen, van Erik; Bentum, Mark J.; Slump, Cornelis H.; Schiphorst, Roel

    2014-01-01

    A novel antenna gain measurement method is described which uses power transfer values that are measured while varying the distance between two antennas (Distance Scan). It can be executed with simple means and is cost-effective. The Distance Scan method yields derived free space antenna gain values

  3. A 3-d laser scanning system and scan data processing method for the monitoring of tunnel deformations

    Science.gov (United States)

    Chmelina, Klaus; Jansa, Josef; Hesina, Gerd; Traxler, Christoph

    2012-11-01

    The paper presents the mobile multi-sensor system Orthos Plus for the monitoring and mapping of tunnel walls, a scan data processing method for the evaluation of 3-d tunnel wall displacements from subsequent wall scans and, finally, a virtual reality tool supporting the interpretation of data. The measuring system consists of a 3-d laser scanner, a motorised total station and a digital camera that are integrated on a light metal frame that is installed on a mobile platform. It has been designed to perform tunnel measurements most efficiently and to meet the special requirements of tunnels under construction. The evaluation of 3-d displacements is based on a 3-d matching algorithm that takes advantage of the particular conditions of tunnel (shotcrete) surfaces. The virtual reality tool allows viewing of data in a 3-d virtual reality tunnel model and their animation in time and space in order supports understanding in an optimal way. The measuring system Orthos Plus has been developed in the course of a national research project, the 3-d matching method in the frame of the Austrian Christian Doppler Laboratory Spatial Data from Laser Scanning and Remote Sensing and the VR tool in the Austrian COMET K1 Competence Center VRVis Center (www.vrvis.at).

  4. A Genome Scan for Modifiers of Age at Onset in Huntington Disease: The HD MAPS Study

    Science.gov (United States)

    Li, Jian-Liang; Hayden, Michael R.; Almqvist, Elisabeth W.; Brinkman, Ryan R.; Durr, Alexandra; Dodé, Catherine; Morrison, Patrick J.; Suchowersky, Oksana; Ross, Christopher A.; Margolis, Russell L.; Rosenblatt, Adam; Gómez-Tortosa, Estrella; Cabrero, David Mayo; Novelletto, Andrea; Frontali, Marina; Nance, Martha; Trent, Ronald J. A.; McCusker, Elizabeth; Jones, Randi; Paulsen, Jane S.; Harrison, Madeline; Zanko, Andrea; Abramson, Ruth K.; Russ, Ana L.; Knowlton, Beth; Djoussé, Luc; Mysore, Jayalakshmi S.; Tariot, Suzanne; Gusella, Michael F.; Wheeler, Vanessa C.; Atwood, Larry D.; Cupples, L. Adrienne; Saint-Hilaire, Marie; Cha, Jang-Ho J.; Hersch, Steven M.; Koroshetz, Walter J.; Gusella, James F.; MacDonald, Marcy E.; Myers, Richard H.

    2003-01-01

    Huntington disease (HD) is caused by the expansion of a CAG repeat within the coding region of a novel gene on 4p16.3. Although the variation in age at onset is partly explained by the size of the expanded repeat, the unexplained variation in age at onset is strongly heritable (h2=0.56), which suggests that other genes modify the age at onset of HD. To identify these modifier loci, we performed a 10-cM density genomewide scan in 629 affected sibling pairs (295 pedigrees and 695 individuals), using ages at onset adjusted for the expanded and normal CAG repeat sizes. Because all those studied were HD affected, estimates of allele sharing identical by descent at and around the HD locus were adjusted by a positionally weighted method to correct for the increased allele sharing at 4p. Suggestive evidence for linkage was found at 4p16 (LOD=1.93), 6p21–23 (LOD=2.29), and 6q24–26 (LOD=2.28), which may be useful for investigation of genes that modify age at onset of HD. PMID:12900792

  5. Method for nanoscale spatial registration of scanning probes with substrates and surfaces

    Science.gov (United States)

    Wade, Lawrence A. (Inventor)

    2010-01-01

    Embodiments in accordance with the present invention relate to methods and apparatuses for aligning a scanning probe used to pattern a substrate, by comparing the position of the probe to a reference location or spot on the substrate. A first light beam is focused on a surface of the substrate as a spatial reference point. A second light beam then illuminates the scanning probe being used for patterning. An optical microscope images both the focused light beam, and a diffraction pattern, shadow, or light backscattered by the illuminated scanning probe tip of a scanning probe microscope (SPM), which is typically the tip of the scanning probe on an atomic force microscope (AFM). Alignment of the scanning probe tip relative to the mark is then determined by visual observation of the microscope image. This alignment process may be repeated to allow for modification or changing of the scanning probe microscope tip.

  6. DNA-free genome editing methods for targeted crop improvement.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala

    2016-07-01

    Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted.

  7. Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains, Spain.

    Science.gov (United States)

    Magdy, M; Werner, O; McDaniel, S F; Goffinet, B; Ros, R M

    2016-03-01

    The common cord moss Funaria hygrometrica has a worldwide distribution and thrives in a wide variety of environments. Here, we studied the genetic diversity in F. hygrometrica along an abiotic gradient in the Mediterranean high mountain of Sierra Nevada (Spain) using a genome scan method. Eighty-four samples from 17 locations from 24 to 2700 m were fingerprinted based on their amplified fragment length polymorphism (AFLP) banding pattern. Using PCA and Bayesian inference we found that the genetic diversity was structured in three or four clusters, respectively. Using a genome scan method we identified 13 outlier loci, which showed a signature of positive selection. Partial Mantel tests were performed between the Euclidean distance matrices of geographic and climatic variables, versus the pair-wise genetic distance of the AFLP dataset and AFLP-positive outliers dataset. AFLP-positive outlier data were significantly correlated with the gradient of the climatic variables, suggesting adaptive variation among populations of F. hygrometrica along the Sierra Nevada Mountains. We highlight the additional analyses necessary to identify the nature of these loci, and their biological role in the adaptation process.

  8. Scanning for genes in large genomic regions: cosmid-based exon trapping of multiple exons in a single product.

    OpenAIRE

    Datson, N.A.; Vosse, E van de; Dauwerse, H.G.; Bout, M; van Ommen, G J; J T den Dunnen

    1996-01-01

    To facilitate the scanning of large genomic regions for the presence of exonic gene segments we have constructed a cosmid-based exon trap vector. The vector serves a dual purpose since it is also suitable for contig construction and physical mapping. The exon trap cassette of vector sCOGH1 consists of the human growth hormone gene driven by the mouse mettallothionein-1 promoter. Inserts are cloned in the multicloning site located in intron 2 of the hGH gene. The efficiency of the system is de...

  9. Microorganism genomics, compositions and methods related thereto

    Science.gov (United States)

    Handelsman, Jo; Goodman, Robert M.; Rondon, Michelle R.

    2001-01-01

    The present invention provides methods and compositions for accessing, in a generally unbaised manner, a diverse genetic pool for genes involved in biosynthetic pathways. The invention also provides compounds which can be identified by cloning biosynthetic pathways.

  10. A Genome-Wide Scan for Breast Cancer Risk Haplotypes among African American Women

    Science.gov (United States)

    Song, Chi; Chen, Gary K.; Millikan, Robert C.; Ambrosone, Christine B.; John, Esther M.; Bernstein, Leslie; Zheng, Wei; Hu, Jennifer J.; Ziegler, Regina G.; Nyante, Sarah; Bandera, Elisa V.; Ingles, Sue A.; Press, Michael F.; Deming, Sandra L.; Rodriguez-Gil, Jorge L.; Chanock, Stephen J.; Wan, Peggy; Sheng, Xin; Pooler, Loreall C.; Van Den Berg, David J.; Le Marchand, Loic; Kolonel, Laurence N.; Henderson, Brian E.; Haiman, Chris A.; Stram, Daniel O.

    2013-01-01

    Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density. PMID:23468962

  11. A large genome scan for rare CNVs in amyotrophic lateral sclerosis.

    NARCIS (Netherlands)

    Blauw, H.M.; Al-Chalabi, A.; Andersen, P.M.; Vught, P.W. van; Diekstra, F.P.; Es, M.A. van; Saris, C.G.J.; Groen, E.J.; Rheenen, W. van; Koppers, M.; Slot, R. van 't; Strengman, E.; Estrada, K.; Rivadeneira, F.; Hofman, A.; Uitterlinden, A.G.; Kiemeney, L.A.L.M.; Vermeulen, H.H.M.; Birve, A.; Waibel, S.; Meyer, T.; Cronin, S.; McLaughlin, R.L.; Hardiman, O.; Sapp, P.C.; Tobin, M.D.; Wain, L.V.; Tomik, B.; Slowik, A.; Lemmens, R.; Rujescu, D.; Schulte, C.; Gasser, T.; Brown Jr., R.H.; Landers, J.E.; Robberecht, W.; Ludolph, A.C.; Ophoff, R.A.; Veldink, J.H.; Berg, L.H. van den

    2010-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease selectively affecting motor neurons in the brain and spinal cord. Recent genome-wide association studies (GWASs) have identified several common variants which increase disease susceptibility. In contrast, rare copy-number

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

    NARCIS (Netherlands)

    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; Boelte, 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; osey, 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, Ines; 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 fa

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

    NARCIS (Netherlands)

    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; Boelte, 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; osey, 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, Ines; 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 fa

  14. 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. 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. 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 evid

  15. 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. 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

  16. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan

    Science.gov (United States)

    Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be easily seen by analyzing the unexpected behaviour of the linkage disequilibrium (LD) decay. A heuristic process was proposed to identify those misassembly signatures and presented the ones found in ...

  17. Genome-wide linkage scan identifies two novel genetic loci for coronary artery disease: in GeneQuest families.

    Directory of Open Access Journals (Sweden)

    Hanxiang Gao

    Full Text Available Coronary artery disease (CAD is the leading cause of death worldwide. Recent genome-wide association studies (GWAS identified >50 common variants associated with CAD or its complication myocardial infarction (MI, but collectively they account for <20% of heritability, generating a phenomena of "missing heritability". Rare variants with large effects may account for a large portion of missing heritability. Genome-wide linkage studies of large families and follow-up fine mapping and deep sequencing are particularly effective in identifying rare variants with large effects. Here we show results from a genome-wide linkage scan for CAD in multiplex GeneQuest families with early onset CAD and MI. Whole genome genotyping was carried out with 408 markers that span the human genome by every 10 cM and linkage analyses were performed using the affected relative pair analysis implemented in GENEHUNTER. Affected only nonparametric linkage (NPL analysis identified two novel CAD loci with highly significant evidence of linkage on chromosome 3p25.1 (peak NPL  = 5.49 and 3q29 (NPL  = 6.84. We also identified four loci with suggestive linkage on 9q22.33, 9q34.11, 17p12, and 21q22.3 (NPL  = 3.18-4.07. These results identify novel loci for CAD and provide a framework for fine mapping and deep sequencing to identify new susceptibility genes and novel variants associated with risk of CAD.

  18. Efficient Haplotype Inference Algorithms in One Whole Genome Scan for Pedigree Data with Non-genotyped Founders

    Institute of Scientific and Technical Information of China (English)

    Yongxi Cheng; Hadi Sabaa; Zhipeng Cai; Randy Goebel; Guohui Lin

    2009-01-01

    An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases where some pedigree founders are not genotyped, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in exactly one nuclear family. The importance of this generalization lies in that such cases frequently happen in real data, because some founders may have passed away and their genotype data can no longer be collected. The algorithm runs in O(m3n3) time, where m is the number of single nucleotide polymorphism (SNP) loci under consideration and n is the number of genotyped members in the pedigree. This zero-recombination haplotyping algorithm is extended to a maximum parsimoniously haplotyping algorithm in one whole genome scan to minimize the total number of breakpoint sites, or equivalently, the number of maximal zero-recombination chromosomal regions. We show that such a whole genome scan haplotyping algorithm can be implemented in O(m3n3) time in a novel incremental fashion,here m denotes the total number of SNP loci along the chromosome.

  19. Genome scan for quantitative trait loci influencing HDL levels: evidence for multilocus inheritance in familial combined hyperlipidemia.

    Science.gov (United States)

    Gagnon, France; Jarvik, Gail P; Badzioch, Michael D; Motulsky, Arno G; Brunzell, John D; Wijsman, Ellen M

    2005-09-01

    Several genome scans in search of high-density lipoprotein (HDL) quantitative trait loci (QTLs) have been performed. However, to date the actual identification of genes implicated in the regulation of common forms of HDL abnormalities remains unsuccessful. This may be due, in part, to the oligogenic and multivariate nature of HDL regulation, and potentially, pleiotropy affecting HDL and other lipid-related traits. Using a Bayesian Markov Chain Monte Carlo (MCMC) approach, we recently provided evidence of linkage of HDL level variation to the APOA1-C3-A4-A5 gene complex, in familial combined hyperlipidemia pedigrees, with an estimated number of two to three large QTLs remaining to be identified. We also presented results consistent with pleiotropy affecting HDL and triglycerides at the APOA1-C3-A4-A5 gene complex. Here we use the same MCMC analytic strategy, which allows for oligogenic trait models, as well as simultaneous incorporation of covariates, in the context of multipoint analysis. We now present results from a genome scan in search for the additional HDL QTLs in these pedigrees. We provide evidence of linkage for additional HDL QTLs on chromosomes 3p14 and 13q32, with results on chromosome 3 further supported by maximum parametric and variance component LOD scores of 3.0 and 2.6, respectively. Weaker evidence of linkage was also obtained for 7q32, 12q12, 14q31-32 and 16q23-24.

  20. 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.

  1. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE

    Directory of Open Access Journals (Sweden)

    Prasad Aparna

    2010-03-01

    Full Text Available Abstract Background Classical bovine spongiform encephalopathy (BSE is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Polymorphisms that alter the prion protein of sheep or humans have been associated with variations in transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that non-synonymous mutations in the bovine prion gene (PRNP are associated with classical BSE disease susceptibility. However, two bovine PRNP insertion/deletion polymorphisms, one within the promoter region and the other in intron 1, have been associated with susceptibility to classical BSE. These associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. To test for associations with BSE susceptibility, we conducted a genome wide scan using a panel of 3,072 single nucleotide polymorphism (SNP markers on 814 animals representing cases and control Holstein cattle from the United Kingdom BSE epidemic. Results Two sets of BSE affected Holstein cattle were analyzed in this study, one set with known family relationships and the second set of paired cases with controls. The family set comprises half-sibling progeny from six sires. The progeny from four of these sires had previously been scanned with microsatellite markers. The results obtained from the current analysis of the family set yielded both some supporting and new results compared with those obtained in the earlier study. The results revealed 27 SNPs representing 18 chromosomes associated with incidence of BSE disease. These results confirm a region previously reported on chromosome 20, and identify additional regions on chromosomes 2, 14, 16, 21 and 28. This study did not identify a significant association near the PRNP in the family sample set. The only association found in the PRNP

  2. New Methods in Genomic Research of Plants

    Institute of Scientific and Technical Information of China (English)

    STEWART J M; KANTARTZI S K; AVILA C A

    2008-01-01

    @@ Association mapping (as opposed to population mapping) is becoming more important in establishing associations between a phenotype and a genotype.The major advantage of association mapping,which depends on novel statistical methods,lies in the ability to use a collection of germplasm directly rather than taking the time and expense of developing a mapping population.Another advantage of association mapping is that the linkage disequilibrium values give a stronger LOD value,hence weak QTLs are more evident.

  3. A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population.

    Science.gov (United States)

    Chen, C Y; Guo, Y M; Zhang, Z Y; Ren, J; Huang, L S

    2010-06-01

    Gestation length and maternal ability are important to improve the sow reproduction efficiency and their offspring survival. To map quantitative trait loci (QTL) for gestation length and maternal ability related traits including piglet survival rate and average body weight of piglets at weaning, more than 200 F2 sows from a White Duroc × Erhualian resource population were phenotyped. A genome-wide scan was performed with 194 microsatellite markers covering the whole pig genome. QTL analysis was carried out using a composite regression interval mapping method via QTL express. The results showed that total number of born piglets was significantly correlated with gestation length (r = -0.13, P gestation length. The QTL on SSC2 achieved the 5% genome-wide significant level and the QTL on SSC8 was consistent with previous reports. Four suggestive QTL were identified for maternal ability related traits including 1 QTL for survival rate of piglets at weaning on SSC8, 3 QTL for average body weight of piglet at weaning on SSC3, 11 and 13.

  4. 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

    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...... 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...

  5. Multiple type 2 diabetes susceptibility genes following genome-wide association scan in UK samples

    OpenAIRE

    Zeggini, Eleftheria; Michael N. Weedon; Lindgren, Cecilia M.; Frayling, Timothy M; Elliott, Katherine S.; Lango, Hana; Nicholas J Timpson; Perry, John R B; Nigel W Rayner; Freathy, Rachel M; Barrett, Jeffrey C.; Shields, Beverley; Andrew P Morris; Ellard, Sian; Groves, Christopher J

    2007-01-01

    The molecular mechanisms involved in the development of type 2 diabetes are poorly understood. Starting from genome-wide genotype data for 1,924 diabetic cases and 2,938 population controls generated by the Wellcome Trust Case Control Consortium, we set out to detect replicated diabetes association signals through analysis of 3,757 additional cases and 5,346 controls, and by integration of our findings with equivalent data from other international consortia. We detected diabetes susceptibilit...

  6. 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.

  7. The difficulty of avoiding false positives in genome scans for natural selection.

    Science.gov (United States)

    Mallick, Swapan; Gnerre, Sante; Muller, Paul; Reich, David

    2009-05-01

    Several studies have found evidence for more positive selection on the chimpanzee lineage compared with the human lineage since the two species split. A potential concern, however, is that these findings may simply reflect artifacts of the data: inaccuracies in the underlying chimpanzee genome sequence, which is of lower quality than human. To test this hypothesis, we generated de novo genome assemblies of chimpanzee and macaque and aligned them with human. We also implemented a novel bioinformatic procedure for producing alignments of closely related species that uses synteny information to remove misassembled and misaligned regions, and sequence quality scores to remove nucleotides that are less reliable. We applied this procedure to re-examine 59 genes recently identified as candidates for positive selection in chimpanzees. The great majority of these signals disappear after application of our new bioinformatic procedure. We also carried out laboratory-based resequencing of 10 of the regions in multiple chimpanzees and humans, and found that our alignments were correct wherever there was a conflict with the published results. These findings throw into question previous findings that there has been more positive selection in chimpanzees than in humans since the two species diverged. Our study also highlights the challenges of searching the extreme tails of distributions for signals of natural selection. Inaccuracies in the genome sequence at even a tiny fraction of genes can produce false-positive signals, which make it difficult to identify loci that have genuinely been targets of selection.

  8. 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.

  9. Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity.

    Science.gov (United States)

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

    2016-08-04

    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.

  10. Comparative analysis of methods for genome-wide nucleosome cartography.

    Science.gov (United States)

    Quintales, Luis; Vázquez, Enrique; Antequera, Francisco

    2015-07-01

    Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use. © The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  11. A novel method for fusion of intra-oral scans and cone-beam computed tomography scans for orthognathic surgery planning.

    NARCIS (Netherlands)

    Waard, O. de; Baan, F.; Verhamme, L.M.; Breuning, H.; Kuijpers-Jagtman, A.M.; Maal, T.J.

    2016-01-01

    AIM: To assess the feasibility of a new method to augment the three-dimensional virtual skull model with a detailed surface model of the dentition produced by intra-oral scanning, compared to the conventional triple scan procedure. MATERIALS & METHODS: In four patients who were planned for

  12. Benchmarking ortholog identification methods using functional genomics data.

    NARCIS (Netherlands)

    Hulsen, T.; Huynen, M.A.; Vlieg, J. de; Groenen, P.M.

    2006-01-01

    BACKGROUND: The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often the defini

  13. Benchmarking ortholog identification methods using functional genomics data.

    NARCIS (Netherlands)

    Hulsen, T.; Huynen, M.A.; Vlieg, J. de; Groenen, P.M.

    2006-01-01

    BACKGROUND: The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often the defini

  14. 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

  15. 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...

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

    OpenAIRE

    Lindgren, Cecilia; Heid, Iris; Randall, Joshua; Lamina, Claudia; Steinthorsdottir, Valgerdur; Qi, Lu; Speliotes, Elizabeth; Thorleifsson, Gudmar; Willer, Cristen; Herrera, Blanca; Jackson, Anne; Lim, Noha; Scheet, Paul; Soranzo, Nicole; Amin, Najaf

    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 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 ...

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

    OpenAIRE

    Lindgren, Cecilia M; Heid, Iris M.; Randall, Joshua C.; Claudia Lamina; Valgerdur Steinthorsdottir; Lu Qi; Speliotes, Elizabeth K.; Gudmar Thorleifsson; Willer, Cristen J.; Herrera, Blanca M; Jackson, Anne U.; Noha Lim; Paul Scheet; Nicole Soranzo; Najaf Amin

    2009-01-01

    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 t...

  18. Modified elliptically polarized light Z-scan method for studying third-order nonlinear susceptibility components.

    Science.gov (United States)

    Yan, Xiao-Qing; Liu, Zhi-Bo; Zhang, Xiao-Liang; Zang, Wei-Ping; Tian, Jian-Guo

    2010-05-10

    The normal elliptically polarized light Z-scan method is modified by adding a quarter-wave plate and an analyzer before the detector. The normalized transmittance formulas of modified elliptically polarized light Z-scan are obtained for media with negligible nonlinear absorption. Compared with normal linearly and elliptically polarized light Z-scan methods, an increase of sensitivity by a factor of larger than 4 is achieved for the real part of third-order susceptibility component's measurements using this modified elliptically polarized light Z-scan method. The analytical results are verified by studying the real part of independent susceptibility components of CS(2) liquid. Moreover, the potential application for cross-polarized wave generation is discussed. (c) 2010 Optical Society of America.

  19. Scan Profiles Based Method for Segmentation and Extraction of Planar Objects in Mobile Laser Scanning Point Clouds

    Science.gov (United States)

    Nguyen, Hoang Long; Belton, David; Helmholz, Petra

    2016-06-01

    The demand for accurate spatial data has been increasing rapidly in recent years. Mobile laser scanning (MLS) systems have become a mainstream technology for measuring 3D spatial data. In a MLS point cloud, the point clouds densities of captured point clouds of interest features can vary: they can be sparse and heterogeneous or they can be dense. This is caused by several factors such as the speed of the carrier vehicle and the specifications of the laser scanner(s). The MLS point cloud data needs to be processed to get meaningful information e.g. segmentation can be used to find meaningful features (planes, corners etc.) that can be used as the inputs for many processing steps (e.g. registration, modelling) that are more difficult when just using the point cloud. Planar features are dominating in manmade environments and they are widely used in point clouds registration and calibration processes. There are several approaches for segmentation and extraction of planar objects available, however the proposed methods do not focus on properly segment MLS point clouds automatically considering the different point densities. This research presents the extension of the segmentation method based on planarity of the features. This proposed method was verified using both simulated and real MLS point cloud datasets. The results show that planar objects in MLS point clouds can be properly segmented and extracted by the proposed segmentation method.

  20. SCAN PROFILES BASED METHOD FOR SEGMENTATION AND EXTRACTION OF PLANAR OBJECTS IN MOBILE LASER SCANNING POINT CLOUDS

    Directory of Open Access Journals (Sweden)

    H. L. Nguyen

    2016-06-01

    Full Text Available The demand for accurate spatial data has been increasing rapidly in recent years. Mobile laser scanning (MLS systems have become a mainstream technology for measuring 3D spatial data. In a MLS point cloud, the point clouds densities of captured point clouds of interest features can vary: they can be sparse and heterogeneous or they can be dense. This is caused by several factors such as the speed of the carrier vehicle and the specifications of the laser scanner(s. The MLS point cloud data needs to be processed to get meaningful information e.g. segmentation can be used to find meaningful features (planes, corners etc. that can be used as the inputs for many processing steps (e.g. registration, modelling that are more difficult when just using the point cloud. Planar features are dominating in manmade environments and they are widely used in point clouds registration and calibration processes. There are several approaches for segmentation and extraction of planar objects available, however the proposed methods do not focus on properly segment MLS point clouds automatically considering the different point densities. This research presents the extension of the segmentation method based on planarity of the features. This proposed method was verified using both simulated and real MLS point cloud datasets. The results show that planar objects in MLS point clouds can be properly segmented and extracted by the proposed segmentation method.

  1. 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.

  2. 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.

  3. An evolutionary genome scan for longevity-related natural selection in mammals.

    Science.gov (United States)

    Jobson, Richard W; Nabholz, Benoit; Galtier, Nicolas

    2010-04-01

    Aging is thought to occur through the accumulation of biochemical damage affecting DNA, proteins, and lipids. The major source of cellular damage involves the generation of reactive oxygen species produced during mitochondrial respiratory activity of the electron transport chain. Energetic metabolism, antioxidative processes, genome maintenance, and cell cycle are the cellular functions most commonly associated with aging, from experimental studies of model organisms. The significance of these experiments with respect to longevity-related selective constraints in nature remains unclear. Here we took a phylogenomic approach to identify the genetic targets of natural selection for elongated life span in mammals. By comparing the nonsynonymous and synonymous evolution of approximately 5.7 million codon sites across 25 species, we identify codons and genes showing a stronger level of amino acid conservation in long-lived than in short-lived lineages. We show that genes involved in lipid composition and (collagen associated) vitamin C binding have collectively undergone increased selective pressure in long-lived species, whereas genes involved in DNA replication/repair or antioxidation have not. Most of the candidate genes experimentally associated with aging (e.g., PolG, Sod, Foxo) have played no detectable role in the evolution of longevity in mammals. A large body of current medical research aims at discovering how to increase longevity in human. In this study, we uncovered the way natural selection has completed this task during mammalian evolution. Cellular membrane and extracellular collagen composition, not genome integrity, have apparently been the optimized features.

  4. 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

  5. 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.

  6. Genome-wide association scan suggests basis for microtia in Awassi sheep.

    Science.gov (United States)

    Jawasreh, K; Boettcher, P J; Stella, A

    2016-08-01

    Hereditary underdevelopment of the ear, a condition also known as microtia, has been observed in several sheep breeds as well as in humans and other species. Its genetic basis in sheep is unknown. The Awassi sheep, a breed native to southwest Asia, carries this phenotype and was targeted for molecular characterization via a genome-wide association study. DNA samples were collected from sheep in Jordan. Eight affected and 12 normal individuals were genotyped with the Illumina OvineSNP50(®) chip. Multilocus analyses failed to identify any genotypic association. In contrast, a single-locus analysis revealed a statistically significant association (P = 0.012, genome-wide) with a SNP at basepair 34 647 499 on OAR23. This marker is adjacent to the gene encoding transcription factor GATA-6, which has been shown to play a role in many developmental processes, including chondrogenesis. The lack of extended homozygosity in this region suggests a fairly ancient mutation, and the time of occurrence was estimated to be approximately 3000 years ago. Many of the earless sheep breeds may thus share the causative mutation, especially within the subgroup of fat-tailed, wool sheep.

  7. 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.

  8. Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction.

    Directory of Open Access Journals (Sweden)

    Vijaykumar Yogesh Muley

    Full Text Available BACKGROUND: Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these methods assume that functionally interacting proteins are likely to have a shared evolutionary history. This history can be traced out for the protein pairs of a query genome by correlating different evolutionary aspects of their homologs in multiple genomes known as the reference genomes. These methods include phylogenetic profiling, gene neighborhood and co-occurrence of the orthologous protein coding genes in the same cluster or operon. These are collectively known as genomic context methods. On the other hand a method called mirrortree is based on the similarity of phylogenetic trees between two interacting proteins. Comprehensive performance analyses of these methods have been frequently reported in literature. However, very few studies provide insight into the effect of reference genome selection on detection of meaningful protein interactions. METHODS: We analyzed the performance of four methods and their variants to understand the effect of reference genome selection on prediction efficacy. We used six sets of reference genomes, sampled in accordance with phylogenetic diversity and relationship between organisms from 565 bacteria. We used Escherichia coli as a model organism and the gold standard datasets of interacting proteins reported in DIP, EcoCyc and KEGG databases to compare the performance of the prediction methods. CONCLUSIONS: Higher performance for predicting protein-protein interactions was achievable even with 100-150 bacterial genomes out of 565 genomes. Inclusion of archaeal genomes in the reference genome set improves performance. We find that in order to obtain a good performance, it is better to sample few genomes of related genera of prokaryotes from the large number of available genomes. Moreover, such a sampling

  9. 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.

  10. Five blood pressure loci identified by an updated genome-wide linkage scan: meta-analysis of the Family Blood Pressure Program.

    Science.gov (United States)

    Simino, Jeannette; Shi, Gang; Kume, Rezart; Schwander, Karen; Province, Michael A; Gu, C Charles; Kardia, Sharon; Chakravarti, Aravinda; Ehret, Georg; Olshen, Richard A; Turner, Stephen T; Ho, Low-Tone; Zhu, Xiaofeng; Jaquish, Cashell; Paltoo, Dina; Cooper, Richard S; Weder, Alan; Curb, J David; Boerwinkle, Eric; Hunt, Steven C; Rao, Dabeeru C

    2011-03-01

    A preliminary genome-wide linkage analysis of blood pressure in the Family Blood Pressure Program (FBPP) was reported previously. We harnessed the power and ethnic diversity of the final pooled FBPP dataset to identify novel loci for blood pressure thereby enhancing localization of genes containing less common variants with large effects on blood pressure levels and hypertension. We performed one overall and 4 race-specific meta-analyses of genome-wide blood pressure linkage scans using data on 4,226 African-American, 2,154 Asian, 4,229 Caucasian, and 2,435 Mexican-American participants (total N = 13,044). Variance components models were fit to measured (raw) blood pressure levels and two types of antihypertensive medication adjusted blood pressure phenotypes within each of 10 subgroups defined by race and network. A modified Fisher's method was used to combine the P values for each linkage marker across the 10 subgroups. Five quantitative trait loci (QTLs) were detected on chromosomes 6p22.3, 8q23.1, 20q13.12, 21q21.1, and 21q21.3 based on significant linkage evidence (defined by logarithm of odds (lod) score ≥3) in at least one meta-analysis and lod scores ≥1 in at least 2 subgroups defined by network and race. The chromosome 8q23.1 locus was supported by Asian-, Caucasian-, and Mexican-American-specific meta-analyses. The new QTLs reported justify new candidate gene studies. They may help support results from genome-wide association studies (GWAS) that fall in these QTL regions but fail to achieve the genome-wide significance.

  11. 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.

  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. Genomic Scans of Zygotic Disequilibrium and Epistatic SNPs in HapMap Phase III Populations.

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    Xin-Sheng Hu

    Full Text Available Previous theory indicates that zygotic linkage disequilibrium (LD is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI possess more significant zygotic LDs for the double-homozygotes (DAABB than any other significant zygotic LDs (DAABb, DAaBB, and DAaBb, while non-Africa populations generally have more significant DAaBb's than any other significant zygotic LDs (DAABB, DAABb, and DAaBB. Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for DAABB and DAaBb than for DAaBB and DAABb in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia, which helps to understand geographical genomic medicine.

  15. Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method.

    Science.gov (United States)

    Zhang, Ren; Ou, Hong-Yu; Gao, Feng; Luo, Hao

    2014-04-01

    The nucleotide composition of genomes undergoes dramatic variations among all three kingdoms of life. GC content, an important characteristic for a genome, is related to many important functions, and therefore GC content and its distribution are routinely reported for sequenced genomes. Traditionally, GC content distribution is assessed by computing GC contents in windows that slide along the genome. Disadvantages of this routinely used window-based method include low resolution and low sensitivity. Additionally, different window sizes result in different GC content distribution patterns within the same genome. We proposed a windowless method, the GC profile, for displaying GC content variations across the genome. Compared to the window-based method, the GC profile has the following advantages: 1) higher sensitivity, because of variation-amplifying procedures; 2) higher resolution, because boundaries between domains can be determined at one single base pair; 3) uniqueness, because the GC profile is unique for a given genome and 4) the capacity to show both global and regional GC content distributions. These characteristics are useful in identifying horizontally-transferred genomic islands and homogenous GC-content domains. Here, we review the applications of the GC profile in identifying genomic islands and genome segmentation points, and in serving as a platform to integrate with other algorithms for genome analysis. A web server generating GC profiles and implementing relevant genome segmentation algorithms is available at: www.zcurve.net.

  16. A method of dynamic chromatic aberration correction in low-voltage scanning electron microscopes.

    Science.gov (United States)

    Khursheed, Anjam

    2005-07-01

    A time-of-flight concept that dynamically corrects for chromatic aberration effects in scanning electron microscopes (SEMs) is presented. The method is predicted to reduce the microscope's chromatic aberration by an order of magnitude. The scheme should significantly improve the spatial resolution of low-voltage scanning electron microscopes (LVSEMs). The dynamic means of correcting for chromatic aberration also allows for the possibility of obtaining high image resolution from electron guns that have relatively large energy spreads.

  17. A novel genomic selection method combining GBLUP and LASSO.

    Science.gov (United States)

    Li, Hengde; Wang, Jingwei; Bao, Zhenmin

    2015-06-01

    Genetic prediction of quantitative traits is a critical task in plant and animal breeding. Genomic selection is an accurate and efficient method of estimating genetic merits by using high-density genome-wide single nucleotide polymorphisms (SNP). In the framework of linear mixed models, we extended genomic best linear unbiased prediction (GBLUP) by including additional quantitative trait locus (QTL) information that was extracted from high-throughput SNPs by using least absolute shrinkage selection operator (LASSO). GBLUP was combined with three LASSO methods-standard LASSO (SLGBLUP), adaptive LASSO (ALGBLUP), and elastic net (ENGBLUP)-that were used for detecting QTLs, and these QTLs were fitted as fixed effects; the remaining SNPs were fitted using a realized genetic relationship matrix. Simulations performed under distinct scenarios revealed that (1) the prediction accuracy of SLGBLUP was the lowest; (2) the prediction accuracies of ALGBLUP and ENGBLUP were equivalent to or higher than that of GBLUP, except under scenarios in which the number of QTLs was large; and (3) the persistence of prediction accuracy over generations was strongest in the case of ENGBLUP. Building on the favorable computational characteristics of GBLUP, ENGBLUP enables robust modeling and efficient computation to be performed for genomic selection.

  18. 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.

    2014-01-01

    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. PMID:25242497

  19. 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

    2014-10-01

    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.

  20. 3D scan line method for identifying void fabric of granular materials

    Science.gov (United States)

    Theocharis, Alexandros I.; Vairaktaris, Emmanouil; Dafalias, Yannis F.

    2017-06-01

    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.

  1. 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.

  2. Genome scan for locus involved in mandibular prognathism in pedigrees from China.

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    Qin Li

    Full Text Available BACKGROUND: It is well known that genetic components play an important role in the etiology of mandibular prognathism, but few susceptibility loci have been mapped. METHODOLOGY: In order to identify linkage regions for mandibular prognathism, we analyzed two Chinese pedigrees with 6,090 genome-wide single-nucleotide polymorphism (SNP markers from Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM. Multipoint parametric and non-parametric (model-free linkage analyses were used for the pedigrees. PRINCIPAL FINDING: The most statistically significant linkage results were with markers on chromosome 4 (LOD=3.166 and NPL=3.65 with rs 875864, 4p16.1, 8.38 cM. Candidate genes within the 4p16.1 include EVC, EVC2. CONCLUSION: We detected a novel suggestive linkage locus for mandibular prognathism in two Chinese pedigrees, and this linkage region provides target for susceptibility gene identification, a process that will provide important insights into the molecular and cellular basis of mandibular prognathism.

  3. A genome-wide scan identifies variants in NFIB associated with metastasis in patients with osteosarcoma

    Science.gov (United States)

    Mirabello, Lisa; Koster, Roelof; Moriarity, Branden S.; Spector, Logan G.; Meltzer, Paul S.; Gary, Joy; Machiela, Mitchell J.; Pankratz, Nathan; Panagiotou, Orestis A.; Largaespada, David; Wang, Zhaoming; Gastier-Foster, Julie M.; Gorlick, Richard; Khanna, Chand; de Toledo, Silvia Regina Caminada; Petrilli, Antonio S.; Patiño-Garcia, Ana; Sierrasesúmaga, Luis; Lecanda, Fernando; Andrulis, Irene L.; Wunder, Jay S.; Gokgoz, Nalan; Serra, Massimo; Hattinger, Claudia; Picci, Piero; Scotlandi, Katia; Flanagan, Adrienne M.; Tirabosco, Roberto; Amary, Maria Fernanda; Halai, Dina; Ballinger, Mandy L.; Thomas, David M.; Davis, Sean; Barkauskas, Donald A.; Marina, Neyssa; Helman, Lee; Otto, George M.; Becklin, Kelsie L.; Wolf, Natalie K.; Weg, Madison T.; Tucker, Margaret; Wacholder, Sholom; Fraumeni, Joseph F.; Caporaso, Neil E.; Boland, Joseph F.; Hicks, Belynda D.; Vogt, Aurelie; Burdett, Laurie; Yeager, Meredith; Hoover, Robert N.; Chanock, Stephen J.; Savage, Sharon A.

    2015-01-01

    Metastasis is the leading cause of death in osteosarcoma patients, the most common pediatric bone malignancy. We conducted a multi-stage genome-wide association study of osteosarcoma metastasis at diagnosis in 935 osteosarcoma patients to determine whether germline genetic variation contributes to risk of metastasis. We identified a SNP, rs7034162, in NFIB significantly associated with metastasis in European osteosarcoma cases, as well as in cases of African and Brazilian ancestry (meta-analysis of all cases: P=1.2×10−9, OR 2.43, 95% CI 1.83–3.24). The risk allele was significantly associated with lowered NFIB expression, which led to increased osteosarcoma cell migration, proliferation, and colony formation. Additionally, a transposon screen in mice identified a significant proportion of osteosarcomas harboring inactivating insertions in Nfib, and had lowered Nfib expression. These data suggest that germline genetic variation at rs7034162 is important in osteosarcoma metastasis, and that NFIB is an osteosarcoma metastasis susceptibility gene. PMID:26084801

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

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    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.

  5. A genome scan for candidate genes involved in the adaptation of turbot (Scophthalmus maximus).

    Science.gov (United States)

    Vilas, Román; Vandamme, Sara G; Vera, Manuel; Bouza, Carmen; Maes, Gregory E; Volckaert, Filip A M; Martínez, Paulino

    2015-10-01

    Partitioning phenotypic variance in genotypic and environmental variance may benefit from the population genomic assignment of genes putatively involved in adaptation. We analyzed a total of 256 markers (120 microsatellites and 136 Single Nucleotide Polymorphisms - SNPs), several of them associated to Quantitative Trait Loci (QTL) for growth and resistance to pathologies, with the aim to identify potential adaptive variation in turbot Scophthalmus maximus L. The study area in the Northeastern Atlantic Ocean, from Iberian Peninsula to the Baltic Sea, involves a gradual change in temperature and an abrupt change in salinity conditions. We detected 27 candidate loci putatively under selection. At least four of the five SNPs identified as outliers are located within genes coding for ribosomal proteins or directly related with the production of cellular proteins. One of the detected outliers, previously identified as part of a QTL for growth, is a microsatellite linked to a gene coding for a growth factor receptor. A similar set of outliers was detected when natural populations were compared with a sample subjected to strong artificial selection for growth along four generations. The observed association between FST outliers and growth-related QTL supports the hypothesis of changes in growth as an adaptation to differences in temperature and salinity conditions. However, further work is needed to confirm this hypothesis.

  6. Genome-Wide Association Scan Meta-Analysis Identifies Three Loci Influencing Adiposity and Fat Distribution

    Science.gov (United States)

    Qi, Lu; Speliotes, Elizabeth K.; Thorleifsson, Gudmar; Willer, Cristen J.; Herrera, Blanca M.; Jackson, Anne U.; Lim, Noha; Scheet, Paul; Soranzo, Nicole; Amin, Najaf; Aulchenko, Yurii S.; Chambers, John C.; Drong, Alexander; Luan, Jian'an; Lyon, Helen N.; Rivadeneira, Fernando; Sanna, Serena; Timpson, Nicholas J.; Zillikens, M. Carola; Zhao, Jing Hua; Almgren, Peter; Bandinelli, Stefania; Bennett, Amanda J.; Bergman, Richard N.; Bonnycastle, Lori L.; Bumpstead, Suzannah J.; Chanock, Stephen J.; Cherkas, Lynn; Chines, Peter; Coin, Lachlan; Cooper, Cyrus; Crawford, Gabriel; Doering, Angela; Dominiczak, Anna; Doney, Alex S. F.; Ebrahim, Shah; Elliott, Paul; Erdos, Michael R.; Estrada, Karol; Ferrucci, Luigi; Fischer, Guido; Forouhi, Nita G.; Gieger, Christian; Grallert, Harald; Groves, Christopher J.; Grundy, Scott; Guiducci, Candace; Hadley, David; Hamsten, Anders; Havulinna, Aki S.; Hofman, Albert; Holle, Rolf; Holloway, John W.; Illig, Thomas; Isomaa, Bo; Jacobs, Leonie C.; Jameson, Karen; Jousilahti, Pekka; Karpe, Fredrik; Kuusisto, Johanna; Laitinen, Jaana; Lathrop, G. Mark; Lawlor, Debbie A.; Mangino, Massimo; McArdle, Wendy L.; Meitinger, Thomas; Morken, Mario A.; Morris, Andrew P.; Munroe, Patricia; Narisu, Narisu; Nordström, Anna; Nordström, Peter; Oostra, Ben A.; Palmer, Colin N. A.; Payne, Felicity; Peden, John F.; Prokopenko, Inga; Renström, Frida; Ruokonen, Aimo; Salomaa, Veikko; Sandhu, Manjinder S.; Scott, Laura J.; Scuteri, Angelo; Silander, Kaisa; Song, Kijoung; Yuan, Xin; Stringham, Heather M.; Swift, Amy J.; Tuomi, Tiinamaija; Uda, Manuela; Vollenweider, Peter; Waeber, Gerard; Wallace, Chris; Walters, G. Bragi; Weedon, Michael N.; Witteman, Jacqueline C. M.; Zhang, Cuilin; Zhang, Weihua; Caulfield, Mark J.; Collins, Francis S.; Davey Smith, George; Day, Ian N. M.; Franks, Paul W.; Hattersley, Andrew T.; Hu, Frank B.; Jarvelin, Marjo-Riitta; Kong, Augustine; Kooner, Jaspal S.; Laakso, Markku; Lakatta, Edward; Mooser, Vincent; Morris, Andrew D.; Peltonen, Leena; Samani, Nilesh J.; Spector, Timothy D.; Strachan, David P.; Tanaka, Toshiko; Tuomilehto, Jaakko; Uitterlinden, André G.; van Duijn, Cornelia M.; Wareham, Nicholas J.; Watkins for the PROCARDIS consortia, Hugh; Waterworth, Dawn M.; Boehnke, Michael; Deloukas, Panos; Groop, Leif; Hunter, David J.; Thorsteinsdottir, Unnur; Schlessinger, David; Wichmann, H.-Erich; Frayling, Timothy M.; Abecasis, Gonçalo R.; Hirschhorn, Joel N.; Loos, Ruth J. F.; Stefansson, Kari; Mohlke, Karen L.; Barroso, Inês; McCarthy for the GIANT consortium, Mark I.

    2009-01-01

    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 = 1.9×10−11) and MSRA (WC, P = 8.9×10−9). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6×10−8). 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. PMID:19557161

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

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    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.

  8. Yeast ancestral genome reconstructions: the possibilities of computational methods II.

    Science.gov (United States)

    Chauve, Cedric; Gavranovic, Haris; Ouangraoua, Aida; Tannier, Eric

    2010-09-01

    Since the availability of assembled eukaryotic genomes, the first one being a budding yeast, many computational methods for the reconstruction of ancestral karyotypes and gene orders have been developed. The difficulty has always been to assess their reliability, since we often miss a good knowledge of the true ancestral genomes to compare their results to, as well as a good knowledge of the evolutionary mechanisms to test them on realistic simulated data. In this study, we propose some measures of reliability of several kinds of methods, and apply them to infer and analyse the architectures of two ancestral yeast genomes, based on the sequence of seven assembled extant ones. The pre-duplication common ancestor of S. cerevisiae and C. glabrata has been inferred manually by Gordon et al. (Plos Genet. 2009). We show why, in this case, a good convergence of the methods is explained by some properties of the data, and why results are reliable. In another study, Jean et al. (J. Comput Biol. 2009) proposed an ancestral architecture of the last common ancestor of S. kluyveri, K. thermotolerans, K. lactis, A. gossypii, and Z. rouxii inferred by a computational method. In this case, we show that the dataset does not seem to contain enough information to infer a reliable architecture, and we construct a higher resolution dataset which gives a good reliability on a new ancestral configuration.

  9. The study of lossy compressive method with different interpolation for holographic reconstruction in optical scanning holography

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    HU Zhijuan

    2015-08-01

    Full Text Available The lossy hologram compression method with three different interpolations is investigated to compress images holographically recorded with optical scanning holography.Without loss of major reconstruction details,results have shown that the lossy compression method is able to achieve high compression ratio of up to 100.

  10. A novel method of estimating effective dose from the point dose method: a case study—parathyroid CT scans

    Science.gov (United States)

    Januzis, Natalie; Nguyen, Giao; Hoang, Jenny K.; Lowry, Carolyn; Yoshizumi, Terry T.

    2015-02-01

    The purpose of this study was to validate a novel approach of applying a partial volume correction factor (PVCF) using a limited number of MOSFET detectors in the effective dose (E) calculation. The results of the proposed PVCF method were compared to the results from both the point dose (PD) method and a commercial CT dose estimation software (CT-Expo). To measure organ doses, an adult female anthropomorphic phantom was loaded with 20 MOSFET detectors and was scanned using the non-contrast and 2 phase contrast-enhanced parathyroid imaging protocols on a 64-slice multi-detector computed tomography scanner. E was computed by three methods: the PD method, the PVCF method, and the CT-Expo method. The E (in mSv) for the PD method, the PVCF method, and CT-Expo method was 2.6  ±  0.2, 1.3  ±  0.1, and 1.1 for the non-contrast scan, 21.9  ±  0.4, 13.9  ±  0.2, and 14.6 for the 1st phase of the contrast-enhanced scan, and 15.5  ±  0.3, 9.8  ±  0.1, and 10.4 for the 2nd phase of the contrast-enhanced scan, respectively. The E with the PD method differed from the PVCF method by 66.7% for the non-contrast scan, by 44.9% and by 45.5% respectively for the 1st and 2nd phases of the contrast-enhanced scan. The E with PVCF was comparable to the results from the CT-Expo method with percent differences of 15.8%, 5.0%, and 6.3% for the non-contrast scan and the 1st and 2nd phases of the contrast-enhanced scan, respectively. To conclude, the PVCF method estimated E within 16% difference as compared to 50-70% in the PD method. In addition, the results demonstrate that E can be estimated accurately from a limited number of detectors.

  11. 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.

  12. A genome-wide linkage scan of theta band activity as an endophenotype for schizophrenia

    NARCIS (Netherlands)

    Aukes, Maartje F.; Boks, Marco P.M.; Willems, Anne E.; Van Lutterveld, Remko; Sommer, Iris E.; Sitskoorn, Margriet M.; Ophoff, Roel A.; Alizadeh, Behrooz Z.; Kahn, Rene S.

    Background: Deviant brain oscillations are candidate endophenotypes for schizophrenia. Our aim was to find new quantitative trait loci for brain oscillations and putatively schizophrenia. Methods: We systematically investigated the genetic characteristics of theta, alpha, and beta oscillations at

  13. Study on the RF Set Point for the PEFP DTL by using a phase scan method

    Science.gov (United States)

    Jang, Ji-Ho; Kwon, Hyeok-Jung; Cho, Yong-Sub

    2012-12-01

    The drift tube linac (DTL) is used to accelerate proton beams from 20 MeV to 100 MeV in the linear accelerator of the Proton Engineering Frontier Project (PEFP). The phase scan signature method is a common technique to determine the radio-frequency (rf) set point, including the rf amplitude and phase, in DTL tanks. In this work, we applied the phase scan method to the first tank of the PEFP's DTL in order to study the procedure for determining the rf set point by using artificial experimental data generated by using the PARMILA code.

  14. Design optimization methods for genomic DNA tiling arrays.

    Science.gov (United States)

    Bertone, Paul; Trifonov, Valery; Rozowsky, Joel S; Schubert, Falk; Emanuelsson, Olof; Karro, John; Kao, Ming-Yang; Snyder, Michael; Gerstein, Mark

    2006-02-01

    A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central issue in designing tiling arrays is that of arriving at a single-copy tile path, as significant sequence cross-hybridization can result from the presence of non-unique probes on the array. Due to the fragmentation of genomic DNA caused by the widespread distribution of repetitive elements, the problem of obtaining adequate sequence coverage increases with the sizes of subsequence tiles that are to be included in the design. This becomes increasingly problematic when considering complex eukaryotic genomes that contain many thousands of interspersed repeats. The general problem of sequence tiling can be framed as finding an optimal partitioning of non-repetitive subsequences over a prescribed range of tile sizes, on a DNA sequence comprising repetitive and non-repetitive regions. Exact solutions to the tiling problem become computationally infeasible when applied to large genomes, but successive optimizations are developed that allow their practical implementation. These include an efficient method for determining the degree of similarity of many oligonucleotide sequences over large genomes, and two algorithms for finding an optimal tile path composed of longer sequence tiles. The first algorithm, a dynamic programming approach, finds an optimal tiling in linear time and space; the second applies a heuristic search to reduce the space complexity to a constant requirement. A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences.

  15. 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, S.C.; Meulen, E.M. van der; Sandkuijl, L.A.; Pauls, D.L.; Monsuur, A.J.; Slot, R. van 't; Minderaa, R.B.; Gunning, W.B.; Pearson, P.L.; Sinke, R.J.

    2003-01-01

    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. Initially

  16. 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

    2003-01-01

    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. Initially

  17. 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....

  18. Genome-wide scan for bovine milk-fat composition. I. Quantitative trait loci for short- and medium-chain fatty acids

    NARCIS (Netherlands)

    Stoop, W.M.; Schennink, A.; Visker, M.H.P.W.; Mullaart, E.; Arendonk, van J.A.M.; Bovenhuis, H.

    2009-01-01

    A genome-wide scan was performed to identify quantitative trait loci (QTL) for short- and medium-chain fatty acids (expressed in wt/wt %). Milk samples were available from 1,905 cows from 398 commercial herds in the Netherlands, and milk-fat composition was measured by gas chromatography. DNA was av

  19. Short communication: Genome-wide scan for bovine milk-fat composition. II. Quantitative trait loci for long-chain fatty acids

    NARCIS (Netherlands)

    Schennink, A.; Stoop, W.M.; Visker, M.H.P.W.; Poel, van der J.J.; Bovenhuis, H.; Arendonk, van J.A.M.

    2009-01-01

    We present the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in long-chain milk fatty acids. Milk-fat composition phenotypes were available on 1,905 Dutch Holstein-Friesian cows. A total of 849 cows and their 7 sires were genotyped for 1

  20. A Method for Identification of Selenoprotein Genes in Archaeal Genomes

    Institute of Scientific and Technical Information of China (English)

    Mingfeng Li; Yanzhao Huang; Yi Xiao

    2009-01-01

    The genetic codon UGA has a dual function: serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should be a real selenoprotein gene. The result shows that Asec-Prediction is effective for the prediction of archaeal selenoprotein genes.

  1. Comparison of a novel surface laser scanning anthropometric technique to traditional methods for facial parameter measurements.

    Science.gov (United States)

    Joe, Paula S; Ito, Yasushi; Shih, Alan M; Oestenstad, Riedar K; Lungu, Claudiu T

    2012-01-01

    This study was designed to determine if three-dimensional (3D) laser scanning techniques could be used to collect accurate anthropometric measurements, compared with traditional methods. The use of an alternative 3D method would allow for quick collection of data that could be used to change the parameters used for facepiece design, improving fit and protection for a wider variety of faces. In our study, 10 facial dimensions were collected using both the traditional calipers and tape method and a Konica-Minolta Vivid9i laser scanner. Scans were combined using RapidForm XOR software to create a single complete facial geometry of the subject as a triangulated surface with an associated texture image from which to obtain measurements. A paired t-test was performed on subject means in each measurement by method. Nine subjects were used in this study: five males (one African-American and four Caucasian females) and four females displaying a range of facial dimensions. Five measurements showed significant differences (pLaser scanning measurements showed high precision and accuracy when compared with traditional methods. Significant differences found can be very small changes in measurements and are unlikely to present a practical difference. The laser scanning technique demonstrated reliable and quick anthropometric data collection for use in future projects in redesigning respirators.

  2. 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.

  3. 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.

  4. 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.

  5. A method for rapid 3D scanning and replication of large paleontological specimens.

    Science.gov (United States)

    Das, Anshuman J; Murmann, Denise C; Cohrn, Kenneth; Raskar, Ramesh

    2017-01-01

    We demonstrate a fast and cost-effective technique to perform three dimensional (3D) scanning and replication of large paleontological specimens, in this case the entire skull of a Tyrannosaurus rex (T.rex) with a volume in the range of 2 m3. The technique involves time-of-flight (TOF) depth sensing using the Kinect scanning module commonly used in gesture recognition in gaming. Raw data from the Kinect sensor was captured using open source software and the reconstruction was done rapidly making this a viable method that can be adopted by museums and researchers in paleontology. The current method has the advantage of being low-cost as compared to industrial scanners and photogrammetric methods but also of accurately scanning a substantial volume range which is well suited for large specimens. The depth resolution from the Kinect sensor was measured to be around 0.6 mm which is ideal for scanning large specimens with reasonable structural detail. We demonstrate the efficacy of this method on the skull of FMNH PR 2081, also known as SUE, a near complete T.rex at the Field Museum of Natural History.

  6. 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

    Abstract Background. In lung cancer radiotherapy, planning on the midventilation (MidV) bin of a four-dimensional (4D) CT scan can reduce the systematic errors introduced by respiratory tumour motion compared to conventional CT. In this study four different methods for MidV bin selection are eval...

  7. 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...

  8. Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.

    Directory of Open Access Journals (Sweden)

    Yannick Allanore

    2011-07-01

    Full Text Available Systemic sclerosis (SSc is an orphan, complex, inflammatory disease affecting the immune system and connective tissue. SSc stands out as a severely incapacitating and life-threatening inflammatory rheumatic disease, with a largely unknown pathogenesis. We have designed a two-stage genome-wide association study of SSc using case-control samples from France, Italy, Germany, and Northern Europe. The initial genome-wide scan was conducted in a French post quality-control sample of 564 cases and 1,776 controls, using almost 500 K SNPs. Two SNPs from the MHC region, together with the 6 loci outside MHC having at least one SNP with a P<10(-5 were selected for follow-up analysis. These markers were genotyped in a post-QC replication sample of 1,682 SSc cases and 3,926 controls. The three top SNPs are in strong linkage disequilibrium and located on 6p21, in the HLA-DQB1 gene: rs9275224, P = 9.18×10(-8, OR = 0.69, 95% CI [0.60-0.79]; rs6457617, P = 1.14×10(-7 and rs9275245, P = 1.39×10(-7. Within the MHC region, the next most associated SNP (rs3130573, P = 1.86×10(-5, OR = 1.36 [1.18-1.56] is located in the PSORS1C1 gene. Outside the MHC region, our GWAS analysis revealed 7 top SNPs (P<10(-5 that spanned 6 independent genomic regions. Follow-up of the 17 top SNPs in an independent sample of 1,682 SSc and 3,926 controls showed associations at PSORS1C1 (overall P = 5.70×10(-10, OR:1.25, TNIP1 (P = 4.68×10(-9, OR:1.31, and RHOB loci (P = 3.17×10(-6, OR:1.21. Because of its biological relevance, and previous reports of genetic association at this locus with connective tissue disorders, we investigated TNIP1 expression. A markedly reduced expression of the TNIP1 gene and also its protein product were observed both in lesional skin tissue and in cultured dermal fibroblasts from SSc patients. Furthermore, TNIP1 showed in vitro inhibitory effects on inflammatory cytokine-induced collagen production. The genetic signal of

  9. A comparison of geochemical core scanning methods on high-grade metamorphic COSC-1 cores

    Science.gov (United States)

    Harms, Ulrich; Hierold, Johannes; Meima, Jeannette; Rammlmair, Dieter; Kollaske, Tina

    2016-04-01

    Micro-XRF core scanning of marine and lacustrine sediment cores provides geochemical data for many elements and has become a standard tool in paleoclimate and environmental studies. In contrast, such investigations are unusual on crystalline cores due to limitations such as crystal lattice reflections. We tested micro-XRF scanning on gneisses and mylonites of the COSC-1 ICDP project in the Swedish Caledonides. The data obtained was compared with new high-resolution half-split core surface mapping using an ED-XRF instrument (50 μm res.) and Laser Induced Breakdown Spectroscopy (LIBS) core scanner (200 μm res.). In addition, an assessment was made with whole-core box oversight XRF scanning (Minalyze AB) with 10 cm resolution. High-grade metamorphic rocks including metasedimentary leucocratic gneisses and intercalated mica-rich mylonites of the lower Seve Nappe drilled during COSC-1 have been investigated to compare scanning methods. All data sets show a clear compositional step between gneiss and mylonite indicating a metasedimentary mixed layer origin (sandy to clayey) of the source rocks with extremely limited metasomatic exchange. Micro-XRF profiles are in full accord with high-resolution mapping data but cannot reproduce the detailed structural information provided by mapping data. LIBS data include light elements such as Li that are not measurable with XRF methods and confirm a sharp non-metasomatic transition between gneisses and mylonite. The whole-core box XRF scans are extremely useful to scan the 2500 m of cored material in a short time compared with other methods, and the data is very helpful, for example, for geochemical reconstructing of lithologies.

  10. Chemoinformatics and chemical genomics: potential utility of in silico methods.

    Science.gov (United States)

    Valerio, Luis G; Choudhuri, Supratim

    2012-11-01

    Computational life sciences and informatics are inseparably intertwined and they lie at the heart of modern biology, predictive quantitative modeling and high-performance computing. Two of the applied biological disciplines that are poised to benefit from such progress are pharmacology and toxicology. This review will describe in silico chemoinformatics methods such as (quantitative) structure-activity relationship modeling and will overview how chemoinformatic technologies are considered in applied regulatory research. Given the post-genomics era and large-scale repositories of omics data that are available, this review will also address potential applications of in silico techniques in chemical genomics. Chemical genomics utilizes small molecules to explore the complex biological phenomena that may not be not amenable to straightforward genetic approach. The reader will gain the understanding that chemoinformatics stands at the interface of chemistry and biology with enabling systems for mapping, statistical modeling, pattern recognition, imaging and database tools. The great potential of these technologies to help address complex issues in the toxicological sciences is appreciated with the applied goal of the protection of public health.

  11. Heterodyne method of apertureless near-field scanning optical microscopy on periodic gold nanowells.

    Energy Technology Data Exchange (ETDEWEB)

    Hall, J. E.; Wiederrecht, G. P.; Gray, S. K.; Chang, S.-H.; Jeon, S.; Rogers, J. A.; Bachelot, R.; Royer, P.; Univ. of Illinois; Univ. of Technology at Troyes; Inst. of Electro-Optical Science and Engineering

    2007-04-02

    Heterodyne detection for apertureless near-field scanning optical microscopy was used to study periodic gold nanowell arrays. Optical near-field amplitude and phase signals were obtained simultaneously with the topography of the gold nanowells and with different polarizations. Theoretical calculations of the near-fields were consistent with the experiments; in particular, the calculated amplitudes were in especially good agreement. The heterodyne method is shown to be particularly effective for these types of periodic photonic structures and other highly scattering media, which can overwhelm the near-field scattered signal when conventional apertureless near-field scanning optical microscopy is used.

  12. 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...... correlation. We compared the power of the methods using empirically fixed significance thresholds (α = 0.05). Our results showed that the multivariate methods implemented in PLINK, SNPTEST, MultiPhen and BIMBAM performed best for the majority of the tested scenarios, with a notable increase in power...

  13. 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.

  14. Scanning for genes in large genomic regions: cosmid-based exon trapping of multiple exons in a single product.

    Science.gov (United States)

    Datson, N A; van de Vosse, E; Dauwerse, H G; Bout, M; van Ommen, G J; den Dunnen, J T

    1996-03-15

    To facilitate the scanning of large genomic regions for the presence of exonic gene segments we have constructed a cosmid-based exon trap vector. The vector serves a dual purpose since it is also suitable for contig construction and physical mapping. The exon trap cassette of vector sCOGH1 consists of the human growth hormone gene driven by the mouse mettallothionein-1 promoter. Inserts are cloned in the multicloning site located in intron 2 of the hGH gene. The efficiency of the system is demonstrated with cosmids containing multiple exons of the Duchenne Muscular Dystrophy gene. All exons present in the inserts were successfully retrieved and no cryptic products were detected. Up to seven exons were isolated simultaneously in a single spliced product. The system has been extended by a transcription-translation-test protocol to determine the presence of large open reading frames in the trapped products, using a combination of tailed PCR primers directing protein synthesis in three different reading frames, followed by in vitro transcription-translation. Having larger stretches of coding sequence in a single exon trap product rather than small single exons greatly facilitates further analysis of potential genes and offers new possibilities for direct mutation analysis of exon trap material.

  15. Genome-wide scan for quantitative trait loci influencing LDL size and plasma triglyceride in familial hypertriglyceridemia.

    Science.gov (United States)

    Austin, Melissa A; Edwards, Karen L; Monks, Stephanie A; Koprowicz, Kent M; Brunzell, John D; Motulsky, Arno G; Mahaney, Michael C; Hixson, James E

    2003-11-01

    Small, dense LDLs and hypertriglyceridemia, two highly correlated and genetically influenced risk factors, are known to predict for risk of coronary heart disease. The objective of this study was to perform a whole-genome scan for linkage to LDL size and triglyceride (TG) levels in 26 kindreds with familial hypertriglyceridemia (FHTG). LDL size was estimated using gradient gel electrophoresis, and genotyping was performed for 355 autosomal markers with an average heterozygosity of 76% and an average spacing of 10.2 centimorgans (cMs). Using variance components linkage analysis, one possible linkage was found for LDL size [logarithm of odds (LOD) = 2.1] on chromosome 6, peak at 140 cM distal to marker F13A1 (closest marker D6S2436). With adjustment for TG and/or HDL cholesterol, the LOD scores were reduced, but remained in exactly the same location. For TG, LOD scores of 2.56 and 2.44 were observed at two locations on chromosome 15, with peaks at 29 and 61 cM distal to marker D15S822 (closest markers D15S643 and D15S211, respectively). These peaks were retained with adjustment for LDL size and/or HDL cholesterol. These findings, if confirmed, suggest that LDL particle size and plasma TG levels could be caused by two different genetic loci in FHTG.

  16. Scanning coherent diffractive imaging methods for actinic extreme ultraviolet mask metrology

    Science.gov (United States)

    Helfenstein, Patrick; Mohacsi, Istvan; Rajeev, Rajendran; Ekinci, Yasin

    2016-07-01

    For the successful implementation of extreme ultraviolet (EUV) lithography in the upcoming technology nodes, a major challenge to overcome is the stable and reliable detection and characterization of mask defects. We have recently presented a reflective mode EUV mask scanning lensless imaging tool (RESCAN) which was installed at the XIL-II beamline of the swiss light source and showed reconstructed aerial images of test patterns on EUV masks. RESCAN uses scanning coherent diffractive imaging (SCDI) methods to obtain actinic aerial images of EUV photomasks and was designed for 80 nm onmask resolution. Our SCDI algorithm reconstructs the measured sample by iteratively solving the phase problem using overdetermined diffraction data gathered by scanning across the specimen with a finite illumination. It provides the phase and amplitude aerial images of EUV photomasks with high resolution without the need to use high numerical aperture (NA) lenses. Contrary to scanning microscopy and full-field microscopy, where the resolution is limited by the spot size or NA of the lens, the achievable resolution with our method depends on the detector noise and NA of the detector. To increase the resolution of our tool, we upgraded RESCAN with a detector and algorithms. Here, we present the results obtained with the tool that is capable of up to 40-nm onmask resolution. We believe that the realization of our prototype marks a significant step toward overcoming the limitations imposed by methods relying on imaging optics and shows a viable solution for actinic mask metrology.

  17. Comparison of covariate adjustment methods using space-time scan statistics for food animal syndromic surveillance

    OpenAIRE

    Alton, Gillian D; Pearl, David L.; Bateman, Ken G.; McNab, Bruce; Berke, Olaf

    2013-01-01

    Background Abattoir condemnation data show promise as a rich source of data for syndromic surveillance of both animal and zoonotic diseases. However, inherent characteristics of abattoir condemnation data can bias results from space-time cluster detection methods for disease surveillance, and may need to be accounted for using various adjustment methods. The objective of this study was to compare the space-time scan statistics with different abilities to control for covariates and to assess t...

  18. Improved method for measuring the ensemble average of strand breaks in genomic DNA.

    Science.gov (United States)

    Bespalov, V A; Conconi, A; Zhang, X; Fahy, D; Smerdon, M J

    2001-01-01

    The cis-syn cyclobutane pyrimidine dimer (CPD) is the major photoproduct induced in DNA by low wavelength ultraviolet radiation. An improved method was developed to detect CPD formation and removal in genomic DNA that avoids the problems encountered with the standard method of endonuclease detection of these photoproducts. Since CPD-specific endonucleases make single-strand cuts at CPD sites, quantification of the frequency of CPDs in DNA is usually done by denaturing gel electrophoresis. The standard method of ethidium bromide staining and gel photography requires more than 10 microg of DNA per gel lane, and correction of the photographic signal for the nonlinear film response. To simplify this procedure, a standard Southern blot protocol, coupled with phosphorimage analysis, was developed. This method uses random hybridization probes to detect genomic sequences with minimal sequence bias. Because of the vast linearity range of phosphorimage detection, scans of the signal profiles for the heterogeneous population of DNA fragments can be integrated directly to determine the number-average size of the population.

  19. Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries.

    Science.gov (United States)

    Branscomb, E; Slezak, T; Pae, R; Galas, D; Carrano, A V; Waterman, M

    1990-10-01

    We present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Our primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, we adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called "contigs." These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.

  20. Axial-scanning low-coherence interferometer method for noncontact thickness measurement of biological samples.

    Science.gov (United States)

    Kim, Do-Hyun; Song, Chul-Gyu; Ilev, Ilko K; Kang, Jin U

    2011-02-20

    We investigated a high-precision optical method for measuring the thickness of biological samples regardless of their transparency. The method is based on the precise measurement of optical path length difference of the end surfaces of objects, using a dual-arm axial-scanning low-coherence interferometer. This removes any consideration of the shape, thickness, or transparency of testing objects when performing the measurement. Scanning the reference simplifies the measurement setup, resulting in unambiguous measurement. Using a 1310 nm wavelength superluminescent diode, with a 65 nm bandwidth, the measurement accuracy was as high as 11.6 μm. We tested the method by measuring the thickness of both transparent samples and nontransparent soft biological tissues.

  1. Axial-scanning low-coherence interferometer method for noncontact thickness measurement of biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Do-Hyun; Song, Chul-Gyu; Ilev, Ilko K.; Kang, Jin U.

    2011-02-20

    We investigated a high-precision optical method for measuring the thickness of biological samples regardless of their transparency. The method is based on the precise measurement of optical path length difference of the end surfaces of objects, using a dual-arm axial-scanning low-coherence interferometer. This removes any consideration of the shape, thickness, or transparency of testing objects when performing the measurement. Scanning the reference simplifies the measurement setup, resulting in unambiguous measurement. Using a 1310 nm wavelength superluminescent diode, with a 65 nm bandwidth, the measurement accuracy was as high as 11.6 {mu}m. We tested the method by measuring the thickness of both transparent samples and nontransparent soft biological tissues.

  2. A new pulsed laser deposition technique: scanning multi-component pulsed laser deposition method.

    Science.gov (United States)

    Fischer, D; de la Fuente, G F; Jansen, M

    2012-04-01

    The scanning multi-component pulsed laser deposition (PLD) method realizes uniform depositions of desired coatings by a modified pulsed laser deposition process, preferably with a femto-second laser-system. Multi-component coatings (single or multilayered) are thus deposited onto substrates via laser induced ablation of segmented targets. This is achieved via horizontal line-scanning of a focused laser beam over a uniformly moving target's surface. This process allows to deposit the desired composition of the coating simultaneously, starting from the different segments of the target and adjusting the scan line as a function of target geometry. The sequence and thickness of multilayers can easily be adjusted by target architecture and motion, enabling inter/intra layer concentration gradients and thus functional gradient coatings. This new, simple PLD method enables the achievement of uniform, large-area coatings. Case studies were performed with segmented targets containing aluminum, titanium, and niobium. Under the laser irradiation conditions applied, all three metals were uniformly ablated. The elemental composition within the rough coatings obtained was fixed by the scanned area to Ti-Al-Nb = 1:1:1. Crystalline aluminum, titanium, and niobium were found to coexist side by side at room temperature within the substrate, without alloy formation up to 600 °C.

  3. Adaptive circle-ellipse fitting method for estimating tree diameter based on single terrestrial laser scanning

    Science.gov (United States)

    Bu, Guochao; Wang, Pei

    2016-04-01

    Terrestrial laser scanning (TLS) has been used to extract accurate forest biophysical parameters for inventory purposes. The diameter at breast height (DBH) is a key parameter for individual trees because it has the potential for modeling the height, volume, biomass, and carbon sequestration potential of the tree based on empirical allometric scaling equations. In order to extract the DBH from the single-scan data of TLS automatically and accurately within a certain range, we proposed an adaptive circle-ellipse fitting method based on the point cloud transect. This proposed method can correct the error caused by the simple circle fitting method when a tree is slanted. A slanted tree was detected by the circle-ellipse fitting analysis, then the corresponding slant angle was found based on the ellipse fitting result. With this information, the DBH of the trees could be recalculated based on reslicing the point cloud data at breast height. Artificial stem data simulated by a cylindrical model of leaning trees and the scanning data acquired with the RIEGL VZ-400 were used to test the proposed adaptive fitting method. The results shown that the proposed method can detect the trees and accurately estimate the DBH for leaning trees.

  4. Morphometric measurements of dragonfly wings: the accuracy of pinned, scanned and detached measurement methods

    Directory of Open Access Journals (Sweden)

    Laura Johnson

    2013-03-01

    Full Text Available Large-scale digitization of museum specimens, particularly of insect collections, is becoming commonplace. Imaging increases the accessibility of collections and decreases the need to handle individual, often fragile, specimens. Another potential advantage of digitization is to make it easier to conduct morphometric analyses, but the accuracy of such methods needs to be tested. Here we compare morphometric measurements of scanned images of dragonfly wings to those obtained using other, more traditional, methods. We assume that the destructive method of removing and slide-mounting wings provides the most accurate method of measurement because it eliminates error due to wing curvature. We show that, for dragonfly wings, hand measurements of pinned specimens and digital measurements of scanned images are equally accurate relative to slide-mounted hand measurements. Since destructive slide-mounting is unsuitable for museum collections, and there is a risk of damage when hand measuring fragile pinned specimens, we suggest that the use of scanned images may also be an appropriate method to collect morphometric data from other collected insect species.

  5. A Flexile and High Precision Calibration Method for Binocular Structured Light Scanning System

    Directory of Open Access Journals (Sweden)

    Jianying Yuan

    2014-01-01

    Full Text Available 3D (three-dimensional structured light scanning system is widely used in the field of reverse engineering, quality inspection, and so forth. Camera calibration is the key for scanning precision. Currently, 2D (two-dimensional or 3D fine processed calibration reference object is usually applied for high calibration precision, which is difficult to operate and the cost is high. In this paper, a novel calibration method is proposed with a scale bar and some artificial coded targets placed randomly in the measuring volume. The principle of the proposed method is based on hierarchical self-calibration and bundle adjustment. We get initial intrinsic parameters from images. Initial extrinsic parameters in projective space are estimated with the method of factorization and then upgraded to Euclidean space with orthogonality of rotation matrix and rank 3 of the absolute quadric as constraint. Last, all camera parameters are refined through bundle adjustment. Real experiments show that the proposed method is robust, and has the same precision level as the result using delicate artificial reference object, but the hardware cost is very low compared with the current calibration method used in 3D structured light scanning system.

  6. 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.

  7. An experimental evaluation method for the performance of a laser line scanning system with multiple sensors

    Science.gov (United States)

    Tian, Qingguo; Yang, Yujie; Zhang, Xiangyu; Ge, Baozhen

    2014-01-01

    Laser line scanning 3D digitising systems have a wide range of applications. Their working performance is mainly determined by the system calibration procedure and is also affected by the working conditions, CCD camera imperfections, and object surface optical characteristics. Therefore, a comprehensive evaluation of working performance is necessary before and during use. This study proposes an experimental method for the performance evaluation of a laser line scanner (LLS) with 8 scanning sensors developed in our laboratory. This method first obtains the dense point clouds of standard parts composed of disks, cylinders, and squares. Next, the single-layer point clouds located in horizontal planes of different heights are fitted using the least squares method to obtain the enclosed contours S. Three parameters, namely, the standard deviation of the distance distribution between points and S, the mean distance of the distance distribution, and the shape feature sizes, are used to evaluate the performance. The proposed method evaluates both the scanner as a whole and each scanning sensor. Using this method, more comprehensive information can be acquired to evaluate the scanner performance. The experimental results show that the absolute dimension size error and relative error are less than 5 mm and 3%, respectively, and the relative shape error is less than 2%; therefore, the evaluated LLS system can meet the requirements for human anthropometry applications. Although each scanning sensor has different random and systematic error, these errors are the function of measurement depth. These conclusions are helpful for the further use of this scanner system and can be utilised to optimise this LLS system further.

  8. Omni-Directional Scanning Localization Method of a Mobile Robot Based on Ultrasonic Sensors

    Directory of Open Access Journals (Sweden)

    Wei-Yi Mu

    2016-12-01

    Full Text Available Improved ranging accuracy is obtained by the development of a novel ultrasonic sensor ranging algorithm, unlike the conventional ranging algorithm, which considers the divergence angle and the incidence angle of the ultrasonic sensor synchronously. An ultrasonic sensor scanning method is developed based on this algorithm for the recognition of an inclined plate and to obtain the localization of the ultrasonic sensor relative to the inclined plate reference frame. The ultrasonic sensor scanning method is then leveraged for the omni-directional localization of a mobile robot, where the ultrasonic sensors are installed on a mobile robot and follow the spin of the robot, the inclined plate is recognized and the position and posture of the robot are acquired with respect to the coordinate system of the inclined plate, realizing the localization of the robot. Finally, the localization method is implemented into an omni-directional scanning localization experiment with the independently researched and developed mobile robot. Localization accuracies of up to ±3.33 mm for the front, up to ±6.21 for the lateral and up to ±0.20° for the posture are obtained, verifying the correctness and effectiveness of the proposed localization method.

  9. Omni-Directional Scanning Localization Method of a Mobile Robot Based on Ultrasonic Sensors.

    Science.gov (United States)

    Mu, Wei-Yi; Zhang, Guang-Peng; Huang, Yu-Mei; Yang, Xin-Gang; Liu, Hong-Yan; Yan, Wen

    2016-12-20

    Improved ranging accuracy is obtained by the development of a novel ultrasonic sensor ranging algorithm, unlike the conventional ranging algorithm, which considers the divergence angle and the incidence angle of the ultrasonic sensor synchronously. An ultrasonic sensor scanning method is developed based on this algorithm for the recognition of an inclined plate and to obtain the localization of the ultrasonic sensor relative to the inclined plate reference frame. The ultrasonic sensor scanning method is then leveraged for the omni-directional localization of a mobile robot, where the ultrasonic sensors are installed on a mobile robot and follow the spin of the robot, the inclined plate is recognized and the position and posture of the robot are acquired with respect to the coordinate system of the inclined plate, realizing the localization of the robot. Finally, the localization method is implemented into an omni-directional scanning localization experiment with the independently researched and developed mobile robot. Localization accuracies of up to ±3.33 mm for the front, up to ±6.21 for the lateral and up to ±0.20° for the posture are obtained, verifying the correctness and effectiveness of the proposed localization method.

  10. Genome-wide SNP-based linkage scan identifies a locus on 8q24 for an age-related hearing impairment trait

    DEFF Research Database (Denmark)

    Huyghe, J.R.; Laer, L. Van; Hendrickx, J.J.

    2008-01-01

    the results of a cross-sectional family-based genetic study employing audiometric data. By using principal component analysis, we were able to reduce the dimensionality of this multivariate phenotype while capturing most of the variation and retaining biologically important features of the audiograms. We...... conducted a genome-wide association as well as a linkage scan with high-density SNP microarrays. Because of the presence of genetic population substructure, association testing was stratified after which evidence was combined by meta-analysis. No association signals reaching genome-wide significance were...

  11. Method and apparatus for differential spectroscopic atomic-imaging using scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kazmerski, Lawrence L. (Lakewood, CO)

    1990-01-01

    A Method and apparatus for differential spectroscopic atomic-imaging is disclosed for spatial resolution and imaging for display not only individual atoms on a sample surface, but also bonding and the specific atomic species in such bond. The apparatus includes a scanning tunneling microscope (STM) that is modified to include photon biasing, preferably a tuneable laser, modulating electronic surface biasing for the sample, and temperature biasing, preferably a vibration-free refrigerated sample mounting stage. Computer control and data processing and visual display components are also included. The method includes modulating the electronic bias voltage with and without selected photon wavelengths and frequency biasing under a stabilizing (usually cold) bias temperature to detect bonding and specific atomic species in the bonds as the STM rasters the sample. This data is processed along with atomic spatial topography data obtained from the STM raster scan to create a real-time visual image of the atoms on the sample surface.

  12. Post-Fragmentation Whole Genome Amplification-Based Method

    Science.gov (United States)

    Benardini, James; LaDuc, Myron T.; Langmore, John

    2011-01-01

    This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at

  13. Advanced three-dimensional scan methods in the nanopositioning and nanomeasuring machine

    Science.gov (United States)

    Hausotte, T.; Percle, B.; Jäger, G.

    2009-08-01

    The nanopositioning and nanomeasuring machine developed at the Ilmenau University of Technology was originally designed for surface measurements within a measuring volume of 25 mm × 25 mm × 5 mm. The interferometric length measuring and drive systems make it possible to move the stage with a resolution of 0.1 nm and a positioning uncertainty of less than 10 nm in all three axes. Various measuring tasks are possible depending on the installed probe system. Most of the sensors utilized are one-dimensional surface probes; however, some tasks require measuring sidewalls and other three-dimensional features. A new control system, based on the I++ DME specification, was implemented in the device. The I++ DME scan functions were improved and special scan functions added to allow advanced three-dimensional scan methods, further fulfilling the demands of scanning force microscopy and micro-coordinate measurements. This work gives an overview of these new functions and the application of them for several different measurements.

  14. [Research on Assessment Methods of Spectrum Data Quality of Core Scan].

    Science.gov (United States)

    Xiu, Lian-cun; Zheng, Zhi-zhong; Yin, Liang; Chen, Chun-xia; Yu, Zheng-kui; Huang, Bin; Zhang, Qiu-ning; Xiu, Xiao-xu; Gao, Yang

    2015-08-01

    Core scan is the instrument used for core spectrum and pictures detection that has been developed in recent years. Cores' data can be digitized with this equipment, then automatic core catalog can be achieved, which provides basis for geological research, mineral deposit study and peripheral deposit prospecting. Meanwhile, an online database of cores can be established by the means of core digitalization to solve the cost problem caused by core preservation and share resources. Quality of core data measurement directly affects the mineral identification, reliability of parameter inversion results. Therefore it's very important to quasi-manage the assessment of data quality with the instrument before cores' spectrum testing services. Combined with the independent R&D of CSD350A type core scan, and on the basis of spectroscopy basic theory, spectrum analysis methods, core spectrum analysis requirements, key issues such as data quality assessment methods, evaluation criteria and target parameters has been discussed in depth, and comprehensive assessment of independent R&D of core scan has been conducted, which indicates the reliability and validity of spectrum measurements of the instrument. Experimental tests show that the methods including test parameters and items can perfectly response the measurements of reflectance spectrum, wavelength accuracy, repeatability and signal to noise ratio with the instrument. Thus the quality of core scan data can be evaluated correctly, and the foundation of data quality for commercial services can be provided. In the case of the current lack of relevant assessment criteria, the method this study proposes for the assessment has great value in the work of core spectrum measurements.

  15. 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

  16. [Genomic DNA extraction from hair sacs of pigs using modified phenol-chloroform method].

    Science.gov (United States)

    Wang, Ji-Ying; Yu, Ying; Feng, Li-Xia; Wang, Huai-Zhong; Zhang, Qin

    2010-07-01

    In referring to various methods for genomic DNA extraction from different tissues, we modified the classical phenol-chloroform procedure and reaction system for use in genomic DNA extraction from pig hair sacs. With the modified the phenol-chloroform method we successfully obtained high quality genomic DNA from pig hair sacs. Genomic DNA can be extracted from sacs of one to six pig hairs with satisfied quantity and quality for the need of PCR-based molecular ex-periment.

  17. 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.

  18. Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce.

    Science.gov (United States)

    Prunier, Julien; Laroche, Jérôme; Beaulieu, Jean; Bousquet, Jean

    2011-04-01

    Outlier detection methods were used to scan the genome of the boreal conifer black spruce (Picea mariana [Mill.] B.S.P.) for gene single-nucleotide polymorphisms (SNPs) potentially involved in adaptations to temperature and precipitation variations. The scan involved 583 SNPs from 313 genes potentially playing adaptive roles. Differentiation estimates among population groups defined following variation in temperature and precipitation were moderately high for adaptive quantitative characters such as the timing of budset or tree height (Q(ST) = 0.189-0.314). Average differentiation estimates for gene SNPs were null, with F(ST) values of 0.005 and 0.006, respectively, among temperature and precipitation population groups. Using two detection approaches, a total of 26 SNPs from 25 genes distributed among 11 of the 12 linkage groups of black spruce were detected as outliers with F(ST) as high as 0.078. Nearly half of the outlier SNPs were located in exons and half of those were nonsynonymous. The functional annotations of genes carrying outlier SNPs and regression analyses between the frequencies of these SNPs and climatic variables supported their implication in adaptive processes. Several genes carrying outlier SNPs belonged to gene families previously found to harbour outlier SNPs in a reproductively isolated but largely sympatric congeneric species, suggesting differential subfunctionalization of gene duplicates. Selection coefficient estimates (S) were moderate but well above the magnitude of drift (>1/N(e)), indicating that the signature of natural selection could be detected at the nucleotide level despite the recent establishment of these populations during the Holocene. © 2011 Blackwell Publishing Ltd.

  19. 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

  20. 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

  1. A novel method of drift-scanning stars suppression based on the standardized linear filter

    Science.gov (United States)

    Lin, Jianlin; Ping, Xijian; Hou, Guanghua; Ma, Debao

    2011-11-01

    A large number of stars in the drift-scanning star image have interfered with the detection of small target, this paper proposes an adaptive linear filtering method to achieve the small target detection by suppressing the stars. Firstly, the characteristics of stars, interest target and noise three different representative objects in the star image are analyzed, then the standardized linear filter is constructed to suppress the stars. For the purpose of decreasing the influence region of stars filtering uniformly, a gradient linear filter is constructed to modify the stars suppression method with the standardized linear filter. Then the filter parameter selection method is given. Finally, a multi-frame target track experiment on the real drift-scanning data is made to testify the validity of the proposed method. With the processing results of different methods, it has been showed that the proposed method for suppressing stars with different length and lean angle has a better effect, higher robustness and easier application than the others.

  2. 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.

  3. A Novel Method of Genomic DNA Extraction for Cactaceae

    Directory of Open Access Journals (Sweden)

    Shannon D. Fehlberg

    2013-03-01

    Full Text Available 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.

  4. 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

  5. Aberration analysis based on pinhole-z-scan method near the focal point of refractive systems

    Science.gov (United States)

    Castro-Marín, Pablo; Garduño-Mejía, Jesús; Rosete-Aguilar, Martha; Bruce, Neil C.; Reid, Derryck T.; Farrell, C.; Sandoval-Romero, Gabriel E.

    2016-09-01

    In this work we present a method used to study the spherical and chromatic aberrations contribution near the focal point of a refractive optical system. The actual focal position is measured by scanning a pinhole attached on the front of a power detector, which are scanned along the optical axis using a motorized stage with 1 μm resolution. Spherical aberration contribution was analyzed by changing the pupil aperture, by modifying the size of the input iris diaphragm and for each case, measuring the actual laser power vs the detector position. Chromatic aberration was analyzed by performing the same procedure but in this case we used an ultra-broad-band femtosecond laser. The results between ML and CW operation were compare. Experimental results are presented.

  6. The low-temperature method for study of coniferous tissues in the environmental scanning electron microscope.

    Science.gov (United States)

    Neděla, Vilém; Tihlaříková, Eva; Hřib, Jiří

    2015-01-01

    The use of non-standard low-temperature conditions in environmental scanning electron microscopy might be promising for the observation of coniferous tissues in their native state. This study is aimed to analyse and evaluate the method based on the principle of low-temperature sample stabilization. We demonstrate that the upper mucous layer is sublimed and a microstructure of the sample surface can be observed with higher resolution at lower gas pressure conditions, thanks to a low-temperature method. An influence of the low-temperature method on sample stability was also studied. The results indicate that high-moisture conditions are not suitable for this method and often cause the collapse of samples. The potential improvement of stability to beam damage has been demonstrated by long-time observation at different operation parameters. We finally show high applicability of the low-temperature method on different types of conifers and Oxalis acetosella. © 2014 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    Furukawa, Takuji; Noda, Koji

    2002-08-01

    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 μs from 700 μs by a usual method. Unwanted dose has been considerably reduced by around a factor of 10 compared with that by the usual method.

  8. Seismic Event Identification Using Scanning Detection: A Comparison of Denoising and Classification Methods

    Science.gov (United States)

    Rowe, C. A.; MacCarthy, J. K.; Giudicepietro, F.

    2005-12-01

    Automatic detection and classification methods are increasingly important in observatory operations, as the volume and rate of incoming data exceed the capacity of human analysis staff to process the data in near-real-time. We explore the success of scanning detection for similar event identification in a variety of seismic waveform catalogs. Several waveform pre-processing methods are applied to previously recorded events which are scanned through triggered and continuous waveform catalogs to determine the success and false alarm rate for detections of repeating signals. Pre-processing approaches include adaptive, cross-coherency filtering, adaptive, auto-associative neural network filtering, discrete wavelet package decomposition and linear predictive coding as well as suites of standard bandpass filters. Classification / detection methods for the various pre-processed signals are applied to investigate the robustness of the individual and combined approaches. The classifiers as applied to the processed waveforms include dendrogram-based clustering and neural network classifiers. We will present findings for the various combinations of methods as applied to tectonic earthquakes, mine blasts and volcanic seismicity.

  9. New method for analyzing recrystallization kinetics of deformed metal by differential scanning calorimeter

    Institute of Scientific and Technical Information of China (English)

    陈建; 马晓光; 李军; 要玉宏; 严文; 范新会

    2015-01-01

    The drawn copper wires have been analyzed by differential scanning calorimeter (DSC) and a new method, which uses DSC measurements to determine the Johnson-Mehl-Avrami-Kolmogorov (JMAK) exponent via introducing Arrhenius behavior and modifying the baseline of DSC curves, has been proposed. The results show that JMAK exponent and recrystallization activation energy of the drawn copper wires with a strain of 2.77 are about 2.39 and 125 kJ/mol, respectively. The line linking the tangency points of DSC curve hypotenuse can be used as the baseline when calculating recrystallization fraction. The JMAK exponent obtained by the DSC method is in a good agreement with that obtained by microhardness measurements. Compared to traditional methods to measure the exponent, the proposed method is faster and less labor intensive.

  10. 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.)

  11. Genome-wide linkage scan and association study of PARL to the expression of LHON families in Thailand.

    Science.gov (United States)

    Phasukkijwatana, Nopasak; Kunhapan, Bussaraporn; Stankovich, Jim; Chuenkongkaew, Wanicha L; Thomson, Russell; Thornton, Timothy; Bahlo, Melanie; Mushiroda, Taisei; Nakamura, Yusuke; Mahasirimongkol, Surakameth; Tun, Aung Win; Srisawat, Chatchawan; Limwongse, Chanin; Peerapittayamongkol, Chayanon; Sura, Thanyachai; Suthammarak, Wichit; Lertrit, Patcharee

    2010-07-01

    Leber hereditary optic neuropathy (LHON) is the most common mitochondrially inherited disease causing blindness, preferentially in young adult males. Most of the patients carry the G11778A mitochondrial DNA (mtDNA) mutation. However, the marked incomplete penetrance and the gender bias indicate some additional genetic and/or environmental factors to disease expression. Herein, we first conducted a genome-wide linkage scan with 400 microsatellite markers in 9 large Thai LHON G11778A pedigrees. Using an affecteds-only nonparametric linkage analysis, 4 regions on chromosomes 3, 12, 13 and 18 showed Zlr scores greater than 2 (P 2 in 10 of 16 allele sharing models tested) was then expanded to include the region 3q26.2-3q28 covering SLC7A14 (3q26.2), MFN1 (3q26.32), MRPL47 (3q26.33), MCCC1 (3q27.1), PARL (3q27.1) and OPA1 (3q28-q29). All of these candidate genes were selected from the Maestro database and had known to be localized in mitochondria. Sixty tag SNPs were genotyped in 86 cases, 211 of their relatives and 32 unrelated Thai controls, by multiplex-PCR-based Invader assay. Analyses using a powerful association testing tool that adjusts for relatedness (the M(QLS) statistic) showed the most evidence of association between two SNPs, rs3749446 and rs1402000 (located in PARL presenilins-associated rhomboid-like) and LHON expression (both P = 8.8 x 10(-5)). The mitochondrial PARL protease has been recently known to play a role with a dynamin-related OPA1 protein in preventing apoptotic events by slowing down the release of cytochrome c out of mitochondrial cristae junctions. Moreover, PARL is required to activate the intramembranous proteolyses resulting in the degradation of an accumulated pro-apoptotic protein in the outer mitochondrial membrane. Under these circumstances, variants of PARL are suggested to influence cell death by apoptosis which has long been believed to intrigue the neurodegeneration of LHON.

  12. Genome scan for loci predisposing to anxiety disorders using a novel multivariate approach: strong evidence for a chromosome 4 risk locus.

    Science.gov (United States)

    Kaabi, Belhassen; Gelernter, Joel; Woods, Scott W; Goddard, Andrew; Page, Grier P; Elston, Robert C

    2006-04-01

    We conducted a 10-centimorgan linkage autosomal genome scan in a set of 19 extended American pedigrees (219 subjects) ascertained through probands with panic disorder. Several anxiety disorders--including social phobia, agoraphobia, and simple phobia--in addition to panic disorder segregate in these families. In previous studies of this sample, linkage analyses were based separately on each of the individual categorical affection diagnoses. Given the substantial comorbidity between anxiety disorders and their probable shared genetic liability, it is clear that this method discards a considerable amount of information. In this article, we propose a new approach that considers panic disorder, simple phobia, social phobia, and agoraphobia as expressions of the same multivariate, putatively genetically influenced trait. We applied the most powerful multipoint Haseman-Elston method, using the grade of membership score generated from a fuzzy clustering of these phenotypes as the dependent variable in Haseman-Elston regression. One region on chromosome 4q31-q34, at marker D4S413 (with multipoint and single-point nominal P values < .00001), showed strong evidence of linkage (genomewide significance at P<.05). The same region is known to be the site of a neuropeptide Y receptor gene, NPY1R (4q31-q32), that was recently connected to anxiolytic-like effects in rats. Several other regions on four chromosomes (4q21.21-22.3, 5q14.2-14.3, 8p23.1, and 14q22.3-23.3) met criteria for suggestive linkage (multipoint nominal P values < .01). Family-by-family analysis did not show any strong evidence of heterogeneity. Our findings support the notion that the major anxiety disorders, including phobias and panic disorder, are complex traits that share at least one susceptibility locus. This method could be applied to other complex traits for which shared genetic-liability factors are thought to be important, such as substance dependencies.

  13. Suspected pulmonary embolism and lung scan interpretation: trial of a Bayesian reporting method.

    Science.gov (United States)

    Becker, D M; Philbrick, J T; Schoonover, F W; Teates, C D

    1990-01-01

    To determine whether a Bayesian method of lung scan (LS) reporting could influence the management of patients with suspected pulmonary embolism (PE). 1) A descriptive study of the diagnostic process for suspected PE using the new reporting method; 2) a non-experimental evaluation of the reporting method comparing prospective patients and historical controls; and 3) a survey of physicians' reactions to the reporting innovation. University of Virginia Hospital. Of 148 consecutive patients enrolled at the time of LS, 129 were completely evaluated; 75 patients scanned the previous year served as controls. The LS results of patients with suspected PE were reported as posttest probabilities of PE calculated from physician-provided pretest probabilities and the likelihood ratios for PE of LS interpretations. Despite the Bayesian intervention, the confirmation or exclusion of PE was often based on inconclusive evidence. PE was considered by the clinician to be ruled out in 98% of patients with posttest probabilities less than 25% and ruled in for 95% of patients with posttest probabilities greater than 75%. Prospective patients and historical controls were similar in terms of tests ordered after the LS (e.g., pulmonary angiography). Patients with intermediate or indeterminate lung scan results had the highest proportion of subsequent testing. Most physicians (80%) found the reporting innovation to be helpful, either because it confirmed clinical judgement (94 cases) or because it led to additional testing (7 cases). Despite the probabilistic guidance provided by the study, the diagnosis of PE was often neither clearly established nor excluded. While physicians appreciated the innovation and were not confused by the terminology, their clinical decision making was not clearly enhanced.

  14. Scanning Tunnelling Microscopy Observation on 10,12-Tricosadiynoic Acid Monolayers Deposited by Schaefer's Method

    Institute of Scientific and Technical Information of China (English)

    张耿民

    2001-01-01

    The Langmuir-Blodgett monolayers of 10, 12-tricosadiynoic acid molecules were deposited onto the basal plane of highly oriented pyrolytic graphite (HOPG) by Schaefer's method and then observed with the scanning tunnelling microscope (STM). With a view to achieving a parallel molecular arrangement on the graphite surface, the deposition was deliberately conducted at a relatively low surface pressure. As exhibited by the STM images, by this approach the 10,12-tricosadiynoic acid molecules could constitute an ordered structure with their molecular chains lying parallel to the substrate. The model of molecular dimer is put forward for the interpretation of the observed phenomena.

  15. Field enhancement analysis of an apertureless near field scanning optical microscope probe with finite element method

    Institute of Scientific and Technical Information of China (English)

    Weibin Chen; Qiwen Zhan

    2007-01-01

    Plasmonic field enhancement in a fully coated dielectric near field scanning optical microscope (NSOM)probe under radial polarization illumination is analyzed using an axially symmetric three-dimensional (3D)finite element method (FEM) model. The enhancement factor strongly depends on the illumination spot size, taper angle of the probe, and the metal film thickness. The tolerance of the alignment angle is investigated. Probe designs with different metal coatings and their enhancement performance are studied as well. The nanometric spot size at the tip apex and high field enhancement of the apertureless NSOM probe have important potential application in semiconductor metrology.

  16. 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.

  17. An interferometric scanning microwave microscope and calibration method for sub-fF microwave measurements.

    Science.gov (United States)

    Dargent, T; Haddadi, K; Lasri, T; Clément, N; Ducatteau, D; Legrand, B; Tanbakuchi, H; Theron, D

    2013-12-01

    We report on an adjustable interferometric set-up for Scanning Microwave Microscopy. This interferometer is designed in order to combine simplicity, a relatively flexible choice of the frequency of interference used for measurements as well as the choice of impedances range where the interference occurs. A vectorial calibration method based on a modified 1-port error model is also proposed. Calibrated measurements of capacitors have been obtained around the test frequency of 3.5 GHz down to about 0.1 fF. Comparison with standard vector network analyzer measurements is shown to assess the performance of the proposed system.

  18. 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)

  19. A novel antibody humanization method based on epitopes scanning and molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    Ding Zhang

    Full Text Available 1-17-2 is a rat anti-human DEC-205 monoclonal antibody that induces internalization and delivers antigen to dendritic cells (DCs. The potentially clinical application of this antibody is limited by its murine origin. Traditional humanization method such as complementarity determining regions (CDRs graft often leads to a decreased or even lost affinity. Here we have developed a novel antibody humanization method based on computer modeling and bioinformatics analysis. First, we used homology modeling technology to build the precise model of Fab. A novel epitope scanning algorithm was designed to identify antigenic residues in the framework regions (FRs that need to be mutated to human counterpart in the humanization process. Then virtual mutation and molecular dynamics (MD simulation were used to assess the conformational impact imposed by all the mutations. By comparing the root-mean-square deviations (RMSDs of CDRs, we found five key residues whose mutations would destroy the original conformation of CDRs. These residues need to be back-mutated to rescue the antibody binding affinity. Finally we constructed the antibodies in vitro and compared their binding affinity by flow cytometry and surface plasmon resonance (SPR assay. The binding affinity of the refined humanized antibody was similar to that of the original rat antibody. Our results have established a novel method based on epitopes scanning and MD simulation for antibody humanization.

  20. Axial segmentation of lungs CT scan images using canny method and morphological operation

    Science.gov (United States)

    Noviana, Rina; Febriani, Rasal, Isram; Lubis, Eva Utari Cintamurni

    2017-08-01

    Segmentation is a very important topic in digital image process. It is found simply in varied fields of image analysis, particularly within the medical imaging field. Axial segmentation of lungs CT scan is beneficial in designation of abnormalities and surgery planning. It will do to ascertain every section within the lungs. The results of the segmentation are accustomed discover the presence of nodules. The method which utilized in this analysis are image cropping, image binarization, Canny edge detection and morphological operation. Image cropping is done so as to separate the lungs areas, that is the region of interest. Binarization method generates a binary image that has 2 values with grey level, that is black and white (ROI), from another space of lungs CT scan image. Canny method used for the edge detection. Morphological operation is applied to smoothing the lungs edge. The segmentation methodology shows an honest result. It obtains an awfully smooth edge. Moreover, the image background can also be removed in order to get the main focus, the lungs.

  1. Evaluation of Wavelet Denoising Methods for Small-Scale Joint Roughness Estimation Using Terrestrial Laser Scanning

    Science.gov (United States)

    Bitenc, M.; Kieffer, D. S.; Khoshelham, K.

    2015-08-01

    The precision of Terrestrial Laser Scanning (TLS) data depends mainly on the inherent random range error, which hinders extraction of small details from TLS measurements. New post processing algorithms have been developed that reduce or eliminate the noise and therefore enable modelling details at a smaller scale than one would traditionally expect. The aim of this research is to find the optimum denoising method such that the corrected TLS data provides a reliable estimation of small-scale rock joint roughness. Two wavelet-based denoising methods are considered, namely Discrete Wavelet Transform (DWT) and Stationary Wavelet Transform (SWT), in combination with different thresholding procedures. The question is, which technique provides a more accurate roughness estimates considering (i) wavelet transform (SWT or DWT), (ii) thresholding method (fixed-form or penalised low) and (iii) thresholding mode (soft or hard). The performance of denoising methods is tested by two analyses, namely method noise and method sensitivity to noise. The reference data are precise Advanced TOpometric Sensor (ATOS) measurements obtained on 20 × 30 cm rock joint sample, which are for the second analysis corrupted by different levels of noise. With such a controlled noise level experiments it is possible to evaluate the methods' performance for different amounts of noise, which might be present in TLS data. Qualitative visual checks of denoised surfaces and quantitative parameters such as grid height and roughness are considered in a comparative analysis of denoising methods. Results indicate that the preferred method for realistic roughness estimation is DWT with penalised low hard thresholding.

  2. Genome-wide scan in Portuguese Island families implicates multiple loci in bipolar disorder: fine mapping adds support on chromosomes 6 and 11.

    Science.gov (United States)

    Pato, Carlos N; Pato, M T; Kirby, A; Petryshen, T L; Medeiros, H; Carvalho, C; Macedo, A; Dourado, A; Coelho, I; Valente, J; Soares, M J; Ferreira, C P; Lei, M; Verner, A; Hudson, T J; Morley, C P; Kennedy, J L; Azevedo, M H; Daly, M J; Sklar, P

    2004-05-15

    As part of an extensive study in the Portuguese Island population of families with multiple patients suffering from bipolar disorder and schizophrenia, we performed an initial genome-wide scan of 16 extended families with bipolar disorder that identified three regions on chromosomes 2, 11, and 19 with genome-wide suggestive linkage and several other regions, including chromosome 6q, also approached suggestive levels of significance. Dick et al. [2003: Am J Hum Genet 73:107-114] recently reported in a study of 250 families with bipolar disorder a maxLOD score of 3.61 near marker D6S1021 on chromosome 6q. This study replicates this finding having detected a peak NPL = 2.02 (P = 0.025) with the same marker D6S1021(104.7 Mb). Higher-density mapping provided additional support for loci on chromosome 6 including marker D6S1021 with an NPL = 2.59 (P = 0.0068) and peaking at marker D6S1639 (125 Mb) with an NPL = 3.06 (P = 0.0019). A similar pattern was detected with higher-density mapping of chromosome 11 with an NPL = 3.15 (P = 0.0014) at marker D11S1883 (63.1 Mb). Simulations at the density of our fine mapping data indicate that less than 1 scan out of 10 would find two such scores genome-wide in the same scan by chance. Our findings provide additional support for a susceptibility locus for bipolar disorder on 6q, as well as, suggesting the importance of denser scans. Published 2004 Wiley-Liss, Inc.

  3. 4D Emittance Measurements Using Multiple Wire and Waist Scan Methods in the ATF Extraction Line

    Energy Technology Data Exchange (ETDEWEB)

    Rimbault, C.; Bambade, P.; Brossard, J.; /Orsay, LAL; Alabau, M.; /Valencia U., IFIC; Kuroda, S.; /KEK, Tsukuba; Scarfe, A.; /Manchester U.; Woodley, M.; /SLAC

    2011-11-02

    Emittance measurements performed in the diagnostic section of the Accelerator Test Facility (ATF) extraction line since 1998 led to vertical emittances three times larger than the expected ones, with a strong dependence on intensity. An experimental program is pursued to investigate potential sources of emittance growth and find possible remedies. This requires efficient and reliable emittance measurement techniques. In the past, several phase-space reconstruction methods developed at SLAC and KEK have been used to estimate the vertical emittance, based on multiple location beam size measurements and dedicated quadrupole scans. These methods have been shown to be very sensitive to measurement errors and other fluctuations in the beam conditions. In this context new emittance measurements have been performed revisiting these methods and newly developed ones with a systematic approach to compare and characterise their performance in the ATF extraction line.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hou, P G; Zhao, J; Liu, M [Electrical Engineering Institute of Yanshan University, QinHuangdao, Hebei (China)

    2006-10-15

    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.

  5. The regularized blind tip reconstruction algorithm as a scanning probe microscopy tip metrology method

    CERN Document Server

    Jozwiak, G; Masalska, A; Gotszalk, T; Ritz, I; Steigmann, H

    2011-01-01

    The problem of an accurate tip radius and shape characterization is very important for determination of surface mechanical and chemical properties on the basis of the scanning probe microscopy measurements. We think that the most favorable methods for this purpose are blind tip reconstruction methods, since they do not need any calibrated characterizers and might be performed on an ordinary SPM setup. As in many other inverse problems also in case of these methods the stability of the solution in presence of vibrational and electronic noise needs application of so called regularization techniques. In this paper the novel regularization technique (Regularized Blind Tip Reconstruction - RBTR) for blind tip reconstruction algorithm is presented. It improves the quality of the solution in presence of isotropic and anisotropic noise. The superiority of our approach is proved on the basis of computer simulations and analysis of images of the Budget Sensors TipCheck calibration standard. In case of characterization ...

  6. Novel method of simultaneous multiple immunogold localization on resin sections in high resolution scanning electron microscopy.

    Science.gov (United States)

    Nebesarova, Jana; Wandrol, Petr; Vancova, Marie

    2016-01-01

    We present a new method of multiple immunolabeling that is suitable for a broad spectrum of biomedical applications. The general concept is to label both sides of the ultrathin section with the thickness of 70-80 nm with different antibodies conjugated to gold nanoparticles and to distinguish the labeled side by advanced imaging methods with high resolution scanning electron microscopy, such as by correlating images acquired at different energies of primary electrons using different signals. From the Clinical Editor: The use of transmission electron microscopy has become an indispensible tool in the detection of cellular proteins. In this short but interesting article, the authors described their new method of labeling and the identification of four different proteins simultaneously, which represents another advance in imaging technique.

  7. Restoration of Scanning Tunneling Microscope Images by means of Two-Dimensional Maximum Entropy Method

    Science.gov (United States)

    Matsumoto, Hisanori; Tokiwano, Kazuo; Hosoi, Hirotaka; Sueoka, Kazuhisa; Mukasa, Koichi

    2002-05-01

    We present a new technique for the restoration of scanning tunneling microscopy (STM) images, which is a two-dimensional extension of a recently developed statistical approach based on the one-dimensional least-squares method (LSM). An STM image is regarded as a realization of a stochastic process and assumed to be a composition of an underlying image and noise. We express the underlying image in terms of a two-dimensional generalized trigonometric polynomial suitable for representing the atomic protrusions in STM images. The optimization of the polynomial is performed by the two-dimensional LSM combined with the power spectral density function estimated by means of the maximum entropy method (MEM) iterative algorithm for two-dimensional signals. The restored images are obtained as the optimum least-squares fitting polynomial which is a continuous surface. We apply this technique to modeled and actual STM data. Results show that the present method yields a reasonable restoration of STM images.

  8. A new method for measurement of the vitrification rate of earthenware texture by scanning electron microscope.

    Science.gov (United States)

    Moon, Eun Jung; Kim, Su Kyeong; Han, Min Su; Lee, Eun Woo; Heo, Jun Su; Lee, Han Hyoung

    2013-08-01

    A new method for determining the vitrification rate of pottery depending on the firing temperature was devised using secondary electron images (SEI) of scanning electron microscope (SEM). Several tests were performed to establish the appropriate operating conditions of SEM and reproducibility as well as to examine the applicability of the method. The grayscale values converted from each pixel of SEI were used to determine the vitrification rate of pottery, which in our study were artificially fired specimens composed of three types of clay. A comparison between the vitrification rate value and appearance temperature of minerals shows that mullite formation starts at 1,100°C, during which the vitrification rate rapidly increases by over 10%. In consequence, the result presented here demonstrates that the new method can be applied to estimate the firing temperature of pottery.

  9. Accuracy of genomic selection using different methods to define haplotypes

    NARCIS (Netherlands)

    Calus, M.P.L.; Meuwissen, T.H.E.; Roos, de S.; Veerkamp, R.F.

    2008-01-01

    Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. In this study the accuracy of predicting breeding values is compared for four different models including a large number of markers, at diffe

  10. Enhanced method to reconstruct mode shapes of continuous scanning measurements using the Hilbert Huang transform and the modal analysis method

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jongsuh; Hussain, Syed Hassaan; Wang, Semyung, E-mail: smwang@gist.ac.kr; Park, Kyihwan [School of Mechatronics, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of)

    2014-09-15

    Generally, it is time consuming to experimentally identify the operating deflection shape or mode shape of a structure. To overcome this problem, the Hilbert Huang transform (HHT) technique has been recently proposed. This technique is used to extract the mode shape from measurements that continuously measure the vibration of a region of interest within a structure using a non-contact laser sensor. In previous research regarding the HHT, two technical processes were needed to obtain the mode shape for each mode. The purpose of this study is to improve and complement our previous research, and for this purpose, a modal analysis approach is adapted without using the two technical processes to obtain an accurate un-damped impulse response of each mode for continuous scanning measurements. In addition, frequency response functions for each type of beam are derived, making it possible to make continuously scanned measurements along a straight profile. In this paper, the technical limitations and drawbacks of the damping compensation technique used in previous research are identified. In addition, the separation of resonant frequency (the Doppler effect) that occurs in continuous scanning measurements and the separation of damping phenomenon are also observed. The proposed method is quantitatively verified by comparing it with the results obtained from a conventional approach to estimate the mode shape with an impulse response.

  11. Enhanced method to reconstruct mode shapes of continuous scanning measurements using the Hilbert Huang transform and the modal analysis method

    Science.gov (United States)

    Lee, Jongsuh; Hussain, Syed Hassaan; Wang, Semyung; Park, Kyihwan

    2014-09-01

    Generally, it is time consuming to experimentally identify the operating deflection shape or mode shape of a structure. To overcome this problem, the Hilbert Huang transform (HHT) technique has been recently proposed. This technique is used to extract the mode shape from measurements that continuously measure the vibration of a region of interest within a structure using a non-contact laser sensor. In previous research regarding the HHT, two technical processes were needed to obtain the mode shape for each mode. The purpose of this study is to improve and complement our previous research, and for this purpose, a modal analysis approach is adapted without using the two technical processes to obtain an accurate un-damped impulse response of each mode for continuous scanning measurements. In addition, frequency response functions for each type of beam are derived, making it possible to make continuously scanned measurements along a straight profile. In this paper, the technical limitations and drawbacks of the damping compensation technique used in previous research are identified. In addition, the separation of resonant frequency (the Doppler effect) that occurs in continuous scanning measurements and the separation of damping phenomenon are also observed. The proposed method is quantitatively verified by comparing it with the results obtained from a conventional approach to estimate the mode shape with an impulse response.

  12. Semi-automated method to measure pneumonia severity in mice through computed tomography (CT) scan analysis

    Science.gov (United States)

    Johri, Ansh; Schimel, Daniel; Noguchi, Audrey; Hsu, Lewis L.

    2010-03-01

    Imaging is a crucial clinical tool for diagnosis and assessment of pneumonia, but quantitative methods are lacking. Micro-computed tomography (micro CT), designed for lab animals, provides opportunities for non-invasive radiographic endpoints for pneumonia studies. HYPOTHESIS: In vivo micro CT scans of mice with early bacterial pneumonia can be scored quantitatively by semiautomated imaging methods, with good reproducibility and correlation with bacterial dose inoculated, pneumonia survival outcome, and radiologists' scores. METHODS: Healthy mice had intratracheal inoculation of E. coli bacteria (n=24) or saline control (n=11). In vivo micro CT scans were performed 24 hours later with microCAT II (Siemens). Two independent radiologists scored the extent of airspace abnormality, on a scale of 0 (normal) to 24 (completely abnormal). Using the Amira 5.2 software (Mercury Computer Systems), a histogram distribution of voxel counts between the Hounsfield range of -510 to 0 was created and analyzed, and a segmentation procedure was devised. RESULTS: A t-test was performed to determine whether there was a significant difference in the mean voxel value of each mouse in the three experimental groups: Saline Survivors, Pneumonia Survivors, and Pneumonia Non-survivors. It was found that the voxel count method was able to statistically tell apart the Saline Survivors from the Pneumonia Survivors, the Saline Survivors from the Pneumonia Non-survivors, but not the Pneumonia Survivors vs. Pneumonia Non-survivors. The segmentation method, however, was successfully able to distinguish the two Pneumonia groups. CONCLUSION: We have pilot-tested an evaluation of early pneumonia in mice using micro CT and a semi-automated method for lung segmentation and scoring system. Statistical analysis indicates that the system is reliable and merits further evaluation.

  13. 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.

  14. 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

    2014-12-01

    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.

  15. Automatic Calibration Method of Voxel Size for Cone-beam 3D-CT Scanning System

    CERN Document Server

    Yang, Min; Liu, Yipeng; Men, Fanyong; Li, Xingdong; Liu, Wenli; Wei, Dongbo

    2013-01-01

    For 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 table along X-ray direction. In order to realize the automatic calibration of the voxel size, a new 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, which reflects the relationship between the rotary table displacement distance from its nominal zero position and the voxel size. Finally, the linear equation is imported into the calibration module of the 3D-CT scanning system, and when the rotary table is moving along X-ray direction, the accurate value of the voxel size is dynamically expo...

  16. The identification of black carbon particles with the analytical scanning electron microscope. Methods and initial results

    Energy Technology Data Exchange (ETDEWEB)

    Stoffyn-Egli, P. [MicroChem, Geochemistry Consultants, East Jeddore, Nova Scotia (Canada); Potter, T.M.; Leonard, J.D.; Pocklington, R. [Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia (Canada)

    1997-04-09

    Combustion of fossil fuel and vegetation produces large quantities of black carbon particles (BCP) which are dispersed by winds over large areas. Once deposited in the sediment, BCP constitute an historic record of anthropogenic activities and wildfires. For BCP to be significant environmental indicators, it is necessary to determine their source as precisely as possible. A method has been developed to differentiate BCP from other carbonaceous particles, and to assign them to coal, oil, or biomass combustion using a scanning electron microscope equipped with an elemental detector (Analytical Scanning Electron Microscope, ASEM). BCP were identified in the ASEM as particles with an O/C atomic ratio of less than 0.15. Morphology (shape and surface texture) and trace element content (S and Cl) were used to classify BCP according to source using samples of known origin (oil, coal and wood fly-ash) and marine sediment samples from Halifax Inlet, which has undergone progressive urbanisation and industrialization over the last 250 years. The method is applicable to a wide size range of BCP and complete isolation of the BCP from the rest of the sample is not necessary

  17. Improved Correction Method for Water-Refracted Terrestrial Laser Scanning Data Acquired in the Mountain Channel

    Science.gov (United States)

    Miura, N.; Asano, Y.; Moribe, Y.

    2016-06-01

    Detailed information of underwater topography is required for better understanding and prediction of water and sediment transport in a mountain channel. Recent research showed promising utility of green-wavelength Terrestrial Laser Scanning (TLS) for measuring submerged stream-bed structure in fluvial environment. However, difficulty in acquiring reliable underwater data has been remained in the part of mountain channel where water surface has some gradient. Since horizontal water surface was a major premise for the existing water refraction correction method, significant error was resulted in such area. Therefore, this paper presents a modified method to correct water-refracted TLS data acquired over mountain channel with complex water-surface slope. Applicability of the modified method was validated using the field data and compared with the existing correction method and non-corrected data. The results showed that the modified method has much smaller error with RMSE value of 3 mm than the existing method (RMSE = 10 mm) and non-corrected data (RMSE = 23 mm). Presented method successfully corrected water-refracted TLS data acquired over sloped channel. This would enable us to quantitatively measure whole units of complex mountain channels, and help us to understand water dynamics better in the area.

  18. Novel scanning electron microscopy methods for analyzing the 3D structure of the Golgi apparatus.

    Science.gov (United States)

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

  19. Scanning genomic areas under selection sweep and association mapping as tools to identify horticultural important genes in watermelon

    Science.gov (United States)

    Watermelon (Citrullus lanatus var. lanatus) contains 88% water, sugars, and several important health-related compounds, including lycopene, citrulline, arginine, and glutathione. The current genetic diversity study uses microsatellites with known map positions to identify genomic regions that under...

  20. A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content.

    Science.gov (United States)

    Zhang, Hui; Wang, Shou-Zhi; Wang, Zhi-Peng; Da, Yang; Wang, Ning; Hu, Xiao-Xiang; Zhang, Yuan-Dan; Wang, Yu-Xiang; Leng, Li; Tang, Zhi-Quan; Li, Hui

    2012-12-15

    Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF. A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (Pchickens. We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.

  1. Application of portable gas detector in point and scanning method to estimate spatial distribution of methane emission in landfill.

    Science.gov (United States)

    Lando, Asiyanthi Tabran; Nakayama, Hirofumi; Shimaoka, Takayuki

    2017-01-01

    Methane from landfills contributes to global warming and can pose an explosion hazard. To minimize these effects emissions must be monitored. This study proposed application of portable gas detector (PGD) in point and scanning measurements to estimate spatial distribution of methane emissions in landfills. The aims of this study were to discover the advantages and disadvantages of point and scanning methods in measuring methane concentrations, discover spatial distribution of methane emissions, cognize the correlation between ambient methane concentration and methane flux, and estimate methane flux and emissions in landfills. This study was carried out in Tamangapa landfill, Makassar city-Indonesia. Measurement areas were divided into basic and expanded area. In the point method, PGD was held one meter above the landfill surface, whereas scanning method used a PGD with a data logger mounted on a wire drawn between two poles. Point method was efficient in time, only needed one person and eight minutes in measuring 400m(2) areas, whereas scanning method could capture a lot of hot spots location and needed 20min. The results from basic area showed that ambient methane concentration and flux had a significant (pmethane emissions in the expanded area by using Kriging method. The average of estimated flux from scanning method was 71.2gm(-2)d(-1) higher than 38.3gm(-2)d(-1) from point method. Further, scanning method could capture the lower and higher value, which could be useful to evaluate and estimate the possible effects of the uncontrolled emissions in landfill.

  2. Spatial temporal clustering for hotspot using kulldorff scan statistic method (KSS): A case in Riau Province

    Science.gov (United States)

    Hudjimartsu, S. A.; Djatna, T.; Ambarwari, A.; Apriliantono

    2017-01-01

    The forest fires in Indonesia occurs frequently in the dry season. Almost all the causes of forest fires are caused by the human activity itself. The impact of forest fires is the loss of biodiversity, pollution hazard and harm the economy of surrounding communities. To prevent fires required the method, one of them with spatial temporal clustering. Spatial temporal clustering formed grouping data so that the results of these groupings can be used as initial information on fire prevention. To analyze the fires, used hotspot data as early indicator of fire spot. Hotspot data consists of spatial and temporal dimensions can be processed using the Spatial Temporal Clustering with Kulldorff Scan Statistic (KSS). The result of this research is to the effectiveness of KSS method to cluster spatial hotspot in a case within Riau Province and produces two types of clusters, most cluster and secondary cluster. This cluster can be used as an early fire warning information.

  3. 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.......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...

  4. Development and Evaluation of Roadside/Obstacle Detection Method Using 3D Scanned Data Processing

    Science.gov (United States)

    Yamamoto, Hiroshi; Ishii, Yoshinori; Yamazaki, Katsuyuki

    In this paper, we have reported the development of a snowblower support system which can safely navigate snowblowers, even during a whiteout, with the combination of a very accurate GPS system, so called RTK-GPS, and a unique and highly accurate map of roadsides and obstacles on roads. Particularly emphasized new techniques in this paper are ways to detect accurate geographical positions of roadsides and obstacles by utilizing and analyzing 3D laser scanned data, whose data has become available in recent days. The experiment has shown that the map created by the methods and RTK-GPS can sufficiently navigate snowblowers, whereby a secure and pleasant social environment can be archived in snow areas of Japan. In addition, proposed methods are expected to be useful for other systems such as a quick development of a highly accurate road map, a safely navigation of a wheeled chair, and so on.

  5. 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

    , genomic codon and amino acid frequencies based comparisons) and proteomes (all-against-all BLAST protein comparisons and pan-genomic analyses). RESULTS: We found that the oligonucleotide based methods gave different results compared to that of the proteome based methods. Differences were also found...... than proteome comparisons between species in genus Brucella and genus Ochrobactrum. Pan-genomic analyses indicated that uptake of DNA from outside genus Brucella appears to be limited. CONCLUSIONS: While both the proteome based methods and the Markov chain based genomic signatures were able to reflect...

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

    Directory of Open Access Journals (Sweden)

    Veerkamp Roel F

    2011-07-01

    Full Text Available Abstract 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 selected for in another environment. The objective of this paper was to develop three models that would permit multi-trait genomic selection by combining scarcely recorded traits with genetically correlated indicator traits, and to compare their performance to single-trait models, using simulated datasets. Methods Three (SNP Single Nucleotide Polymorphism based models were used. Model G and BCπ0 assumed that contributed (covariances of all SNP are equal. Model BSSVS sampled SNP effects from a distribution with large (or small effects to model SNP that are (or not associated with a quantitative trait locus. For reasons of comparison, model A including pedigree but not SNP information was fitted as well. Results In terms of accuracies for animals without phenotypes, the models generally ranked as follows: BSSVS > BCπ0 > G > > A. Using multi-trait SNP-based models, the accuracy for juvenile animals without any phenotypes increased up to 0.10. For animals with phenotypes on an indicator trait only, accuracy increased up to 0.03 and 0.14, for genetic correlations with the evaluated trait of 0.25 and 0.75, respectively. Conclusions When the indicator trait had a genetic correlation lower than 0.5 with the trait of interest in our simulated data, the accuracy was higher if genotypes rather than phenotypes were obtained for the indicator trait. However, when genetic correlations were higher than 0.5, using an indicator trait led to higher accuracies for selection candidates. For different combinations of traits, the level of genetic correlation below which genotyping selection candidates is more effective than obtaining phenotypes for an indicator

  7. INVESTIGATION OF NANO- AND MICROSTRUCTURE OF BIOMATERIALS FOR REGENERATIVE MEDICINE BY METHOD OF SCANNING PROBE NANOTOMOGRAPHY

    Directory of Open Access Journals (Sweden)

    A. E. Efimov

    2014-01-01

    Full Text Available Aim. To perform a study of three-dimensional micro- and nanostructure of porous biocompatible scaffolds and quantitative analysis of nanoscale porosity parameters.Materials and methods. Three-dimensional porous scaffolds made from spidroin rS1/9 (recombinant analog of spider dragline protein were produced by salt leaching technique. Dimensions of macropores in produced three-imensional scaffolds were in range from 200 to 400 microns. The study of three-dimensional structure of scaffolds was carried out by scanning probe nanotomography technique with the use of experimental setup combining ultramicrotome and scanning probe microscope. Results. Three-dimensional nanotomographical reconstruction of scaffold macropore wall structure is obtained. The formation of three-dimensional network of interconnected pores and channels with characteristic dimensions in range from 20 to 700 nm in the volume of macropore walls of studied scaffolds is observed. Mean pore diameter is 150 nm. Volume porosity of macropore walls is 22% while volume fraction of pores interconnected in large pore clusters is about 20% of all pore volume.Conclusion. Obtained as a result of the study quantitative characteristics of porous micro- and nanostructure of scaffolds show signifi cant degree of nanoscale porosity and percolation of macropore walls what correlates with reported high effi ciency of tissue regeneration on such scaffolds implanted in vivo. Use of scanning probe nanotomography technique for analysis of characteristics and topology of micro- and nanopore systems enables to improve effi ciency of development of novel biocompatible and biodegradable materials with predicted morphological, physical, chemical and biological characteristics.

  8. 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.

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

    Science.gov (United States)

    Lenda, Grzegorz; Uznański, Andrzej; Strach, Michał; Lewińska, Paulina

    2016-06-01

    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.

  10. Tissue sampling methods and standards for vertebrate genomics

    Directory of Open Access Journals (Sweden)

    Wong Pamela BY

    2012-07-01

    Full Text Available Abstract The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual; three-star (RNA as above and frozen tissue for 1 mg of DNA; two-star (frozen tissue for at least 700 μg of DNA; and one-star (ethanol-preserved tissue for 700 μg of DNA or less of mixed quality. At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species’ natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.

  11. A method to find groups of orthogous genes across multiple genomes

    Directory of Open Access Journals (Sweden)

    ALMEIDA, N.F.

    2013-12-01

    Full Text Available In this work we propose a simple method to obtain groups of homologous genes across multiple (k organisms, called kGC. Our method takes as input all-against-all Blastp comparisons and produces groups of homologous sequences. First, homologies among groups of paralogs of all the k compared genomes are found, followed by homologies of groups among k - 1 genomes and so on, until groups belonging exclusively to only one genome, that is, groups of one genome not presenting strong similarities with any group of any other genome, are identified. We have used our method to determine homologous groups across six Actinobacterial complete genomes. To validate kGC, we first investigate the Pfam classification of the homologous groups, and after compare our results with those produced by OrthoMCL. Although kGC is much simpler than OrthoMCL it presented similar results with respect to Pfam classification.

  12. Third-order nonlinear optical properties of acid green 25 dye by Z-scan method

    Science.gov (United States)

    Jeyaram, S.; Geethakrishnan, T.

    2017-03-01

    Third-order nonlinear optical (NLO) properties of aqueous solutions of an anthraquinone dye (Acid green 25 dye, color index: 61570) have been studied by Z-scan method with a 5 mW continuous wave (CW) diode laser operating at 635 nm. The nonlinear refractive index (n2) and the absorption coefficient (β) have been evaluated respectively from the closed and open aperture Z-scan data and the values of these parameters are found to increase with increase in concentration of the dye solution. The negative sign of the observed nonlinear refractive index (n2) indicates that the aqueous solution of acid green 25 dye exhibits self-defocusing type optical nonlinearity. The mechanism of the observed nonlinear absorption (NLA) and nonlinear refraction (NLR) is attributed respectively to reverse saturable absorption (RSA) and thermal nonlinear effects. The magnitudes of n2 and β are found to be of the order of 10-7 cm2/W and 10-3 cm/W respectively. With these experimental results, the authors suggest that acid green 25 dye may have potential applications in nonlinear optics.

  13. Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

    Science.gov (United States)

    Durowoju, Ibrahim B.; Bhandal, Kamaljit S.; Hu, Jian; Carpick, Bruce; Kirkitadze, Marina

    2017-01-01

    Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural “fingerprint” that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; ∆H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process. PMID:28287565

  14. Differential Scanning Calorimetry - A Method for Assessing the Thermal Stability and Conformation of Protein Antigen.

    Science.gov (United States)

    Durowoju, Ibrahim B; Bhandal, Kamaljit S; Hu, Jian; Carpick, Bruce; Kirkitadze, Marina

    2017-03-04

    Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural "fingerprint" that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; ∆H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process.

  15. Effects of different application durations of scanning laser method on debonding strength of laminate veneers.

    Science.gov (United States)

    Oztoprak, Mehmet Oguz; Tozlu, Murat; Iseri, Ufuk; Ulkur, Feyza; Arun, Tulin

    2012-07-01

    Porcelain laminate veneers as esthetic and minimally invasive restorations are being used as an alternative to full veneer crowns. However, the removal of porcelain veneers that have failed may be an uncomfortable and time-consuming procedure because of the high bond strength between the porcelain laminate veneers and the tooth surface. The purpose of this study was to prepare a simple and reliable method for porcelain laminate veneer debonding by using an Er:YAG laser with the scanning method and to determine the amount of lasing time required. Eighty cylindrical specimens with a thickness of 0.7 mm and a diameter of 5 mm were fabricated from Empress II ceramic material. They were cemented on the labial surface of extracted bovine mandibular incisors using Variolink II (Ivoclar Vivadent AG, Schaan, Liechtenstein) and light cured for 40 s. The specimens were randomly divided into four groups of 20. The first group was assigned as the control group and no laser application was performed. The Er:YAG laser was applied on each specimen in the other three study groups for 3, 6, and 9 s by using the scanning method. One second after the lasing, a mechanical force was applied to remove the laminate veneers by using an Instron Universal Testing machine. Results of this study exhibited statistically significant differences between the control group and the three study groups. Intergroup comparison of shear bond strengths of the three study groups showed a statistically significant difference (p = 0.0001). This study showed that all three application times of Er-YAG laser were effective for debonding ceramic laminate veneers by softening the adhesive resin.

  16. Evaluation of anisotropic chitosan hydrogels using analytical Mueller matrix method and scanned laser pico-projector.

    Science.gov (United States)

    Huang, Chih-Ling; Chuang, Chin-Ho; Lo, Yu-Lung

    2013-07-25

    Chitosan has excellent biodegradable, biocompatible and bio-absorbable properties and has been found increasing use in the biomedical field in recent decades. The linear birefringence (LB), linear diattenuation (LD), circular birefringence (CB), circular diattenuation (CD), and depolarization properties of chitosan hydrogel films crosslinked in citrate acid buffer solution (CBS) are extracted using an analytical Mueller matrix method. It is shown that the optical phase retardance property of the hydrogel films provides a reliable indication of both the chitosan concentration of the film and the pH value of the CBS crosslinking environment. In addition, chitosan hydrogel suspension with low-concentration crosslinked in CBS environments with various pH values are studied by the speckle contrast of the projected images obtained when illuminating the suspension with a scanned laser pico-projector (SLPP). It is found that for the samples crosslinked in an acidic environment, the speckle contrast decreases with an increasing pH value. By contrast, for the samples crosslinked in an alkaline CBS environment, the speckle contrast increases as the pH value increases. It is concluded that both the phase retardance and the speckle contrast enable the pH value of the CBS crosslinking solution to be reliably determined. However, of the two methods, the SLPP method yields improved measurement sensitivity. Overall, the results presented in this study show that the analytical Mueller matrix method and SLPP method provide an effective means of characterizing the optical properties, concentration and crosslinking environment of chitosan hydrogel films and suspensions.

  17. 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.

  18. A dual growing method for the automatic extraction of individual trees from mobile laser scanning data

    Science.gov (United States)

    Li, Lin; Li, Dalin; Zhu, Haihong; Li, You

    2016-10-01

    Street trees interlaced with other objects in cluttered point clouds of urban scenes inhibit the automatic extraction of individual trees. This paper proposes a method for the automatic extraction of individual trees from mobile laser scanning data, according to the general constitution of trees. Two components of each individual tree - a trunk and a crown can be extracted by the dual growing method. This method consists of coarse classification, through which most of artifacts are removed; the automatic selection of appropriate seeds for individual trees, by which the common manual initial setting is avoided; a dual growing process that separates one tree from others by circumscribing a trunk in an adaptive growing radius and segmenting a crown in constrained growing regions; and a refining process that draws a singular trunk from the interlaced other objects. The method is verified by two datasets with over 98% completeness and over 96% correctness. The low mean absolute percentage errors in capturing the morphological parameters of individual trees indicate that this method can output individual trees with high precision.

  19. A genome-wide linkage scan for distinct subsets of schizophrenia characterized by age at onset and neurocognitive deficits.

    Directory of Open Access Journals (Sweden)

    Yin-Ju Lien

    Full Text Available BACKGROUND: As schizophrenia is genetically and phenotypically heterogeneous, targeting genetically informative phenotypes may help identify greater linkage signals. The aim of the study is to evaluate the genetic linkage evidence for schizophrenia in subsets of families with earlier age at onset or greater neurocognitive deficits. METHODS: Patients with schizophrenia (n  =  1,207 and their first-degree relatives (n  =  1,035 from 557 families with schizophrenia were recruited from six data collection field research centers throughout Taiwan. Subjects completed a face-to-face semi-structured interview, the Continuous Performance Test (CPT, the Wisconsin Card Sorting Test, and were genotyped with 386 microsatellite markers across the genome. RESULTS: A maximum nonparametric logarithm of odds (LOD score of 4.17 at 2q22.1 was found in 295 families ranked by increasing age at onset, which had significant increases in the maximum LOD score compared with those obtained in initial linkage analyses using all available families. Based on this subset, a further subsetting by false alarm rate on the undegraded and degraded CPT obtained further increase in the nested subset-based LOD on 2q22.1, with a score of 7.36 in 228 families and 7.71 in 243 families, respectively. CONCLUSION: We found possible evidence of linkage on chromosome 2q22.1 in families of schizophrenia patients with more CPT false alarm rates nested within the families with younger age at onset. These results highlight the importance of incorporating genetically informative phenotypes in unraveling the complex genetics of schizophrenia.

  20. Research on the influence and correction method of depth scanning error to the underwater acoustic image measurement

    Institute of Scientific and Technical Information of China (English)

    MEI Jidan; ZHAI Chunpin; WANGYilin; HUI Junying

    2011-01-01

    The technology of underwater acoustic image measurement was a passive locating method with high precision in near field. To improve the precision of underwater acoustic image measurement, the influence of the depth scan error was analyzed and the correcti

  1. 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.

  2. 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.

  3. A total station spatial positioning method based on rotary laser scanning and ultrasonic ranging

    Science.gov (United States)

    Wu, Jun; Zhu, Jigui; Yu, Zhijing; Zhuge, Jingchang; Xue, Bin

    2016-11-01

    Total station spatial coordinator measuring technology is extensively applied in the large-scale measurement of industrial assembly and manufacturing for its flexibility and adaptability. The existing total station technology has some principal limits such as poor efficiency and single tasking; in order to achieve the total station spatial coordinator measuring technology with the advantages of multi-task, real-time measurement, and high accuracy, this paper presents a novel total station measurement method by using multi-laser plane constraints established through rotating planar planes and distance information obtained with an ultrasonic ranging method. With the spatial divergence angles of the optoelectronic scanning and ultrasonic arrays, this method can measure the spatial coordinates in multi-task and real-time with a single station and a portable target bar. Experimental results show that the proposed method is feasible and valid with satisfactory accuracy. The maximum distance measurement error is less than 0.2 mm in a volume that is 5 m far away from the station.

  4. Railway Tunnel Clearance Inspection Method Based on 3D Point Cloud from Mobile Laser Scanning.

    Science.gov (United States)

    Zhou, Yuhui; Wang, Shaohua; Mei, Xi; Yin, Wangling; Lin, Chunfeng; Hu, Qingwu; Mao, Qingzhou

    2017-09-07

    Railway tunnel clearance is directly related to the safe operation of trains and upgrading of freight capacity. As more and more railway are put into operation and the operation is continuously becoming faster, the railway tunnel clearance inspection should be more precise and efficient. In view of the problems existing in traditional tunnel clearance inspection methods, such as low density, slow speed and a lot of manual operations, this paper proposes a tunnel clearance inspection approach based on 3D point clouds obtained by a mobile laser scanning system (MLS). First, a dynamic coordinate system for railway tunnel clearance inspection has been proposed. A rail line extraction algorithm based on 3D linear fitting is implemented from the segmented point cloud to establish a dynamic clearance coordinate system. Second, a method to seamlessly connect all rail segments based on the railway clearance restrictions, and a seamless rail alignment is formed sequentially from the middle tunnel section to both ends. Finally, based on the rail alignment and the track clearance coordinate system, different types of clearance frames are introduced for intrusion operation with the tunnel section to realize the tunnel clearance inspection. By taking the Shuanghekou Tunnel of the Chengdu-Kunming Railway as an example, when the clearance inspection is carried out by the method mentioned herein, its precision can reach 0.03 m, and difference types of clearances can be effectively calculated. This method has a wide application prospects.

  5. Evaluation of different methods to clean titanium abutments. A scanning electron microscopic study.

    Science.gov (United States)

    Speelman, J A; Collaert, B; Klinge, B

    1992-09-01

    The cleaning effectiveness of different treatment methods for titanium abutments was evaluated using scanning electron microscopy (SEM). In the mandible of 4 beagle dogs, 25 titanium abutments were installed (modum Brånemark). After 16 weeks of plaque accumulation, mineralized deposits had formed on 23 abutments. Each of these abutments was subjected to one of the following treatment methods: scaling with (1) metal, (2) plastic, or (3) ultrasonic instruments; (4) air-polishing, (5) weekly rubber cup polishing or (6) daily brushing with a conventional toothbrush. Fourteen abutments were removed immediately after treatment. On 9 abutments, the scaling procedures and air-polishing were repeated after another 16 weeks of plaque accumulation. The abutments were prepared for SEM, and each of them was viewed and photographed at 3 different magnifications. The photomicrographs were evaluated by 3 examiners who, guided by reference pictures, gave each abutment a "cleanliness" score, ranking from 0 to 5. Regular rubber cup polishing and regular brushing resulted in the highest surface cleanliness, while the air-polishing procedure showed the lowest cleanliness score. None of the 3 scaling methods created a cleanliness score better than 3. The 3 scaling methods were considered equal in their cleaning effectiveness. No differences could be observed between surfaces treated 1 x or 2 x. Taken the present findings and those of other studies concerning the effects of scaling on the surface roughness and biocompatibility into consideration, it was concluded that plastic scalers may be the instruments of choice for debridement of titanium implant surfaces.

  6. Polymorphism in nimodipine raw materials: development and validation of a quantitative method through differential scanning calorimetry.

    Science.gov (United States)

    Riekes, Manoela Klüppel; Pereira, Rafael Nicolay; Rauber, Gabriela Schneider; Cuffini, Silvia Lucia; de Campos, Carlos Eduardo Maduro; Silva, Marcos Antonio Segatto; Stulzer, Hellen Karine

    2012-11-01

    Due to the physical-chemical and therapeutic impacts of polymorphism, its monitoring in raw materials is necessary. The purpose of this study was to develop and validate a quantitative method to determine the polymorphic content of nimodipine (NMP) raw materials based on differential scanning calorimetry (DSC). The polymorphs required for the development of the method were characterized through DSC, X-ray powder diffraction (XRPD) and Raman spectroscopy and their polymorphic identity was confirmed. The developed method was found to be linear, robust, precise, accurate and specific. Three different samples obtained from distinct suppliers (NMP 1, NMP 2 and NMP 3) were firstly characterized through XRPD and DSC as polymorphic mixtures. The determination of their polymorphic identity revealed that all samples presented the Modification I (Mod I) or metastable form in greatest proportion. Since the commercial polymorph is Mod I, the polymorphic characteristic of the samples analyzed needs to be investigated. Thus, the proposed method provides a useful tool for the monitoring of the polymorphic content of NMP raw materials. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. 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.

    Science.gov (United States)

    Oh, Taekjun; Lee, Donghwa; Kim, Hyungjin; Myung, Hyun

    2015-07-03

    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.

  8. 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

    Science.gov (United States)

    Oh, Taekjun; Lee, Donghwa; Kim, Hyungjin; Myung, Hyun

    2015-01-01

    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. PMID:26151203

  9. 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.

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

    Science.gov (United States)

    Ryu, Young Shin; Biswas, Rajesh Kumar; Shin, Kwangsu; Parisutham, Vinuselvi; Kim, Suk Min; Lee, Sung Kuk

    2014-01-01

    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.

  11. 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.

  12. Understanding Spatial Genome Organization:Methods and Insights

    Institute of Scientific and Technical Information of China (English)

    Vijay Ramani; Jay Shendure; Zhijun Duan

    2016-01-01

    The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher-order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains (TADs) appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.

  13. A fast and robust method for whole genome sequencing of the Aleutian Mink Disease Virus (AMDV) genome

    DEFF Research Database (Denmark)

    Hagberg, Emma Elisabeth; Krarup, Anders; Fahnøe, Ulrik;

    2016-01-01

    have focused on limited regions of the viral genome. This paper describes a robust, reliable, and fast protocol for amplification of the full AMDV genome using long-range PCR. The method was used to generate next generation sequencing data for the non-virulent cell-culture adapted AMDV-G strain as well......Aleutian Mink Disease Virus (AMDV) is a frequently encountered pathogen associated with commercial mink breeding. AMDV infection leads to increased mortality and compromised animal health and welfare. Currently little is known about the molecular evolution of the virus, and the few existing studies...

  14. 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...

  15. Topographical surveys: Classical method versus 3D laser scanning. Case study - An application in civil engineering

    Science.gov (United States)

    Grigoraş, I.-R.; Covăsnianu, A.; Pleşu, G.; Benedict, B.

    2009-04-01

    The paper describes an experiment which took place in Iasi town, Romania, consisted in two different topographical survey techniques applied for one and the same objective placed in a block within the city (western part) - a thermal power station. The purpose was to compare those methods and to determine which one is proper to be used in this domain in terms of fastness, optimization and speed of data processing. First technique applied for our survey was the classical one, with a total station. Using the CAD technique, we obtained a final product (a dwg file) and a list of coordinates (a text file). The second method, which we focused our attention more, was the measurement with a very precise 3D laser scanstation, also very suitable in archeology. The data obtained were processed with special software. Result was a 3D model of the thermal power plant composed of measurable cloud point data. Finally, analyzing the advantages and disadvantages of each method, we came to the conclusion that the 3D laser scanning which we used matches well the application, in this case civil engineering, but the future of accepting and implementing this technique is in the hands of Romanian authorities.

  16. 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.

  17. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition

    Directory of Open Access Journals (Sweden)

    Moradi Mohammad Hossein

    2012-02-01

    Full Text Available Abstract Background Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds. Results Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. Conclusions In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication.

  18. A novel sedimentological method based on CT-scanning: Use for tomographic characterization of the Galicia Interior Basin

    Science.gov (United States)

    Mena, Anxo; Francés, Guillermo; Pérez-Arlucea, Marta; Aguiar, Pablo; Barreiro-Vázquez, José Daniel; Iglesias, Alfredo; Barreiro-Lois, Andrés

    2015-05-01

    Non-destructive techniques of core analysis, especially of marine cores, are being broadly employed for sedimentary, paleoceanographic and paleoclimate research. In particular, Computed Tomography scanning (CT-scanning) allows acquisition of 3D and 2D images, according to desired planes, and thus the identification of sedimentary structures, large grains and their distributions as well as direct measurements of material densities. The most significant contribution of this technique is the possibility of getting results before opening the core. In this work CT-scan data obtained for five cores from the Galicia Interior Basin (GIB, NW Peninsula Iberia) are presented and discussed, focussing on (1) methodology of the CT-scan use, (2) tomographic description of sedimentary facies identified in the GIB, (3) treatment of the numeric data obtained with CT-scanning using specific software (anidoC), and (4) comparison of tomographic data with data obtained by conventional methodologies of core analysis. The most singular feature of GIB cores is the presence of Ice Rafted Debris (IRD) deposited during late Pleistocene Heinrich Events (HE), which can be easily recognized using the CT-scan by the presence of high radio-density grains immersed in a low radio-density matrix. Comparison of CT-scan data with analytical sedimentary data and HE proxies performed on the cores validates the CT-scanning method as a powerful tool to improve correlations, identify well-constrained events, and make more accurate basin reconstructions without opening all the cores in an oceanographic study.

  19. Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef.

    Science.gov (United States)

    Taye, Mengistie; Kim, Jaemin; Yoon, Sook Hee; Lee, Wonseok; Hanotte, Olivier; Dessie, Tadelle; Kemp, Stephen; Mwai, Okeyo Ally; Caetano-Anolles, Kelsey; Cho, Seoae; Oh, Sung Jong; Lee, Hak-Kyo; Kim, Heebal

    2017-02-09

    Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods. We identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness. Results revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes

  20. Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein x Jersey crossbred population.

    Science.gov (United States)

    Maltecca, C; Weigel, K A; Khatib, H; Cowan, M; Bagnato, A

    2009-02-01

    We herein report results from a daughter design genome-scan study aiming to identify quantitative trait loci (QTL) associated with birth weight, direct gestation length and passive immune transfer in a backcross (Holstein x Jersey) x Holstein population. Two-hundred and seventy-six calves, offspring of seven crossbred sires, were genotyped for 161 microsatellite markers distributed along the 29 bovine autosomes. The genome scan was performed through interval mapping using an animal model in order to identify QTL accounting for phenotypic differences between individual animals. Based on significant chi-squared values, we identified putative QTL on BTA7 and BTA14 for gestation length, on BTA2, BTA6 and BTA14 for birth weight and on BTA20 for passive immune transfer. In total, these QTL accounted for 12%, 18% and 1% of the phenotypic variance in gestation length, birth weight and passive immune transfer respectively. We also report results from a supplementary and independent influential grand-daughter Holstein family. In this family, findings on BTA7 and BTA14 for direct gestation length were in agreement with results in the crossbred population. Two other regions on BTA6 and BTA21 putatively underlying QTL for direct gestation length variability were discovered with this analysis.

  1. A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions

    Directory of Open Access Journals (Sweden)

    Zhao Zhongming

    2006-12-01

    Full Text Available Abstract Background The local environment of single nucleotide polymorphisms (SNPs contains abundant genetic information for the study of mechanisms of mutation, genome evolution, and causes of diseases. Recent studies revealed that neighboring-nucleotide biases on SNPs were strong and the genome-wide bias patterns could be represented by a small subset of the total SNPs. It remains unsolved for the estimation of the effective SNP size, the number of SNPs that are sufficient to represent the bias patterns observed from the whole SNP data. Results To estimate the effective SNP size, we developed a novel statistical method, SNPKS, which considers both the statistical and biological significances. SNPKS consists of two major steps: to obtain an initial effective size by the Kolmogorov-Smirnov test (KS test and to find an intermediate effective size by interval evaluation. The SNPKS algorithm was implemented in computer programs and applied to the real SNP data. The effective SNP size was estimated to be 38,200, 39,300, 38,000, and 38,700 in the human, chimpanzee, dog, and mouse genomes, respectively, and 39,100, 39,600, 39,200, and 42,200 in human intergenic, genic, intronic, and CpG island regions, respectively. Conclusion SNPKS is the first statistical method to estimate the effective SNP size. It runs efficiently and greatly outperforms the algorithm implemented in SNPNB. The application of SNPKS to the real SNP data revealed the similar small effective SNP size (38,000 – 42,200 in the human, chimpanzee, dog, and mouse genomes as well as in human genomic regions. The findings suggest strong influence of genetic factors across vertebrate genomes.

  2. Use of scanning LIMM (Laser Intensity Modulation Method) to characterise polarisation variability in dielectric materials

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, Mark; Cain, Markys, E-mail: mark.stewart@npl.co.u [National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW (United Kingdom)

    2009-08-01

    The Laser Intensity Modulation Method (LIMM) has traditionally been used to characterise the depth dependence of polarisation of piezoelectric materials{sup 1}. Although the technique is simple, it is difficult to extract the polarisation / depth data from the measured pyroelectric current because of the complex mathematics pertaining to the physics of the technique. However, the laser probe may still be used as a comparative or qualitative tool in mapping out the polarisation across the surface of a material. A novel scanning LIMM system has been developed to map the variation in piezoelectric activity across a range of samples. The system has been upgraded with a galvanometer mirror scanner to increase speed and reduce sensitivity to acoustic noise. The improvements are discussed and tested on a range of case studies. The technique can be used to show differences in piezoelectric activity caused by features such as inhomogeneous material composition, porosity and mechanical damage. The method has application as a quality control tool for materials and device manufacturers.

  3. [Research on absolute calibration of sun channel of sun photometer using laser raster scanning method].

    Science.gov (United States)

    Xu, Wen-Bin; Li, Jian-Jun; Zheng, Xiao-Bing

    2013-01-01

    In the present paper, a new calibration method of absolute spectral irradiance responsivity of sun channel of sun photometer was developed. A tunable laser was used as source and a standard tranfer detector, calibrated against cryogenic absolute radiometer, was used to measure laser beam power. By raster scanning of a single collimated laser beam to generate the uniform irradiance field at the plane of effective aperture stop of sun photometer, the absolute irradiance responsivity of center wavelength of the 870 nm unpolarized sun channels of sun photometer was obtained accurately. The relative spectral irradiance responsivity of corresponding channel was obtained by using lamp-monochromator system and then used to acquire the absolute spectral irradiance responsivity in the laboratory. On the basis of the above results, the top-of-the-atmosphere responsive constant V0 was obtained by integration with extraterrestrial solar spectral irradiance data. Comparing the calibration result with that from GSFC, NASA in 2009, the difference is only 3.75%. In the last, the uncertainties of calibration were evaluated and reached to 2.06%. The principle feasibility of the new method was validated.

  4. Parallel Processing Method for Airborne Laser Scanning Data Using a PC Cluster and a Virtual Grid

    Directory of Open Access Journals (Sweden)

    Kiyun Yu

    2009-04-01

    Full Text Available In this study, a parallel processing method using a PC cluster and a virtual grid is proposed for the fast processing of enormous amounts of airborne laser scanning (ALS data. The method creates a raster digital surface model (DSM by interpolating point data with inverse distance weighting (IDW, and produces a digital terrain model (DTM by local minimum filtering of the DSM. To make a consistent comparison of performance between sequential and parallel processing approaches, the means of dealing with boundary data and of selecting interpolation centers were controlled for each processing node in parallel approach. To test the speedup, efficiency and linearity of the proposed algorithm, actual ALS data up to 134 million points were processed with a PC cluster consisting of one master node and eight slave nodes. The results showed that parallel processing provides better performance when the computational overhead, the number of processors, and the data size become large. It was verified that the proposed algorithm is a linear time operation and that the products obtained by parallel processing are identical to those produced by sequential processing.

  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. Superhydrophobic and adhesive properties of surfaces: testing the quality by an elaborated scanning electron microscopy method.

    Science.gov (United States)

    Ensikat, Hans J; Mayser, Matthias; Barthlott, Wilhelm

    2012-10-09

    In contrast to advancements in the fabrication of new superhydrophobic materials, the characterization of their water repellency and quality is often coarse and unsatisfactory. In view of the problems and inaccuracies, particularly in the measurement of very high contact angles, we developed alternative methods for the characterization of superhydrophobic surfaces. It was found that adhering water remnants after immersion are a useful criterion in determining the repellency quality. In this study, we introduce microscopy methods to detect traces of water-resembling test liquids on superhydrophobic surfaces by scanning electron microscopy (SEM) or fluorescence light microscopy (FLM). Diverse plant surfaces and some artificial superhydrophobic samples were examined. Instead of pure water, we used aqueous solutions containing a detectable stain and glycerol in order to prevent immediate evaporation of the microdroplets. For the SEM examinations, aqueous solutions of lead acetate were used, which could be detected in a frozen state at -90 °C with high sensitivity using a backscattered electron detector. For fluorescence microscopy, aqueous solutions of auramine were used. On different species of superhydrophobic plants, varying patterns of remaining microdroplets were found on their leaves. On some species, drop remnants occurred only on surface defects such as damaged epicuticular waxes. On others, microdroplets regularly decorated the locations of increased adhesion, particularly on hierarchically structured surfaces. Furthermore, it is demonstrated that the method is suitable for testing the limits of repellency under harsh conditions, such as drop impact or long-enduring contact. The supplementation of the visualization method by the measurement of the pull-off force between a water drop and the sample allowed us to determine the adhesive properties of superhydrophobic surfaces quantitatively. The results were in good agreement with former studies of the water

  7. Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption

    OpenAIRE

    Nicola Pirastu; Maarten Kooyman; Antonietta Robino; Ashley van der Spek; Luciano Navarini; Najaf Amin; Lennart C. Karssen; Cornelia M van Duijn; Paolo Gasparini

    2016-01-01

    Coffee is one of the most consumed beverages world-wide and one of the primary sources of caffeine intake. Given its important health and economic impact, the underlying genetics of its consumption has been widely studied. Despite these efforts, much has still to be uncovered. In particular, the use of non-additive genetic models may uncover new information about the genetic variants driving coffee consumption. We have conducted a genome-wide association study in two Italian populations using...

  8. 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.

  9. Family based genome-wide copy number scan identifies complex rearrangements at 17q21.31 in dyslexics.

    Science.gov (United States)

    Veerappa, Avinash M; Saldanha, Marita; Padakannaya, Prakash; Ramachandra, Nallur B

    2014-10-01

    Developmental dyslexia (DD) is a complex heritable disorder with unexpected difficulty in learning to read and spell despite adequate intelligence, education, environment, and normal senses. We performed genome-wide screening for copy number variations (CNVs) in 10 large Indian dyslexic families using Affymetrix Genome-Wide Human SNP Array 6.0. Results revealed the complex genomic rearrangements due to one non-contiguous deletion and five contiguous micro duplications and micro deletions at 17q21.31 region in three dyslexic families. CNVs in this region harbor the genes KIAA1267, LRRC37A, ARL17A/B, NSFP1, and NSF. The CNVs in case 1 and case 2 at this locus were found to be in homozygous state and case 3 was a de novo CNV. These CNVs were found with at least one CNV having a common break and end points in the parents. This cluster of genes containing NSF is implicated in learning, cognition, and memory, though not formally associated with dyslexia. Molecular network analysis of these and other dyslexia related module genes suggests NSF and other genes to be associated with cellular/vesicular membrane fusion and synaptic transmission. Thus, we suggest that NSF in this cluster would be the nearest gene responsible for the learning disability phenotype.

  10. 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

  11. 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.

  12. 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.

  13. SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk genetic epistasis in bipolar disorder

    Institute of Scientific and Technical Information of China (English)

    Xiaohan Hu; Qiang Liu; Zhao Zhang; Zhiqiang Li; Shilin Wang; Lin He; Yongyong Shi

    2010-01-01

    @@ Dear Editor, We developed a GPU-based analytical method, named as SHEsisEpi, which purely focuses on risk epistasis in a genome-wide association study (GWAS) of complex traits, excluding the contamination of marginal effects caused by single-locus association. We analyzed the Wellcome Trust Case Control Consortium's (WTCCC)GWAS data of bipolar disorder (BPD) with 500K SNPs.

  14. A new centering method of the measuring probe for spiral scanning-based surface profile measurement systems

    Science.gov (United States)

    Du, Hui-Lin; Zeng, Pei-Yang; Ju, Bing-Feng; Zhou, Zhao-Zhong; Xu, Shaoning; Sun, Anyu

    2017-02-01

    Spiral scanning is a high-efficiency scanning mode for surface profile measurement systems. The most important priority to realize the spiral scanning mode is to accurately align the measuring probe with the rotational centre of the spindle. This paper proposes a novel centre alignment method of the measuring probe, which is considered to be suitable for any type of spiral scanning surface measurement systems. The proposed method, which only needs a tilted flat mirror as the artefact, makes the time-consuming centre alignment process of the measuring probe become much easier and faster. The operational steps of the proposed method are presented. Experiments have also been carried out based on a self-developed optical profiler with spiral scanning operation to verity the feasibility of the proposed method. The experimental results show that the proposed method is capable of conducting a fast alignment (only takes 3 min) while maintaining a high alignment accuracy. Evaluation of the alignment accuracy shows that the centering error is less than 10 µm on the mechanical guide rail stage and about 1.7 µm on the air-bearing stage.

  15. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences

    Science.gov (United States)

    Eisenberg, David; Marcotte, Edward M.; Pellegrini, Matteo; Thompson, Michael J.; Yeates, Todd O.

    2002-10-15

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  16. AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha.

    Directory of Open Access Journals (Sweden)

    Ting Wang

    Full Text Available Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae, one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

  17. Methods for visual mining of genomic and proteomic data atlases.

    Science.gov (United States)

    Boyle, John; Kreisberg, Richard; Bressler, Ryan; Killcoyne, Sarah

    2012-04-23

    As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations

  18. Methods for visual mining of genomic and proteomic data atlases

    Directory of Open Access Journals (Sweden)

    Boyle John

    2012-04-01

    Full Text Available Abstract Background As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. Results This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas and the genomic characterization of cancer (The Cancer Genome Atlas. Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. Conclusions The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make

  19. 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.

  20. Scanning Measurement Method of Dispersion Mini-spot by Quadrant Photodetector

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Quadrant photodetector is a new type position detector, which has already been applied to many fields such as measurement, target tracking, control, laser collimation, guidance, etc. System performance is related to laser spot area received by the quadrant photodetector. The optimum linear output signal of system is gotten only when the size of laser dispersion spot is well-proportioned to the detector photosensitive area. A method to measure the mini-spot received by detector and to adjust it in real time is presented, which is based on the quadrant geometrical and optical structure, making use of tilting mirror scanning, the sequence output signal of detector is gotten, then measurement model is built with rate of signal change as characteristic variable, the radius of the laser dispersion spot and adjustable value of dispersion are calculated. The experiment result shows that the maximum error is 0.58μm in measurement range of 0.5mm±0.1mm.

  1. A new quantitative method to measure activity of ice structuring proteins using differential scanning calorimetry.

    Science.gov (United States)

    Hassa-Roudsari, Majid; Goff, H Douglas

    2012-01-01

    There are very few quantitative assays to measure the activity of antifreeze proteins (AFPs, or Ice Structuring Proteins, ISPs) and these can be prone to various inaccuracies and inconsistencies. Some methods rely only on unassisted visual assessment. When microscopy is used to measure ice crystal size, it is critical that standardized procedures be adopted, especially when image analysis software is used to quantify sizes. Differential Scanning Calorimetry (DSC) has been used to measure the thermal hysteresis activity (TH) of AFPs. In this study, DSC was used isothermally to measure enthalpic changes associated with structural rearrangements as a function of time. Differences in slopes of isothermal heat flow vs. time between winter wheat ISP or AFP type I containing samples, and those without ISP or AFP type I were demonstrated. ISP or AFP type I containing samples had significantly higher slopes compared to those without ISP or AFP type I. Samples with higher concentration of ISP or AFP type I showed higher slope values during the first hour and took up to 3 hr to attain equilibrium. Differences were attributed to activity of the proteins at the ice interface. Proteinaceous activity of ISPs or AFP type I was confirmed by loss of activity after treatment with protease.

  2. 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

  3. Whole-genome scan to detect quantitative trait loci associated with milk protein composition in 3 French dairy cattle breeds.

    Science.gov (United States)

    Sanchez, M P; Govignon-Gion, A; Ferrand, M; Gelé, M; Pourchet, D; Amigues, Y; Fritz, S; Boussaha, M; Capitan, A; Rocha, D; Miranda, G; Martin, P; Brochard, M; Boichard, D

    2016-10-01

    In the context of the PhénoFinLait project, a genome-wide analysis was performed to detect quantitative trait loci (QTL) that affect milk protein composition estimated using mid-infrared spectrometry in the Montbéliarde (MO), Normande (NO), and Holstein (HO) French dairy cattle breeds. The 6 main milk proteins (α-lactalbumin, β-lactoglobulin, and αS1-, αS2-, β-, and κ-caseins) expressed as grams per 100g of milk (% of milk) or as grams per 100g of protein (% of protein) were estimated in 848,068 test-day milk samples from 156,660 cows. Genotyping was performed for 2,773 MO, 2,673 NO, and 2,208 HO cows using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). Individual test-day records were adjusted for environmental effects and then averaged per cow to define the phenotypes analyzed. Quantitative trait loci detection was performed within each breed using a linkage disequilibrium and linkage analysis approach. A total of 39 genomic regions distributed on 20 of the 29 Bos taurus autosomes (BTA) were significantly associated with milk protein composition at a genome-wide level of significance in at least 1 of the 3 breeds. The 9 most significant QTL were located on BTA2 (133 Mbp), BTA6 (38, 47, and 87 Mbp), BTA11 (103 Mbp), BTA14 (1.8 Mbp), BTA20 (32 and 58 Mbp), and BTA29 (8 Mbp). The BTA6 (87 Mbp), BTA11, and BTA20 (58 Mbp) QTL were found in all 3 breeds, and they had highly significant effects on κ-casein, β-lactoglobulin, and α-lactalbumin, expressed as a percentage of protein, respectively. Each of these QTL explained between 13% (BTA14) and 51% (BTA11) of the genetic variance of the trait. Many other QTL regions were also identified in at least one breed. They were located on 14 additional chromosomes (1, 3, 4, 5, 7, 15, 17, 19, 21, 22, 24, 25, 26, and 27), and they explained 2 to 8% of the genetic variance of 1 or more protein composition traits. Concordance analyses, performed between QTL status and sequence-derived polymorphisms from

  4. A scanning electron microscopy comparison of enamel polishing methods after air-rotor stripping.

    Science.gov (United States)

    Piacentini, C; Sfondrini, G

    1996-01-01

    In the last few years, orthodontic literature has shown particular interest in the interproximal enamel reduction technique described as stripping or slenderizing. Most researchers have shown, by scanning electron microscopy (SEM) studies, the difficulties encountered while attempting to remove coarse abrasions left after stripping with the first instrument. The objective of this SEM study was to compare the different polishing methods proposed in the literature and to assess the efficiency of our own procedure. For this purpose, 48 healthy human teeth (premolars and molars) were used after removal for orthodontic or periodontal reasons. The teeth were divided into eight groups of six teeth each (two molars and four premolars), and mounted on a typodont to simulate a clinical situation. Each group underwent stripping according to one of the following techniques: 16-blade tungsten carbide bur and fine and ultrafine diamond burs; coarse diamond bur and fine and ultrafine diamond burs; coarse diamond disk and Sof-Lex disks (Dental products/3M, St. Paul, Minn.); 16-blade tungsten carbide bur and phosphoric acid on finishing strip; and 8-straight blade tungsten carbide diamond bur and Sof-Lex disks. The SEM investigations demonstrated that it is not possible to eliminate, with normal polishing and cleaning methods, the furrows left on the enamel both by the diamond burs and the diamond disks and the 16-blade tungsten carbide burs. Mechanical and chemical stripping as well did not prove to be effective. By contrast, with the use of a 8-straight blade tungsten carbide bur followed by Sof-Lex disks for polishing the enamel, it is possible to obtain well-polished surfaces that many times appear smoother than the intact or untreated enamel.

  5. Stability augmentation and mosaic method of forward-scan sonar images

    Science.gov (United States)

    Xie, Shaorong; Luo, Jun; Chen, Jinbo; Xu, Yuanyu

    2012-06-01

    In recent years, forward-scan sonar is widely applied to the underwater inspection, which is not subject to the influence of light and turbidity. For expanding the monitoring scope, the image sonar is generally mounted on the pan-tilt platform of a ROV (Remotely Operated Vehicle) or survey boat. However, there are still some problems such as: 1) The field-of-view is narrow, i.e. the horizontal view angle of DIDSON (Dual-frequency identification sonar) is 29° 2) The dynamic change of a ROV or survey boat by the water disturbances will cause the target to escape from the sonar image easily; 3) The image sonar is fixed on the pan-tilt platform, and its position and posture are unceasingly changed. As a result of these problems, the obtained images may be distorted and not on the same plane. To solve the above problems, stability augmentation of pan-tilt platform based on the principle of bionic eye movements and a mosaic method of sonar images are presented. According to the principle of the vestibule-ocular reflex, an active compensation control system of the mechanical pan-tilt platform is developed. It can compensate the sonar image instability resulting from attitude variation of a ROV or survey boat during operation. Applying multi-sensor fusion technology can rectify the sonar images with different position and posture to be on a single geodetic coordinate frame for image matching. Finally, sonar images can be mosaic. A stable large-scale sonar image can be obtained. The experimental results validate that the presented method is valid.

  6. 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

  7. Genome scan for cognitive trait loci of dyslexia: rapid naming and rapid switching of letters, numbers, and colors

    Science.gov (United States)

    Rubenstein, Kevin; Raskind, Wendy H.; Berninger, Virginia W.; Matsushita, Mark M.; Wijsman, Ellen M.

    2014-01-01

    Dyslexia, or specific reading disability, is a common developmental disorder that affects 5–12% of school-aged children. Dyslexia and its component phenotypes, assessed categorically or quantitatively, have complex genetic bases. The ability to rapidly name letters, numbers, and colors from rows presented visually correlates strongly with reading in multiple languages and is a valid predictor of reading and spelling impairment. Performance on measures of rapid naming and switching, RAN and RAS, is stable throughout elementary school years, with slowed performance persisting in adults who still manifest dyslexia. Targeted analyses of dyslexia candidate regions have included RAN measures, but only one other genome-wide linkage study has been reported. As part of a broad effort to identify genetic contributors to dyslexia, we performed combined oligogenic segregation and linkage analyses of measures of RAN and RAS in a family-based cohort ascertained through probands with dyslexia. We obtained strong evidence for linkage of RAN letters to the DYX3 locus on chromosome 2p and RAN colors to chromosome 10q, but were unable to confirm the chromosome 6p21 linkage detected for a composite measure of RAN colors and objects in the previous genome-wide study. PMID:24807833

  8. Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.].

    Science.gov (United States)

    Scotti-Saintagne, Caroline; Mariette, Stéphanie; Porth, Ilga; Goicoechea, Pablo G; Barreneche, Teresa; Bodénès, Catherine; Burg, Kornel; Kremer, Antoine

    2004-11-01

    Interspecific differentiation values (G(ST)) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution of G(ST) values followed an L-shaped curve with most markers exhibiting low species differentiation (G(ST) 10% levels. Twelve percent of the loci exhibited significant G(ST) deviations to neutral expectations, suggesting that selection contributed to species divergence. Coding regions expressed higher differentiation than noncoding regions. Among the 389 markers, 158 could be mapped on the 12 linkage groups of the existing Q. robur genetic map. Outlier loci with large G(ST) values were distributed over 9 linkage groups. One cluster of three outlier loci was found within 0.51 cM; but significant autocorrelation of G(ST) was observed at distances <2 cM. The size and distribution of genomic regions involved in species divergence are discussed in reference to hitchhiking effects and disruptive selection.

  9. Genome scan for cognitive trait loci of dyslexia: Rapid naming and rapid switching of letters, numbers, and colors.

    Science.gov (United States)

    Rubenstein, Kevin B; Raskind, Wendy H; Berninger, Virginia W; Matsushita, Mark M; Wijsman, Ellen M

    2014-06-01

    Dyslexia, or specific reading disability, is a common developmental disorder that affects 5-12% of school-aged children. Dyslexia and its component phenotypes, assessed categorically or quantitatively, have complex genetic bases. The ability to rapidly name letters, numbers, and colors from rows presented visually correlates strongly with reading in multiple languages and is a valid predictor of reading and spelling impairment. Performance on measures of rapid naming and switching, RAN and RAS, is stable throughout elementary school years, with slowed performance persisting in adults who still manifest dyslexia. Targeted analyses of dyslexia candidate regions have included RAN measures, but only one other genome-wide linkage study has been reported. As part of a broad effort to identify genetic contributors to dyslexia, we performed combined oligogenic segregation and linkage analyses of measures of RAN and RAS in a family-based cohort ascertained through probands with dyslexia. We obtained strong evidence for linkage of RAN letters to the DYX3 locus on chromosome 2p and RAN colors to chromosome 10q, but were unable to confirm the chromosome 6p21 linkage detected for a composite measure of RAN colors and objects in the previous genome-wide study. © 2014 Wiley Periodicals, Inc.

  10. Extraction of human genomic DNA from whole blood using a magnetic microsphere method.

    Science.gov (United States)

    Gong, Rui; Li, Shengying

    2014-01-01

    With the rapid development of molecular biology and the life sciences, magnetic extraction is a simple, automatic, and highly efficient method for separating biological molecules, performing immunoassays, and other applications. Human blood is an ideal source of human genomic DNA. Extracting genomic DNA by traditional methods is time-consuming, and phenol and chloroform are toxic reagents that endanger health. Therefore, it is necessary to find a more convenient and efficient method for obtaining human genomic DNA. In this study, we developed urea-formaldehyde resin magnetic microspheres and magnetic silica microspheres for extraction of human genomic DNA. First, a magnetic microsphere suspension was prepared and used to extract genomic DNA from fresh whole blood, frozen blood, dried blood, and trace blood. Second, DNA content and purity were measured by agarose electrophoresis and ultraviolet spectrophotometry. The human genomic DNA extracted from whole blood was then subjected to polymerase chain reaction analysis to further confirm its quality. The results of this study lay a good foundation for future research and development of a high-throughput and rapid extraction method for extracting genomic DNA from various types of blood samples.

  11. Genomic instability of human embryonic stem cell lines using different passaging culture methods.

    Science.gov (United States)

    Tosca, Lucie; Feraud, Olivier; Magniez, Aurélie; Bas, Cécile; Griscelli, Frank; Bennaceur-Griscelli, Annelise; Tachdjian, Gérard

    2015-01-01

    Human embryonic stem cells exhibit genomic instability that can be related to culture duration or to the passaging methods used for cell dissociation. In order to study the impact of cell dissociation techniques on human embryonic stem cells genomic instability, we cultured H1 and H9 human embryonic stem cells lines using mechanical/manual or enzymatic/collagenase-IV dissociation methods. Genomic instability was evaluated at early (p60) passages by using oligonucleotide based array-comparative genomic hybridization 105 K with a mean resolution of 50 Kb. DNA variations were mainly located on subtelomeric and pericentromeric regions with sizes <100 Kb. In this study, 9 recurrent genomic variations were acquired during culture including the well known duplication 20q11.21. When comparing cell dissociation methods, we found no significant differences between DNA variations number and size, DNA gain or DNA loss frequencies, homozygous loss frequencies and no significant difference on the content of genes involved in development, cell cycle tumorigenesis and syndrome disease. In addition, we have never found any malignant tissue in 4 different teratoma representative of the two independent stem cell lines. These results show that the occurrence of genomic instability in human embryonic stem cells is similar using mechanical or collagenase IV-based enzymatic cell culture dissociation methods. All the observed genomic variations have no impact on the development of malignancy.

  12. 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

    Aim: To ascertain the role of Enterococcus faecalis in persistent infection and a possible method to prevent the penetration of E. faecalis into root cementum. Methodology: 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. Results: 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. Conclusion: 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. PMID:27994316

  13. Laser-scanning velocimetry: A confocal microscopy method for quantitative measurement of cardiovascular performance in zebrafish embryos and larvae

    Directory of Open Access Journals (Sweden)

    Linney Elwood

    2007-07-01

    Full Text Available Abstract Background The zebrafish Danio rerio is an important model system for drug discovery and to study cardiovascular development. Using a laser-scanning confocal microscope, we have developed a non-invasive method of measuring cardiac performance in zebrafish embryos and larvae that obtains cardiovascular parameters similar to those obtained using Doppler echocardiography in mammals. A laser scan line placed parallel to the path of blood in the dorsal aorta measures blood cell velocity, from which cardiac output and indices of vascular resistance and contractility are calculated. Results This technique, called laser-scanning velocimetry, was used to quantify the effects of pharmacological, developmental, and genetic modifiers of cardiac function. Laser-scanning velocimetry was applied to analyze the cardiovascular effects of morpholino knockdown of osmosensing scaffold for MEKK3 (OSM, which when mutated causes the human vascular disease cerebral cavernous malformations. OSM-deficient embryos had a constricted aortic arch and markedly increased peak cell velocity, a characteristic indicator of aortic stenosis. Conclusion These data validate laser-scanning velocimetry as a quantitative tool to measure cardiovascular performance for pharmacological and genetic analysis in zebrafish, which requires no specialized equipment other than a laser-scanning confocal microscope.

  14. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases.

    Directory of Open Access Journals (Sweden)

    Roberto Amato

    Full Text Available Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or F(ST. We performed a genome-wide estimation of F(ST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of F(ST values between autosomes and heterochromosomes. When we compared the F(ST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of F(ST, while several pathways related to cell signalling, growth and morphogenesis showed high F(ST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.

  15. Sex-specific variability and a 'cage effect' independently mask a neuropathic pain quantitative trait locus detected in a whole genome scan.

    Science.gov (United States)

    Devor, Marshall; Gilad, Amit; Arbilly, Michal; Nissenbaum, Jonathan; Yakir, Benjamin; Raber, Pnina; Minert, Anne; Pisanté, Anne; Darvasi, Ariel

    2007-08-01

    Sex and environment may dramatically affect genetic studies, and thus should be carefully considered. Beginning with two inbred mouse strains with contrasting phenotype in the neuroma model of neuropathic pain (autotomy), we established a backcross population on which we conducted a genome-wide scan. The backcross population was partially maintained in small social groups and partially in isolation. The genome scan detected one previously reported quantitative trait locus (QTL) on chromosome 15 (pain1), but no additional QTLs were found. Interestingly, group caging introduced phenotypic noise large enough to completely mask the genetic effect of the chromosome 15 QTL. The reason appears to be that group-caging animals from the low-autotomy strain together with animals from the high-autotomy strain dramatically increases autotomy in the otherwise low-autotomy mice (males or females). The converse, suppression of pain behaviour in the high-autotomy strain when caged with the low-autotomy strain was also observed, but only in females. Even in isolated mice, the genetic effect of the chromosome 15 QTL was significant only in females. To determine why, we evaluated autotomy levels of females in 12 different inbred stains of mice and compared them to previously reported levels for males. Strikingly larger environmental variation was observed in males than in females for this pain phenotype. The high baseline variance in males can explain the difficulty in detecting the genetic effect, which was readily seen in females. Our study emphasizes the importance of sex and environment in the genetic analysis of pain.

  16. 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.

  17. A rapid scan vacuum FTIR method for determining diffusion coefficients in viscous and glassy aerosol particles.

    Science.gov (United States)

    Zhang, Yun; Cai, Chen; Pang, Shu-Feng; Reid, Jonathan P; Zhang, Yun-Hong

    2017-09-25

    We report a new method to investigate water transport kinetics in aerosol particles by using rapid scan FTIR spectroscopy combined with a custom-built pulse relative humidity (RH) control system. From real time in situ measurements of RH and composition using high time resolution infrared spectroscopy (0.12 s for one spectrum), and through achieving a high rate of RH change (as fast as 60% per second), we are able to investigate the competition between the gas and condensed phase diffusive transport limits of water for particles with mean diameter ∼3 μm and varying phase and viscosity. The characteristic time (τ) for equilibration in particle composition following a step change in RH is measured to quantify dissolution timescales for crystalline particles and to probe the kinetics of water evaporation and condensation in amorphous particles. We show that the dissolution kinetics are prompt for crystalline inorganic salt particles following an increase in RH from below to above the deliquescence RH, occurring on a timescale comparable to the timescale of the RH change (particles, we show that the timescales for both the drying and condensation processes can be delayed by many orders of magnitude, depending on the viscosity of the particles in the range 10(1) to 10(9) Pa s considered here. For amorphous particles, these kinetics are shown to be consistent with previous measurements of mass transfer rates in larger single particles. More specifically, the consistency suggests that fully understanding and modelling the complex microphysical processes and heterogeneities that form in viscous particles may not be necessary for estimating timescales for particle equilibration. A comparison of the kinetics for crystalline and amorphous particles illustrates the interplay of the rates of gas and condensed phase diffusion in determining the mass transport rates of water in aerosols.

  18. Helix Scan: A Scan Design for Diagnosis

    Institute of Scientific and Technical Information of China (English)

    WANG Fei; HU Yu; LI Xiaowei

    2007-01-01

    Scan design is a widely used design-for-testability technique to improve test quality and efficiency. For the scan-designed circuit, test and diagnosis of the scan chain and the circuit is an important process for silicon debug and yield learning. However, conventional scan designs and diagnosis methods abort the subsequent diagnosis process after diagnosing the scan chain if the scan chain is faulty. In this work, we propose a design-for-diagnosis scan strategy called helix scan and a diagnosis algorithm to address this issue. Unlike previous proposed methods, helix scan has the capability to carry on the diagnosis process without losing information when the scan chain is faulty. What is more, it simplifies scan chain diagnosis and achieves high diagnostic resolution as well as accuracy. Experimental results demonstrate the effectiveness of our design.

  19. 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

    BACKGROUND: The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. A set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. The statistical methods we are concerned......, 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...... measure was a good measure to detect horizontally transferred regions, and when used to compare the phylogenetic relationships between plasmids and hosts, significant correlation (R2 = 0.4) was found with genomic GC content and intra-chromosomal homogeneity. CONCLUSION: The statistical methods examined...

  20. An efficient method for genomic DNA extraction from different molluscs species.

    Science.gov (United States)

    Pereira, Jorge C; Chaves, Raquel; Bastos, Estela; Leitão, Alexandra; Guedes-Pinto, Henrique

    2011-01-01

    The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others.

  1. An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

    Directory of Open Access Journals (Sweden)

    Henrique Guedes-Pinto

    2011-11-01

    Full Text Available The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills or quantity of tissue, can explain the lack of efficiency (quality and yield in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia and Muricidae (Gastropoda, with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others.

  2. GONAD: Genome-editing via Oviductal Nucleic Acids Delivery system: a novel microinjection independent genome engineering method in mice.

    Science.gov (United States)

    Takahashi, Gou; Gurumurthy, Channabasavaiah B; Wada, Kenta; Miura, Hiromi; Sato, Masahiro; Ohtsuka, Masato

    2015-06-22

    Microinjection is considered the gold standard technique for delivery of nucleic acids (NAs; transgenes or genome editing tools such as CRISPR/Cas9 systems) into embryos, for creating genetically modified organisms. It requires sophisticated equipment as well as well-trained and highly skilled personnel to perform the micro-injection technique. Here, we describe a novel and simple microinjection-independent technique, called Genome-editing via Oviductal Nucleic Acids Delivery (GONAD). Using GONAD, we show that NAs (e.g., eGFP mRNA or Cas9 mRNA/sgRNAs) can be effectively delivered to pre-implantation embryos within the intact mouse oviduct by a simple electroporation method, and result in the desired genetic modification in the embryos. Thus GONAD can bypass many complex steps in transgenic technology such as isolation of zygotes, microinjection of NAs into them, and their subsequent transfer to pseudo-pregnant animals. Furthermore, this method can potentially be used for genome editing in species other than mice.

  3. A novel method to screen genomic libraries that combines genomic immunization with the prime-boost strategy.

    Science.gov (United States)

    Yero, Daniel; Pajón, Rolando; Caballero, Evelin; González, Sonia; Cobas, Karem; Fariñas, Mildrey; Lopez, Yamilé; Acosta, Armando

    2007-08-01

    We employed a prime-boost regimen in combination with the expression library immunization protocol to improve the protective effectiveness of a genomic library used as immunogen. To demonstrate the feasibility of this novel strategy, we used as a prime a serogroup B Neisseria meningitidis random genomic library constructed in a eukaryotic expression vector. Mice immunized with different fractions of this library and boosted with a single dose of meningococcal outer membrane vesicles elicited higher bactericidal antibody titers compared with mice primed with the empty vector. After the boost, passive administration of sera from mice primed with two of these fractions significantly reduced the number of viable bacteria in the blood of infant rats challenged with live N. meningitidis. The method proposed could be applied to the identification of subimmunogenic antigens during vaccine candidate screening by employing expression library immunization.

  4. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation

    Science.gov (United States)

    Adhikari, Kaustubh; Fuentes-Guajardo, Macarena; Quinto-Sánchez, Mirsha; Mendoza-Revilla, Javier; Camilo Chacón-Duque, Juan; Acuña-Alonzo, Victor; Jaramillo, Claudia; Arias, William; Lozano, Rodrigo Barquera; Pérez, Gastón Macín; Gómez-Valdés, Jorge; Villamil-Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria- Cátira; Canizales-Quinteros, Samuel; Cheeseman, Michael; Rosique, Javier; Bedoya, Gabriel; Rothhammer, Francisco; Headon, Denis; González-José, Rolando; Balding, David; Ruiz-Linares, Andrés

    2016-01-01

    We report a genome-wide association scan for facial features in ∼6,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P values<5 × 10−8) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of ∼3,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion. PMID:27193062

  5. 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.

  6. 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.

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

    Science.gov (United States)

    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, genomic codon and amino acid frequencies based comparisons) and proteomes (all-against-all BLAST protein comparisons and pan-genomic analyses). Results We found that the oligonucleotide based methods gave different results compared to that of the proteome based methods. Differences were also found 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 could be detected between all genera included in this study using the codon and amino acid frequencies based methods. Proteome comparisons were found to be in strong accordance with current Brucella taxonomy indicating a remarkable association between gene gain or loss on one hand and mutations in marker genes on the other. The proteome based methods found greater similarity between Brucella species and Ochrobactrum species than between species within genus Agrobacterium compared to each other. In other words, proteome comparisons of species within genus Agrobacterium were found to be more diverse than proteome comparisons between species in genus Brucella and genus Ochrobactrum. Pan-genomic analyses indicated that uptake of DNA from outside genus Brucella appears to be

  8. Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection.

    Science.gov (United States)

    Li, Zitong; Sillanpää, Mikko J

    2012-08-01

    Quantitative trait loci (QTL)/association mapping aims at finding genomic loci associated with the phenotypes, whereas genomic selection focuses on breeding value prediction based on genomic data. Variable selection is a key to both of these tasks as it allows to (1) detect clear mapping signals of QTL activity, and (2) predict the genome-enhanced breeding values accurately. In this paper, we provide an overview of a statistical method called least absolute shrinkage and selection operator (LASSO) and two of its generalizations named elastic net and adaptive LASSO in the contexts of QTL mapping and genomic breeding value prediction in plants (or animals). We also briefly summarize the Bayesian interpretation of LASSO, and the inspired hierarchical Bayesian models. We illustrate the implementation and examine the performance of methods using three public data sets: (1) North American barley data with 127 individuals and 145 markers, (2) a simulated QTLMAS XII data with 5,865 individuals and 6,000 markers for both QTL mapping and genomic selection, and (3) a wheat data with 599 individuals and 1,279 markers only for genomic selection.

  9. Measurement of blood-brain barrier permeability using dynamic Gd-DTPA scanning--a comparison of methods

    DEFF Research Database (Denmark)

    Larsson, H B; Tofts, P S

    1992-01-01

    Two recently published methods of blood-brain barrier permeability measurement using Gd-DTPA scanning are compared by authors representing each group. The physiological models are reconciled. Results from both groups agree. These show that the transfer constant (the permeability surface area prod...

  10. 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.

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

    Science.gov (United States)

    de Brito, Daniel M.; Maracaja-Coutinho, Vinicius; de Farias, Savio T.; Batista, Leonardo V.; do Rêgo, Thaís G.

    2016-01-01

    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. PMID:26731657

  12. 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.

  13. GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome.

    Science.gov (United States)

    Folkersen, Lasse; Diez, Diego; Wheelock, Craig E; Haeggström, Jesper Z; Goto, Susumu; Eriksson, Per; Gabrielsen, Anders

    2009-08-01

    Whole-genome microarrays allow us to interrogate the entire transcriptome of a cell. Affymetrix microarrays are constructed using several probes that match to different regions of a gene and a summarization step reduces this complexity into a single value, representing the expression level of the gene or the expression level of an exon in the case of exon arrays. However, this simplification eliminates information that might be useful when focusing on specific genes of interest. To address these limitations, we present a software package for the R platform that allows detailed analysis of expression at the probe level. The package matches the probe sequences against a target gene sequence (either mRNA or DNA) and shows the expression levels of each probe along the gene. It also features functions to fit a linear regression based on several genetic models that enables study of the relationship between gene expression and genotype. The software is implemented as a platform-independent R package available through the Bioconductor repository at http://www.bioconductor.org/. It is licensed as GPL 2.0. Supplementary data are available at Bioinformatics online.

  14. Genome-wide scan for bats and dolphin to detect their genetic basis for new locomotive styles.

    Directory of Open Access Journals (Sweden)

    Yong-Yi Shen

    Full Text Available For most mammals, running is their major locomotive style, however, cetaceans and bats are two mammalian groups that have independently developed new locomotive styles (swimming and flying from their terrestrial ancestors. In this study, we used a genome-wide comparative analysis in an attempt to identify the selective imprint of the development of new locomotive styles by cetaceans and bats to adapt to their new ecological niches. We found that an elevated proportion of mitochondrion-associated genes show evidence of adaptive evolution in cetaceans and on the common ancestral lineage leading to bats, compared to other terrestrial mammals. This result is consistent with the fact that during the independent developments of swimming and flying in these two groups, the changes of energy metabolism ratios would be among the most important factors to overcome elevated energy demands. Furthermore, genes that show evidence of sequence convergence or parallel evolution in these two lineages were overrepresented in the categories of energy metabolism, muscle contraction, heart, and glucose metabolism, genes that perform functions which are essential for locomotion. In conclusion, our analyses showed that on the dolphin and bat lineages, genes associated with locomotion not only both show a greater propensity to adaptively evolve, but also show evidence of sequence convergence, which likely reflects a response to a common requirement during their development of these two drastic locomotive styles.

  15. AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection.

    Science.gov (United States)

    Tollenaere, C; Duplantier, J-M; Rahalison, L; Ranjalahy, M; Brouat, C

    2011-03-01

    The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining P-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci. © 2010 Blackwell Publishing Ltd.

  16. 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.

  17. Efficient method for the extraction of genomic DNA from wormwood ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-09-17

    Sep 17, 2008 ... Faculty of Agro-technology and Food Science, Universiti Malaysia Terengganu, ... showed high purity and high quantity in Sarkosyl method compare the other methods. ... Isolation of plant nucleic acids for use in Southen blot.

  18. Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

    Science.gov (United States)

    Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

    2016-08-15

    Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities.

  19. 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

  20. Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach

    Directory of Open Access Journals (Sweden)

    Shong Huang

    2013-04-01

    Full Text Available The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct.

  1. 探讨MSCT腰椎间盘的扫描方法%Investigating the Lumbar Explore MSCT scan Method

    Institute of Scientific and Technical Information of China (English)

    吕淑华

    2013-01-01

    Objective:To investigate MSCT scan lumbar disc the best method .Methods:16-slice CT use of non -vertebral space spiral plain and reconstruction gap volume scanning method ,measuring L5/S1 disc and the angle of the horizontal plane .Results:Spiral volume scanning reconstruction gap ,to more clearly show that the disc disease ,found that more than 250 measuring the angle between the angle of about 28 percent.Conclusion:The volume scanning space of more help to rebuild the diagnosis of lumbar disc herniation .%目的:探讨MSCT腰椎间盘的最佳扫描方法。方法:16排CT采用非螺旋椎间隙平扫和容积扫描间隙重建的方法;测量L5/S1椎间盘与水平面的夹角分析。结果:螺旋容积扫描间隙重建法,能更清晰地显示椎间盘的病变情况;夹角测量发现大于25°角的约为28%。结论:容积扫描间隙重建法更有助于腰椎间盘突出的诊断。

  2. An automatic scanning method for high throughput microscopic system to facilitate medical genetic diagnosis: an initial study

    Science.gov (United States)

    Qiu, Yuchen; Chen, Xiaodong; Li, Zheng; Li, Yuhua; Chen, Wei R.; Zheng, Bin; Li, Shibo; Liu, Hong

    2012-03-01

    The purpose of this paper is to report a new automatic scanning scheme for high throughput microscopic systems aiming to facilitate disease diagnosis in genetic laboratories. To minimize the impact of the random vibration and mechanical drifting of the scanning stage in microscopic image acquisition, auto-focusing operations are usually applied repeatedly during the scanning process. Such methods ensure the acquisition of well focused images for clinical diagnosis, but are time consuming. The technique investigated in this preliminary study applies the auto-focusing operations at a limited number of locations on the slide. For the rest of the imaging field, the focusing position is quickly adjusted through linear interpolation. In this initial validation study, blood pathological slides containing both metaphase and interphase cells are scanned. For a selected area of 6.9mm×6.9mm, a number of 2×2, 3×2, 3×3, and 4×4 positions are evenly sampled for auto-focusing operations. Respectively, 25, 29, 40, and 41 clinically meaningful cells are identified for each sampling scheme. For the specific case investigated, the results demonstrate that the 4 position auto-focusing scheme could obtain the adequate number of clinically meaningful cells for the diagnosis. The schemes with more auto-focusing operations provide an option for high reliability diagnosis when clinically necessary. More comprehensive research is planned, and that may lead to optimal design of trade-off for developing the scanning scheme of the high throughput microscopic systems.

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

    Science.gov (United States)

    Fukuda, Shingo; Uchihashi, Takayuki; Ando, Toshio

    2015-06-01

    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 α3β3 subcomplex of F1-ATPase in dynamic action at ˜7 frames/s.

  4. 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.

  5. Using MLPA method for determining unbalanced changes in genome

    OpenAIRE

    KŘÍHOVÁ, Miroslava

    2015-01-01

    Unbalanced chromosomal structural changes are connected with the presence of supernumerary particular part of chromosome, or the chromosome is absenting. MLPA is a method based on PCR principal, which amplifies MLPA probes, not the target sequences. MLPA probes hybridize to target sequences and then ligate them. Only one pair of primers is used. In the theoretical part the MLPA method is presented. Additionally, other diagnostics method of clinical genetic are mentioned (for example PCR, FISH...

  6. 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.

  7. Fast and reliable method of conductive carbon nanotube-probe fabrication for scanning probe microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Dremov, Vyacheslav, E-mail: dremov@issp.ac.ru; Fedorov, Pavel; Grebenko, Artem [Institute of Solid State Physics, RAS, 142432 Chernogolovka (Russian Federation); Interdisciplinary Center for Basic Research, Moscow Institute of Physics and Technology, 141700 Dolgoprudniy (Russian Federation); Fedoseev, Vitaly [Institute of Solid State Physics, RAS, 142432 Chernogolovka (Russian Federation)

    2015-05-15

    We demonstrate the procedure of scanning probe microscopy (SPM) conductive probe fabrication with a single multi-walled carbon nanotube (MWNT) on a silicon cantilever pyramid. The nanotube bundle reliably attached to the metal-covered pyramid is formed using dielectrophoresis technique from the MWNT suspension. It is shown that the dimpled aluminum sample can be used both for shortening/modification of the nanotube bundle by applying pulse voltage between the probe and the sample and for controlling the probe shape via atomic force microscopy imaging the sample. Carbon nanotube attached to cantilever covered with noble metal is suitable for SPM imaging in such modulation regimes as capacitance contrast microscopy, Kelvin probe microscopy, and scanning gate microscopy. The majority of such probes are conductive with conductivity not degrading within hours of SPM imaging.

  8. Morphometric measurements of dragonfly wings: the accuracy of pinned, scanned and detached measurement methods.

    Science.gov (United States)

    Johnson, Laura; Mantle, Beth L; Gardner, Janet L; Backwell, Patricia R Y

    2013-01-01

    Large-scale digitization of museum specimens, particularly of insect collections, is becoming commonplace. Imaging increases the accessibility of collections and decreases the need to handle individual, often fragile, specimens. Another potential advantage of digitization is to make it easier to conduct morphometric analyses, but the accuracy of such methods needs to be tested. Here we compare morphometric measurements of scanned images of dragonfly wings to those obtained using other, more traditional, methods. We assume that the destructive method of removing and slide-mounting wings provides the most accurate method of measurement because it eliminates error due to wing curvature. We show that, for dragonfly wings, hand measurements of pinned specimens and digital measurements of scanned images are equally accurate relative to slide-mounted hand measurements. Since destructive slide-mounting is unsuitable for museum collections, and there is a risk of damage when hand measuring fragile pinned specimens, we suggest that the use of scanned images may also be an appropriate method to collect morphometric data from other collected insect species.

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

    African Journals Online (AJOL)

    aghomotsegin

    2014-02-05

    Feb 5, 2014 ... Technology, Federal Polytechnic Bali, Taraba State, Nigeria. Accepted ... (CTAB) method is used to isolate DNA from tissues containing high levels of polysaccharides. The ... Isolation of plant nucleic acids for use in Southern.

  10. An improved method for detecting and delineating genomic regions with altered gene expression in cancer

    OpenAIRE

    2008-01-01

    Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method combines top-notch detection performance with an ability to delineate relevant regions without excessive over-segmentation, making it a significant advance over existing methods. ...

  11. Comparison of eight methods of genomic DNA extraction from babassu.

    Science.gov (United States)

    Viana, J P G; Borges, A N C; Lopes, A C A; Gomes, R L F; Britto, F B; Lima, P S C; Valente, S E S

    2015-12-22

    Babassu (Orbignya phalerata Martius) is one of the most important palms in Brazil because of the largest morphological variation, wide geographic distribution, and high socio-economic importance. The diversity present in babassu germplasm should be protected against loss to ensure their use with high productivity. Study of the available variability in populations of babassu is necessary to develop conservation strategies. The study of genetic variability can be conducted using molecular markers and many of these studies require significant quantity of high-quality DNA. The present study aimed to effect comparison among eight DNA extraction methods in case of O. phalerata. The quality and concentration of nucleic acids were analyzed by spectrophotometry and integrity of DNA was ascertained by agarose gel electrophoresis. The spectrophotometry revealed that some methods resulted in high levels of concentration of nucleic acids, in which values of the ratio A260/280 and A260/230 were outside the range of purity. The agarose gel electrophoresis established the concentration and integrity of DNA. The methods of Murray and Thompson (1980) and Ferreira and Grattapaglia (1998) did not result in satisfactory quantities of DNA. Conversely, the method proposed by Khanuja et al. (1999) resulted in DNA of adequate quality and quantity that could be satisfactorily used for amplification reactions performed with two ISSR primers.

  12. 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

    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...

  13. 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

  14. Comparison of methods for high quantity and quality genomic DNA extraction from raw cow milk.

    Science.gov (United States)

    Usman, T; Yu, Y; Liu, C; Fan, Z; Wang, Y

    2014-04-29

    Isolation of sufficient quantities of high quality DNA is a prerequisite for molecular studies. Milk somatic cells can be used; however, inhibitors such as fats and proteins make milk a difficult medium for extracting large amounts of quality DNA. We optimized, evaluated and compared three methods, Modified Nucleospin Blood Kit method, Modified TianGen Kit method and Phenol-Chloroform method for genomic DNA extraction from bovine milk. Individual cows' milk and bulk milk samples were collected from a China agricultural university dairy farm. Genomic DNA extracted from each milk sample by the three methods was evaluated for quantity and purity by spectrophotometry and gel electrophoresis, as well as PCR and sequencing. All the three methods were found suitable for genomic DNA isolation from bovine milk, PCR applications, and sequencing. Comparing the three methods, we found that the Modified Nucleospin Blood Kit method was significantly better than the Phenol-Chloroform method in terms of quantity as well as quality (amount, concentration, 260/280 nm and 260/230 nm absorbance ratio), whereas, the Modified TianGen Kit method was more efficient than the Phenol-Chloroform method and cheaper than the Modified Nucleospine Blood Kit method; it yielded reasonably good quantities of good quality DNA and would be suitable for large-scale genotyping of lactating cows.

  15. Scanning and three-dimensional electron microscopy methods for the study of Trypanosoma brucei and Leishmania mexicana flagella.

    Science.gov (United States)

    Gluenz, Eva; Wheeler, Richard John; Hughes, Louise; Vaughan, Sue

    2015-01-01

    Three-dimensional electron microscopy tools have revolutionized our understanding of cell structure and molecular complexes in biology. Here, we describe methods for studying flagellar ultrastructure and biogenesis in two unicellular parasites-Trypanosoma brucei and Leishmania mexicana. We describe methods for the preparation of these parasites for scanning electron microscopy cellular electron tomography, and serial block face scanning electron microscopy (SBFSEM). These parasites have a highly ordered cell shape and form, with a defined positioning of internal cytoskeletal structures and organelles. We show how knowledge of these can be used to dissect cell cycles in both parasites and identify the old flagellum from the new in T. brucei. Finally, we demonstrate the use of SBFSEM three-dimensional models for analysis of individual whole cells, demonstrating the excellent potential this technique has for future studies of mutant cell lines.

  16. Scanning electron microscopic study of the surface of feline gastric epithelium: a simple method of removing the coating material.

    Science.gov (United States)

    Al-Tikriti, M; Henry, R W; Al-Bagdadi, F K; Hoskins, J; Titkemeyer, C

    1986-01-01

    Scanning electron microscopic examination of the gastric surface epithelial cells is often hindered by the presence of a coating material. Several methods for removal of coating material on feline gastric mucosa were utilized. The cleansed tissues were evaluated using the scanning electron microscope to assess damage caused by the use of various cleansing methods to surface epithelial cells. The stretched stomach washed several times, including rubbing the mucosal surface with gloved fingers, yielded the best results with no apparent damage to the surface epithelial cells. Flushing unstretched stomachs with saline only did not adequately remove coating material. Flushing unstretched stomachs with saline while stroking the surface with a cotton tipped applicator stick removed debris but damaged the surface epithelium.

  17. Methods and Strategies to Impute Missing Genotypes for Improving Genomic Prediction

    DEFF Research Database (Denmark)

    Ma, Peipei

    Genomic prediction has been widely used in dairy cattle breeding. Genotype imputation is a key procedure to efficently utilize marker data from different chips and obtain high density marker data with minimizing cost. This thesis investigated methods and strategies to genotype imputation for impr......Genomic prediction has been widely used in dairy cattle breeding. Genotype imputation is a key procedure to efficently utilize marker data from different chips and obtain high density marker data with minimizing cost. This thesis investigated methods and strategies to genotype imputation...

  18. A Novel Method of Genomic DNA Extraction for Cactaceae

    OpenAIRE

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

    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 compl...

  19. 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.

  20. 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.

  1. An efficient de-convolution reconstruction method for spatiotemporal-encoding single-scan 2D MRI.

    Science.gov (United States)

    Cai, Congbo; Dong, Jiyang; Cai, Shuhui; Li, Jing; Chen, Ying; Bao, Lijun; Chen, Zhong

    2013-03-01

    Spatiotemporal-encoding single-scan MRI method is relatively insensitive to field inhomogeneity compared to EPI method. Conjugate gradient (CG) method has been used to reconstruct super-resolved images from the original blurred ones based on coarse magnitude-calculation. In this article, a new de-convolution reconstruction method is proposed. Through removing the quadratic phase modulation from the signal acquired with spatiotemporal-encoding MRI, the signal can be described as a convolution of desired super-resolved image and a point spread function. The de-convolution method proposed herein not only is simpler than the CG method, but also provides super-resolved images with better quality. This new reconstruction method may make the spatiotemporal-encoding 2D MRI technique more valuable for clinic applications. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Scanning thermal probe microscope method for the determination of thermal diffusivity of nanocomposite thin films.

    Science.gov (United States)

    Varandani, Deepak; Agarwal, Khushboo; Brugger, Juergen; Mehta, Bodh Raj

    2016-08-01

    A commercial scanning thermal microscope has been upgraded to facilitate its use in estimating the radial thermal diffusivity of thin films close to room temperature. The modified setup includes a microcontroller driven microhotplate coupled with a Bluetooth module for wireless control. The microcontroller board (Arduino Leonardo) is used to generate a bias of suitable voltage amplitude and pulse duration which is applied across the microhotplate contact pads. A corresponding heat pulse from the Pt heating element (1 mm(2)) embedded within the microhotplate is delivered to the lower surface of the thin film (25 mm(2)) deposited over it. The large difference in the dimensions of the heating source and the thin film surface causes heat to flow radially outwards on the top surface of the latter. The decay of this radial heat wave as it flows outwards is recorded by the scanning thermal microscope in terms of temperature-time (T-t) profiles at varying positions around the central heating zone. A fitting procedure is suggested to extract the thermal diffusivity value from the array of T-t profiles. The efficacy of the above setup has been established by evaluating the thermal diffusivities of Bi2Te3 and Bi2Te3:Si thin film samples. Further, with only minor alterations in design the capabilities of the above setup can be extended to estimate the axial thermal diffusivity and specific heat of thin films, as a function of temperature.

  3. Scanning thermal probe microscope method for the determination of thermal diffusivity of nanocomposite thin films

    Science.gov (United States)

    Varandani, Deepak; Agarwal, Khushboo; Brugger, Juergen; Mehta, Bodh Raj

    2016-08-01

    A commercial scanning thermal microscope has been upgraded to facilitate its use in estimating the radial thermal diffusivity of thin films close to room temperature. The modified setup includes a microcontroller driven microhotplate coupled with a Bluetooth module for wireless control. The microcontroller board (Arduino Leonardo) is used to generate a bias of suitable voltage amplitude and pulse duration which is applied across the microhotplate contact pads. A corresponding heat pulse from the Pt heating element (1 mm2) embedded within the microhotplate is delivered to the lower surface of the thin film (25 mm2) deposited over it. The large difference in the dimensions of the heating source and the thin film surface causes heat to flow radially outwards on the top surface of the latter. The decay of this radial heat wave as it flows outwards is recorded by the scanning thermal microscope in terms of temperature-time (T-t) profiles at varying positions around the central heating zone. A fitting procedure is suggested to extract the thermal diffusivity value from the array of T-t profiles. The efficacy of the above setup has been established by evaluating the thermal diffusivities of Bi2Te3 and Bi2Te3:Si thin film samples. Further, with only minor alterations in design the capabilities of the above setup can be extended to estimate the axial thermal diffusivity and specific heat of thin films, as a function of temperature.

  4. High-Accuracy, Compact Scanning Method and Circuit for Resistive Sensor Arrays

    Directory of Open Access Journals (Sweden)

    Jong-Seok Kim

    2016-01-01

    Full Text Available The zero-potential scanning circuit is widely used as read-out circuit for resistive sensor arrays because it removes a well known problem: crosstalk current. The zero-potential scanning circuit can be divided into two groups based on type of row drivers. One type is a row driver using digital buffers. It can be easily implemented because of its simple structure, but we found that it can cause a large read-out error which originates from on-resistance of the digital buffers used in the row driver. The other type is a row driver composed of operational amplifiers. It, very accurately, reads the sensor resistance, but it uses a large number of operational amplifiers to drive rows of the sensor array; therefore, it severely increases the power consumption, cost, and system complexity. To resolve the inaccuracy or high complexity problems founded in those previous circuits, we propose a new row driver which uses only one operational amplifier to drive all rows of a sensor array with high accuracy. The measurement results with the proposed circuit to drive a 4 × 4 resistor array show that the maximum error is only 0.1% which is remarkably reduced from 30.7% of the previous counterpart.

  5. Image reconstruction based on total-variation minimization and alternating direction method in linear scan computed tomography

    Institute of Scientific and Technical Information of China (English)

    Zhang Han-Ming; Wang Lin-Yuan; Yah Bin; Li Lei; Xi Xiao-Qi; Lu Li-Zhong

    2013-01-01

    Linear scan computed tomography (LCT) is of great benefit to online industrial scanning and security inspection due to its characteristics of straight-line source trajectory and high scanning speed.However,in practical applications of LCT,there are challenges to image reconstruction due to limited-angle and insufficient data.In this paper,a new reconstruction algorithm based on total-variation (TV) minimization is developed to reconstruct images from limited-angle and insufficient data in LCT.The main idea of our approach is to reformulate a TV problem as a linear equality constrained problem where the objective function is separable,and then minimize its augmented Lagrangian function by using alternating direction method (ADM) to solve subproblems.The proposed method is robust and efficient in the task of reconstruction by showing the convergence of ADM.The numerical simulations and real data reconstructions show that the proposed reconstruction method brings reasonable performance and outperforms some previous ones when applied to an LCT imaging problem.

  6. A genome-wide admixture scan identifies MYH9 as a candidate locus associated with non-diabetic end stage renal disease in African Americans

    Science.gov (United States)

    Linda Kao, WH; Klag, Michael J; Meoni, Lucy A; Reich, David; Berthier-Schaad, Yvette; Li, Man; Coresh, Josef; Patterson, Nick; Tandon, Arti; Powe, Neil R; Fink, Nancy E; Sadler, John H; Weir, Matthew R; Abboud, Hanna E; Adler, Sharon; Divers, Jasmin; Iyengar, Sudha K; Freedman, Barry I; Kimmel, Paul L; Knowler, William C; Kohn, Orly F; Kramp, Kristopher; Leehey, David J; Nicholas, Susanne; Pahl, Madeleine; Schelling, Jeffrey R; Sedor, John R; Thornley-Brown, Denyse; Winkler, Cheryl A; Smith, Michael W.; Parekh, Rulan S.

    2008-01-01

    End stage renal disease (ESRD) has a four times higher incidence in African Americans compared to European Americans. This led to the hypothesis that susceptibility alleles for ESRD have a higher frequency in West African than European gene pool. We performed a genome-wide admixture scan in 1,372 ESRD cases and 806 controls and demonstrated a highly significant association between excess African ancestry and non-diabetic ESRD (LOD 5.70) but not diabetic ESRD (LOD 0.47) on chromosome 22q12. Each copy of the European ancestral allele conferred a relative risk of 0.50 (95% credible interval 0.39 – 0.63) compared to African ancestry. Multiple common SNPs (allele frequency ranging from 0.2 to 0.6) in the gene that encodes non-muscle myosin heavy chain type II isoform A (MYH9) were associated with 2-4 times greater risk of non-diabetic ESRD and accounted for a large proportion of the excess risk of ESRD observed in African compared to European Americans. PMID:18794854

  7. 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

    . 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...... from human and H1N1 virus from swine, on a single lane of a GAIIx flow cell to an average depth of 122-fold. This technique can be applied to cultivated and uncultivated virus.......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...

  8. 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.

  9. Thermal conductivity profile determination in proton-irradiated ZrC by spatial and frequency scanning thermal wave methods

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, C. [GRESPI, Multiscale Thermophysics Lab., Université de Reims Champagne-Ardenne URCA, Moulin de la Housse BP 1039, Reims 51687 (France); Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322 (United States); Chirtoc, M.; Horny, N.; Antoniow, J. S.; Pron, H. [GRESPI, Multiscale Thermophysics Lab., Université de Reims Champagne-Ardenne URCA, Moulin de la Housse BP 1039, Reims 51687 (France); Ban, H. [Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322 (United States)

    2013-10-07

    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{sup −1} K{sup −1} and 26.7 ±1 W m{sup −1} K{sup −1}, respectively. A thermal resistance evidenced in the frequency spectra of the PTR results was calculated to be (1.58 ± 0.1) × 10{sup −6} m{sup 2} K W{sup −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.

  10. 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.).

  11. Efficient genomic correction methods in human iPS cells using CRISPR-Cas9 system.

    Science.gov (United States)

    Li, Hongmei Lisa; Gee, Peter; Ishida, Kentaro; Hotta, Akitsu

    2016-05-15

    Precise gene correction using the CRISPR-Cas9 system in human iPS cells holds great promise for various applications, such as the study of gene functions, disease modeling, and gene therapy. In this review article, we summarize methods for effective editing of genomic sequences of iPS cells based on our experiences correcting dystrophin gene mutations with the CRISPR-Cas9 system. Designing specific sgRNAs as well as having efficient transfection methods and proper detection assays to assess genomic cleavage activities are critical for successful genome editing in iPS cells. In addition, because iPS cells are fragile by nature when dissociated into single cells, a step-by-step confirmation during the cell recovery process is recommended to obtain an adequate number of genome-edited iPS cell clones. We hope that the techniques described here will be useful for researchers from diverse backgrounds who would like to perform genome editing in iPS cells.

  12. [Investigation on remote measurement of air pollution by a method of infrared passive scanning imaging].

    Science.gov (United States)

    Jiao, Yang; Xu, Liang; Gao, Min-Guang; Feng, Ming-Chun; Jin, Ling; Tong, Jing-Jing; Li, Sheng

    2012-07-01

    Passive remote sensing by Fourier-transform infrared (FTIR) spectrometry allows detection of air pollution. However, for the localization of a leak and a complete assessment of the situation in the case of the release of a hazardous cloud, information about the position and the distribution of a cloud is essential. Therefore, an imaging passive remote sensing system comprising an interferometer, a data acquisition and processing software, scan system, a video system, and a personal computer has been developed. The remote sensing of SF6 was done. The column densities of all directions in which a target compound has been identified may be retrieved by a nonlinear least squares fitting algorithm and algorithm of radiation transfer, and a false color image is displayed. The results were visualized by a video image, overlaid by false color concentration distribution image. The system has a high selectivity, and allows visualization and quantification of pollutant clouds.

  13. Method and apparatus for differential spectroscopic atomic-imaging using scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kazmerski, L.L.

    1990-07-17

    This patent describes a spectroscopic scanning tunneling microscope (SSTM) apparatus for differential atomic imaging the surface of a material sample. It comprises: a mounting stage for mounting the sample; a fine-point electrode probe positioned adjacent the mounting stage and being positionable very closely adjacent a sample that is mounted on the stage to accommodate a tunneling current between the sample and the probe; tunable electronic surface bias means connected to the surface of the sample and to the probe for electronically biasing the surface of the sample in relation to the probe with a surface voltage bias; photon bias means adjacent the stage for providing photon biasing of selected wavelengths and frequencies on the surface of the sample adjacent the probe; instrumentation means for measuring tunneling current through the probe and electronic voltage bias; data processing means; and display means.

  14. 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.

  15. 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 (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.

  16. Assessment of the absorbed dose to organs from bone mineral density scan by using TLDS and the Monte Carlo method

    Directory of Open Access Journals (Sweden)

    Karimian Alireza

    2014-01-01

    Full Text Available Nowadays, dual energy X-ray absorptiometry is used in bone mineral density systems to assess the amount of osteoporosis. The purpose of this research is to evaluate patient organ doses from dual X-ray absorptiometry by thermoluminescence dosimeters chips and Monte Carlo method. To achieve this goal, in the first step, the surface dose of the cervix, kidney, abdomen region, and thyroid were measured by using TLD-GR 200 at various organ locations. Then, to evaluate the absorbed dose by simulation, the BMD system, patient's body, X-ray source and radiosensitive tissues were simulated by the Monte Carlo method. The results showed, for the spine (left femur bone mineral density scan by using thermoluminescence dosimeters, the absorbed doses of the cervix and kidney were 4.5 (5.64 and 162.17 (3.99(mGy, respectively. For spine (left femur bone mineral density scan in simulation, the absorbed doses of the cervix and kidney were 4.19 (5.88 and 175 (3.68(mGy, respectively. The data obtained showed that the absorbed dose of the kidney in the spine scan is noticeable. Furthermore, because of the small relative difference between the simulation and experimental results, the radiation absorbed dose may be assessed by simulation and software, especially for internal organs, and at different depths of otherwise inaccessible organs which is not possible in experiments.

  17. 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.

  18. Evaluation method for the potential functionome harbored in the genome and metagenome

    Directory of Open Access Journals (Sweden)

    Takami Hideto

    2012-12-01

    Full Text Available Abstract Background One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG functional modules. Results Distribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules, indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host. Conclusions The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics

  19. 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

    BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleoti...

  20. Tc-99m-Sestamibi scanning with SDZ PSC 833 as a functional detection method for resistance modulation in patients with solid tumours

    NARCIS (Netherlands)

    Bakker, M; Van der Graaf, WTA; Piers, DA; Franssen, EJF; Groen, HJM; Smit, EF; Kool, W; Hollema, H; Muller, EA; de Vries, EGE

    1999-01-01

    Background: Our aim was to determine the value of 99mTc-Sestamibi scanning as functional detection method of P-glycoprotein (Pgp) blockade by PSC 833 in solid tumour patients. Patients and methods: Day 1 and day 4 after 2,200 mg orally administered PSC 833 the tumour area was scanned after intraveno

  1. The research on calibration methods of dual-CCD laser three-dimensional human face scanning system

    Science.gov (United States)

    Wang, Jinjiang; Chang, Tianyu; Ge, Baozhen; Tian, Qingguo; Yang, Fengting; Shi, Shendong

    2013-09-01

    In this paper, on the basis of considering the performance advantages of two-step method, we combines the stereo matching of binocular stereo vision with active laser scanning to calibrate the system. Above all, we select a reference camera coordinate system as the world coordinate system and unity the coordinates of two CCD cameras. And then obtain the new perspective projection matrix (PPM) of each camera after the epipolar rectification. By those, the corresponding epipolar equation of two cameras can be defined. So by utilizing the trigonometric parallax method, we can measure the space point position after distortion correction and achieve stereo matching calibration between two image points. Experiments verify that this method can improve accuracy and system stability is guaranteed. The stereo matching calibration has a simple process with low-cost, and simplifies regular maintenance work. It can acquire 3D coordinates only by planar checkerboard calibration without the need of designing specific standard target or using electronic theodolite. It is found that during the experiment two-step calibration error and lens distortion lead to the stratification of point cloud data. The proposed calibration method which combining active line laser scanning and binocular stereo vision has the both advantages of them. It has more flexible applicability. Theory analysis and experiment shows the method is reasonable.

  2. 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.

  3. Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Julie M Struble

    Full Text Available BACKGROUND: The ability of bacteria to rapidly evolve resistance to antibiotics is a critical public health problem. Resistance leads to increased disease severity and death rates, as well as imposes pressure towards the discovery and development of new antibiotic therapies. Improving understanding of the evolution and genetic basis of resistance is a fundamental goal in the field of microbiology. RESULTS: We have applied a new genomic method, Scalar Analysis of Library Enrichments (SCALEs, to identify genomic regions that, given increased copy number, may lead to aminoglycoside resistance in Pseudomonas aeruginosa at the genome scale. We report the result of selections on highly representative genomic libraries for three different aminoglycoside antibiotics (amikacin, gentamicin, and tobramycin. At the genome-scale, we show significant (p<0.05 overlap in genes identified for each aminoglycoside evaluated. Among the genomic segments identified, we confirmed increased resistance associated with an increased copy number of several genomic regions, including the ORF of PA5471, recently implicated in MexXY efflux pump related aminoglycoside resistance, PA4943-PA4946 (encoding a probable GTP-binding protein, a predicted host factor I protein, a delta 2-isopentenylpyrophosphate transferase, and DNA mismatch repair protein mutL, PA0960-PA0963 (encoding hypothetical proteins, a probable cold shock protein, a probable DNA-binding stress protein, and aspartyl-tRNA synthetase, a segment of PA4967 (encoding a topoisomerase IV subunit B, as well as a chimeric clone containing two inserts including the ORFs PA0547 and PA2326 (encoding a probable transcriptional regulator and a probable hypothetical protein, respectively. CONCLUSIONS: The studies reported here demonstrate the application of new a genomic method, SCALEs, which can be used to improve understanding of the evolution of antibiotic resistance in P. aeruginosa. In our demonstration studies, we

  4. Application of chemometric methods to differential scanning calorimeter (DSC) to estimate nimodipine polymorphs from cosolvent system.

    Science.gov (United States)

    Siddiqui, Akhtar; Rahman, Ziyaur; Khan, Mansoor A

    2015-06-01

    The focus of this study was to evaluate the applicability of chemometrics to differential scanning calorimetry data (DSC) to evaluate nimodipine polymorphs. Multivariate calibration models were built using DSC data from known mixtures of the nimodipine modification. The linear baseline correction treatment of data was used to reduce dispersion in thermograms. Principal component analysis of the treated and untreated data explained 96% and 89% of the data variability, respectively. Score and loading plots correlated variability between samples with change in proportion of nimodipine modifications. The R(2) for principal component regression (PCR) and partial lease square regression (PLS) were found to be 0.91 and 0.92. The root mean square of standard error of the treated samples for calibration and validation in PCR and PLS was found to be lower than the untreated sample. These models were applied to samples recrystallized from a cosolvent system, which indicated different proportion of modifications in the mixtures than those obtained by placing samples under different storage conditions. The model was able to predict the nimodipine modifications with known margin of error. Therefore, these models can be used as a quality control tool to expediently determine the nimodipine modification in an unknown mixture.

  5. Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.

    Science.gov (United States)

    Uchino, Yoshihito; Miura, Takamasa; Hosoyama, Akira; Ohji, Shoko; Yamazoe, Atsushi; Ito, Masako; Takahata, Yoh; Suzuki, Ken-Ichiro; Fujita, Nobuyuki

    2015-01-01

    A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

  6. Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta

    Directory of Open Access Journals (Sweden)

    Cohen Nadine

    2009-03-01

    Full Text Available Abstract Background The monogenic disease osteogenesis imperfecta (OI is due to single mutations in either of the collagen genes ColA1 or ColA2, but within the same family a given mutation is accompanied by a wide range of disease severity. Although this phenotypic variability implies the existence of modifier gene variants, genome wide scanning of DNA from OI patients has not been reported. Promising genome wide marker-independent physical methods for identifying disease-related loci have lacked robustness for widespread applicability. Therefore we sought to improve these methods and demonstrate their performance to identify known and novel loci relevant to OI. Results We have improved methods for enriching regions of identity-by-descent (IBD shared between related, afflicted individuals. The extent of enrichment exceeds 10- to 50-fold for some loci. The efficiency of the new process is shown by confirmation of the identification of the Col1A2 locus in osteogenesis imperfecta patients from Amish families. Moreover the analysis revealed additional candidate linkage loci that may harbour modifier genes for OI; a locus on chromosome 1q includes COX-2, a gene implicated in osteogenesis. Conclusion Technology for physical enrichment of IBD loci is now robust and applicable for finding genes for monogenic diseases and genes for complex diseases. The data support the further investigation of genetic loci other than collagen gene loci to identify genes affecting the clinical expression of osteogenesis imperfecta. The discrimination of IBD mapping will be enhanced when the IBD enrichment procedure is coupled with deep resequencing.

  7. Application of imputation methods to genomic selection in Chinese Holstein cattle

    Directory of Open Access Journals (Sweden)

    Weng Ziqing

    2012-02-01

    Full Text Available Abstract Missing genotypes are a common feature of high density SNP datasets obtained using SNP chip technology and this is likely to decrease the accuracy of genomic selection. This problem can be circumvented by imputing the missing genotypes with estimated genotypes. When implementing imputation, the criteria used for SNP data quality control and whether to perform imputation before or after data quality control need to consider. In this paper, we compared six strategies of imputation and quality control using different imputation methods, different quality control criteria and by changing the order of imputation and quality control, against a real dataset of milk production traits in Chinese Holstein cattle. The results demonstrated that, no matter what imputation method and quality control criteria were used, strategies with imputation before quality control performed better than strategies with imputation after quality control in terms of accuracy of genomic selection. The different imputation methods and quality control criteria did not significantly influence the accuracy of genomic selection. We concluded that performing imputation before quality control could increase the accuracy of genomic selection, especially when the rate of missing genotypes is high and the reference population is small.

  8. Rotated-Random-Scanning: a simple method for set-valued model calibration

    NARCIS (Netherlands)

    Janssen PHM; Heuberger PSC; CWM

    1995-01-01

    Een eenvoudige methode wordt voorgesteld voor het kalibreren van modellen in slecht-gedefinieerde en informatie-arme situaties, die veelvuldig worden aangetroffen bij milieu-onderzoek. De methode volvoert een efficiente zoekaktie in de parameterruimte op basis van Monte Carlo trekkingen in combi

  9. 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...... conventional far-field detectors provides information on centre of mass, crystallographic orientation and stress state of the individual grains [5], at the expense of high spatial resolution. However, far-field detectors have much higher efficiency than near-field detectors, and as such are suitable...

  10. Novel Digital Driving Method Using Dual Scan for Active Matrix Organic Light-Emitting Diode Displays

    Science.gov (United States)

    Jung, Myoung Hoon; Choi, Inho; Chung, Hoon-Ju; Kim, Ohyun

    2008-11-01

    A new digital driving method has been developed for low-temperature polycrystalline silicon, transistor-driven, active-matrix organic light-emitting diode (AM-OLED) displays by time-ratio gray-scale expression. This driving method effectively increases the emission ratio and the number of subfields by inserting another subfield set into nondisplay periods in the conventional digital driving method. By employing the proposed modified gravity center coding, this method can be used to effectively compensate for dynamic false contour noise. The operation and performance were verified by current measurement and image simulation. The simulation results using eight test images show that the proposed approach improves the average peak signal-to-noise ratio by 2.61 dB, and the emission ratio by 20.5%, compared with the conventional digital driving method.

  11. A rapid, non enzymatic method for genomic DNA extraction from whole blood and mammalian tissues

    Directory of Open Access Journals (Sweden)

    Adnan F. N Al-azawy

    2011-05-01

    Full Text Available Although several methods have been exist for DNA extraction from blood or animal tissues samples, traditionally most of these methods consume long time and using expensive chemicals such as proteinase K or toxic organic solvent such as phenol. On the other hand, there is no rapid, simple one method for the extraction of genomic DNA from blood and animal tissues samples in the same time. Since the objective of this study was to development easy modified method for DNA extraction from difference mammalian tissues such as fresh or frozen whole blood, kidney, liver, heart, muscles. The description method have many advantages, reducing the time, using inexpensive materials, no phenol, in addition to small amount of mammalian tissue is required (100-200 mg and 2 ml from whole blood. Genomic DNA was obtained having high molecular weight and good quality, shown by agarose gel electrophoresis and spectrophtometric analysis. These results shown that the modified method is simple, fast, safe, most economical, resulting in a high molecular genomic DNA of good quality from several mammalian tissues and can be used in medical laboratories and research centers.

  12. 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.

  13. 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.

  14. Genome-wide linkage scan for loci of musical aptitude in Finnish families: evidence for a major locus at 4q22.

    Science.gov (United States)

    Pulli, K; Karma, K; Norio, R; Sistonen, P; Göring, H H H; Järvelä, I

    2008-07-01

    Music perception and performance are comprehensive human cognitive functions and thus provide an excellent model system for studying human behaviour and brain function. However, the molecules involved in mediating music perception and performance are so far uncharacterised. To unravel the biological background of music perception, using molecular and statistical genetic approaches. 15 Finnish multigenerational families (with a total of 234 family members) were recruited via a nationwide search. The phenotype of all family members was determined using three tests used in defining musical aptitude: a test for auditory structuring ability (Karma Music test; KMT) commonly used in Finland, and the Seashore pitch and time discrimination subtests (SP and ST respectively) used internationally. We calculated heritabilities and performed a genome-wide variance components-based linkage scan using genotype data for 1113 microsatellite markers. The heritability estimates were 42% for KMT, 57% for SP, 21% for ST and 48% for the combined music test scores. Significant evidence of linkage was obtained on chromosome 4q22 (LOD 3.33) and suggestive evidence of linkage at 8q13-21 (LOD 2.29) with the combined music test scores, using variance component linkage analyses. The major contribution of the 4q22 locus was obtained for the KMT (LOD 2.91). Interestingly, a positive LOD score of 1.69 was shown at 18q, a region previously linked to dyslexia (DYX6) using combined music test scores. Our results show that there is a genetic contribution to musical aptitude that is likely to be regulated by several predisposing genes or variants.

  15. Terrestrial Laser Scanning for Measuring Stream Bank Erosion within Legacy Sediments: Data Processing and Analysis Methods

    Science.gov (United States)

    Starek, M. J.; Mitasova, H.; Wegmann, K. W.

    2011-12-01

    Land clearing for agricultural purposes following European settlement of America resulted in upland erosion rates 50-400 times above long-term geologic rates in much of the North Carolina Piedmont region. A considerable amount of the eroded sediment was subsequently aggraded on floodplains and impounded in the slackwater ponds behind milldams. This trapped "legacy" sediment is commonly mistaken for natural floodplain deposition and has remained largely unrecognized as a potential source of accelerated sediment erosion contributing to modern water quality impairment. In this study, terrestrial laser scanning (TLS) is utilized to monitor stream bank evolution along a reach that has breached a former millpond. Due to the unique surface geometry and orientation of the stream bank, vegetation occlusion, and true 3D structure of the point cloud, a systematic data processing approach is implemented to compute the change in sediment volume between repeat TLS surveys. The processing approach consists of the following four steps: 1) segmentation of the stream bank point cloud; 2) transformation of the point cloud such that the xy plane is parallel to the trend of the bank; 3) filter vegetation by selecting local lowest point within a grid cell; 4) smooth high frequency noise 5) generate bare earth digital elevation model (DEM). From the DEMs, change in volume was quantified for a 13 m x 3.5 m section of the stream bank providing an estimate on erosion rates and slumping between surveys. The major mechanisms for the observed changes are freeze-thaw events and fluvial entrainment. To evaluate the surface evolution between the distinct sedimentary layers (legacy vs non-legacy) that comprise the stream bank, elevation change is modeled as a continuous trivariate function z = f(x,y,t) where x,y is horizontal location, t is time, and z is a first-surface referenced elevation. Hence, z=0 for all x,y at t=0, time of first survey. The filtered, transformed, and first

  16. [A novel method of the genome-wide prediction for the target genes and its application].

    Science.gov (United States)

    Zhang, Jing-Jing; Feng, Jing; Zhu, Ying-Guo; Li, Yang-Sheng

    2006-10-01

    Based on the protein databases of several model species, this study developed a new method of the Genome-wide prediction for the target genes, using Hidden Markov model by Perl programming. The advantages of this method are high throughput, high quality and easy prediction, especially in the case of multi-domains proteins families. By this method, we predicted the PPR and TPR proteins families in whole genome of several model species. There were 536 PPR proteins and 199 TPR proteins in Oryza sativa ssp. japonica, 519 PPR proteins and 177 TPR proteins in Oryza sativa L. ssp. indica, 735 PPR proteins and 292 TPR proteins in Arabidopsis thaliana, 6 PPR proteins and 32 TPR proteins in Cyanidioschyzon merolae. Synechococcus and Thermophilic archaebacterium did not have PPR proteins. By contrast, 10 TPR proteins were found in Synechococcus and 4 TPR proteins were found in Thermophilic archaebacterium. Moreover, of these results, some further bioinformatics analyses were conducted.

  17. Pantograph: A template-based method for genome-scale metabolic model reconstruction.

    Science.gov (United States)

    Loira, Nicolas; Zhukova, Anna; Sherman, David James

    2015-04-01

    Genome-scale metabolic models are a powerful tool to study the inner workings of biological systems and to guide applications. The advent of cheap sequencing has brought the opportunity to create metabolic maps of biotechnologically interesting organisms. While this drives the development of new methods and automatic tools, network reconstruction remains a time-consuming process where extensive manual curation is required. This curation introduces specific knowledge about the modeled organism, either explicitly in the form of molecular processes, or indirectly in the form of annotations of the model elements. Paradoxically, this knowledge is usually lost when reconstruction of a different organism is started. We introduce the Pantograph method for metabolic model reconstruction. This method combines a template reaction knowledge base, orthology mappings between two organisms, and experimental phenotypic evidence, to build a genome-scale metabolic model for a target organism. Our method infers implicit knowledge from annotations in the template, and rewrites these inferences to include them in the resulting model of the target organism. The generated model is well suited for manual curation. Scripts for evaluating the model with respect to experimental data are automatically generated, to aid curators in iterative improvement. We present an implementation of the Pantograph method, as a toolbox for genome-scale model reconstruction, curation and validation. This open source package can be obtained from: http://pathtastic.gforge.inria.fr.

  18. Geometric correction method of rotary scanning hyperspectral image in agriculture application

    Science.gov (United States)

    Wan, Peng; Yang, Guijun; Xu, Bo; Feng, Haikuan; Yu, Haiyang

    2015-04-01

    In order to meet the demand of farmland plot experiments hyperspectral images acquisition, an equipment that incorporating an aerial lift vehicle with hyperspectral imager was proposed. In this manner, high spatial resolution (in millimeter) imageries were collected, which meets the need of spatial resolution on farm experiments, but also improves the efficiency of image acquisition. In allusion to the image circular geometric distortion which produced by telescopic arm rotation, an image rectification method that based on mounted position and orientation system was proposed. Experimental results shows that the image rectification method is effective.

  19. Dating the age of admixture via wavelet transform analysis of genome-wide data

    NARCIS (Netherlands)

    I. Pugach (Irina); R. Matveyev (Rostislav); A. Wollstein (Andreas); M.H. Kayser (Manfred); M. Stoneking (Mark)

    2011-01-01

    textabstractWe describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixe

  20. 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...

  1. 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.)

  2. 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.

  3. Improving the efficiency and relevance of evidence-based recommendations in the era of whole-genome sequencing: an EGAPP methods update.

    Science.gov (United States)

    Veenstra, David L; Piper, Margaret; Haddow, James E; Pauker, Stephen G; Klein, Roger; Richards, Carolyn Sue; Tunis, Sean R; Djulbegovic, Benjamin; Marrone, Michael; Lin, Jennifer S; Berg, Alfred O; Calonge, Ned

    2013-01-01

    To provide an update on recent revisions to Evaluation of Genomic Applications in Practice and Prevention (EGAPP) methods designed to improve efficiency, and an assessment of the implications of whole genome sequencing for evidence-based recommendation development. Improvements to the EGAPP approach include automated searches for horizon scanning, a quantitative ranking process for topic prioritization, and the development of a staged evidence review and evaluation process. The staged process entails (i) triaging tests with minimal evidence of clinical validity, (ii) using and updating existing reviews, (iii) evaluating clinical validity prior to analytic validity or clinical utility, (iv) using decision modeling to assess potential clinical utility when direct evidence is not available. EGAPP experience to date suggests the following approaches will be critical for the development of evidence based recommendations in the whole genome sequencing era: (i) use of triage approaches and frameworks to improve efficiency, (ii) development of evidence thresholds that consider the value of further research, (iii) incorporation of patient preferences, and (iv) engagement of diverse stakeholders. The rapid advances in genomics present a significant challenge to traditional evidence based medicine, but also an opportunity for innovative approaches to recommendation development.

  4. Femtosecond laser fabrication of long period fiber gratings by a transversal-scanning inscription method and the research of its orientational bending characteristics

    Science.gov (United States)

    Dong, Xin-Ran; Sun, Xiao-Yan; Li, Hai-Tao; Hu, You-Wang; Duan, Ji-An; Zhou, Jian-Ying; Wang, Cong

    2015-08-01

    In order to make the whole fiber core modified, an improved point-by-point inscription method (called a transversal-scanning inscription method) is proposed to fabricate long period fiber gratings (LPFGs) by using femtosecond laser. LPFGs with an attenuation depth of 16 dB are achieved within the wavelength range of 1580-1680 nm. We have compared the bending properties of LPFGs fabricated by the line-by-line scanning inscription method and the transversal-scanning inscription method at the orthogonal directions. It is found that increasing scanning area using the transversal-scanning method can enhance the bend sensitivity obviously. The resulting curvature sensitivities are -4.82 nm/m-1 and -1.63 nm/m-1 at the 0° and 90° bend orientations respectively, within the curvature range from 1.75 m-1 to 3 m-1 in the experiment. The LPFG-I fabricated by the line-by-line scanning inscription method experiences red-shift, while the LPFG-II fabricated by the transversal-scanning inscription method experiences blue-shift.

  5. Application of dose kernel calculation using a simplified Monte Carlo method to treatment plan for scanned proton beams.

    Science.gov (United States)

    Mizutani, Shohei; Takada, Yoshihisa; Kohno, Ryosuke; Hotta, Kenji; Tansho, Ryohei; Akimoto, Tetsuo

    2016-03-01

    Full Monte Carlo (FMC) calculation of dose distribution has been recognized to have superior accuracy, compared with the pencil beam algorithm (PBA). However, since the FMC methods require long calculation time, it is difficult to apply them to routine treatment planning at present. In order to improve the situation, a simplified Monte Carlo (SMC) method has been introduced to the dose kernel calculation applicable to dose optimization procedure for the proton pencil beam scanning. We have evaluated accuracy of the SMC calculation by comparing a result of the dose kernel calculation using the SMC method with that using the FMC method in an inhomogeneous phantom. The dose distribution obtained by the SMC method was in good agreement with that obtained by the FMC method. To assess the usefulness of SMC calculation in clinical situations, we have compared results of the dose calculation using the SMC with those using the PBA method for three clinical cases of tumor treatment. The dose distributions calculated with the PBA dose kernels appear to be homogeneous in the planning target volumes (PTVs). In practice, the dose distributions calculated with the SMC dose kernels with the spot weights optimized with the PBA method show largely inhomogeneous dose distributions in the PTVs, while those with the spot weights optimized with the SMC method have moderately homogeneous distributions in the PTVs. Calculation using the SMC method is faster than that using the GEANT4 by three orders of magnitude. In addition, the graphic processing unit (GPU) boosts the calculation speed by 13 times for the treatment planning using the SMC method. Thence, the SMC method will be applicable to routine clinical treatment planning for reproduction of the complex dose distribution more accurately than the PBA method in a reasonably short time by use of the GPU-based calculation engine. PACS number(s): 87.55.Gh.

  6. 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

  7. Insulating method using cataphoretic paint for tungsten tips for electrochemical scanning tunnelling microscopy (ECSTM)

    Science.gov (United States)

    Zhu, L.; Claude-Montigny, B.; Gattrell, M.

    2005-12-01

    A new tip insulating process for active metal tips allowing atomic resolution ECSTM imaging has been developed. This new method using cathodic cataphoretic paint deposition has been tested successfully. The insulating deposited film appears homogeneous under optical microscopy and it has been characterised by infra red and SEM analysis. The depositing layer of the paint is sufficiently dense to effectively resist electrolyte ion penetration and resists corrosion in various acidic, basic aqueous or non-aqueous media. The coating film does not reduce the imaging capability of the ECSTM even to atomic resolution. This new insulating method adds to the approaches available to those preparing tips for ECSTM. This approach would also be of great utility for the preparation of microelectrodes using active metals.

  8. A new iterative method for liver segmentation from perfusion CT scans

    Science.gov (United States)

    Draoua, Ahmed; Albouy-Kissi, Adélaïde; Vacavant, Antoine; Sauvage, Vincent

    2014-03-01

    Liver cancer is the third most common cancer in the world, and the majority of patients with liver cancer will die within one year as a result of the cancer. Liver segmentation in the abdominal area is critical for diagnosis of tumor and for surgical procedures. Moreover, it is a challenging task as liver tissue has to be separated from adjacent organs and substantially the heart. In this paper we present a novel liver segmentation iterative method based on Fuzzy C-means (FCM) coupled with a fast marching segmentation and mutual information. A prerequisite for this method is the determination of slice correspondences between ground truth that is, a few images segmented by an expert, and images that contain liver and heart at the same time.

  9. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

    Science.gov (United States)

    Lin, Michael F; Jungreis, Irwin; Kellis, Manolis

    2011-07-01

    As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE, and as interest grows in long non-coding RNAs, often initially recognized by their lack of protein coding potential rather than conserved RNA secondary structures. The Objective Caml source code and executables for GNU/Linux and Mac OS X are freely available at http://compbio.mit.edu/PhyloCSF CONTACT: mlin@mit.edu; manoli@mit.edu.

  10. A Hybrid Method for Segmentation and Visualization of Teeth in Multi-Slice CT scan Images

    Directory of Open Access Journals (Sweden)

    Mohammad Hosntalab

    2009-12-01

    Full Text Available Introduction: Various computer assisted medical procedures such as dental implant, orthodontic planning, face, jaw and cosmetic surgeries require automatic quantification and volumetric visualization of teeth. In this regard, segmentation is a major step. Material and Methods: In this paper, inspired by our previous experiences and considering the anatomical knowledge of teeth and jaws, we propose a hybrid technique for teeth segmentation and visualization in CT volumetric data. The major steps of the proposed techniques are as follows: (1 Separation of teeth in CT dataset; (2 Initial segmentation of teeth in panoramic projection; (3 Final segmentation of teeth in CT dataset; (4 3D visualization of teeth. Results: The proposed algorithm was evaluated in 30 multi-slice CT datasets. Segmented images were compared with manually outlined contours. In order to evaluate the proposed method, we utilized several common performance measures such as sensitivity, specificity, precision, accuracy and mean error rate. The experimental results reveal the effectiveness of the proposed method. Discussion and Conclusion: In the proposed algorithm, the variationallevel set technique was utilized to trace the contour of the teeth. In view of the fact that this technique is based on the characteristics of the overall region of the tooth image, it is possible to extract a very smooth and accurate tooth contour using this technique. For the available datasets, the proposed technique was more successful in teeth segmentation compared to previous techniques.

  11. Ultrasonic lateral modulation imaging, speckle reduction, and displacement vector measurements using simple single-beam scanning or plural crossed-beam scanning with new spectra frequency division processing methods

    Directory of Open Access Journals (Sweden)

    Sumi C

    2012-10-01

    Full Text Available Chikayoshi Sumi, Yousuke IshiiDepartment of Information and Communication Sciences, Faculty of Science and Technology, Sophia University, Tokyo, JapanAbstract: The development of effective ultrasonic tissue displacement measurement methods increases the number of possible applications for various tissue displacement and strain measurements. These applications include measurements of spontaneous motions/deformations generated by heart motion; pulsations from phenomena such as blood flow (intracardiac, intravascular, and carotid; heart, blood vessel, and liver motion; and motion from artificial sources such as motions/deformations generated by applying static compression/stretching forces, vibration or acoustic radiation forces (breast and liver. For arbitrary orthogonal coordinate systems obtained using arbitrary transducer types (eg, linear, convex, sector, arc, or radial array types, or single aperture types with a mechanical scan, several lateral modulation (LM methods (eg, scanning with plural crossed or steered beams over a region of interest have been developed that can be used with new echo imaging methods for tissue displacement/deformation measurements. Specifically, by using such beamforming methods, in addition to highly accurate displacement vector and lateral displacement measurements, LM echo imaging with a high lateral carrier frequency and a high lateral resolution has been developed. Another new beamforming method, referred to as “a steering angle (ASTA method,” ie, scanning with a defined steering angle, is also described. In addition to conventional non-steered-beam scanning (ie, a version of ASTA and conventional steered-beam scanning with a variable steering angle (eg, sector, arc, radial scan, a simple, single-beam scanning method also permits the use of LM, which yields an accurate displacement vector measurement with fewer calculations than the original LM methods. This is accomplished by using a previously developed

  12. 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 ...

  13. Comparative assessment of performance and genome dependence among phylogenetic profiling methods

    Directory of Open Access Journals (Sweden)

    Wu Jie

    2006-09-01

    Full Text Available Abstract Background The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. With the increasing number of sequenced eukaryotic genomes comes a need for bioinformatic techniques to aid in functional annotation. Ideally, genome context based techniques such as proximity, fusion, and phylogenetic profiling, which have been so successful in prokaryotes, could be utilized in eukaryotes. Here we explore the application of phylogenetic profiling, a method that exploits the evolutionary co-occurrence of genes in the assignment of functional linkages, to eukaryotic genomes. Results In order to evaluate the performance of phylogenetic profiling in eukaryotes, we assessed the relative performance of commonly used profile construction techniques and genome compositions in predicting functional linkages in both prokaryotic and eukaryotic organisms. When predicting linkages in E. coli with a prokaryotic profile, the use of continuous values constructed from transformed BLAST bit-scores performed better than profiles composed of discretized E-values; the use of discretized E-values resulted in more accurate linkages when using S. cerevisiae as the query organism. Extending this analysis by incorporating several eukaryotic genomes in profiles containing a majority of prokaryotes resulted in similar overall accuracy, but with a surprising reduction in pathway diversity among the most significant linkages. Furthermore, the application of phylogenetic profiling using profiles composed of only eukaryotes resulted in the loss of the strong correlation between common KEGG pathway membership and profile similarity score. Profile construction methods, orthology definitions, ontology and domain complexity were explored as possible sources of the poor performance of eukaryotic profiles, but with no improvement in results. Conclusion Given the current set of

  14. A three-stage method for the 3D reconstruction of the tracheobronchial tree from CT scans.

    Science.gov (United States)

    Rosell, Jan; Cabras, Paolo

    2013-01-01

    This paper proposes a method for segmenting the airways from CT scans of the chest to obtain a 3D model that can be used in the virtual bronchoscopy for the exploration and the planning of paths to the lesions. The method is composed of 3 stages: a gross segmentation that reconstructs the main airway tree using adaptive region growing, a finer segmentation that identifies any potential airway region based on a 2D process that enhances bronchi walls using local information, and a final process to connect any isolated bronchus to the main airways using a morphologic reconstruction process and a path planning technique. The paper includes two examples for the evaluation and discussion of the proposal.

  15. 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.)

  16. Genome-wide identification of new Wnt/β-catenin target genes in the human genome using CART method

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    Inestrosa Nibaldo C

    2010-06-01

    Full Text Available Abstract Background The importance of in silico predictions for understanding cellular processes is now widely accepted, and a variety of algorithms useful for studying different biological features have been designed. In particular, the prediction of cis regulatory modules in non-coding human genome regions represents a major challenge for understanding gene regulation in several diseases. Recently, studies of the Wnt signaling pathway revealed a connection with neurodegenerative diseases such as Alzheimer's. In this article, we construct a classification tool that uses the transcription factor binding site motifs composition of some gene promoters to identify new Wnt/β-catenin pathway target genes potentially involved in brain diseases. Results In this study, we propose 89 new Wnt/β-catenin pathway target genes predicted in silico by using a method based on multiple Classification and Regression Tree (CART analysis. We used as decision variables the presence of transcription factor binding site motifs in the upstream region of each gene. This prediction was validated by RT-qPCR in a sample of 9 genes. As expected, LEF1, a member of the T-cell factor/lymphoid enhancer-binding factor family (TCF/LEF1, was relevant for the classification algorithm and, remarkably, other factors related directly or indirectly to the inflammatory response and amyloidogenic processes also appeared to be relevant for the classification. Among the 89 new Wnt/β-catenin pathway targets, we found a group expressed in brain tissue that could be involved in diverse responses to neurodegenerative diseases, like Alzheimer's disease (AD. These genes represent new candidates to protect cells against amyloid β toxicity, in agreement with the proposed neuroprotective role of the Wnt signaling pathway. Conclusions Our multiple CART strategy proved to be an effective tool to identify new Wnt/β-catenin pathway targets based on the study of their regulatory regions in the human

  17. A comprehensive uncertainty analysis and method of geometric calibration for a circular scanning airborne lidar

    Science.gov (United States)

    Gonsalves, Michael Oliver

    This dissertation describes an automated technique for ascertaining the values of the geometric calibration parameters of an airborne lidar. A least squares approach is employed that adjusts the point cloud to a single planar surface which could be either a narrow airport runway or a dynamic sea surface. Going beyond the customary three boresight angles, the proposed adjustment can determine up to eleven calibration parameters to a precision that renders a negligible contribution to the point cloud's positional uncertainty. Presently under development is the Coastal Zone Mapping and Imaging Lidar (CZMIL), which, unlike most contemporary systems that use oscillating mirrors to reflect the beam, will use a circular spinning prism to refract the laser in the desired direction. This departure from the traditional scanner presents the potential for internal geometric misalignments not previously experienced. Rather than relying on past calibration practices (like requiring data be acquired over a pitched-roof), a more robust method of calibration is established which does not depend on the presence of any cultural features. To develop this new method of calibration, the laser point positioning equation for this lidar was developed first. The system was then simulated in the MATLAB environment. Using these artificial datasets, the behavior of each geometric parameter iii was systematically manipulated, understood and calibrated, while an optimal flight strategy for the calibration acquisition was simultaneously developed. Finally, the total propagated uncertainty (TPU) of the point cloud was determined using a propagation of variances. Using this TPU module, the strength of the calibration solution was assessed. For example, four flight lines each of 20 seconds in duration contained sufficient information to determine the calibration parameters to such a degree of confidence that their contribution to the final point cloud uncertainty was only 0.012m in the horizontal

  18. A segmentation method for 3D visualization of neurons imaged with a confocal laser scanning microscope

    Science.gov (United States)

    Anderson, Jeffrey R.; Barrett, Steven F.; Wilcox, Michael J.

    2005-04-01

    Our understanding of the world around us is based primarily on three-dimensional information because of the environment in which we live and interact. Medical or biological image information is often collected in the form of two-dimensional, serial section images. As such, it is difficult for the observer to mentally reconstruct the three dimensional features of each object. Although many image rendering software packages allow for 3D views of the serial sections, they lack the ability to segment, or isolate different objects in the data set. Segmentation is the key to creating 3D renderings of distinct objects from serial slice images, like separate pieces to a puzzle. This paper describes a segmentation method for objects recorded with serial section images. The user defines threshold levels and object labels on a single image of the data set that are subsequently used to automatically segment each object in the remaining images of the same data set, while maintaining boundaries between contacting objects. The performance of the algorithm is verified using mathematically defined shapes. It is then applied to the visual neurons of the housefly, Musca domestica. Knowledge of the fly"s visual system may lead to improved machine visions systems. This effort has provided the impetus to develop this segmentation algorithm. The described segmentation method can be applied to any high contrast serial slice data set that is well aligned and registered. The medical field alone has many applications for rapid generation of 3D segmented models from MRI and other medical imaging modalities.

  19. Choosing a suitable method for the identification of replication origins in microbial genomes

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    Chengcheng eSong

    2015-09-01

    Full Text Available As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. Using various in silico approaches such as Ori-Finder 2, and databases such as DoriC and oriDB, researchers have predicted the locations of replication origins sites for thousands bacterial chromosomes and archaeal genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.

  20. Comparison of Two Methods for the Isolation of Genomic DNA from Cyathostomin Adult Parasites

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    Juliana Bana ISHII

    2017-07-01

    Full Text Available Cyathostomins are the most common and important group of large intestine nematodes, infecting horses worldwide. The current control strategy is associated with the development of anthelmintic resistance, which has been reported worldwide. Therefore, experiments with this family of parasites have become progressively important to provide their monitoring and control strategies. The aim of the present study was to propose a faster and more economic assay for isolation of genomic DNA from the adult stage of Cyathostomin parasites than reported. Adult parasites were collected from a single horse from a farm in São José dos Pinhais, PR, Brazil, and were identified. Genomic DNA was isolated from ten individual female adult parasites using a standardized procedure developed. Then, extraction from ten individual female was carried out by another DNA extraction method. DNA concentration from both methods were measured and compared. We obtained a good DNA quality with this standardized procedure. As a result of this analysis, we propose a modified phenol-chloroform method, which will contribute to assays that require DNA extraction from adult worms for genomic DNA sequences of cyathostomin, or species-specific identification.

  1. 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......-scan and from laser scans) are alike to different observers. We found the best inter-observer agreement for the bones versus 3D visualizations, with the highest values for the auricular surface. Between the 3D modalities, less variability was obtained for the 3D laser visualizations. Fair inter...

  2. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection

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    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 redu