WorldWideScience

Sample records for digital genome scanning

  1. Human Digital Modeling & Hand Scanning Lab

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory incorporates specialized scanning equipment, computer workstations and software applications for the acquisition and analysis of digitized models of...

  2. 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

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  4. Out-of-Print Digital Scanning.

    Science.gov (United States)

    Kellerman, L. Suzanne

    2002-01-01

    Describes the in-house operational procedures developed at the Penn State University libraries to produce facsimiles of hard-to-locate, out-of-print titles using digital scanning technologies. Highlights include identification and selection, costs, copyright issues, interlibrary loan, materials preparation, and future trends. (Author/LRW)

  5. Digital X-Radiography Scanning Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Generates digital X-radiographic images of sediment cores that portray density variations, sediment stratigraphy, bioturbation, and inclusions.DESCRIPTION:...

  6. PC-based digital feedback control for scanning force microscope

    International Nuclear Information System (INIS)

    Mohd Ashhar Khalid

    2002-01-01

    In the past, most digital feedback implementation for scanned-probe microscope were based on a digital signal processor (DSP). At present DSP plug-in card with the input-output interface module is still expensive compared to a fast pentium PC motherboard. For a magnetic force microscope (MFM) digital feedback has an advantage where the magnetic signal can be easily separated from the topographic signal. In this paper, a simple low-cost PC-based digital feedback and imaging system for Scanning Force Microscope (SFM) is presented. (Author)

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

    Science.gov (United States)

    2010-06-01

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

  8. Genome-wide DNA polymorphism analyses using VariScan

    Directory of Open Access Journals (Sweden)

    Vilella Albert J

    2006-09-01

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

  9. Surpassing digital holography limits by lensless object scanning holography.

    Science.gov (United States)

    Micó, Vicente; Ferreira, Carlos; García, Javier

    2012-04-23

    We present lensless object scanning holography (LOSH) as a fully lensless method, capable of improving image quality in reflective digital Fourier holography, by means of an extremely simplified experimental setup. LOSH is based on the recording and digital post-processing of a set of digital lensless holograms and results in a synthetic image with improved resolution, field of view (FOV), signal-to-noise ratio (SNR), and depth of field (DOF). The superresolution (SR) effect arises from the generation of a synthetic aperture (SA) based on the linear movement of the inspected object. The same scanning principle enlarges the object FOV. SNR enhancement is achieved by speckle suppression and coherent artifacts averaging due to the coherent addition of the multiple partially overlapping bandpass images. And DOF extension is performed by digital refocusing to different object's sections. Experimental results showing an impressive image quality improvement are reported for a one-dimensional reflective resolution test target. © 2012 Optical Society of America

  10. Scanning negatives and slides digitizing your photographic archive

    CERN Document Server

    Steinhoff, Sascha

    2009-01-01

    Many photographers have either moved into digital photography exclusively or use both analog and digital media in their work. In either case, there is sure to be an archive of slides and negatives that cannot be directly integrated into the new digital workflow, nor can it be archived in a digital format. Increasingly, photographers are trying to bridge this gap with the use of high-performance film scanners. In this 2nd edition, you will learn how to achieve the best possible digital image from a negative or a slide, and how to build a workflow to make this process efficient, repeatable, and reliable. The author uses Nikon's film scanners, but all steps can easily be accomplished while using a different scanner. The most common software tools for scanning (SilverFast, VueScan, NikonScan) are not only covered extensively in the book, but trial versions are also provided on a DVD, which also contains other useful tools for image editing, as well as numerous sample scans.

  11. Comparison of dimensional accuracy of digital dental models produced from scanned impressions and scanned stone casts

    Science.gov (United States)

    Subeihi, Haitham

    Introduction: Digital models of dental arches play a more and more important role in dentistry. A digital dental model can be generated by directly scanning intraoral structures, by scanning a conventional impression of oral structures or by scanning a stone cast poured from the conventional impression. An accurate digital scan model is a fundamental part for the fabrication of dental restorations. Aims: 1. To compare the dimensional accuracy of digital dental models produced by scanning of impressions versus scanning of stone casts. 2. To compare the dimensional accuracy of digital dental models produced by scanning of impressions made of three different materials (polyvinyl siloxane, polyether or vinyl polyether silicone). Methods and Materials: This laboratory study included taking addition silicone, polyether and vinyl polyether silicone impressions from an epoxy reference model that was created from an original typodont. Teeth number 28 and 30 on the typodont with a missing tooth number 29 were prepared for a metal-ceramic three-unit fixed dental prosthesis with tooth #29 being a pontic. After tooth preparation, an epoxy resin reference model was fabricated by duplicating the typodont quadrant that included the tooth preparations. From this reference model 12 polyvinyl siloxane impressions, 12 polyether impressions and 12 vinyl polyether silicone impressions were made. All 36 impressions were scanned before pouring them with dental stone. The 36 dental stone casts were, in turn, scanned to produce digital models. A reference digital model was made by scanning the reference model. Six groups of digital models were produced. Three groups were made by scanning of the impressions obtained with the three different materials, the other three groups involved the scanning of the dental casts that resulted from pouring the impressions made with the three different materials. Groups of digital models were compared using Root Mean Squares (RMS) in terms of their

  12. Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR.

    Science.gov (United States)

    Decraene, Charles; Silveira, Amanda B; Bidard, François-Clément; Vallée, Audrey; Michel, Marc; Melaabi, Samia; Vincent-Salomon, Anne; Saliou, Adrien; Houy, Alexandre; Milder, Maud; Lantz, Olivier; Ychou, Marc; Denis, Marc G; Pierga, Jean-Yves; Stern, Marc-Henri; Proudhon, Charlotte

    2018-02-01

    Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited. We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan ® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events. The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations. This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy. © 2017 American Association for Clinical Chemistry.

  13. Uninformative polymorphisms bias genome scans for signatures of selection

    Directory of Open Access Journals (Sweden)

    Roesti Marius

    2012-06-01

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

  14. A digital gigapixel large-format tile-scan camera.

    Science.gov (United States)

    Ben-Ezra, M

    2011-01-01

    Although the resolution of single-lens reflex (SLR) and medium-format digital cameras has increased in recent years, applications for cultural-heritage preservation and computational photography require even higher resolutions. Addressing this issue, a large-format cameras' large image planes can achieve very high resolution without compromising pixel size and thus can provide high-quality, high-resolution images.This digital large-format tile scan camera can acquire high-quality, high-resolution images of static scenes. It employs unique calibration techniques and a simple algorithm for focal-stack processing of very large images with significant magnification variations. The camera automatically collects overlapping focal stacks and processes them into a high-resolution, extended-depth-of-field image.

  15. Digital radiographic scanning installation with multiwire proportional chamber

    International Nuclear Information System (INIS)

    Babichev, E.A.; Baru, S.E.; Khabakhpashev, A.G.; Kolachev, G.M.; Savinov, G.A.; Shekhtman, L.I.; Sidorov, V.A.; Volobuev, A.I.

    1991-01-01

    A digital radiographic installation for medical diagnostics is described. Distribution of X-ray intensity in horizontal direction is measured by a one-coordinate MWPC with a 1.2 mm channel. A two-dimensional image is produced by mechanical scanning with 1 mm channel width in vertical direction. The number of pixels in the image is 320x256. The MWPC works in count mode with quantum efficiency 25% (50 keV) and count rate capability 600 kHz/channel. Results of testing a prototype with 64 channels 0.6 mm width are also presented. (orig.)

  16. Accuracy of a computed tomography scanning procedure to manufacture digital models.

    NARCIS (Netherlands)

    Darroudi, A.M.; Kuijpers-Jagtman, A.M.; Ongkosuwito, E.M.; Suttorp, C.M.; Bronkhorst, E.M.; Breuning, K.H.

    2017-01-01

    INTRODUCTION: Accurate articulation of the digital dental casts is crucial in orthodontic diagnosis and treatment planning. We aimed to determine the accuracy of manufacturing digital dental casts from computed tomography scanning of plaster casts regarding linear dimensions and interarch

  17. Digital examination and transvaginal scan - competing or complementary for predicting preterm birth?

    DEFF Research Database (Denmark)

    Reiter, Eva; Nielsen, Kurt Aagaard; Fedder, Jens

    2012-01-01

    The transvaginal ultrasonographic cervix scan has partly replaced digital examination for diagnosing preterm birth; conflicting results are reported about their respective contribution to birth prediction....

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

    Science.gov (United States)

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

    2009-06-02

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

  19. Automatic scanning of Cerenkov light photograms from a multistep avalanche chamber using a television digitizer

    International Nuclear Information System (INIS)

    Vascon, M.; Zanella, G.

    1980-01-01

    A television digitizer and its application to automatic scanning of Cerenkov imaging using the multistep avalanche chamber in front of optical spark chamber are described. The results are of interest in the adoption of the automatic scanning of photographic plates of these events or for the on-line application of the television digitizer itself. (orig.)

  20. Integration of Digital Dental Casts in Cone-Beam Computed Tomography Scans

    OpenAIRE

    Rangel, Frits A.; Maal, Thomas J. J.; Bergé, Stefaan J.; Kuijpers-Jagtman, Anne Marie

    2012-01-01

    Cone-beam computed tomography (CBCT) is widely used in maxillofacial surgery. The CBCT image of the dental arches, however, is of insufficient quality to use in digital planning of orthognathic surgery. Several authors have described methods to integrate digital dental casts into CBCT scans, but all reported methods have drawbacks. The aim of this feasibility study is to present a new simplified method to integrate digital dental casts into CBCT scans. In a patient scheduled for orthognathic ...

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Jingjing Gu

    2009-06-01

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

  3. Digital acquisition and processing of electron micrographs using a scanning transmission electron microscope

    International Nuclear Information System (INIS)

    Engel, A.; Christen, F.; Michel, B.

    1981-01-01

    A digital acquisition system that collects multichannel information from a scanning transmission electron microscope (STEM) and its application are described. The hardware comprises (i) single electron counting detectors, (ii) a digital scan generator, (iii) a digital multi-channel on-line processor, (iv) an interface to a minicomputer, and (v) a display system. Experimental results characterizing these components are presented, and their performance is discussed. The software includes assembler coded programs for dynamic file maintenance and fast acquisition of image data, a display driver, and FORTRAN coded application programs. The usefulness of digitized STEM is illustrated by a variety of biological applications. (orig.)

  4. Digital Conically Scanned L-Band Radar, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed effort seeks to develop a digitally steered polarimetric phased array L-Band radar utilizing a novel, high performance architecture leveraging recent...

  5. 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.

  6. Integration of digital dental casts in cone-beam computed tomography scans

    NARCIS (Netherlands)

    Rangel, F.A.; Maal, T.J.J.; Berge, S.J.; Kuijpers-Jagtman, A.M.

    2012-01-01

    Cone-beam computed tomography (CBCT) is widely used in maxillofacial surgery. The CBCT image of the dental arches, however, is of insufficient quality to use in digital planning of orthognathic surgery. Several authors have described methods to integrate digital dental casts into CBCT scans, but all

  7. 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

  8. Benefits and unexpected artifacts of biplanar digital slot-scanning imaging in children

    Energy Technology Data Exchange (ETDEWEB)

    Blumer, Steven L. [Nemours/A.I duPont Hospital for Children, Department of Medical Imaging, Wilmington, DE (United States); Dinan, David [Nemours Children' s Hospital, Orlando, FL (United States); Grissom, Leslie E. [Nemours/Alfred I. duPont Hospital for Children, Department of Radiology, Wilmington, DE (United States)

    2014-07-15

    Biplanar digital slot-scanning allows for relatively low-dose orthopedic imaging, an advantage in imaging children given the growing concerns regarding radiosensitivity. We have used this system for approximately 1 year for orthopedic imaging of the spine and lower extremities. We have noted advantages of using the digital slot-scanning system when compared with computed radiographic and standard digital radiographic imaging systems, but we also found unexpected but common imaging artifacts that are the direct result of the imaging method and that have not been reported. This pictorial essay serves to familiarize radiologists with the advantages of the digital slot-scanning system as well as imaging artifacts common with this new technology. (orig.)

  9. Integration of Digital Dental Casts in Cone-Beam Computed Tomography Scans

    Science.gov (United States)

    Rangel, Frits A.; Maal, Thomas J. J.; Bergé, Stefaan J.; Kuijpers-Jagtman, Anne Marie

    2012-01-01

    Cone-beam computed tomography (CBCT) is widely used in maxillofacial surgery. The CBCT image of the dental arches, however, is of insufficient quality to use in digital planning of orthognathic surgery. Several authors have described methods to integrate digital dental casts into CBCT scans, but all reported methods have drawbacks. The aim of this feasibility study is to present a new simplified method to integrate digital dental casts into CBCT scans. In a patient scheduled for orthognathic surgery, titanium markers were glued to the gingiva. Next, a CBCT scan and dental impressions were made. During the impression-taking procedure, the titanium markers were transferred to the impression. The impressions were scanned, and all CBCT datasets were exported in DICOM format. The two datasets were matched, and the dentition derived from the scanned impressions was transferred to the CBCT of the patient. After matching the two datasets, the average distance between the corresponding markers was 0.1 mm. This novel method allows for the integration of digital dental casts into CBCT scans, overcoming problems such as unwanted extra radiation exposure, distortion of soft tissues due to the use of bite jigs, and time-consuming digital data handling. PMID:23050159

  10. Impact of digital intraoral scan strategies on the impression accuracy using the TRIOS Pod scanner.

    Science.gov (United States)

    Müller, Philipp; Ender, Andreas; Joda, Tim; Katsoulis, Joannis

    2016-04-01

    Little information is available on the impact of different scan strategies on the accuracy of full-arch scans with intraoral scanners. The aim of this in-vitro study was to investigate the trueness and precision of full-arch maxillary digital impressions comparing three scan strategies. Three scan strategies (A, B, and C) were applied each five times on one single model (A, first buccal surfaces, return from occlusal-palatal; B, first occlusal-palatal, return buccal; C, S-type one-way). The TRIOS Pod scanner (3shape, Copenhagen, Denmark) with a color detector was used for these digital impressions. A cast of a maxillary dentate jaw was fabricated and scanned with an industrial reference scanner. This full-arch data record was digitally superimposed with the test scans (trueness) and within-group comparison was performed for each group (precision). The values within the 90/10 percentiles from the digital superimposition were used for calculation and group comparisons with nonparametric tests (ANOVA, post-hoc Bonferroni). The trueness (mean ± standard deviation) was 17.9 ± 16.4 μm for scan strategy A, 17.1 ± 13.7 μm for B, and 26.8 ± 14.7 μm for C without statistically significant difference. The precision was lowest for scan strategy A (35.0 ± 51.1 μm) and significantly different to B (7.9 ± 5.6 μm) and C (8.5 ± 6.3 μm). Scan strategy B may be recommended as it provides the highest trueness and precision in full-arch scans and therefore minimizes inaccuracies in the final reconstruction.

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

    Indian Academy of Sciences (India)

    reviewer

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

  12. Optical scanning holography based on compressive sensing using a digital micro-mirror device

    Science.gov (United States)

    A-qian, Sun; Ding-fu, Zhou; Sheng, Yuan; You-jun, Hu; Peng, Zhang; Jian-ming, Yue; xin, Zhou

    2017-02-01

    Optical scanning holography (OSH) is a distinct digital holography technique, which uses a single two-dimensional (2D) scanning process to record the hologram of a three-dimensional (3D) object. Usually, these 2D scanning processes are in the form of mechanical scanning, and the quality of recorded hologram may be affected due to the limitation of mechanical scanning accuracy and unavoidable vibration of stepper motor's start-stop. In this paper, we propose a new framework, which replaces the 2D mechanical scanning mirrors with a Digital Micro-mirror Device (DMD) to modulate the scanning light field, and we call it OSH based on Compressive Sensing (CS) using a digital micro-mirror device (CS-OSH). CS-OSH can reconstruct the hologram of an object through the use of compressive sensing theory, and then restore the image of object itself. Numerical simulation results confirm this new type OSH can get a reconstructed image with favorable visual quality even under the condition of a low sample rate.

  13. Optimization of scanning strategy of digital Shack-Hartmann wavefront sensing.

    Science.gov (United States)

    Guo, Wenjiang; Zhao, Liping; Li, Xiang; Chen, I-Ming

    2012-01-01

    In the traditional Shack-Hartmann wavefront sensing (SHWS) system, a lenslet array with a bigger configuration is desired to achieve a higher lateral resolution. However, practical implementation limits the configuration and this parameter is contradicted with the measurement range. We have proposed a digital scanning technique by making use of the high flexibility of a spatial light modulator to sample the reflected wavefront [X. Li, L. P. Zhao, Z. P. Fang, and C. S. Tan, "Improve lateral resolution in wavefront sensing with digital scanning technique," in Asia-Pacific Conference of Transducers and Micro-Nano Technology (2006)]. The lenslet array pattern is programmed to laterally scan the whole aperture. In this paper, the methodology to optimize the scanning step for the purpose of form measurement is proposed. The correctness and effectiveness are demonstrated in numerical simulation and experimental investigation. © 2012 Optical Society of America

  14. prokaryote genome annotation with GeneScan and GLIMMER

    Indian Academy of Sciences (India)

    Unknown

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

  15. Precision of guided scanning procedures for full-arch digital impressions in vivo.

    Science.gov (United States)

    Zimmermann, Moritz; Koller, Christina; Rumetsch, Moritz; Ender, Andreas; Mehl, Albert

    2017-11-01

    System-specific scanning strategies have been shown to influence the accuracy of full-arch digital impressions. Special guided scanning procedures have been implemented for specific intraoral scanning systems with special regard to the digital orthodontic workflow. The aim of this study was to evaluate the precision of guided scanning procedures compared to conventional impression techniques in vivo. Two intraoral scanning systems with implemented full-arch guided scanning procedures (Cerec Omnicam Ortho; Ormco Lythos) were included along with one conventional impression technique with irreversible hydrocolloid material (alginate). Full-arch impressions were taken three times each from 5 participants (n = 15). Impressions were then compared within the test groups using a point-to-surface distance method after best-fit model matching (OraCheck). Precision was calculated using the (90-10%)/2 quantile and statistical analysis with one-way repeated measures ANOVA and post hoc Bonferroni test was performed. The conventional impression technique with alginate showed the lowest precision for full-arch impressions with 162.2 ± 71.3 µm. Both guided scanning procedures performed statistically significantly better than the conventional impression technique (p Cerec Omnicam Ortho were 74.5 ± 39.2 µm and for group Ormco Lythos 91.4 ± 48.8 µm. The in vivo precision of guided scanning procedures exceeds conventional impression techniques with the irreversible hydrocolloid material alginate. Guided scanning procedures may be highly promising for clinical applications, especially for digital orthodontic workflows.

  16. Fine Metal Mask 3-Dimensional Measurement by using Scanning Digital Holographic Microscope

    Science.gov (United States)

    Shin, Sanghoon; Yu, Younghun

    2018-04-01

    For three-dimensional microscopy, fast and high axial resolution are very important. Extending the depth of field for digital holographic is necessary for three-dimensional measurements of thick samples. We propose an optical sectioning method for optical scanning digital holography that is performed in the frequency domain by spatial filtering of a reconstructed amplitude image. We established a scanning dual-wavelength off-axis digital holographic microscope to measure samples that exhibit a large amount of coherent noise and a thickness larger than the depth of focus of the objective lens. As a demonstration, we performed a three-dimensional measurement of a fine metal mask with a reconstructed sectional phase image and filtering with a reconstructed amplitude image.

  17. Reliability of capturing foot parameters using digital scanning and the neutral suspension casting technique

    Science.gov (United States)

    2011-01-01

    Background A clinical study was conducted to determine the intra and inter-rater reliability of digital scanning and the neutral suspension casting technique to measure six foot parameters. The neutral suspension casting technique is a commonly utilised method for obtaining a negative impression of the foot prior to orthotic fabrication. Digital scanning offers an alternative to the traditional plaster of Paris techniques. Methods Twenty one healthy participants volunteered to take part in the study. Six casts and six digital scans were obtained from each participant by two raters of differing clinical experience. The foot parameters chosen for investigation were cast length (mm), forefoot width (mm), rearfoot width (mm), medial arch height (mm), lateral arch height (mm) and forefoot to rearfoot alignment (degrees). Intraclass correlation coefficients (ICC) with 95% confidence intervals (CI) were calculated to determine the intra and inter-rater reliability. Measurement error was assessed through the calculation of the standard error of the measurement (SEM) and smallest real difference (SRD). Results ICC values for all foot parameters using digital scanning ranged between 0.81-0.99 for both intra and inter-rater reliability. For neutral suspension casting technique inter-rater reliability values ranged from 0.57-0.99 and intra-rater reliability values ranging from 0.36-0.99 for rater 1 and 0.49-0.99 for rater 2. Conclusions The findings of this study indicate that digital scanning is a reliable technique, irrespective of clinical experience, with reduced measurement variability in all foot parameters investigated when compared to neutral suspension casting. PMID:21375757

  18. Full arch scans: conventional versus digital impressions--an in-vitro study.

    Science.gov (United States)

    Ender, A; Mehl, A

    2011-01-01

    The digital intraoral impression has become a central part of the CAD/CAM technique. The objective of the present study was to compare the accuracy (trueness and precision) of digital impressions of the full arch with that of conventional impressions on the in-vitro model. For this purpose, a master model was acquired with a new reference scanning process, the measuring trueness of which was +/- 4.1 microm and the precision +/- 2.5 microm. On the one hand, conventional impressions and then plaster models (n = 5) were produced from this master model, and on the other hand, digital impressions were made with the Cerec AC Bluecam and the Lava COS system (each n = 5). The plaster models were also scanned with the reference scanner. The available data records were superimposed and the differences determined. The deviation from the master model defines the trueness of the impression method. The deviations of the models among one another demonstrate the precision of the method. The trueness of the impressions was 55 +/- 21.8 microm in the conventional impression group, for digital impressions with Cerec Bluecam it was 49 +/- 14.2 microm and for digital impressions with Lava COS 40.3 +/- 14.1 microm. The precision was 61.3 +/- 17.9 microm for conventional impression with Impregum, 30.9 +/- 7.1 microm for digital impression with the Cerec Bluecam and 60.1 +/- 31.3 microm for digital impression with Lava COS. These in-vitro results show that accuracy of the digital impression is similar to that of the conventional impression. These results will have to be confirmed in further clinical studies.

  19. Three-Dimensional Digital Documentation of Heritage Sites Using Terrestrial Laser Scanning and Unmanned Aerial Vehicle Photogrammetry

    Science.gov (United States)

    Jo, Y. H.; Kim, J. Y.

    2017-08-01

    Three-dimensional digital documentation is an important technique for the maintenance and monitoring of cultural heritage sites. This study focuses on the three-dimensional digital documentation of the Magoksa Temple, Republic of Korea, using a combination of terrestrial laser scanning and unmanned aerial vehicle (UAV) photogrammetry. Terrestrial laser scanning mostly acquired the vertical geometry of the buildings. In addition, the digital orthoimage produced by UAV photogrammetry had higher horizontal data acquisition rate than that produced by terrestrial laser scanning. Thus, the scanning and UAV photogrammetry were merged by matching 20 corresponding points and an absolute coordinate system was established using seven ground control points. The final, complete threedimensional shape had perfect horizontal and vertical geometries. This study demonstrates the potential of integrating terrestrial laser scanning and UAV photogrammetry for three-dimensional digital documentation. This new technique is expected to contribute to the three-dimensional digital documentation and spatial analysis of cultural heritage sites.

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

    NARCIS (Netherlands)

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

    2013-01-01

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

  1. T-scan III system diagnostic tool for digital occlusal analysis in orthodontics - a modern approach.

    Science.gov (United States)

    Trpevska, Vesna; Kovacevska, Gordana; Benedeti, Alberto; Jordanov, Bozidar

    2014-01-01

    This systematic literature review was performed to establish the mechanism, methodology, characteristics, clinical application and opportunities of the T-Scan III System as a diagnostic tool for digital occlusal analysis in different fields of dentistry, precisely in orthodontics. Searching of electronic databases, using MEDLINE and PubMed, hand searching of relevant key journals, and screening of reference lists of included studies with no language restriction was performed. Publications providing statistically examined data were included for systematic review. Twenty potentially relevant Randomized Controlled Trials (RCTs) were identified. Only ten met the inclusion criteria. The literature demonstrates that using digital occlusal analysis with T-Scan III System in orthodontics has significant advantage with regard to the capability of measuring occlusal parameters in static positions and during dynamic of the mandible. Within the scope of this systematic review, there is evidence to support that T-Scan system is rapid and accurate in identifying the distribution of the tooth contacts and it shows great promise as a clinical diagnostic screening device for occlusion and for improving the occlusion after various dental treatments. Additional clinical studies are required to advance the indication filed of this system. Importance of using digital occlusal T-Scan analysis in orthodontics deserves further investigation.

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

    Science.gov (United States)

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

    2017-07-01

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

  5. Evaluation of the effect scan pattern has on the trueness and precision of six intraoral digital impression systems.

    Science.gov (United States)

    Mennito, Anthony S; Evans, Zachary P; Lauer, Abigail W; Patel, Ravi B; Ludlow, Mark E; Renne, Walter G

    2018-03-01

    Clinicians have been slow to adopt digital impression technologies due possibly to perceived technique sensitivities involved in data acquisition. This research has two aims: determine whether scan pattern and sequence affects the accuracy of the three-dimensional (3D) model created from this digital impression and to compare the 5 imaging systems with regards to their scanning accuracy for sextant impressions. Six digital intraoral impression systems were used to scan a typodont sextant with optical properties similar to natural teeth. The impressions were taken using five different scan patterns and the resulting digital models were overlayed on a master digital model to determine the accuracy of each scanner performing each scan pattern. Furthermore, regardless of scan pattern, each digital impression system was evaluated for accuracy to the other systems in this same manner. No differences of significance were noted in the accuracy of 3D models created using six distinct scan patterns with one exception involving the CEREC Omnicam. Planmeca Planscan was determined to be the truest scanner while 3Shape Trios was determined to be the most precise for sextant impression making. Scan pattern does not significantly affect the accuracy of the resulting digital model for sextant scanning. Companies who make digital impression systems often recommend a scan pattern specific for their system. However, every clinical scanning scenario is different and may require a different approach. Knowing how important scan pattern is with regards to accuracy would be helpful for guiding a growing number of practitioners who are utilizing this technology. © 2018 Wiley Periodicals, Inc.

  6. Synchronous digitization for high dynamic range lock-in amplification in beam-scanning microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Muir, Ryan D.; Sullivan, Shane Z.; Oglesbee, Robert A.; Simpson, Garth J., E-mail: gsimpson@purdue.edu [Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907 (United States)

    2014-03-15

    Digital lock-in amplification (LIA) with synchronous digitization (SD) is shown to provide significant signal to noise (S/N) and linear dynamic range advantages in beam-scanning microscopy measurements using pulsed laser sources. Direct comparisons between SD-LIA and conventional LIA in homodyne second harmonic generation measurements resulted in S/N enhancements consistent with theoretical models. SD-LIA provided notably larger S/N enhancements in the limit of low light intensities, through the smooth transition between photon counting and signal averaging developed in previous work. Rapid beam scanning instrumentation with up to video rate acquisition speeds minimized photo-induced sample damage. The corresponding increased allowance for higher laser power without sample damage is advantageous for increasing the observed signal content.

  7. Effects of scanning resolution and digital image magnification on photostimulable phosphor imaging system

    International Nuclear Information System (INIS)

    Sakurai, Takashi; Inagaki, Masafumi; Asai, Hideomi; Koyama, Atsushi; Kashima, Isamu

    2000-01-01

    The purpose of this study is to examine the effects of changes in scanning resolution and digital magnification on the image quality and diagnostic ability of the photostimulable phosphor imaging system. Using a photostimulable phosphor imaging system, images of a human adult dried mandible phantom embedded in a 25 mm-thick epoxy resin block were made. The latent images on the photostimulable phosphor imaging plate were scanned using four different pixel sizes as follows: 25 μm x 25 μm, 50 μm x 50 μm, 100 μm x 100 μm and 200 μm x 200 μm. A primary image was produced for each pixel size. These images were also digitally magnified at powers of 2, 4 and 8 times. The gradient range, brightness and contrast of each image were adjusted to optimum levels on a cathode ray tube display, and hard copies were produced with a writing pixel size of 60 μm x 60 μm. The granularity, sharpness and anatomical diagnostic ability of the images were assessed subjectively by eight dentists. Increasing the scanning resolution tended to generally improve image quality and diagnostic ability. Visual image quality was maintained up to a pixel size of 50 μm, and diagnostic ability was maintained up to a pixel size of 100 μm. Digital image magnification degraded image quality, and more than 2-times magnification degraded diagnostic ability. Under the present experimental conditions, increasing the scanning resolution did not always lead to an improvement in image quality or diagnostic ability, and digital image magnification degraded image quality and diagnostic ability. (author)

  8. Digitally controlled analog proportional-integral-derivative (PID) controller for high-speed scanning probe microscopy

    Science.gov (United States)

    Dukic, Maja; Todorov, Vencislav; Andany, Santiago; Nievergelt, Adrian P.; Yang, Chen; Hosseini, Nahid; Fantner, Georg E.

    2017-12-01

    Nearly all scanning probe microscopes (SPMs) contain a feedback controller, which is used to move the scanner in the direction of the z-axis in order to maintain a constant setpoint based on the tip-sample interaction. The most frequently used feedback controller in SPMs is the proportional-integral (PI) controller. The bandwidth of the PI controller presents one of the speed limiting factors in high-speed SPMs, where higher bandwidths enable faster scanning speeds and higher imaging resolution. Most SPM systems use digital signal processor-based PI feedback controllers, which require analog-to-digital and digital-to-analog converters. These converters introduce additional feedback delays which limit the achievable imaging speed and resolution. In this paper, we present a digitally controlled analog proportional-integral-derivative (PID) controller. The controller implementation allows tunability of the PID gains over a large amplification and frequency range, while also providing precise control of the system and reproducibility of the gain parameters. By using the analog PID controller, we were able to perform successful atomic force microscopy imaging of a standard silicon calibration grating at line rates up to several kHz.

  9. An improved three-dimensional non-scanning laser imaging system based on digital micromirror device

    Science.gov (United States)

    Xia, Wenze; Han, Shaokun; Lei, Jieyu; Zhai, Yu; Timofeev, Alexander N.

    2018-01-01

    Nowadays, there are two main methods to realize three-dimensional non-scanning laser imaging detection, which are detection method based on APD and detection method based on Streak Tube. However, the detection method based on APD possesses some disadvantages, such as small number of pixels, big pixel interval and complex supporting circuit. The detection method based on Streak Tube possesses some disadvantages, such as big volume, bad reliability and high cost. In order to resolve the above questions, this paper proposes an improved three-dimensional non-scanning laser imaging system based on Digital Micromirror Device. In this imaging system, accurate control of laser beams and compact design of imaging structure are realized by several quarter-wave plates and a polarizing beam splitter. The remapping fiber optics is used to sample the image plane of receiving optical lens, and transform the image into line light resource, which can realize the non-scanning imaging principle. The Digital Micromirror Device is used to convert laser pulses from temporal domain to spatial domain. The CCD with strong sensitivity is used to detect the final reflected laser pulses. In this paper, we also use an algorithm which is used to simulate this improved laser imaging system. In the last, the simulated imaging experiment demonstrates that this improved laser imaging system can realize three-dimensional non-scanning laser imaging detection.

  10. Rapid Prototyping — A Tool for Presenting 3-Dimensional Digital Models Produced by Terrestrial Laser Scanning

    Directory of Open Access Journals (Sweden)

    Juho-Pekka Virtanen

    2014-07-01

    Full Text Available Rapid prototyping has received considerable interest with the introduction of affordable rapid prototyping machines. These machines can be used to manufacture physical models from three-dimensional digital mesh models. In this paper, we compare the results obtained with a new, affordable, rapid prototyping machine, and a traditional professional machine. Two separate data sets are used for this, both of which were acquired using terrestrial laser scanning. Both of the machines were able to produce complex and highly detailed geometries in plastic material from models based on terrestrial laser scanning. The dimensional accuracies and detail levels of the machines were comparable, and the physical artifacts caused by the fused deposition modeling (FDM technique used in the rapid prototyping machines could be found in both models. The accuracy of terrestrial laser scanning exceeded the requirements for manufacturing physical models of large statues and building segments at a 1:40 scale.

  11. Digital Processing for Modifying and Rearranging Rectilinear and Section Scan Data under Direct Observation

    Energy Technology Data Exchange (ETDEWEB)

    Kuhl, D. E.; Edwards, R. Q. [University of Pennsylvania, Philadelphia, PA (United States)

    1969-01-15

    Our digital processor for scan data is an on-site instrument that is intermediate in complexity between conventional optical processing devices and large digital computers. It is designed to provide for a wide and flexible range of secondary data operations, direct picture display on a CRT screen, and full operator control of both processing and display operations at the time of viewing. The instrument does not require the user to learn complicated programing schemes. The operator is expected to be a physician who will control the parameters of interest by punching preset buttons on a keyboard while observing changes displayed on a CRT screen. The system functions primarily as an investigative tool for studying perception of scan information and ways of making this information more meaningful. Data operations include data bounding, spatial averaging, iso-count line generation, image addition and subtraction, and several forms of quantitative read-out for analysis of regional data. The instrument is intended to serve as a central processor and reader for data from several units. Investigations with this processor have served as a source of information leading to the design of more simple processing devices suitable for wider acceptance. For example, the Mark III rectilinear and transverse section brain scanner that has evolved from this project is expected to be a practical improvement of the brain study method. This instrument is designed especially for rapid brain scanning using {sup 99m}Tc pertechnetate. It has a self-contained computer, integrated digital circuits for compactness and economy, and provision for transverse section scanning. The advantages of this system are that it provides a more thorough study using both transverse section and rectilinear modes, rapid performance, precise orientation of section and rectilinear views to the patient position, efficient transfer of information between physician and machine during studies, and economy of design

  12. A simplified digital lock-in amplifier for the scanning grating spectrometer.

    Science.gov (United States)

    Wang, Jingru; Wang, Zhihong; Ji, Xufei; Liu, Jie; Liu, Guangda

    2017-02-01

    For the common measurement and control system of a scanning grating spectrometer, the use of an analog lock-in amplifier requires complex circuitry and sophisticated debugging, whereas the use of a digital lock-in amplifier places a high demand on the calculation capability and storage space. In this paper, a simplified digital lock-in amplifier based on averaging the absolute values within a complete period is presented and applied to a scanning grating spectrometer. The simplified digital lock-in amplifier was implemented on a low-cost microcontroller without multipliers, and got rid of the reference signal and specific configuration of the sampling frequency. Two positive zero-crossing detections were used to lock the phase of the measured signal. However, measurement method errors were introduced by the following factors: frequency fluctuation, sampling interval, and integer restriction of the sampling number. The theoretical calculation and experimental results of the signal-to-noise ratio of the proposed measurement method were 2055 and 2403, respectively.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-10-01

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

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

  15. Influence of scanning system and dentist's level of training in the accuracy of digital impressions

    Science.gov (United States)

    Hategan, Simona; Gabor, Alin; Zaharia, Cristian; Sinescu, Cosmin; Negrutiu, Meda Lavinia; Jivanescu, Anca

    2016-03-01

    Background: The principal aim of our study was to evaluate digital impressions, taken with spray powder and powderfree scan systems, in order to determine the influence of the dentist's commitment to training as a critical factor regarding quality. Material and method: Two digital intraoral impression systems from the same manufacture (Sirona) : Apollo DI and CEREC Omnicam, were used to scan 16 crown preparations on teeth on a typodont maxillary model. Because an Apollo Di intraoral camera is a powder system, an adhesive was applied before using the powder spray. Three groups were used to scan the crown preparations in order to determine coating thickness homogeneity. One group consisted of senior year dental students, a second consisted of prosthodontics residents, and the third consisted of prosthodontics specialists. The same procedure was applied with a CEREC Omnicam intraoral camera, which is a powder-free system. By using the two systems software parameters we were able to determine the scanning precision. Results: Homogeneity scores for Apollo Di regarding the spray layer was significantly thinner for all dental surfaces in the first group, while the second group had thinner coatings for buccal and distal surfaces. For the third group, the crown preparations were coated more homogeneously than the first two groups. The powder-free system CEREC Omnicam can, to a degree, mask the lack of experience in direct optical impressions by avoiding the poor quality coating, which can lead to defective marginal adaptation of definitive restoration. Conclusions: The dentist's lack of experience can be mitigated, and partially avoided, by using powder-free systems. At the same time, the dentist can give more time towards learning how to integrate computerized fabricated restoration into the practice. The commitment to training is a critical factor in the successful integration of the technology. In addition, scanning marginal preparation details needs time in order to

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

    Directory of Open Access Journals (Sweden)

    Frits A Rangel

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

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

    Science.gov (United States)

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

    2013-01-01

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

  18. 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.)

  19. Digitization of medical documents: an X-Windows application for fast scanning.

    Science.gov (United States)

    Muñoz, A; Salvador, C H; Gonzalez, M A; Dueñas, A

    1992-01-01

    This paper deals with digitization, using a commercial scanner, of medical documents as still images for introduction into a computer-based Information System. Document management involves storing, editing and transmission. This task has usually been approached from the perspective of the difficulties posed by radiologic images because of their indisputable qualitative and quantitative significance. However, healthcare activities require the management of many other types of documents and involve the requirements of numerous users. One key to document management will be the availability of a digitizer to deal with the greatest possible number of different types of documents. This paper describes the relevant aspects of documents and the technical specifications that digitizers must fulfill. The concept of document type is introduced as the ideal set of digitizing parameters for a given document. The use of document type parameters can drastically reduce the time the user spends in scanning sessions. Presentation is made of an application based on Unix, X-Windows and OSF/Motif, with a GPIB interface, implemented around the document type concept. Finally, the results of the evaluation of the application are presented, focusing on the user interface, as well as on the viewing of color images in an X-Windows environment and the use of lossy algorithms in the compression of medical images.

  20. Digitally generated excitation and near-baseband quadrature detection of rapid scan EPR signals.

    Science.gov (United States)

    Tseitlin, Mark; Yu, Zhelin; Quine, Richard W; Rinard, George A; Eaton, Sandra S; Eaton, Gareth R

    2014-12-01

    The use of multiple synchronized outputs from an arbitrary waveform generator (AWG) provides the opportunity to perform EPR experiments differently than by conventional EPR. We report a method for reconstructing the quadrature EPR spectrum from periodic signals that are generated with sinusoidal magnetic field modulation such as continuous wave (CW), multiharmonic, or rapid scan experiments. The signal is down-converted to an intermediate frequency (IF) that is less than the field scan or field modulation frequency and then digitized in a single channel. This method permits use of a high-pass analog filter before digitization to remove the strong non-EPR signal at the IF, that might otherwise overwhelm the digitizer. The IF is the difference between two synchronized X-band outputs from a Tektronix AWG 70002A, one of which is for excitation and the other is the reference for down-conversion. To permit signal averaging, timing was selected to give an exact integer number of full cycles for each frequency. In the experiments reported here the IF was 5kHz and the scan frequency was 40kHz. To produce sinusoidal rapid scans with a scan frequency eight times IF, a third synchronized output generated a square wave that was converted to a sine wave. The timing of the data acquisition with a Bruker SpecJet II was synchronized by an external clock signal from the AWG. The baseband quadrature signal in the frequency domain was reconstructed. This approach has the advantages that (i) the non-EPR response at the carrier frequency is eliminated, (ii) both real and imaginary EPR signals are reconstructed from a single physical channel to produce an ideal quadrature signal, and (iii) signal bandwidth does not increase relative to baseband detection. Spectra were obtained by deconvolution of the reconstructed signals for solid BDPA (1,3-bisdiphenylene-2-phenylallyl) in air, 0.2mM trityl OX63 in water, 15 N perdeuterated tempone, and a nitroxide with a 0.5G partially-resolved proton

  1. Automated detection of analyzable metaphase chromosome cells depicted on scanned digital microscopic images

    Science.gov (United States)

    Qiu, Yuchen; Wang, Xingwei; Chen, Xiaodong; Li, Yuhua; Liu, Hong; Li, Shibo; Zheng, Bin

    2010-02-01

    Visually searching for analyzable metaphase chromosome cells under microscopes is quite time-consuming and difficult. To improve detection efficiency, consistency, and diagnostic accuracy, an automated microscopic image scanning system was developed and tested to directly acquire digital images with sufficient spatial resolution for clinical diagnosis. A computer-aided detection (CAD) scheme was also developed and integrated into the image scanning system to search for and detect the regions of interest (ROI) that contain analyzable metaphase chromosome cells in the large volume of scanned images acquired from one specimen. Thus, the cytogeneticists only need to observe and interpret the limited number of ROIs. In this study, the high-resolution microscopic image scanning and CAD performance was investigated and evaluated using nine sets of images scanned from either bone marrow (three) or blood (six) specimens for diagnosis of leukemia. The automated CAD-selection results were compared with the visual selection. In the experiment, the cytogeneticists first visually searched for the analyzable metaphase chromosome cells from specimens under microscopes. The specimens were also automated scanned and followed by applying the CAD scheme to detect and save ROIs containing analyzable cells while deleting the others. The automated selected ROIs were then examined by a panel of three cytogeneticists. From the scanned images, CAD selected more analyzable cells than initially visual examinations of the cytogeneticists in both blood and bone marrow specimens. In general, CAD had higher performance in analyzing blood specimens. Even in three bone marrow specimens, CAD selected 50, 22, 9 ROIs, respectively. Except matching with the initially visual selection of 9, 7, and 5 analyzable cells in these three specimens, the cytogeneticists also selected 41, 15 and 4 new analyzable cells, which were missed in initially visual searching. This experiment showed the feasibility of

  2. Terrestrial scanning or digital images in inventory of monumental objects? - case study

    Science.gov (United States)

    Markiewicz, J. S.; Zawieska, D.

    2014-06-01

    Cultural heritage is the evidence of the past; monumental objects create the important part of the cultural heritage. Selection of a method to be applied depends on many factors, which include: the objectives of inventory, the object's volume, sumptuousness of architectural design, accessibility to the object, required terms and accuracy of works. The paper presents research and experimental works, which have been performed in the course of development of architectural documentation of elements of the external facades and interiors of the Wilanów Palace Museum in Warszawa. Point clouds, acquired from terrestrial laser scanning (Z+F 5003h) and digital images taken with Nikon D3X and Hasselblad H4D cameras were used. Advantages and disadvantages of utilisation of these technologies of measurements have been analysed with consideration of the influence of the structure and reflectance of investigated monumental surfaces on the quality of generation of photogrammetric products. The geometric quality of surfaces obtained from terrestrial laser scanning data and from point clouds resulting from digital images, have been compared.

  3. 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.

  4. Synchronous-digitization for video rate polarization modulated beam scanning second harmonic generation microscopy

    Science.gov (United States)

    Sullivan, Shane Z.; DeWalt, Emma L.; Schmitt, Paul D.; Muir, Ryan D.; Simpson, Garth J.

    2015-03-01

    Fast beam-scanning non-linear optical microscopy, coupled with fast (8 MHz) polarization modulation and analytical modeling have enabled simultaneous nonlinear optical Stokes ellipsometry (NOSE) and linear Stokes ellipsometry imaging at video rate (15 Hz). NOSE enables recovery of the complex-valued Jones tensor that describes the polarization-dependent observables, in contrast to polarimetry, in which the polarization stated of the exciting beam is recorded. Each data acquisition consists of 30 images (10 for each detector, with three detectors operating in parallel), each of which corresponds to polarization-dependent results. Processing of this image set by linear fitting contracts down each set of 10 images to a set of 5 parameters for each detector in second harmonic generation (SHG) and three parameters for the transmittance of the fundamental laser beam. Using these parameters, it is possible to recover the Jones tensor elements of the sample at video rate. Video rate imaging is enabled by performing synchronous digitization (SD), in which a PCIe digital oscilloscope card is synchronized to the laser (the laser is the master clock.) Fast polarization modulation was achieved by modulating an electro-optic modulator synchronously with the laser and digitizer, with a simple sine-wave at 1/10th the period of the laser, producing a repeating pattern of 10 polarization states. This approach was validated using Z-cut quartz, and NOSE microscopy was performed for micro-crystals of naproxen.

  5. Image quality characteristics of a novel colour scanning digital ophthalmoscope (SDO) compared with fundus photography.

    Science.gov (United States)

    Strauss, Rupert W; Krieglstein, Tina R; Priglinger, Siegfried G; Reis, Werner; Ulbig, Michael W; Kampik, Anselm; Neubauer, Aljoscha S

    2007-11-01

    To establish a set of quality parameters for grading image quality and apply those to evaluate the fundus image quality obtained by a new scanning digital ophthalmoscope (SDO) compared with standard slide photography. On visual analogue scales a total of eight image characteristics were defined: overall quality, contrast, colour brilliance, focus (sharpness), resolution and details, noise, artefacts and validity of clinical assessment. Grading was repeated after 4 months to assess repeatability. Fundus images of 23 patients imaged digitally by SDO and by Zeiss 450FF fundus camera using Kodak film were graded side-by-side by three graders. Lens opacity was quantified with the Interzeag Lens Opacity Meter 701. For all of the eight scales of image quality, good repeatability within the graders (mean Kendall's W 0.69) was obtained after 4 months. Inter-grader agreement ranged between 0.31 and 0.66. Despite the SDO's limited nominal image resolution of 720 x 576 pixels, the Zeiss FF 450 camera performed better in only two of the subscales - noise (p = 0.001) and artefacts (p = 0.01). Lens opacities significantly influenced only the two subscales 'resolution' and 'details', which deteriorated with increasing media opacities for both imaging systems. Distinct scales to grade image characteristics of different origin were developed and validated. Overall SDO digital imaging was found to provide fundus pictures of a similarly high level of quality as expert photography on slides.

  6. APPLICATION OF 3D DIGITAL SCANNING AND CAD/CAM SYSTEMS FOR ZIRCONIA INDIRECT RESTORATIONS

    Directory of Open Access Journals (Sweden)

    Mariela Tsanova

    2016-09-01

    Full Text Available Object: To study the CAD/CAM systems’ possibilities for manufacturing Zirconia indirect restorations for restoring vital, vastly devastated teeth. Material and methods: Five patients with vital, heavily destroyed molars were included in the clinical study. The teeth were prepared according to requirements for Zirconia restorations. The impressions were taken with 3D intraoral scanner. The acquired data is transmitted electronically for designing the future restoration by the CAD software. After designing, the restoration is milled by the CAM module and sintered, according to a specially projected programme in accordance with the manufacturing demands. After clinical check-up, the restorations are glazed, air-blasted and cemented. Results: Setting up an individual protocol for working with CAD/CAM systems for restoring vital, severely devastated teeth with Zirconia indirect restorations. A research is made on 3D digital scanning, occlusal and proximal modeling, virtual articulation, analyzing the incline of the cavity walls, the thickness of the restoration and the possibilities for restoring the anatomy of the tooth according to patient’s individual characteristics of the teeth’s arch. Conclusion: The scanning and design process should be evaluated with the same quality control as when using traditional methods. The CAD software requires excellent preparation of the tooth cavity and digital scanning. This is the reason why these systems require a thorough understanding of CAD/CAM calibration and parameters of the product to be clinically acceptable. Once understood, CAD/CAM dentistry can create detailed and accurate restorations that function and perform with great success and longevity.

  7. Virology: The Next Generation from Digital PCR to Single Virion Genomics

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard A.; Brazelton De Cardenas, Jessica N.; Hayden, Randall T.

    2015-10-01

    In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. Using the principle of limiting dilution, digital PCR amplifies single molecules of DNA in highly partitioned endpoint reactions and reads each of those reactions as either positive or negative based on the presence or absence of target fluorophore. In this review, digital PCR will be highlighted along with current studies, advantages/disadvantages, and future perspectives with regard to digital PCR, viral load testing, and the possibility of single virion genomics.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  9. 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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    DEFF Research Database (Denmark)

    Perola, Markus; Sammalisto, Sampo; Hiekkalinna, Tero

    2007-01-01

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

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

    Science.gov (United States)

    Ambrosini, Giovanna; Groux, Romain; Bucher, Philipp

    2018-03-05

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

  13. Comparison of conventional study model measurements and 3D digital study model measurements from laser scanned dental impressions

    Science.gov (United States)

    Nugrahani, F.; Jazaldi, F.; Noerhadi, N. A. I.

    2017-08-01

    The field of orthodontics is always evolving,and this includes the use of innovative technology. One type of orthodontic technology is the development of three-dimensional (3D) digital study models that replace conventional study models made by stone. This study aims to compare the mesio-distal teeth width, intercanine width, and intermolar width measurements between a 3D digital study model and a conventional study model. Twelve sets of upper arch dental impressions were taken from subjects with non-crowding teeth. The impressions were taken twice, once with alginate and once with polivinylsiloxane. The alginate impressions used in the conventional study model and the polivinylsiloxane impressions were scanned to obtain the 3D digital study model. Scanning was performed using a laser triangulation scanner device assembled by the School of Electrical Engineering and Informatics at the Institut Teknologi Bandung and David Laser Scan software. For the conventional model, themesio-distal width, intercanine width, and intermolar width were measured using digital calipers; in the 3D digital study model they were measured using software. There were no significant differences between the mesio-distal width, intercanine width, and intermolar width measurments between the conventional and 3D digital study models (p>0.05). Thus, measurements using 3D digital study models are as accurate as those obtained from conventional study models

  14. A CdZnTe slot-scanned detector for digital mammography

    International Nuclear Information System (INIS)

    Mainprize, James G.; Ford, Nancy L.; Yin Shi; Gordon, Eli E.; Hamilton, William J.; Tuemer, Tuemay O.; Yaffe, Martin J.

    2002-01-01

    A new high-resolution detector has been developed for use in a slot-scanned digital mammography system. The detector is a hybrid device that consists of a CCD operating in time-delay integration mode that is bonded to a 150-μm-thick CdZnTe photoconductor array. The CCD was designed with a detector element pitch of 50 μm. Two devices were evaluated with differing crystalline quality. Incomplete charge collection was a source of reduction in DQE. This occurs in both devices due to characteristically low mobility-lifetime products for CdZnTe, with the greatest losses demonstrated by the multicrystalline sample. The mobility-lifetime products for the multicrystalline device were found to be 2.4x10 -4 and 4.0x10 -7 cm 2 /V for electrons and holes, respectively. The device constructed with higher quality single crystal CdZnTe demonstrated mobility-lifetime products of 1.0x10 -4 and 4.4x10 -6 cm 2 /V for electrons and holes. The MTF and DQE for the device were measured at several exposures and results were compared to predictions from a linear systems model of signal and noise propagation. The MTF at a spatial frequency of 10 mm -1 exceeded 0.18 and 0.56 along the scan and slot directions, respectively. Scanning motion and CCD design limited the resolution along the scan direction. For an x-ray beam from a tungsten target tube with 40 μm molybdenum filtration operated at 26 kV, the single crystal device demonstrated a DQE(0) of 0.70±0.02 at 7.1x10 -6 C/kg (27 mR) exposure to the detector, despite its relatively poor charge collection efficiency

  15. Digital elevation model production from scanned topographic contour maps via thin plate spline interpolation

    International Nuclear Information System (INIS)

    Soycan, Arzu; Soycan, Metin

    2009-01-01

    GIS (Geographical Information System) is one of the most striking innovation for mapping applications supplied by the developing computer and software technology to users. GIS is a very effective tool which can show visually combination of the geographical and non-geographical data by recording these to allow interpretations and analysis. DEM (Digital Elevation Model) is an inalienable component of the GIS. The existing TM (Topographic Map) can be used as the main data source for generating DEM by amanual digitizing or vectorization process for the contours polylines. The aim of this study is to examine the DEM accuracies, which were obtained by TMs, as depending on the number of sampling points and grid size. For these purposes, the contours of the several 1/1000 scaled scanned topographical maps were vectorized. The different DEMs of relevant area have been created by using several datasets with different numbers of sampling points. We focused on the DEM creation from contour lines using gridding with RBF (Radial Basis Function) interpolation techniques, namely TPS as the surface fitting model. The solution algorithm and a short review of the mathematical model of TPS (Thin Plate Spline) interpolation techniques are given. In the test study, results of the application and the obtained accuracies are drawn and discussed. The initial object of this research is to discuss the requirement of DEM in GIS, urban planning, surveying engineering and the other applications with high accuracy (a few deci meters). (author)

  16. Simultaneous measurement of refractive index and thickness distributions using low-coherence digital holography and vertical scanning

    International Nuclear Information System (INIS)

    Watanabe, Kaho; Ohshima, Masashi; Nomura, Takanori

    2014-01-01

    The simultaneous measurement method of a refractive index distribution and a thickness distribution using low-coherence digital holography with a vertical scanning is proposed. The proposed method consists of a combination of digital holography and low-coherence interferometry. The introduction of a datum plane enables the measurement of both a refractive index distribution and a thickness distribution. By the optical experiment, the potential of the proposed method is confirmed. (paper)

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

    Directory of Open Access Journals (Sweden)

    Ethan M Lange

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

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

    Science.gov (United States)

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

    2006-08-01

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

  19. Fundamental imaging characteristics of a slot-scan digital chest radiographic system

    International Nuclear Information System (INIS)

    Samei, Ehsan; Saunders, Robert S.; Lo, Joseph Y.; Dobbins, James T. III; Jesneck, Jonathan L.; Floyd, Carey E.; Ravin, Carl E.

    2004-01-01

    Our purpose in this study was to evaluate the fundamental image quality characteristics of a new slot-scan digital chest radiography system (ThoraScan, Delft Imaging Systems/Nucletron, Veenendaal, The Netherlands). The linearity of the system was measured over a wide exposure range at 90, 117, and 140 kVp with added Al filtration. System uniformity and reproducibility were established with an analysis of images from repeated exposures. The modulation transfer function (MTF) was evaluated using an established edge method. The noise power spectrum (NPS) and the detective quantum efficiency (DQE) of the system were evaluated at the three kilo-voltages over a range of exposures. Scatter fraction (SF) measurements were made using a posterior beam stop method and a geometrical chest phantom. The system demonstrated excellent linearity, but some structured nonuniformities. The 0.1 MTF values occurred between 3.3-3.5 mm -1 . The DQE(0.15) and DQE(2.5) were 0.21 and 0.07 at 90 kVp, 0.18 and 0.05 at 117 kVp, and 0.16 and 0.03 at 140 kVp, respectively. The system exhibited remarkably lower SFs compared to conventional full-field systems with anti-scatter grid, measuring 0.13 in the lungs and 0.43 in the mediastinum. The findings indicated that the slot-scan design provides marked scatter reduction leading to high effective DQE (DQE eff ) of the system and reduced patient dose required to achieve high image quality

  20. Comparison of scatter rejection and low-contrast performance of scan equalization digital radiography (SEDR), slot-scan digital radiography, and full-field digital radiography systems for chest phantom imaging

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xinming; Shaw, Chris C.; Lai, Chao-Jen; Wang Tianpeng [Department of Imaging Physics, Digital Imaging Research Laboratory, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030-4009 (United States)

    2011-01-15

    Purpose: To investigate and compare the scatter rejection properties and low-contrast performance of the scan equalization digital radiography (SEDR) technique to the slot-scan and conventional full-field digital radiography techniques for chest imaging. Methods: A prototype SEDR system was designed and constructed with an a-Se flat-panel (FP) detector to improve image quality in heavily attenuating regions of an anthropomorphic chest phantom. Slot-scanning geometry was used to reject scattered radiation without attenuating primary x rays. The readout scheme of the FP was modified to erase accumulated scatter signals prior to image readout. A 24-segment beam width modulator was developed to regulate x-ray exposures regionally and compensate for the low x-ray flux in heavily attenuating regions. To measure the scatter-to-primary ratios (SPRs), a 2 mm thick lead plate with a 2-D array of aperture holes was used to measure the primary signals, which were then subtracted from those obtained without the lead plate to determine scatter components. A 2-D array of aluminum beads (3 mm in diameter) was used as the low-contrast objects to measure the contrast ratios (CRs) and contrast-to-noise ratios (CNRs) for evaluating the low-contrast performance in chest phantom images. A set of two images acquired with the same techniques were subtracted from each other to measure the noise levels. SPRs, CRs, and CNRs of the SEDR images were measured in four anatomical regions of chest phantom images and compared to those of slot-scan images and full-field images acquired with and without antiscatter grid. Results: The percentage reduction of SPR (percentage of SPRs reduced with scatter removal/rejection methods relative to that for nongrid full-field imaging) averaged over four anatomical regions was measured to be 80%, 83%, and 71% for SEDR, slot-scan, and full-field with grid, respectively. The average CR over four regions was found to improve over that for nongrid full

  1. Comparison of scatter rejection and low-contrast performance of scan equalization digital radiography (SEDR), slot-scan digital radiography, and full-field digital radiography systems for chest phantom imaging

    International Nuclear Information System (INIS)

    Liu Xinming; Shaw, Chris C.; Lai, Chao-Jen; Wang Tianpeng

    2011-01-01

    Purpose: To investigate and compare the scatter rejection properties and low-contrast performance of the scan equalization digital radiography (SEDR) technique to the slot-scan and conventional full-field digital radiography techniques for chest imaging. Methods: A prototype SEDR system was designed and constructed with an a-Se flat-panel (FP) detector to improve image quality in heavily attenuating regions of an anthropomorphic chest phantom. Slot-scanning geometry was used to reject scattered radiation without attenuating primary x rays. The readout scheme of the FP was modified to erase accumulated scatter signals prior to image readout. A 24-segment beam width modulator was developed to regulate x-ray exposures regionally and compensate for the low x-ray flux in heavily attenuating regions. To measure the scatter-to-primary ratios (SPRs), a 2 mm thick lead plate with a 2-D array of aperture holes was used to measure the primary signals, which were then subtracted from those obtained without the lead plate to determine scatter components. A 2-D array of aluminum beads (3 mm in diameter) was used as the low-contrast objects to measure the contrast ratios (CRs) and contrast-to-noise ratios (CNRs) for evaluating the low-contrast performance in chest phantom images. A set of two images acquired with the same techniques were subtracted from each other to measure the noise levels. SPRs, CRs, and CNRs of the SEDR images were measured in four anatomical regions of chest phantom images and compared to those of slot-scan images and full-field images acquired with and without antiscatter grid. Results: The percentage reduction of SPR (percentage of SPRs reduced with scatter removal/rejection methods relative to that for nongrid full-field imaging) averaged over four anatomical regions was measured to be 80%, 83%, and 71% for SEDR, slot-scan, and full-field with grid, respectively. The average CR over four regions was found to improve over that for nongrid full

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

    Science.gov (United States)

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

    2016-05-01

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

  3. Genome complexity, robustness and genetic interactions in digital organisms

    Science.gov (United States)

    Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

    1999-08-01

    Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

  4. 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...

  5. 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.

  6. 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.

  7. Decreasing medication turnaround time with digital scanning technology in a canadian health region.

    Science.gov (United States)

    Neville, Heather; Nodwell, Lisa; Alsharif, Sahar

    2014-11-01

    Reducing medication turnaround time can improve efficiency, patient safety, and quality of care in the hospital setting. Digital scanning technology (DST) can be used to electronically transmit scanned prescriber orders to a pharmacy computer queue for verification and processing, which may help to improve medication turnaround time. To evaluate medication turnaround time before and after implementation of DST for all medications and for antibiotics only. Medication turnaround times were evaluated retrospectively for periods before (June 6-10, 2011) and after (September 26-30, 2011) implementation of DST at 2 hospital sites in 1 health region. Medication turnaround time was defined as the time from composition of a medication order by the prescriber to its verification by the pharmacy (phase 1) and the time from prescriber composition to administration to the patient by a nurse (total). Median turnaround times were analyzed with SPSS software using the Mann-Whitney U test. In total, 304 and 244 medication orders were audited before and after DST implementation, respectively. Median phase 1 turnaround time for all medications declined significantly, from 2 h 23 min before DST implementation to 1 h 33 min after DST implementation (p < 0.001). Antibiotics were also processed significantly faster (1 h 51 min versus 1 h 9 min, p = 0.015). However, total turnaround time for all medications did not differ significantly (5 h 15 min versus 5 h 0 min, p = 0.42). Implementation of DST was associated with a 50-min decrease in medication turnaround time for the period from when an order was prescribed to the time it was processed by the pharmacy. Regular evaluation of medication turnaround times is recommended to compare with benchmarks, to ensure that hospital standards are being met, and to measure the effects of policy changes and implementation of new technology on medication-use processes.

  8. 3D digital image processing for biofilm quantification from confocal laser scanning microscopy: Multidimensional statistical analysis of biofilm modeling

    Science.gov (United States)

    Zielinski, Jerzy S.

    The dramatic increase in number and volume of digital images produced in medical diagnostics, and the escalating demand for rapid access to these relevant medical data, along with the need for interpretation and retrieval has become of paramount importance to a modern healthcare system. Therefore, there is an ever growing need for processed, interpreted and saved images of various types. Due to the high cost and unreliability of human-dependent image analysis, it is necessary to develop an automated method for feature extraction, using sophisticated mathematical algorithms and reasoning. This work is focused on digital image signal processing of biological and biomedical data in one- two- and three-dimensional space. Methods and algorithms presented in this work were used to acquire data from genomic sequences, breast cancer, and biofilm images. One-dimensional analysis was applied to DNA sequences which were presented as a non-stationary sequence and modeled by a time-dependent autoregressive moving average (TD-ARMA) model. Two-dimensional analyses used 2D-ARMA model and applied it to detect breast cancer from x-ray mammograms or ultrasound images. Three-dimensional detection and classification techniques were applied to biofilm images acquired using confocal laser scanning microscopy. Modern medical images are geometrically arranged arrays of data. The broadening scope of imaging as a way to organize our observations of the biophysical world has led to a dramatic increase in our ability to apply new processing techniques and to combine multiple channels of data into sophisticated and complex mathematical models of physiological function and dysfunction. With explosion of the amount of data produced in a field of biomedicine, it is crucial to be able to construct accurate mathematical models of the data at hand. Two main purposes of signal modeling are: data size conservation and parameter extraction. Specifically, in biomedical imaging we have four key problems

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

    Science.gov (United States)

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

    2012-01-01

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

  10. ODK Scan: Digitizing Data Collection and Impacting Data Management Processes in Pakistan’s Tuberculosis Control Program

    Directory of Open Access Journals (Sweden)

    Syed Mustafa Ali

    2016-10-01

    Full Text Available The present grievous tuberculosis situation can be improved by efficient case management and timely follow-up evaluations. With the advent of digital technology, this can be achieved through quick summarization of the patient-centric data. The aim of our study was to assess the effectiveness of the ODK Scan paper-to-digital system during a testing period of three months. A sequential, explanatory mixed-method research approach was employed to elucidate technology use. Training, smartphones, the application and 3G-enabled SIMs were provided to the four field workers. At the beginning, baseline measures of the data management aspects were recorded and compared with endline measures to determine the impact of ODK Scan. Additionally, at the end of the study, users’ feedback was collected regarding app usability, user interface design and workflow changes. A total of 122 patients’ records were retrieved from the server and analysed in terms of quality. It was found that ODK Scan recognized 99.2% of multiple choice fill-in bubble responses and 79.4% of numerical digit responses correctly. However, the overall quality of the digital data was decreased in comparison to manually entered data. Using ODK Scan, a significant time reduction is observed in data aggregation and data transfer activities, but data verification and form-filling activities took more time. Interviews revealed that field workers saw value in using ODK Scan, but they were more concerned about the time-consuming aspects of the use of ODK Scan. Therefore, it is concluded that minimal disturbance in the existing workflow, continuous feedback and value additions are the important considerations for the implementing organization to ensure technology adoption and workflow improvements.

  11. Scan equalization digital radiography (SEDR) implemented with an amorphous selenium flat-panel detector: initial experience

    Energy Technology Data Exchange (ETDEWEB)

    Liu Xinming; Lai Chaojen; Chen Lingyun; Han Tao; Zhong Yuncheng; Shen Youtao; Wang Tianpeng; Shaw, Chris C [Department of Imaging Physics, Digital Imaging Research Laboratory, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030-4009 (United States)], E-mail: xliu@di.mdacc.tmc.edu

    2009-11-21

    It is well recognized in projection radiography that low-contrast detectability suffers in heavily attenuating regions due to excessively low x-ray fluence to the image receptor and higher noise levels. Exposure equalization can improve image quality by increasing the x-ray exposure to heavily attenuating regions, resulting in a more uniform distribution of exposure to the detector. Image quality is also expected to be improved by using the slot-scan geometry to reject scattered radiation effectively without degrading primary x-rays. This paper describes the design of a prototype scan equalization digital radiography (SEDR) system implemented with an amorphous silicon (a-Si) thin-film transistor (TFT) array-based flat-panel detector. With this system, slot-scan geometry with alternate line erasure and readout (ALER) technique was used to achieve scatter rejection. A seven-segment beam height modulator assembly was mounted onto the fore collimator to regulate exposure regionally for chest radiography. The beam modulator assembly, consisting of micro linear motors, lead screw cartridge with lead (Pb) beam blockers attached, position feedback sensors and motor driver circuitry, has been tested and found to have an acceptable response for exposure equalization in chest radiography. An anthropomorphic chest phantom was imaged in the posterior-anterior (PA) view under clinical conditions. Scatter component, primary x-rays, scatter-to-primary ratios (SPRs) and primary signal-to-noise ratios (PSNRs) were measured in the SEDR images to evaluate the rejection and redistribution of scattered radiation, and compared with those for conventional full-field imaging with and without anti-scatter grid methods. SPR reduction ratios (SPRRRs, defined as the differences between the non-grid full-field SPRs and the reduced SPRs divided by the former) yielded approximately 59% for the full-field imaging with grid and 82% for the SEDR technique in the lungs, and 77% for the full

  12. Scanning-beam digital x-ray (SBDX) technology for interventional and diagnostic cardiac angiography

    International Nuclear Information System (INIS)

    Speidel, Michael A.; Wilfley, Brian P.; Star-Lack, Josh M.; Heanue, Joseph A.; Van Lysel, Michael S.

    2006-01-01

    The scanning-beam digital x-ray (SBDX) system is designed for x-ray dose reduction in cardiac angiographic applications. Scatter reduction, efficient detection of primary x-rays, and an inverse beam geometry are the main components of the entrance dose reduction strategy. This paper reports the construction of an SBDX prototype, image reconstruction techniques, and measurements of spatial resolution and x-ray output. The x-ray source has a focal spot that is electronically scanned across a large-area transmission target. A multihole collimator beyond the target defines a series of x-ray beams directed at a distant small-area detector array. The prototype has a 23 cmx23 cm target, 100x100 focal spot positions, and a 5 cmx5 cm CdTe detector positioned 150 cm from the target. With this nonmechanical method of beam scanning, patient images with low detected scatter are generated at up to 30 frame/s. SBDX data acquisition is tomosynthetic. The prototype simultaneously reconstructs 16 planes spaced throughout the cardiac volume using shift-and-add backprojection. Image frames analogous to conventional projection images are generated with a multiplane compositing algorithm. Single-plane versus multiplane reconstruction of contrast-filled coronary arteries is demonstrated with images of the porcine heart. Phantom and porcine imaging studies show multiplane reconstruction is practicable under clinically realistic levels of patient attenuation and cardiac motion. The modulation transfer function for an in-plane slit at mechanical isocenter measured 0.41-0.56 at 1 cycle/mm, depending on the detector element to image pixel interpolation technique. Modeling indicates that desired gains in spatial resolution are achievable by halving the detector element width. The x-ray exposure rate 15 cm below isocenter, without table or patient in the beam, measured 11.5 R/min at 120 kVp, 24.3 kWp and 3.42 R/min at 70 kVp, 14.2 kWp

  13. Technique for evaluation of spatial resolution and microcalcifications in digital and scanned images of a standard breast phantom

    International Nuclear Information System (INIS)

    Santana, Priscila do C.; Gomes, Danielle S.; Oliveira, Marcio A.; Oliveira, Paulo Marcio C. de; Meira-Belo, Luiz C.; Nogueira-Tavares, Maria S.

    2011-01-01

    In this work, an automated methodology to evaluate digital and scanned images of a standard phantom (Phantom Mama) was studied. The Phantom Mama was used as an important tool to check the quality of mammographs. The scanned images were digitized using a ScanMaker 9800XL, with resolution of 900 dpi. The aim of this work is to test an automatic methodology for evaluation of spatial resolution and microcalcifications group of phantom mama images acquired with the same parameters in the same equipment. In order to analyze the images we have used the ImageJ software (in Java) which is public domain. We have used the Fast Fourier transform technique to evaluate the spatial resolution and used the ImageJ function Subtract Background and the Light Background plus Sliding Paraboloid on the evaluation of the five groups of microcalcifications on the breast phantom to assess the viability of using automated methods for both types of images. The methodology was adequate for evaluated the microcalcifications group and the spatial resolution in scanned and digital images, but the Phantom Mama doesn't provide sufficient parameters to evaluate the spatial resolution in this images. (author)

  14. Evaluation of digital dental models obtained from dental cone-beam computed tomography scan of alginate impressions.

    Science.gov (United States)

    Jiang, Tingting; Lee, Sang-Mi; Hou, Yanan; Chang, Xin; Hwang, Hyeon-Shik

    2016-05-01

    To investigate the dimensional accuracy of digital dental models obtained from the dental cone-beam computed tomography (CBCT) scan of alginate impressions according to the time elapse when the impressions are stored under ambient conditions. Alginate impressions were obtained from 20 adults using 3 different alginate materials, 2 traditional alginate materials (Alginoplast and Cavex Impressional) and 1 extended-pour alginate material (Cavex ColorChange). The impressions were stored under ambient conditions, and scanned by CBCT immediately after the impressions were taken, and then at 1 hour intervals for 6 hours. After reconstructing three-dimensional digital dental models, the models were measured and the data were analyzed to determine dimensional changes according to the elapsed time. The changes within the measurement error were regarded as clinically acceptable in this study. All measurements showed a decreasing tendency with an increase in the elapsed time after the impressions. Although the extended-pour alginate exhibited a less decreasing tendency than the other 2 materials, there were no statistically significant differences between the materials. Changes above the measurement error occurred between the time points of 3 and 4 hours after the impressions. The results of this study indicate that digital dental models can be obtained simply from a CBCT scan of alginate impressions without sending them to a remote laboratory. However, when the impressions are not stored under special conditions, they should be scanned immediately, or at least within 2 to 3 hours after the impressions are taken.

  15. Evaluation of digital dental models obtained from dental cone-beam computed tomography scan of alginate impressions

    Science.gov (United States)

    Jiang, Tingting; Lee, Sang-Mi; Hou, Yanan; Chang, Xin

    2016-01-01

    Objective To investigate the dimensional accuracy of digital dental models obtained from the dental cone-beam computed tomography (CBCT) scan of alginate impressions according to the time elapse when the impressions are stored under ambient conditions. Methods Alginate impressions were obtained from 20 adults using 3 different alginate materials, 2 traditional alginate materials (Alginoplast and Cavex Impressional) and 1 extended-pour alginate material (Cavex ColorChange). The impressions were stored under ambient conditions, and scanned by CBCT immediately after the impressions were taken, and then at 1 hour intervals for 6 hours. After reconstructing three-dimensional digital dental models, the models were measured and the data were analyzed to determine dimensional changes according to the elapsed time. The changes within the measurement error were regarded as clinically acceptable in this study. Results All measurements showed a decreasing tendency with an increase in the elapsed time after the impressions. Although the extended-pour alginate exhibited a less decreasing tendency than the other 2 materials, there were no statistically significant differences between the materials. Changes above the measurement error occurred between the time points of 3 and 4 hours after the impressions. Conclusions The results of this study indicate that digital dental models can be obtained simply from a CBCT scan of alginate impressions without sending them to a remote laboratory. However, when the impressions are not stored under special conditions, they should be scanned immediately, or at least within 2 to 3 hours after the impressions are taken. PMID:27226958

  16. Beyond the Scanned Image: A Needs Assessment of Scholarly Users of Digital Collections

    Science.gov (United States)

    Green, Harriett E.; Courtney, Angela

    2015-01-01

    This paper presents an analysis of how humanities scholars use digital collections in their research and the ways in which digital collections could be enhanced for scholarly use. The authors surveyed and interviewed humanities faculty from twelve research universities about their research practices with digital collections and present analysis of…

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

    NARCIS (Netherlands)

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

    2008-01-01

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

  19. DIGITAL TERRAIN MODELS FROM MOBILE LASER SCANNING DATA IN MORAVIAN KARST

    Directory of Open Access Journals (Sweden)

    N. Tyagur

    2016-06-01

    Full Text Available During the last ten years, mobile laser scanning (MLS systems have become a very popular and efficient technology for capturing reality in 3D. A 3D laser scanner mounted on the top of a moving vehicle (e.g. car allows the high precision capturing of the environment in a fast way. Mostly this technology is used in cities for capturing roads and buildings facades to create 3D city models. In our work, we used an MLS system in Moravian Karst, which is a protected nature reserve in the Eastern Part of the Czech Republic, with a steep rocky terrain covered by forests. For the 3D data collection, the Riegl VMX 450, mounted on a car, was used with integrated IMU/GNSS equipment, which provides low noise, rich and very dense 3D point clouds. The aim of this work is to create a digital terrain model (DTM from several MLS data sets acquired in the neighbourhood of a road. The total length of two covered areas is 3.9 and 6.1 km respectively, with an average width of 100 m. For the DTM generation, a fully automatic, robust, hierarchic approach was applied. The derivation of the DTM is based on combinations of hierarchical interpolation and robust filtering for different resolution levels. For the generation of the final DTMs, different interpolation algorithms are applied to the classified terrain points. The used parameters were determined by explorative analysis. All MLS data sets were processed with one parameter set. As a result, a high precise DTM was derived with high spatial resolution of 0.25 x 0.25 m. The quality of the DTMs was checked by geodetic measurements and visual comparison with raw point clouds. The high quality of the derived DTM can be used for analysing terrain changes and morphological structures. Finally, the derived DTM was compared with the DTM of the Czech Republic (DMR 4G with a resolution of 5 x 5 m, which was created from airborne laser scanning data. The vertical accuracy of the derived DTMs is around 0.10 m.

  20. The Role of Digital 3D Scanned Models in Dental Students' Self-Assessments in Preclinical Operative Dentistry.

    Science.gov (United States)

    Lee, Cliff; Kobayashi, Hiro; Lee, Samuel R; Ohyama, Hiroe

    2018-04-01

    The aim of this study was to determine how dental student self-assessment and faculty assessment of operative preparations compared for conventional visual assessment versus assessment of scanned digital 3D models. In 2016, all third-year students in the Class of 2018 (N=35) at Harvard School of Dental Medicine performed preclinical exams of Class II amalgam preparations (C2AP) and Class III composite preparations (C3CP) and completed self-assessment forms; in 2017, all third-year students in the Class of 2019 (N=34) performed the same exams. Afterwards, the prepared typodont teeth were digitally scanned. Students self-assessed their preparations digitally, and four faculty members graded the preparations conventionally and digitally. The results showed that, overall, the students assessed their preparations higher than the faculty assessments. The mean student-faculty gaps for C2AP and C3CP in the conventional assessments were 11% and 5%, respectively. The mean digital student-faculty gap for C2AP and C3CP were 8% and 2%, respectively. In the conventional assessments, preclinical performance was negatively correlated with the student-faculty gap (r=-0.47, pStudents in the bottom quartile significantly improved their self-assessment accuracy using digital self-assessments over conventional assessments (C2AP 10% vs. 17% and C3CP 3% vs. 10%, respectively). These results suggest that digital assessments offered a significant learning opportunity for students to critically self-assess themselves in operative preclinical dentistry. The lower performing students benefitted the most, improving their assessment ability to the level of the rest of the class.

  1. 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

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

    Science.gov (United States)

    Haasl, Ryan J.; Payseur, Bret A.

    2016-01-01

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

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

    Science.gov (United States)

    Mao, Hongliang; Wang, Hao

    2017-03-01

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

  4. Rotational scanning and multiple-spot focusing through a multimode fiber based on digital optical phase conjugation

    Science.gov (United States)

    Ma, Chaojie; Di, Jianglei; Li, Ying; Xiao, Fajun; Zhang, Jiwei; Liu, Kaihui; Bai, Xuedong; Zhao, Jianlin

    2018-06-01

    We demonstrate, for the first time, the rotational memory effect of a multimode fiber (MMF) based on digital optical phase conjugation (DOPC) to achieve multiple-spot focusing. An implementation interferometer is used to address the challenging alignments in DOPC. By rotating the acquired phase conjugate pattern, rotational scanning through a MMF could be achieved by recording a single off-axis hologram. The generation of two focal spots through a MMF is also demonstrated by combining the rotational memory effect with the superposition principle. The results may be useful for ultrafast scanning imaging and optical manipulation of multiple objects through a MMF.

  5. TU-CD-207-05: A Novel Digital Tomosynthesis System Using Orthogonal Scanning Technique: A Feasibility Study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J [Samsung Medical Center, Seoul (Korea, Republic of); Park, C [University of Florida Health Science Center, Gainesville, FL (United States); Kauweloa, K [UTHSCSA, San Antonio, TX (United States); Chung, Y; Han, Y [Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Ju, S [Samsung Medical Center, Seoul, Seoul (Korea, Republic of)

    2015-06-15

    Purpose: As an alternative to full tomographic imaging technique such as cone-beam computed tomography (CBCT), there is growing interest to adopt digital tomosynthesis (DTS) for the use of diagnostic as well as therapeutic applications. The aim of this study is to propose a new DTS system using novel orthogonal scanning technique, which can provide superior image quality DTS images compared to the conventional DTS scanning system. Methods: Unlike conventional DTS scanning system, the proposed DTS is reconstructed with two sets of orthogonal patient scans. 1) X-ray projections that are acquired along transverse trajectory and 2) an additional sets of X-ray projections acquired along the vertical direction at the mid angle of the previous transverse scan. To reconstruct DTS, we have used modified filtered backprojection technique to account for the different scanning directions of each projection set. We have evaluated the performance of our method using numerical planning CT data of liver cancer patient and a physical pelvis phantom experiment. The results were compared with conventional DTS techniques with single transverse and vertical scanning. Results: The experiments on both numerical simulation as well as physical experiment showed that the resolution as well as contrast of anatomical structures was much clearer using our method. Specifically, the image quality comparing with transversely scanned DTS showed that the edge and contrast of anatomical structures along Left-Right (LR) directions was comparable however, considerable discrepancy and enhancement could be observed along Superior-Inferior (SI) direction using our method. The opposite was observed when vertically scanned DTS was compared. Conclusion: In this study, we propose a novel DTS system using orthogonal scanning technique. The results indicated that the image quality of our novel DTS system was superior compared to conventional DTS system. This makes our DTS system potentially useful in various

  6. Evaluation of digital dental models obtained from dental cone-beam computed tomography scan of alginate impressions

    OpenAIRE

    Jiang, Tingting; Lee, Sang-Mi; Hou, Yanan; Chang, Xin; Hwang, Hyeon-Shik

    2016-01-01

    Objective To investigate the dimensional accuracy of digital dental models obtained from the dental cone-beam computed tomography (CBCT) scan of alginate impressions according to the time elapse when the impressions are stored under ambient conditions. Methods Alginate impressions were obtained from 20 adults using 3 different alginate materials, 2 traditional alginate materials (Alginoplast and Cavex Impressional) and 1 extended-pour alginate material (Cavex ColorChange). The impressions wer...

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

    Science.gov (United States)

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

    2012-07-01

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

  8. SCAN- a maintenance-free flowrate meter with direct digital read-out for computerised control applications in radiochemical plants

    Energy Technology Data Exchange (ETDEWEB)

    Shah, B V; Siddiqui, I A; Theyyunni, T K [Process Engineering and Systems Division, Bhabha Atomic Research Centre, Mumbai (India)

    1994-06-01

    In radiochemical plants, the choice of flowrate sensor is subject to stringent requirements of fail-safe design and freedom from maintenance. The SCAN remote digital direct indicating flowrate meter described in this paper was developed to meet the requirements of flowrate and transmitting it to the control room, and to a computerised control system. SCAN is designed on the principle that flowrate through an orifice is a function of the head of liquid acting upon it. SCAN consists of a small chamber which receives the flow, and discharges it through an orifice located in bottom. The level of liquid in the pot represents the flowrate of the input stream. SCAN has been developed into an accurate, rugged and practical device by refinements in the design of internals, and by introducing a special end-section which makes the calibration insensitive to location. An important feature of SCAN is that it is passive, maintenance free, fail-safe device and contains no moving parts. There is no liquid hold up in the SCAN when idle, which is a desirable feature for the radiochemical plant environment. (author). 3 figs., 2 tabs.

  9. Patient dose simulations for scanning-beam digital x-ray tomosynthesis of the lungs

    International Nuclear Information System (INIS)

    Nelson, Geoff; Fahrig, Rebecca; Yoon, Sungwon; Krishna, Ganesh; Wilfley, Brian

    2013-01-01

    Purpose: An improved method of image guidance for lung tumor biopsies could help reduce the high rate of false negatives. The aim of this work is to optimize the geometry of the scanning-beam digital tomography system (SBDX) for providing real-time 3D tomographic reconstructions for target verification. The unique geometry of the system requires trade-offs between patient dose, imaging field of view (FOV), and tomographic angle.Methods: Tomosynthetic angle as a function of tumor-to-detector distance was calculated. Monte Carlo Software (PCXMC) was used to calculate organ doses and effective dose for source-to-detector distances (SDDs) from 90 to 150 cm, patient locations with the tumor at 20 cm from the source to 20 cm from the detector, and FOVs centered on left lung and right lung as well as medial and distal peripheries of the lungs. These calculations were done for two systems, a SBDX system and a GE OEC-9800 C-arm fluoroscopic unit. To evaluate the dose effect of the system geometry, results from PCXMC were calculated using a scan of 300 mAs for both SBDX and fluoroscopy. The Rose Criterion was used to find the fluence required for a tumor SNR of 5, factoring in scatter, air-gap, system geometry, and patient position for all models generated with PCXMC. Using the calculated fluence for constant tumor SNR, the results from PCXMC were used to compare the patient dose for a given SNR between SBDX and fluoroscopy.Results: Tomographic angle changes with SDD only in the region near the detector. Due to their geometry, the source array and detector have a peak tomographic angle for any given SDD at a source to tumor distance that is 69.7% of the SDD assuming constant source and detector size. Changing the patient location in order to increase tomographic angle has a significant effect on organ dose distribution due to geometrical considerations. With SBDX and fluoroscopy geometries, the dose to organs typically changes in an opposing manner with changing patient

  10. Patient dose simulations for scanning-beam digital x-ray tomosynthesis of the lungs

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Geoff; Fahrig, Rebecca [Department of Radiology, Stanford University, Stanford, California 94305 (United States); Yoon, Sungwon [Varian Medical Systems, Palo Alto, California 94304 (United States); Krishna, Ganesh [Palo Alto Medical Foundation, Mountain View, California 94040 (United States); Wilfley, Brian [Triple Ring Technologies, Inc., Newark, California 94560 (United States)

    2013-11-15

    Purpose: An improved method of image guidance for lung tumor biopsies could help reduce the high rate of false negatives. The aim of this work is to optimize the geometry of the scanning-beam digital tomography system (SBDX) for providing real-time 3D tomographic reconstructions for target verification. The unique geometry of the system requires trade-offs between patient dose, imaging field of view (FOV), and tomographic angle.Methods: Tomosynthetic angle as a function of tumor-to-detector distance was calculated. Monte Carlo Software (PCXMC) was used to calculate organ doses and effective dose for source-to-detector distances (SDDs) from 90 to 150 cm, patient locations with the tumor at 20 cm from the source to 20 cm from the detector, and FOVs centered on left lung and right lung as well as medial and distal peripheries of the lungs. These calculations were done for two systems, a SBDX system and a GE OEC-9800 C-arm fluoroscopic unit. To evaluate the dose effect of the system geometry, results from PCXMC were calculated using a scan of 300 mAs for both SBDX and fluoroscopy. The Rose Criterion was used to find the fluence required for a tumor SNR of 5, factoring in scatter, air-gap, system geometry, and patient position for all models generated with PCXMC. Using the calculated fluence for constant tumor SNR, the results from PCXMC were used to compare the patient dose for a given SNR between SBDX and fluoroscopy.Results: Tomographic angle changes with SDD only in the region near the detector. Due to their geometry, the source array and detector have a peak tomographic angle for any given SDD at a source to tumor distance that is 69.7% of the SDD assuming constant source and detector size. Changing the patient location in order to increase tomographic angle has a significant effect on organ dose distribution due to geometrical considerations. With SBDX and fluoroscopy geometries, the dose to organs typically changes in an opposing manner with changing patient

  11. Optimization Of Scan Range For 3d Point Localization In Statscan Digital Medical Radiology

    Directory of Open Access Journals (Sweden)

    Jacinta S. Kimuyu

    2015-08-01

    Full Text Available The emergence of computerized medical imaging in early 1970s which merged with digital technology in the 1980s was celebrated as a major breakthrough in three-dimensional 3D medicine. However a recent South African innovation the high speed scanning Lodox Statscan Critical Digital Radiology modality posed challenges in X-ray photogrammetry due to the systems intricate imaging geometry. The study explored the suitability of the Direct Linear Transformation as a method for the determination of 3D coordinates of targeted points from multiple images acquired with the Statscan X-ray system and optimization of the scan range. This investigation was carried out as a first step towards the development of a method to determine the accurate positions of points on or inside the human body. The major causes of errors in three-dimensional point localization using Statscan images were firstly the X-ray beam divergence and secondly the position of the point targets above the X-ray platform. The experiments carried out with two reference frames showed that point positions could be established with RMS values in the mm range in the middle axis of the X-ray patient platform. This range of acceptable mm accuracies extends about 15 to 20 cm sideways towards the edge of the X-ray table and to about 20 cm above the table surface. Beyond this range accuracy deteriorated significantly reaching RMS values of 30mm to 40 mm. The experiments further showed that the inclusion of control points close to the table edges and more than 20 cm above the table resulted in lower accuracies for the L - parameters of the DLT solution than those derived from points close to the center axis only. As the accuracy of the L - parameters propagates into accuracy of the final coordinates of newly determined points it is essential to restrict the space of the control points to the above described limits. If one adopts the usual approach of surrounding the object by known control points then

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

    Directory of Open Access Journals (Sweden)

    Kunzhe Dong

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

  13. Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping

    Directory of Open Access Journals (Sweden)

    Maruoka Shuichiro

    2008-12-01

    Full Text Available Abstract Background The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are limited and not always within reach. In this study, we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK, a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. MSDK is a sequenced based method that allows a comprehensive and unbiased methylation profiling. The method generates 21 base pairs long sequence tags derived from specific locations in the genome. The resulting tag frequencies determine in a quantitative manner the methylation level of the corresponding loci. Results Genomic DNA from whole lung was isolated and subjected to MSDK analysis using the methylation-sensitive enzyme Not I as the mapping enzyme and Nla III as the fragmenting enzyme. In a pair wise comparison of the generated mouse MSDK libraries we identified 158 loci that are significantly differentially methylated (P-value = 0.05 after perinatal dietary changes in our mouse model. Quantitative methylation specific PCR and sequence analysis of bisulfate modified genomic DNA confirmed changes in methylation at specific loci. Differences in genomic MSDK tag counts for a selected set of genes, correlated well with changes in transcription levels as measured by real-time PCR. Furthermore serial analysis of gene expression profiling demonstrated a dramatic difference in expressed transcripts in mice exposed to perinatal nutritional changes. Conclusion The genome-wide methylation survey applied in this study allowed for an unbiased methylation profiling revealing subtle changes in DNA methylation in mice maternally exposed to dietary changes in methyl-donor content. The MSDK method is applicable for mouse models

  14. Fast-scan em with digital image processing for dynamic experiments

    Science.gov (United States)

    Charles W. McMillin; Fred C. Billingsley; Robert E. Frazer

    1973-01-01

    The recent introduction of accessory instrumentation capable of display at television scan rates suggests a broadened application for the scanning electron microscope - the direct observation of motion (dynamic events) at magnifactions otherwise unattainable. In one illustrative experiment, the transverse surface of southern pine was observed when subjected to large...

  15. Comparison of Bolton analysis and Little’s irregularity index on laser scanned three-dimensional digital study models with conventional study models

    Science.gov (United States)

    Kurnia, H.; Noerhadi, N. A. I.

    2017-08-01

    Three-dimensional digital study models were introduced following advances in digital technology. This study was carried out to assess the reliability of digital study models scanned by a laser scanning device newly assembled. The aim of this study was to compare the digital study models and conventional models. Twelve sets of dental impressions were taken from patients with mild-to-moderate crowding. The impressions were taken twice, one with alginate and the other with polyvinylsiloxane. The alginate impressions were made into conventional models, and the polyvinylsiloxane impressions were scanned to produce digital models. The mesiodistal tooth width and Little’s irregularity index (LII) were measured manually with digital calipers on the conventional models and digitally on the digital study models. Bolton analysis was performed on each study models. Each method was carried out twice to check for intra-observer variability. The reproducibility (comparison of the methods) was assessed using independent-sample t-tests. The mesiodistal tooth width between conventional and digital models did not significantly differ (p > 0.05). Independent-sample t-tests did not identify statistically significant differences for Bolton analysis and LII (p = 0.603 for Bolton and p = 0894 for LII). The measurements of the digital study models are as accurate as those of the conventional models.

  16. 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

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Aihong eYang

    2016-05-01

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

  19. Validity, reliability, and reproducibility of linear measurements on digital models obtained from intraoral and cone-beam computed tomography scans of alginate impressions

    NARCIS (Netherlands)

    Wiranto, Matthew G.; Engelbrecht, W. Petrie; Nolthenius, Heleen E. Tutein; van der Meer, W. Joerd; Ren, Yijin

    INTRODUCTION: Digital 3-dimensional models are widely used for orthodontic diagnosis. The aim of this study was to assess the validity, reliability, and reproducibility of digital models obtained from the Lava Chairside Oral scanner (3M ESPE, Seefeld, Germany) and cone-beam computed tomography scans

  20. Evaluating Digital PCR for the Quantification of Human Genomic DNA: Accessible Amplifiable Targets.

    Science.gov (United States)

    Kline, Margaret C; Romsos, Erica L; Duewer, David L

    2016-02-16

    Polymerase chain reaction (PCR) multiplexed assays perform best when the input quantity of template DNA is controlled to within about a factor of √2. To help ensure that PCR assays yield consistent results over time and place, results from methods used to determine DNA quantity need to be metrologically traceable to a common reference. Many DNA quantitation systems can be accurately calibrated with solutions of DNA in aqueous buffer. Since they do not require external calibration, end-point limiting dilution technologies, collectively termed "digital PCR (dPCR)", have been proposed as suitable for value assigning such DNA calibrants. The performance characteristics of several commercially available dPCR systems have recently been documented using plasmid, viral, or fragmented genomic DNA; dPCR performance with more complex materials, such as human genomic DNA, has been less studied. With the goal of providing a human genomic reference material traceably certified for mass concentration, we are investigating the measurement characteristics of several dPCR systems. We here report results of measurements from multiple PCR assays, on four human genomic DNAs treated with four endonuclease restriction enzymes using both chamber and droplet dPCR platforms. We conclude that dPCR does not estimate the absolute number of PCR targets in a given volume but rather the number of accessible and amplifiable targets. While enzymatic restriction of human genomic DNA increases accessibility for some assays, in well-optimized PCR assays it can reduce the number of amplifiable targets and increase assay variability relative to uncut sample.

  1. Diagnostic performance of digital breast tomosynthesis with a wide scan angle compared to full-field digital mammography for the detection and characterization of microcalcifications

    International Nuclear Information System (INIS)

    Clauser, Paola; Nagl, Georg; Helbich, Thomas H.; Pinker-Domenig, Katja; Weber, Michael; Kapetas, Panagiotis; Bernathova, Maria; Baltzer, Pascal A.T.

    2016-01-01

    Highlights: • Wide scan-angle DBT alone shows a high detection rate for microcalcifications. • DBT and FFDM can characterize microcalcifications at a comparable level. • Characterization is influenced by reader and by lesion type (benign vs malignant). • DBT might be used as a stand-alone technique for the assessment of microcalcifications. - Abstract: Objectives: To assess the diagnostic performance of digital breast tomosynthesis (DBT), with a wide scan-angle, compared to full-field digital mammography (FFDM), for the detection and characterization of microcalcifications. Methods: IRB approval was obtained for this retrospective study. We selected 150 FFDM and DBT (50 benign and 50 malignant histologically verified microcalcifications, 50 cases classified as BI-RADS 1). Four radiologists evaluated, in separate sessions and blinded to patients’ history and histology, the presence of microcalcifications. Cases with microcalcifications were assessed for visibility, characteristics, and grade of suspicion using BI-RADS categories. Detection rate and diagnostic performance were calculated. Visibility, lesions’ characteristics and reading time were analysed. Results: Detection rate and visibility were good for both FFDM and DBT, without intra-reader differences (P = 0.510). Inter-reader differences were detected (P < 0.018). Only two lesions were not detected by any reader on either FFDM or DBT. Diagnostic performance with DBT was as good as that of FFDM, but a significant inter-reader difference was found (P = 0.041). High inter-reader variability in the use of the descriptors was found. Reading time for DBT was almost twice that for FFDM (44 and 25 s, respectively). Conclusion: Wide scan-angle DBT enabled the detection and characterization of microcalcifications with no significant differences from FFDM. Inter-reader variability was seen.

  2. Diagnostic performance of digital breast tomosynthesis with a wide scan angle compared to full-field digital mammography for the detection and characterization of microcalcifications

    Energy Technology Data Exchange (ETDEWEB)

    Clauser, Paola, E-mail: paola.clauser@meduniwien.ac.at [Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria); Nagl, Georg [Department for Radiology and Interventional Radiology, Landesklinikum Horn, Spitalgasse 10, 3580 Horn (Austria); Helbich, Thomas H., E-mail: thomas.helbich@meduniwien.ac.at [Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria); Pinker-Domenig, Katja [Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria); Weber, Michael [Department of Biomedical Imaging and Image-Guided Therapy, Division of General and Pediatric Radiology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria); Kapetas, Panagiotis; Bernathova, Maria; Baltzer, Pascal A.T. [Department of Biomedical Imaging and Image-Guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna (Austria)

    2016-12-15

    Highlights: • Wide scan-angle DBT alone shows a high detection rate for microcalcifications. • DBT and FFDM can characterize microcalcifications at a comparable level. • Characterization is influenced by reader and by lesion type (benign vs malignant). • DBT might be used as a stand-alone technique for the assessment of microcalcifications. - Abstract: Objectives: To assess the diagnostic performance of digital breast tomosynthesis (DBT), with a wide scan-angle, compared to full-field digital mammography (FFDM), for the detection and characterization of microcalcifications. Methods: IRB approval was obtained for this retrospective study. We selected 150 FFDM and DBT (50 benign and 50 malignant histologically verified microcalcifications, 50 cases classified as BI-RADS 1). Four radiologists evaluated, in separate sessions and blinded to patients’ history and histology, the presence of microcalcifications. Cases with microcalcifications were assessed for visibility, characteristics, and grade of suspicion using BI-RADS categories. Detection rate and diagnostic performance were calculated. Visibility, lesions’ characteristics and reading time were analysed. Results: Detection rate and visibility were good for both FFDM and DBT, without intra-reader differences (P = 0.510). Inter-reader differences were detected (P < 0.018). Only two lesions were not detected by any reader on either FFDM or DBT. Diagnostic performance with DBT was as good as that of FFDM, but a significant inter-reader difference was found (P = 0.041). High inter-reader variability in the use of the descriptors was found. Reading time for DBT was almost twice that for FFDM (44 and 25 s, respectively). Conclusion: Wide scan-angle DBT enabled the detection and characterization of microcalcifications with no significant differences from FFDM. Inter-reader variability was seen.

  3. Digital Droplet Multiple Displacement Amplification (ddMDA for Whole Genome Sequencing of Limited DNA Samples.

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available Multiple displacement amplification (MDA is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  4. 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.

  5. 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.

  6. 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....

  7. Comparison of digital scanning and polyvinyl siloxane impression techniques by dental students: instructional efficiency and attitudes towards technology.

    Science.gov (United States)

    Marti, A M; Harris, B T; Metz, M J; Morton, D; Scarfe, W C; Metz, C J; Lin, W-S

    2017-08-01

    With increasing use of digital scanning with restorative procedures in the dental office, it becomes necessary that educational institutions adopt instructional methodology for introducing this technology together with conventional impression techniques. To compare the time differences between instructing dental students on digital scanning (DS) (LAVA C.O.S. digital impression system) and a conventional impression technique (CI) (polyvinyl siloxane), and to compare students' attitudes and beliefs towards both techniques. Volunteer sophomore dental students (n = 25) with no prior experience in clinical impressions were recruited and IRB consent obtained. Participants responded to a pre-and post-exposure questionnaire. Participants were instructed on the use of both DS and CI for a single tooth full coverage crown restoration using a consecutive sequence of video lecture, investigator-led demonstration and independent impression exercise. The time necessary for each step (minutes) was recorded. Statistical significance was calculated using dependent t-tests (time measurements) and 2-sample Mann-Whitney (questionnaire responses). The time spent teaching students was greater for DS than CI for video lecture (15.95 and 10.07 min, P = 0.0000), demonstration time (9.06 and 4.70 min, P = 0.0000) and impression time (18.17 and 8.59 min, P = 0.0000). Prior to the instruction and practice, students considered themselves more familiar with CI (3.96) than DS (1.96) (P = 0.0000). After the instruction and practice, participants reported CI technique proved significantly easier than expected (pre-instruction: 3.52 and post-instruction: 4.08, P = 0.002). However, overall participants' perception of ease of use for DS was not influenced by this instruction and practice experience (pre-instruction: 3.84 and post-instruction: 3.56, P = 0.106). Despite the results, 96% of participants expressed an expectation that DS will become their predominant impression technique during their

  8. Detector, collimator and real-time reconstructor for a new scanning-beam digital x-ray (SBDX) prototype.

    Science.gov (United States)

    Speidel, Michael A; Tomkowiak, Michael T; Raval, Amish N; Dunkerley, David A P; Slagowski, Jordan M; Kahn, Paul; Ku, Jamie; Funk, Tobias

    Scanning-beam digital x-ray (SBDX) is an inverse geometry fluoroscopy system for low dose cardiac imaging. The use of a narrow scanned x-ray beam in SBDX reduces detected x-ray scatter and improves dose efficiency, however the tight beam collimation also limits the maximum achievable x-ray fluence. To increase the fluence available for imaging, we have constructed a new SBDX prototype with a wider x-ray beam, larger-area detector, and new real-time image reconstructor. Imaging is performed with a scanning source that generates 40,328 narrow overlapping projections from 71 × 71 focal spot positions for every 1/15 s scan period. A high speed 2-mm thick CdTe photon counting detector was constructed with 320×160 elements and 10.6 cm × 5.3 cm area (full readout every 1.28 μs), providing an 86% increase in area over the previous SBDX prototype. A matching multihole collimator was fabricated from layers of tungsten, brass, and lead, and a multi-GPU reconstructor was assembled to reconstruct the stream of captured detector images into full field-of-view images in real time. Thirty-two tomosynthetic planes spaced by 5 mm plus a multiplane composite image are produced for each scan frame. Noise equivalent quanta on the new SBDX prototype measured 63%-71% higher than the previous prototype. X-ray scatter fraction was 3.9-7.8% when imaging 23.3-32.6 cm acrylic phantoms, versus 2.3-4.2% with the previous prototype. Coronary angiographic imaging at 15 frame/s was successfully performed on the new SBDX prototype, with live display of either a multiplane composite or single plane image.

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

    OpenAIRE

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

    2008-01-01

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

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  11. 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.

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

    NARCIS (Netherlands)

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

    2009-01-01

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  14. Correction of phase-shifting error in wavelength scanning digital holographic microscopy

    Science.gov (United States)

    Zhang, Xiaolei; Wang, Jie; Zhang, Xiangchao; Xu, Min; Zhang, Hao; Jiang, Xiangqian

    2018-05-01

    Digital holographic microscopy is a promising method for measuring complex micro-structures with high slopes. A quasi-common path interferometric apparatus is adopted to overcome environmental disturbances, and an acousto-optic tunable filter is used to obtain multi-wavelength holograms. However, the phase shifting error caused by the acousto-optic tunable filter reduces the measurement accuracy and, in turn, the reconstructed topographies are erroneous. In this paper, an accurate reconstruction approach is proposed. It corrects the phase-shifting errors by minimizing the difference between the ideal interferograms and the recorded ones. The restriction on the step number and uniformity of the phase shifting is relaxed in the interferometry, and the measurement accuracy for complex surfaces can also be improved. The universality and superiority of the proposed method are demonstrated by practical experiments and comparison to other measurement methods.

  15. Determination of tire cross-sectional geometric characteristics from a digitally scanned image

    Science.gov (United States)

    Danielson, Kent T.

    1995-08-01

    A semi-automated procedure is described for the accurate determination of geometrical characteristics using a scanned image of the tire cross-section. The procedure can be useful for cases when CAD drawings are not available or when a description of the actual cured tire is desired. Curves representing the perimeter of the tire cross-section are determined by an edge tracing scheme, and the plyline and cord-end positions are determined by locations of color intensities. The procedure provides an accurate description of the perimeter of the tire cross-section and the locations of plylines and cord-ends. The position, normals, and curvatures of the cross-sectional surface are included in this description. The locations of the plylines provide the necessary information for determining the ply thicknesses and relative position to a reference surface. Finally, the locations of the cord-ends provide a means to calculate the cord-ends per inch (epi). Menu driven software has been developed to facilitate the procedure using the commercial code, PV-Wave by Visual Numerics, Inc., to display the images. From a single user interface, separate modules are executed for image enhancement, curve fitting the edge trace of the cross-sectional perimeter, and determining the plyline and cord-end locations. The code can run on SUN or SGI workstations and requires the use of a mouse to specify options or identify items on the scanned image.

  16. QUANTIFICATION OF BIOFILMS IN MULTI-SPECTRAL DIGITAL1 VOLUMES FROM CONFOCAL LASER-SCANNING MICROSCOPES

    Directory of Open Access Journals (Sweden)

    Karsten Rodenacker

    2011-05-01

    Full Text Available Populations of bacteria in sludge flocs and biofilm marked by fluorescence marked with fluorescent probes are digitised with a confocal laser scanning microscope. These data are used to analyse the microbial community structure, to obtain information on the localisation of specific bacterial groups and to examine gene expression. This information is urgently required for an in-depth understanding of the function and, more generally, the microbial ecology of biofilms. Methods derived from quantitative image analysis are applied to digitised data from confocal laser scanning microscopes to obtain quantitative descriptions of volumetric, topological (and topographical properties of different compartments of the components under research. In addition to free-moving flocs, also biofilms attached to a substratum in an experimental environment are analysed. Growth form as well as interaction of components are quantitatively described. Classical measurements of volume and intensity (shape, distribution and distance dependent interaction measurements using methods from mathematical morphology are performed. Mainly image (volume processing methods are outlined. Segmented volumes are globally and individually (in terms of 3Dconnected components measured and used for distance mapping transform as well as for estimation of geodesic distances from the substrate. All transformations are applied on the 3D data set. Resulting distance distributions are quantified and related to information on the identity and activity of the probe-identified bacteria.

  17. Estimating the chlorophyll content in the waters of Guanabara Bay from the LANDSAT multispectral scanning digital data

    Science.gov (United States)

    Dejesusparada, N. (Principal Investigator); Bentancurt, J. J. V.; Herz, B. R.; Molion, L. B.

    1980-01-01

    Detection of water quality in Guanabara Bay using multispectral scanning digital data taken from LANDSAT satellites was examined. To test these processes, an empirical (statistical) approach was choosen to observe the degree of relationship between LANDSAT data and the in situ data taken simultaneously. The linear and nonlinear regression analyses were taken from among those developed by INPE in 1978. Results indicate that the major regression was in the number six MSS band, atmospheric effects, which indicated a correction coefficient of 0.99 and an average error of 6.59 micrograms liter. This error was similar to that obtained in the laboratory. The chlorophyll content was between 0 and 100 micrograms/liter, as taken from the MSS of LANDSAT.

  18. Comparison between a digital scanning system and a conventional screen film system in the full spine radiological procedure in pediatrics

    International Nuclear Information System (INIS)

    Espana, M. L.; Gomez, G.; Romero, A.; Minambres, A.; Albi, G.; Floriano, A.; Rodirguez, A.; Lopez Franco, P.

    2004-01-01

    To compare from both dosimetry and image quality standpoints, a digital scanning system with a conventional screen film system, in the full spine radiological procedure. The standard patient is considered to be 12 years old, and a sample of forty patients referred for full spine radiological procedure has been studied. Gonad shielding has been used in all the patients, and its efficiency has been evaluated. Dosimetric study includes Kerma-area product, and thorax and gonad entrance surface dose. Kerma area product has been measured using a transmission camera, and for entrance surface dose estimation both thermoluminescent dosemeter LiF: Mg, Cu, P and LiF: Mg, Ti have been utilized. Three radiologists have evaluated the image quality according to the degree of fulfilment of the image quality criteria. (Author) 22 refs

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

    Directory of Open Access Journals (Sweden)

    Hari Deo eUpadhyaya

    2016-03-01

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

  20. The rf sigmameter: A digital phase-locked technique for accurate long-range laser scanning

    International Nuclear Information System (INIS)

    Zhu, M.; Hall, J.L.

    1986-01-01

    The authors use a new version of a sigmameter, the two-channel field-widened rf sigmameter, to map optical frequency into the phase of an rf signal. This enables them to lock the laser frequency on the interferometer by using a phase-locked loop (PLL). Controlling the reference phase of the PLL electronically, they are able to scan the laser frequency over a long range step by step or with substeps. The systematic error of each substep is cancelled automatically when the authors change one step (which is ten substeps, for example), and that of each step is cancelled when they change the reference phase by 2π (which corresponds to 256 steps in their scheme)

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Daniëlle van Manen

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

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

    Science.gov (United States)

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

    2011-01-01

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

  4. Second generation stationary digital breast tomosynthesis system with faster scan time and wider angular span.

    Science.gov (United States)

    Calliste, Jabari; Wu, Gongting; Laganis, Philip E; Spronk, Derrek; Jafari, Houman; Olson, Kyle; Gao, Bo; Lee, Yueh Z; Zhou, Otto; Lu, Jianping

    2017-09-01

    The aim of this study was to characterize a new generation stationary digital breast tomosynthesis system with higher tube flux and increased angular span over a first generation system. The linear CNT x-ray source was designed, built, and evaluated to determine its performance parameters. The second generation system was then constructed using the CNT x-ray source and a Hologic gantry. Upon construction, test objects and phantoms were used to characterize system resolution as measured by the modulation transfer function (MTF), and artifact spread function (ASF). The results indicated that the linear CNT x-ray source was capable of stable operation at a tube potential of 49 kVp, and measured focal spot sizes showed source-to-source consistency with a nominal focal spot size of 1.1 mm. After construction, the second generation (Gen 2) system exhibited entrance surface air kerma rates two times greater the previous s-DBT system. System in-plane resolution as measured by the MTF is 7.7 cycles/mm, compared to 6.7 cycles/mm for the Gen 1 system. As expected, an increase in the z-axis depth resolution was observed, with a decrease in the ASF from 4.30 mm to 2.35 mm moving from the Gen 1 system to the Gen 2 system as result of an increased angular span. The results indicate that the Gen 2 stationary digital breast tomosynthesis system, which has a larger angular span, increased entrance surface air kerma, and faster image acquisition time over the Gen 1 s-DBT system, results in higher resolution images. With the detector operating at full resolution, the Gen 2 s-DBT system can achieve an in-plane resolution of 7.7 cycles per mm, which is better than the current commercial DBT systems today, and may potentially result in better patient diagnosis. © 2017 American Association of Physicists in Medicine.

  5. Dimensional accuracy of digital dental models from cone-beam computed tomography scans of alginate impressions according to time elapsed after the impressions.

    Science.gov (United States)

    Lee, Sang-Mi; Hou, Yanan; Cho, Jin-Hyoung; Hwang, Hyeon-Shik

    2016-02-01

    Our objective was to investigate the dimensional accuracy of digital dental models obtained from the cone-beam computed tomography (CBCT) scans of alginate impressions according to the time elapsed after the impressions were taken. Alginate impressions were obtained of 20 adults using 2 alginate materials: Alginoplast (Heraeus Kulzer, Hanau, Germany) and Cavex (Cavex Holland, Haarlem, The Netherlands). These impressions were stored in wet conditions and scanned by CBCT immediately after impression-taking and after storage times of 12, 24, 36, 48, 60, and 72 hours. After reconstruction of the 3-dimensional digital dental models, the models were measured, and the data were analyzed to determine the dimensional changes according to the time elapsed. The changes within the measurement error were regarded as clinically acceptable in this study. The measurement errors ranged from 0.27 to 0.29 mm in the digital dental models obtained from CBCT scans of the alginate impressions. All measurements showed decreasing accuracy with greater elapsed time after the impressions were taken. Changes above the measurement error occurred at 24 and 36 hours for Cavex and Alginoplast, respectively. Digital dental models can be obtained from CBCT scans of alginate impressions without sending them to a remote laboratory. However, the impressions need to be scanned within 24 hours; otherwise, dimensional changes lead to errors that exceed the error of measurement. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2012-01-01

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

  7. 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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

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

    DEFF Research Database (Denmark)

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

    2005-01-01

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

  11. Detection of Aspens Using High Resolution Aerial Laser Scanning Data and Digital Aerial Images

    Directory of Open Access Journals (Sweden)

    Kalle Eerikäinen

    2008-08-01

    Full Text Available The aim was to use high resolution Aerial Laser Scanning (ALS data and aerial images to detect European aspen (Populus tremula L. from among other deciduous trees. The field data consisted of 14 sample plots of 30 m × 30 m size located in the Koli National Park in the North Karelia, Eastern Finland. A Canopy Height Model (CHM was interpolated from the ALS data with a pulse density of 3.86/m2, low-pass filtered using Height-Based Filtering (HBF and binarized to create the mask needed to separate the ground pixels from the canopy pixels within individual areas. Watershed segmentation was applied to the low-pass filtered CHM in order to create preliminary canopy segments, from which the non-canopy elements were extracted to obtain the final canopy segmentation, i.e. the ground mask was analysed against the canopy mask. A manual classification of aerial images was employed to separate the canopy segments of deciduous trees from those of coniferous trees. Finally, linear discriminant analysis was applied to the correctly classified canopy segments of deciduous trees to classify them into segments belonging to aspen and those belonging to other deciduous trees. The independent variables used in the classification were obtained from the first pulse ALS point data. The accuracy of discrimination between aspen and other deciduous trees was 78.6%. The independent variables in the classification function were the proportion of vegetation hits, the standard deviation of in pulse heights, accumulated intensity at the 90th percentile and the proportion of laser points reflected at the 60th height percentile. The accuracy of classification corresponded to the validation results of earlier ALS-based studies on the classification of individual deciduous trees to tree species.

  12. 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

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Mahmood Gholami

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

  15. 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.

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

    Science.gov (United States)

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

    2015-02-25

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

  17. 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.

  18. Digitization

    DEFF Research Database (Denmark)

    Finnemann, Niels Ole

    2014-01-01

    what a concept of digital media might add to the understanding of processes of mediatization and what the concept of mediatization might add to the understanding of digital media. It is argued that digital media open an array of new trajectories in human communication, trajectories which were...

  19. A digital repository with an extensible data model for biobanking and genomic analysis management.

    Science.gov (United States)

    Izzo, Massimiliano; Mortola, Francesco; Arnulfo, Gabriele; Fato, Marco M; Varesio, Luigi

    2014-01-01

    Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management. We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing. Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2001-01-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Velculescu Victor E

    2008-04-01

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

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2017-12-01

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

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

    Science.gov (United States)

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

    2014-10-02

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

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

    Science.gov (United States)

    Gould, Billie A; Stinchcombe, John R

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2009-08-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Bumstead Nat

    2005-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Cecilia M Lindgren

    2009-06-01

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

  13. Investigation of renovascular hypertension with 99mTC-DTPA dynamic renal scanning and digital subtraction angiography

    International Nuclear Information System (INIS)

    Stavraka-Kakavakis, A.; Vlontjou, E.; Apostolopoulos, D.; Mourikis, D.; Venetsanakis, N.; Lazarou, S.; Vlahos, L.

    1989-01-01

    Sixty-four selected hypertensive patients, aged 17-45 years, were evaluated for renovascular hypertension. They were studied with 99m TC-DTPA dynamic renal scanning (DRS) and intravenous digital subtraction angiography (IV-DSA). Intra-arterial DSA was further performed to demonstrate renal vascular anatomy in all disputable cases. Agreement of diagnosis occurred in 58 patients (32 with renal artery stenosis). There was one false positive with DRS and one false positive with IV-DSA. In another four patients with proven renovascular disease, IV-DSA was positive while DRS negative, but in two of them the stenotic lesion was considered insignificant, as they failed to respond to percutaneous transluminal dilatation (PTA). In contrast, nearly all patients whose hypertension improved after PTA or surgery had positive DRS and greater than 40% reduction of relative function of the affected kidney. IV-DSA yielded better results than DRS in the detection of renal arterial stenosis (especially whenever bilateral stenosis or rich collateral circulation was present), but DRS showed better correlation with the functional significance of a certain vascular abnormality. Thus the combination of the two methods seems to be a reasonable diagnostic approach to hypertensive patients with the aim of selecting those with curable hypertension due to renal vascular disease. (orig.)

  14. Printing line/space patterns on nonplanar substrates using a digital micromirror device-based point-array scanning technique

    Science.gov (United States)

    Kuo, Hung-Fei; Kao, Guan-Hsuan; Zhu, Liang-Xiu; Hung, Kuo-Shu; Lin, Yu-Hsin

    2018-02-01

    This study used a digital micromirror device (DMD) to produce point-array patterns and employed a self-developed optical system to define line-and-space patterns on nonplanar substrates. First, field tracing was employed to analyze the aerial images of the lithographic system, which comprised an optical system and the DMD. Multiobjective particle swarm optimization was then applied to determine the spot overlapping rate used. The objective functions were set to minimize linewidth and maximize image log slope, through which the dose of the exposure agent could be effectively controlled and the quality of the nonplanar lithography could be enhanced. Laser beams with 405-nm wavelength were employed as the light source. Silicon substrates coated with photoresist were placed on a nonplanar translation stage. The DMD was used to produce lithographic patterns, during which the parameters were analyzed and optimized. The optimal delay time-sequence combinations were used to scan images of the patterns. Finally, an exposure linewidth of less than 10 μm was successfully achieved using the nonplanar lithographic process.

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

    Directory of Open Access Journals (Sweden)

    Chan Juliana CN

    2010-02-01

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

  16. Feasibility study for image reconstruction in circular digital tomosynthesis (CDTS) from limited-scan angle data based on compressed-sensing theory

    Energy Technology Data Exchange (ETDEWEB)

    Park, Yeonok; Je, Uikyu; Cho, Hyosung, E-mail: hscho1@yonsei.ac.kr; Hong, Daeki; Park, Chulkyu; Cho, Heemoon; Choi, Sungil; Woo, Taeho

    2015-03-21

    In this work, we performed a feasibility study for image reconstruction in a circular digital tomosynthesis (CDTS) from limited-scan angle data based on compressed-sensing (CS) theory. Here, the X-ray source moves along an arc within a limited-scan angle (≤ 180°) on a circular path set perpendicularly to the axial direction during the image acquisition. This geometry, compared to full-angle (360°) scan geometry, allows imaging system to be designed more compactly and gives better tomographic quality than conventional linear digital tomosynthesis (DTS). We implemented an efficient CS-based reconstruction algorithm for the proposed geometry and performed systematic simulations to investigate the image characteristics. We successfully reconstructed CDTS images with incomplete projections acquired at several selected limited-scan angles of 45°, 90°, 135°, and 180° for a given tomographic angle of 80° and evaluated the reconstruction quality. Our simulation results indicate that the proposed method can provide superior tomographic quality for axial view and even for the other views (i.e., sagittal and coronal), as in computed tomography, to conventional DTS. - Highlights: • Image reconstruction is done in circular digital tomosynthesis (CDTS). • The designed geometry allows imaging system to be the better image. • An efficient compressed-sensing (CS)-based reconstruction algorithm is performed. • Proposed method can provide superior tomographic quality for the axial view.

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

    NARCIS (Netherlands)

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

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

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Angelo Scuteri

    2007-07-01

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

  1. Compaction bands in shale revealed through digital volume correlation of time-resolved X-ray tomography scans

    Science.gov (United States)

    McBeck, J.; Kobchenko, M.; Hall, S.; Tudisco, E.; Cordonnier, B.; Renard, F.

    2017-12-01

    Previous studies have identified compaction bands primarily within sandstones, and in fewer instances, within other porous rocks and sediments. Using Digital Volume Correlation (DVC) of X-ray microtomography scans, we find evidence of localized zones of high axial contraction that form tabular structures sub-perpendicular to maximum compression, σ1, in Green River shale. To capture in situ strain localization throughout loading, two shale cores were deformed in the HADES triaxial deformation apparatus installed on the X-ray microtomography beamline ID19 at the European Synchrotron Radiation Facility. In these experiments, we increase σ1 in increments of two MPa, with constant confining pressure (20 MPa), until the sample fails in macroscopic shear. After each stress step, a 3D image of the sample inside the rig is acquired at a voxel resolution of 6.5 μm. The evolution of lower density regions within 3D reconstructions of linear attenuation coefficients reveal the development of fractures that fail with some opening. If a fracture produces negligible dilation, it may remain undetected in image segmentation of the reconstructions. We use the DVC software TomoWarp2 to identify undetected fractures and capture the 3D incremental displacement field between each successive pair of microtomography scans acquired in each experiment. The corresponding strain fields reveal localized bands of high axial contraction that host minimal shear strain, and thus match the kinematic definition of compaction bands. The bands develop sub-perpendicular to σ1 in the two samples in which pre-existing bedding laminations were oriented parallel and perpendicular to σ1. As the shales deform plastically toward macroscopic shear failure, the number of bands and axial contraction within the bands increase, while the spacing between the bands decreases. Compaction band development accelerates the rate of overall axial contraction, increasing the mean axial contraction throughout the sample

  2. Experimental study of water sorption and clays swelling by environmental scanning electron microscopy (ESEM) and digital image analysis

    International Nuclear Information System (INIS)

    Montes-Hernandez, G.

    2002-10-01

    This work deals with the study of water sorption and clays swelling (MX80 bentonite and Paris basin argilites). A new approach by environmental scanning electron microscopy (ESEM) coupled to digital image analysis is proposed to estimate the swelling with time and the relative humidity. The ESEM is a new generation tool, not much used in the clays domain, which allows to study hydrated materials in different conditions of relative humidity. In this work, it is shown that qualitative and quantitative information about clays swelling at the aggregate scale can be obtained. The study of the kinetics allows to identify three swelling steps which are described by a first order kinetic model. The study of water sorption by raw bentonite and the exchange of different cation (Na + , Li + , K + , Ca 2+ , Mg 2+ ) has permitted to analyze the cation influence on the swelling potential. The adsorption kinetics, described by a second order model, depends directly on the relative humidity, on the mass of the sample and on the compensating cation. The study of the texture of the compacted MX80 bentonite in dry and humid conditions has permitted to observe the morphological evolution of the porous network (macro-porosity) during the hydration/dehydration. From different analytical approaches, a diminution of the macro-pores and/or meso-pores size and the opening of inter-aggregate pores is observed when the apparent density increases. The study of the influence of the instantaneous water condensation/evaporation on the argilites shows that the sensitiveness to water increases when the proportion of clay increases. In particular, it is characterized by a cracking partially reversible or irreversible after several condensation/evaporation cycles. (J.S.)

  3. Validation of digit-length ratio (2D:4D) assessments on the basis of DXA-derived hand scans

    International Nuclear Information System (INIS)

    Romann, Michael; Fuchslocher, Jörg

    2015-01-01

    The second-to-fourth digit-length ratio (2D:4D) may be a correlate of prenatal sex steroids, and it has been linked to sporting prowess. The aim of the study was to validate dual-energy X-ray-absorptiometry (DXA) as a technique to assess 2D:4D in soccer players under 15 years of age (U-15). Paired X-ray and DXA scans of the left hands of 63 male U-15 elite soccer players (age: 14.0 ± 0.3 years) were performed, and 2D:4D was then compared between the two techniques. The 2D:4D measurements were performed twice by two blinded raters. Intrarater and interrater reliability, as well as agreement between the X-ray and the DXA assessments, were tested. Intrarater reliabilities of both raters using X-ray with intraclass correlation coefficients (ICCs) of 0.97 and 0.90 were excellent. Using DXA, the ICCs were 0.90 and 0.91 thus also showing excellent reliability. Interrater reliabilities were excellent using both the X-ray (ICC of 0.94) and the DXA (ICC of 0.90), assessments respectively. Bland-Altman plots demonstrated that the 2D:4D ratios of the two raters did not differ significantly between the X-ray and the DXA assessments. The standard errors of estimate were 0.01 for both techniques. The 95% limits of agreement of ±0.018 (±2.0%) and ±0.023 (±2.6%), respectively, were within the acceptable tolerance of 5%, and showed very good agreement. DXA offered a replicable technique for assessing 2D:4D in youth soccer players. Therefore, the DXA technique seems to be an alternative method for evaluating 2D:4D in youth sports

  4. Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments.

    Science.gov (United States)

    Li, Chunmei; Yu, Zhilong; Fu, Yusi; Pang, Yuhong; Huang, Yanyi

    2017-04-26

    We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multifraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infer CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of a reaction mix before amplification. By examining the sequencing result of each fraction for a specific fragment and applying a segment-merge maximum likelihood algorithm to the calculation of copy number, we digitize the sequencing-depth-based CNV identification and thus provide a method that is less sensitive to the amplification bias. In this paper, we demonstrate a mfA platform through multiple displacement amplification (MDA) chemistry. When performing the mfA platform, the noise of MDA is reduced; therefore, the resolution of single-cell CNV identification can be improved to 100 kb. We can also determine the genomic region free of allelic drop-out with mfA platform, which is impossible for conventional single-cell amplification methods.

  5. DIGITAL

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Digital Flood Insurance Rate Map (DFIRM) Database depicts flood risk information and supporting data used to develop the risk data. The primary risk...

  6. Micro computed tomography (CT) scanned anatomical gateway to insect pest bioinformatics

    Science.gov (United States)

    An international collaboration to establish an interactive Digital Video Library for a Systems Biology Approach to study the Asian citrus Psyllid and psyllid genomics/proteomics interactions is demonstrated. Advances in micro-CT, digital computed tomography (CT) scan uses X-rays to make detailed pic...

  7. 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

  8. Digital curation and online resources: digital scanning of surgical tools at the royal college of physicians and surgeons of Glasgow for an open university learning resource.

    Science.gov (United States)

    Earley, Kirsty; Livingstone, Daniel; Rea, Paul M

    2017-01-01

    Collection preservation is essential for the cultural status of any city. However, presenting a collection publicly risks damage. Recently this drawback has been overcome by digital curation. Described here is a method of digitisation using photogrammetry and virtual reality software. Items were selected from the Royal College of Physicians and Surgeons of Glasgow archives, and implemented into an online learning module for the Open University. Images were processed via Agisoft Photoscan, Autodesk Memento, and Garden Gnome Object 2VR. Although problems arose due to specularity, 2VR digital models were developed for online viewing. Future research must minimise the difficulty of digitising specular objects.

  9. Patients' preferences when comparing analogue implant impressions using a polyether impression material versus digital impressions (Intraoral Scan) of dental implants

    NARCIS (Netherlands)

    Wismeijer, D.; Mans, R.S.; Van Genuchten, M.J.I.M; Reijers, H.A.

    2014-01-01

    Objectives: The primary objective of this clinical study was to assess the patients' perception of the difference between an analogue impression approach on the one hand and an intra-oral scan (IO scan) on the other when restoring implants in the non-aesthetic zone. A second objective was to analyse

  10. Patients' preferences when comparing analogue implant impressions using a polyether impression material versus digital impressions (Intraoral Scan) of dental implants

    NARCIS (Netherlands)

    Wismeijer, D.; Mans, R.; van Genugten, M.; Reijers, H.A.

    2014-01-01

    Objectives The primary objective of this clinical study was to assess the patients' perception of the difference between an analogue impression approach on the one hand and an intra-oral scan (IO scan) on the other when restoring implants in the non-aesthetic zone. A second objective was to analyse

  11. Patients' preferences when comparing analogue implant impressions using a polyether impression material versus digital impressions (Intraoral Scan) of dental implants.

    Science.gov (United States)

    Wismeijer, Daniel; Mans, Ronny; van Genuchten, Michiel; Reijers, Hajo A

    2014-10-01

    The primary objective of this clinical study was to assess the patients' perception of the difference between an analogue impression approach on the one hand and an intra-oral scan (IO scan) on the other when restoring implants in the non-aesthetic zone. A second objective was to analyse the difference in time needed to perform these two procedures. Thirty consecutive patients who had received 41 implants (Straumann tissue level) in the non-aesthetic zone in an implant-based referral practice setting in the Netherlands. As they were to receive crown and or bridge work on the implants, in one session, the final impressions were taken with both an analogue technique and with an intraoral scan. Patients were also asked if, directly after the treatment was carried out, they would be prepared to fill out a questionnaire on their perception of both techniques. The time involved following these two procedures was also recorded. The preparatory activities of the treatment, the taste of the impression material and the overall preference of the patients were significantly in favour of the IO scan. The bite registration, the scan head and gag reflex positively tended to the IO scan, but none of these effects were significant. The overall time involved with the IO scan was more negatively perceived than the analogue impression. Overall less time was involved when following the analogue impression technique than with the IO scan. The overall preference of the patients in our sample is significantly in favour of the approach using the IO scan. This preference relates mainly to the differences between the compared approaches with respect to taste effects and their preparatory activities. The patients did perceive the duration of IO scan more negatively than the analogue impression approach. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Development of an image intensifier-TV digital imaging system with a multiple-slit scanning x-ray beam

    International Nuclear Information System (INIS)

    Kume, Y.; Doi, K.

    1986-01-01

    The authors are developing a new digital x-ray imaging system employing a multiple-slit assembly (MSA) and an image intensifier (II)-TV digital system. The final image consisting of primary radiation is digitally reconstructed from multiple slit images obtained with the MSA. This system can significantly reduce the scattered radiation from an object and the veiling glare from II-TV system. The quality of the reconstructed image is related to many parameters, such as slit width, the number of image frames, and the image reconstruction algorithm. They present the effect of these various parameters on basic imaging properties and the practicability of the method in comparison with conventional wide beam imaging

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

    Science.gov (United States)

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

    2017-09-01

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

  14. Digital radiography

    International Nuclear Information System (INIS)

    Brody, W.R.

    1984-01-01

    Digital Radiography begins with an orderly introduction to the fundamental concepts of digital imaging. The entire X-ray digital imagining system is described, from an overall characterization of image quality to specific components required for a digital radiographic system. Because subtraction is central to digital radiographic systems, the author details the use of various subtraction methods for image enhancement. Complex concepts are illustrated with numerous examples and presented in terms that can readily be understood by physicians without an advanced mathematics background. The second part of the book discusses implementations and applications of digital imagining systems based on area and scanned detector technologies. This section includes thorough coverage of digital fluoroscopy, scanned projection radiography, and film-based digital imaging systems, and features a state-of-the-art synopsis of the applications of digital subtraction angiography. The book concludes with a timely assessment of anticipated technological advances

  15. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

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

  16. Valley of the unicorns: consumer genomics, venture capital and digital disruption

    OpenAIRE

    Hogarth, Stuart James

    2017-01-01

    Drawing on the sociology of expectations and sociology of conventions, this paper explores issues of worth and value in the bioeconomy, and the promissory character of contemporary capitalism. Arguing that the literature on biocapital has paid insufficient attention to geographical differentiation in capital accumulation strategies, this paper situates the consumer genomics firm 23andme in the entrepreneurial culture of Silicon Valley. The paper suggests that in Silicon Valley the relationshi...

  17. Quantitative investigation of the effects of the scanning parameters in the digitization of EBT and EBT2 Gafchromic film dosimetry with flatbed scanners.

    Science.gov (United States)

    Hu, Yida; Ahmad, Salahuddin; Ali, Imad

    2012-01-01

    With increasing popularity and complexity of intensity-modulated radiation therapy (IMRT) delivery modalities including regular and arc therapies, there is a growing challenge for validating the accuracy of dose distributions. Gafchromic films have superior characteristics for dose verification over other conventional dosimeters. In order to optimize the use of Gafchromic films in clinical IMRT quality assurance procedures, the scanning parameters of EBT and EBT2 films with a flatbed scanner were investigated. The effects of several parameters including scanning position, orientation, uniformity, film sensitivity and optical density (OD) growth after irradiation were quantified. The profiles of the EBT and EBT2 films had a noise level of 0.6% and 0.7%, respectively. Considerable orientation dependence was observed and the scanner value difference between landscape and portrait modes were about 12% and 10% for EBT and EBT2 films, respectively. The highest response sensitivity was observed using digitized red color images of the EBT2 film scanned with landscape mode. The total system non-uniformity composed of contributions from the film and the scanner was less than 1.7%. OD variations showed that EBT gray scale grew slower, however, reached higher growth values of 15% when compared with EBT2 gray scale which grew 12% after a long time (480 hours) post-irradiation. The EBT film using the red color channel showed the minimal growth where OD increased up to 3% within 3 days after irradiation, and took one week to stabilize.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Eui-Soo Kim

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

  20. Method for dose-reduced 3D catheter tracking on a scanning-beam digital x-ray system using dynamic electronic collimation

    Science.gov (United States)

    Dunkerley, David A. P.; Funk, Tobias; Speidel, Michael A.

    2016-03-01

    Scanning-beam digital x-ray (SBDX) is an inverse geometry x-ray fluoroscopy system capable of tomosynthesis-based 3D catheter tracking. This work proposes a method of dose-reduced 3D tracking using dynamic electronic collimation (DEC) of the SBDX scanning x-ray tube. Positions in the 2D focal spot array are selectively activated to create a regionof- interest (ROI) x-ray field around the tracked catheter. The ROI position is updated for each frame based on a motion vector calculated from the two most recent 3D tracking results. The technique was evaluated with SBDX data acquired as a catheter tip inside a chest phantom was pulled along a 3D trajectory. DEC scans were retrospectively generated from the detector images stored for each focal spot position. DEC imaging of a catheter tip in a volume measuring 11.4 cm across at isocenter required 340 active focal spots per frame, versus 4473 spots in full-FOV mode. The dose-area-product (DAP) and peak skin dose (PSD) for DEC versus full field-of-view (FOV) scanning were calculated using an SBDX Monte Carlo simulation code. DAP was reduced to 7.4% to 8.4% of the full-FOV value, consistent with the relative number of active focal spots (7.6%). For image sequences with a moving catheter, PSD was 33.6% to 34.8% of the full-FOV value. The root-mean-squared-deviation between DEC-based 3D tracking coordinates and full-FOV 3D tracking coordinates was less than 0.1 mm. The 3D distance between the tracked tip and the sheath centerline averaged 0.75 mm. Dynamic electronic collimation can reduce dose with minimal change in tracking performance.

  1. Assessing the Accuracy of High Resolution Digital Surface Models Computed by PhotoScan® and MicMac® in Sub-Optimal Survey Conditions

    Directory of Open Access Journals (Sweden)

    Marion Jaud

    2016-06-01

    Full Text Available For monitoring purposes and in the context of geomorphological research, Unmanned Aerial Vehicles (UAV appear to be a promising solution to provide multi-temporal Digital Surface Models (DSMs and orthophotographs. There are a variety of photogrammetric software tools available for UAV-based data. The objective of this study is to investigate the level of accuracy that can be achieved using two of these software tools: Agisoft PhotoScan® Pro and an open-source alternative, IGN© MicMac®, in sub-optimal survey conditions (rugged terrain, with a large variety of morphological features covering a range of roughness sizes, poor GPS reception. A set of UAV images has been taken by a hexacopter drone above the Rivière des Remparts, a river on Reunion Island. This site was chosen for its challenging survey conditions: the topography of the study area (i involved constraints on the flight plan; (ii implied errors on some GPS measurements; (iii prevented an optimal distribution of the Ground Control Points (GCPs and; (iv was very complex to reconstruct. Several image processing tests are performed with different scenarios in order to analyze the sensitivity of each software package to different parameters (image quality, numbers of GCPs, etc.. When computing the horizontal and vertical errors within a control region on a set of ground reference targets, both methods provide rather similar results. A precision up to 3–4 cm is achievable with these software packages. The DSM quality is also assessed over the entire study area comparing PhotoScan DSM and MicMac DSM with a Terrestrial Laser Scanner (TLS point cloud. PhotoScan and MicMac DSM are also compared at the scale of particular features. Both software packages provide satisfying results: PhotoScan is more straightforward to use but its source code is not open; MicMac is recommended for experimented users as it is more flexible.

  2. Personal experience with whole-body, low-dosage, digital X-ray scanning (LODOX-Statscan in trauma

    Directory of Open Access Journals (Sweden)

    Zimmermann Heinz

    2009-09-01

    Full Text Available Abstract Background Lodox-Statscan is a whole-body, skeletal and soft-tissue, low-dose X-ray scanner Anterior-posterior and lateral thoraco-abdominal studies are obtained in 3-5 minutes with only about one-third of the radiation required for conventional radiography. Since its approval by the Food and Drug Administration (FDA in the USA, several trauma centers have incorporated this technology into their Advanced Trauma Life Support protocols. This review provides a brief overview of the system, and describes the authors' own experience with the system. Methods We performed a PubMed search to retrieve all references with 'Lodox' and 'Stat-scan' used as search terms. We furthermore used the google search engine to identify existing alternatives. To the best of our knowledge, this is the only FDA-approved device of its kind currently used in trauma. Results and Conclusion The intention of our review has been to sensitize the readership that such alternative devices exist. The key message is that low dosage full body radiography may be an alternative to conventional resuscitation room radiography which is usually a prelude to CT scanning (ATLS algorithm. The combination of both is radiation intensive and therefore we consider any reduction of radiation a success. But only the future will show whether LS will survive in the face of low-dose radiation CT scanners and magnetic resonance imaging devices that may eventually completely replace conventional radiography.

  3. 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.

  4. Digital dissection - using contrast-enhanced computed tomography scanning to elucidate hard- and soft-tissue anatomy in the Common Buzzard Buteo buteo.

    Science.gov (United States)

    Lautenschlager, Stephan; Bright, Jen A; Rayfield, Emily J

    2014-04-01

    Gross dissection has a long history as a tool for the study of human or animal soft- and hard-tissue anatomy. However, apart from being a time-consuming and invasive method, dissection is often unsuitable for very small specimens and often cannot capture spatial relationships of the individual soft-tissue structures. The handful of comprehensive studies on avian anatomy using traditional dissection techniques focus nearly exclusively on domestic birds, whereas raptorial birds, and in particular their cranial soft tissues, are essentially absent from the literature. Here, we digitally dissect, identify, and document the soft-tissue anatomy of the Common Buzzard (Buteo buteo) in detail, using the new approach of contrast-enhanced computed tomography using Lugol's iodine. The architecture of different muscle systems (adductor, depressor, ocular, hyoid, neck musculature), neurovascular, and other soft-tissue structures is three-dimensionally visualised and described in unprecedented detail. The three-dimensional model is further presented as an interactive PDF to facilitate the dissemination and accessibility of anatomical data. Due to the digital nature of the data derived from the computed tomography scanning and segmentation processes, these methods hold the potential for further computational analyses beyond descriptive and illustrative proposes. © 2013 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

  5. Absolute determination of single-stranded and self-complementary adeno-associated viral vector genome titers by droplet digital PCR.

    Science.gov (United States)

    Lock, Martin; Alvira, Mauricio R; Chen, Shu-Jen; Wilson, James M

    2014-04-01

    Accurate titration of adeno-associated viral (AAV) vector genome copies is critical for ensuring correct and reproducible dosing in both preclinical and clinical settings. Quantitative PCR (qPCR) is the current method of choice for titrating AAV genomes because of the simplicity, accuracy, and robustness of the assay. However, issues with qPCR-based determination of self-complementary AAV vector genome titers, due to primer-probe exclusion through genome self-annealing or through packaging of prematurely terminated defective interfering (DI) genomes, have been reported. Alternative qPCR, gel-based, or Southern blotting titering methods have been designed to overcome these issues but may represent a backward step from standard qPCR methods in terms of simplicity, robustness, and precision. Droplet digital PCR (ddPCR) is a new PCR technique that directly quantifies DNA copies with an unparalleled degree of precision and without the need for a standard curve or for a high degree of amplification efficiency; all properties that lend themselves to the accurate quantification of both single-stranded and self-complementary AAV genomes. Here we compare a ddPCR-based AAV genome titer assay with a standard and an optimized qPCR assay for the titration of both single-stranded and self-complementary AAV genomes. We demonstrate absolute quantification of single-stranded AAV vector genomes by ddPCR with up to 4-fold increases in titer over a standard qPCR titration but with equivalent readout to an optimized qPCR assay. In the case of self-complementary vectors, ddPCR titers were on average 5-, 1.9-, and 2.3-fold higher than those determined by standard qPCR, optimized qPCR, and agarose gel assays, respectively. Droplet digital PCR-based genome titering was superior to qPCR in terms of both intra- and interassay precision and is more resistant to PCR inhibitors, a desirable feature for in-process monitoring of early-stage vector production and for vector genome biodistribution

  6. Comparison of vessel contrast measured with a scanning-beam digital x-ray system and an image intensifier/television system

    International Nuclear Information System (INIS)

    Speidel, Michael A.; Wilfley, Brian P.; Heanue, Joseph A.; Betts, Timothy D.; Van Lysel, Michael S.

    2001-01-01

    Vessel contrast was measured in the fluoroscopic images produced by a scanning-beam digital x-ray (SBDX) system and an image intensifier/television (II/TV) based system. The SBDX system electronically scans a series of pencil x-ray beams across the patient, each of which is directed at a distant small-area detector array. The reduction in detected scatter achieved with this geometry was expected to provide an increase in image contrast. Vessel contrast was evaluated from images of a phantom containing iodinated tubes. The vessels were inserted into an acrylic stack to provide a patient-mimicking scattering medium. Vessel diameter ranged from 0.3 to 3.1 mm. Images were acquired at 100 kVp with the SBDX and II/TV systems and averaged to reduce x-ray noise. The II/TV system was operated in the 6-in. image intensifier mode with an anti-scatter grid. The increase in contrast in the SBDX images, expressed as a ratio of the measured SBDX and II/TV contrasts, ranged from 1.63 to 1.79 for individual vessels. This agreed well with a prediction of the contrast improvement ratio for this experiment, based on measurements of the scatter fraction, object-plane line spread functions, and consideration of the source spectrum and detector absorption properties. The predicted contrast improvement ratio for SBDX relative to II/TV images was 1.62 to 1.77

  7. Development of digital reconstructed radiography software at new treatment facility for carbon-ion beam scanning of National Institute of Radiological Sciences.

    Science.gov (United States)

    Mori, Shinichiro; Inaniwa, Taku; Kumagai, Motoki; Kuwae, Tsunekazu; Matsuzaki, Yuka; Furukawa, Takuji; Shirai, Toshiyuki; Noda, Koji

    2012-06-01

    To increase the accuracy of carbon ion beam scanning therapy, we have developed a graphical user interface-based digitally-reconstructed radiograph (DRR) software system for use in routine clinical practice at our center. The DRR software is used in particular scenarios in the new treatment facility to achieve the same level of geometrical accuracy at the treatment as at the imaging session. DRR calculation is implemented simply as the summation of CT image voxel values along the X-ray projection ray. Since we implemented graphics processing unit-based computation, the DRR images are calculated with a speed sufficient for the particular clinical practice requirements. Since high spatial resolution flat panel detector (FPD) images should be registered to the reference DRR images in patient setup process in any scenarios, the DRR images also needs higher spatial resolution close to that of FPD images. To overcome the limitation of the CT spatial resolution imposed by the CT voxel size, we applied image processing to improve the calculated DRR spatial resolution. The DRR software introduced here enabled patient positioning with sufficient accuracy for the implementation of carbon-ion beam scanning therapy at our center.

  8. A reference gene set for sex pheromone biosynthesis and degradation genes from the diamondback moth, Plutella xylostella, based on genome and transcriptome digital gene expression analyses

    OpenAIRE

    He, Peng; Zhang, Yun-Fei; Hong, Duan-Yang; Wang, Jun; Wang, Xing-Liang; Zuo, Ling-Hua; Tang, Xian-Fu; Xu, Wei-Ming; He, Ming

    2017-01-01

    Background Female moths synthesize species-specific sex pheromone components and release them to attract male moths, which depend on precise sex pheromone chemosensory system to locate females. Two types of genes involved in the sex pheromone biosynthesis and degradation pathways play essential roles in this important moth behavior. To understand the function of genes in the sex pheromone pathway, this study investigated the genome-wide and digital gene expression of sex pheromone biosynthesi...

  9. Information Life-Cycle Management at the Erasmus Medical Center : Collaboratively Managing Digital Data for Care, Research, Education and the International Development of the GLOBE 3D Genome Viewer

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); P. Walgemoed; H.J.F.M.M. Eussen (Bert)

    2006-01-01

    textabstractInformation Lifecycle Management at the Erasmus University Medical Centre. Collaboratively managing digital data for care, research and education using the international development of the GLOBE 3D Genome Viewer and Erasmus Computing Grid as catalyzing initiatives. The

  10. Application of Digital (Motic and Scanning electron microscope in histological study of leaf of Tecoma gaudichaudi DC (Bignoniaceae

    Directory of Open Access Journals (Sweden)

    Kedar Kalyani Abhimanyu

    2016-03-01

    Full Text Available Tecoma gaudichaudi DC (Bignoniaceae is a shrub or a small tree found in various regions of Maharashtra. The objective of the study was to develop various standardization parameters for the evaluation of leaves of this plant. Microscopy, powder characteristics and scanning electron microscopy (SEM of leaves were observed and results were recorded. Histological study of leaves shows underlined palisade cells on the upper epidermal surface, anomocytic stomata on the lower epidermis with covering (2–3 cells and glandular trichomes etc. The specific observed characteristics such as types of stomata and trichomes were predominantly observed on the lower epidermal surface of the leaf. Physicochemical analysis such as extractive value includes petroleum ether, ethanol, ethyl acetate and aqueous soluble extractive values of 3.08, 10.50, 8.5, and 13.4% w/w respectively; extracts were analysed by chemical test and showed presence of flavonoids, tannins, steroids and triterpenoids etc. Fluorescence analysis is one of the parameters that help in the analysis of chemical constituents. So these parameters are useful in the authentication of T. gaudichaudi DC and can play a vital role in authentication and standardization of botanicals.

  11. 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.

  12. Measurement of effective detective quantum efficiency for a photon counting scanning mammography system and comparison with two flat panel full-field digital mammography systems

    Science.gov (United States)

    Wood, Tim J.; Moore, Craig S.; Saunderson, John R.; Beavis, Andrew W.

    2018-01-01

    Effective detective quantum efficiency (eDQE) describes the resolution and noise properties of an imaging system along with scatter and primary transmission, all measured under clinically appropriate conditions. Effective dose efficiency (eDE) is the eDQE normalised to mean glandular dose and has been proposed as a useful metric for the optimisation of clinical imaging systems. The aim of this study was to develop a methodology for measuring eDQE and eDE on a Philips microdose mammography (MDM) L30 photon counting scanning system, and to compare performance with two conventional flat panel systems. A custom made lead-blocker was manufactured to enable the accurate determination of dose measurements, and modulation transfer functions were determined free-in-air at heights of 2, 4 and 6 cm above the breast support platform. eDQE were calculated for a Philips MDM L30, Hologic Dimensions and Siemens Inspiration digital mammography system for 2, 4 and 6 cm thick poly(methyl methacrylate) (PMMA). The beam qualities (target/filter and kilovoltage) assessed were those selected by the automatic exposure control, and anti-scatter grids were used where available. Measurements of eDQE demonstrate significant differences in performance between the slit- and scan-directions for the photon counting imaging system. MTF has been shown to be the limiting factor in the scan-direction, which results in a rapid fall in eDQE at mid-to-high spatial frequencies. A comparison with two flat panel mammography systems demonstrates that this may limit image quality for small details, such as micro-calcifications, which correlates with a more conventional image quality assessment with the CDMAM phantom. eDE has shown the scanning photon counting system offers superior performance for low spatial frequencies, which will be important for the detection of large low contrast masses. Both eDQE and eDE are proposed as useful metrics that should enable optimisation of the Philips MDM L30.

  13. 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.

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

    Science.gov (United States)

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

    2013-12-01

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

  15. 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.

  16. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  18. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    1981-01-01

    This patent specification relates to a tomographic scanning apparatus using a fan beam and digital output signal, and particularly to the design of the gas-pressurized ionization detection system. (U.K.)

  19. Assessment of statistical agreement of three techniques for the study of cut marks: 3D digital microscope, laser scanning confocal microscopy and micro-photogrammetry.

    Science.gov (United States)

    Maté-González, Miguel Ángel; Aramendi, Julia; Yravedra, José; Blasco, Ruth; Rosell, Jordi; González-Aguilera, Diego; Domínguez-Rodrigo, Manuel

    2017-09-01

    In the last few years, the study of cut marks on bone surfaces has become fundamental for the interpretation of prehistoric butchery practices. Due to the difficulties in the correct identification of cut marks, many criteria for their description and classification have been suggested. Different techniques, such as three-dimensional digital microscope (3D DM), laser scanning confocal microscopy (LSCM) and micro-photogrammetry (M-PG) have been recently applied to the study of cut marks. Although the 3D DM and LSCM microscopic techniques are the most commonly used for the 3D identification of cut marks, M-PG has also proved to be very efficient and a low-cost method. M-PG is a noninvasive technique that allows the study of the cortical surface without any previous preparation of the samples, and that generates high-resolution models. Despite the current application of microscopic and micro-photogrammetric techniques to taphonomy, their reliability has never been tested. In this paper, we compare 3D DM, LSCM and M-PG in order to assess their resolution and results. In this study, we analyse 26 experimental cut marks generated with a metal knife. The quantitative and qualitative information registered is analysed by means of standard multivariate statistics and geometric morphometrics to assess the similarities and differences obtained with the different methodologies. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

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

    Science.gov (United States)

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

    2004-05-01

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

  1. Accuracy and efficiency of full-arch digitalization and 3D printing: A comparison between desktop model scanners, an intraoral scanner, a CBCT model scan, and stereolithographic 3D printing.

    Science.gov (United States)

    Wesemann, Christian; Muallah, Jonas; Mah, James; Bumann, Axel

    2017-01-01

    The primary objective of this study was to compare the accuracy and time efficiency of an indirect and direct digitalization workflow with that of a three-dimensional (3D) printer in order to identify the most suitable method for orthodontic use. A master model was measured with a coordinate measuring instrument. The distances measured were the intercanine width, the intermolar width, and the dental arch length. Sixty-four scans were taken with each of the desktop scanners R900 and R700 (3Shape), the intraoral scanner TRIOS Color Pod (3Shape), and the Promax 3D Mid cone beam computed tomography (CBCT) unit (Planmeca). All scans were measured with measuring software. One scan was selected and printed 37 times on the D35 stereolithographic 3D printer (Innovation MediTech). The printed models were measured again using the coordinate measuring instrument. The most accurate results were obtained by the R900. The R700 and the TRIOS intraoral scanner showed comparable results. CBCT-3D-rendering with the Promax 3D Mid CBCT unit revealed significantly higher accuracy with regard to dental casts than dental impressions. 3D printing offered a significantly higher level of deviation than digitalization with desktop scanners or an intraoral scanner. The chairside time required for digital impressions was 27% longer than for conventional impressions. Conventional impressions, model casting, and optional digitization with desktop scanners remains the recommended workflow process. For orthodontic demands, intraoral scanners are a useful alternative for full-arch scans. For prosthodontic use, the scanning scope should be less than one quadrant and three additional teeth.

  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. Real-time out-of-plane artifact subtraction tomosynthesis imaging using prior CT for scanning beam digital x-ray system

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Meng, E-mail: mengwu@stanford.edu [Department of Electrical Engineering, Stanford University, Stanford, California 94305 (United States); Fahrig, Rebecca [Department of Radiology, Stanford University, Stanford, California 94305 (United States)

    2014-11-01

    Purpose: The scanning beam digital x-ray system (SBDX) is an inverse geometry fluoroscopic system with high dose efficiency and the ability to perform continuous real-time tomosynthesis in multiple planes. This system could be used for image guidance during lung nodule biopsy. However, the reconstructed images suffer from strong out-of-plane artifact due to the small tomographic angle of the system. Methods: The authors propose an out-of-plane artifact subtraction tomosynthesis (OPAST) algorithm that utilizes a prior CT volume to augment the run-time image processing. A blur-and-add (BAA) analytical model, derived from the project-to-backproject physical model, permits the generation of tomosynthesis images that are a good approximation to the shift-and-add (SAA) reconstructed image. A computationally practical algorithm is proposed to simulate images and out-of-plane artifacts from patient-specific prior CT volumes using the BAA model. A 3D image registration algorithm to align the simulated and reconstructed images is described. The accuracy of the BAA analytical model and the OPAST algorithm was evaluated using three lung cancer patients’ CT data. The OPAST and image registration algorithms were also tested with added nonrigid respiratory motions. Results: Image similarity measurements, including the correlation coefficient, mean squared error, and structural similarity index, indicated that the BAA model is very accurate in simulating the SAA images from the prior CT for the SBDX system. The shift-variant effect of the BAA model can be ignored when the shifts between SBDX images and CT volumes are within ±10 mm in the x and y directions. The nodule visibility and depth resolution are improved by subtracting simulated artifacts from the reconstructions. The image registration and OPAST are robust in the presence of added respiratory motions. The dominant artifacts in the subtraction images are caused by the mismatches between the real object and the prior CT

  4. Evaluating droplet digital PCR for the quantification of human genomic DNA: converting copies per nanoliter to nanograms nuclear DNA per microliter.

    Science.gov (United States)

    Duewer, David L; Kline, Margaret C; Romsos, Erica L; Toman, Blaza

    2018-05-01

    The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI). Unlike values assigned using conventional relationships between ultraviolet absorbance and DNA mass concentration, entity-based ddPCR measurements are expected to be stable over time. However, the forensic community expects DNA quantity to be stated in terms of mass concentration rather than entity concentration. The transformation can be accomplished given SI-traceable values and uncertainties for the number of nucleotide bases per human haploid genome equivalent (HHGE) and the average molar mass of a nucleotide monomer in the DNA polymer. This report presents the considerations required to establish the metrological traceability of ddPCR-based mass concentration estimates of human nuclear DNA. Graphical abstract The roots of metrological traceability for human nuclear DNA mass concentration results. Values for the factors in blue must be established experimentally. Values for the factors in red have been established from authoritative source materials. HHGE stands for "haploid human genome equivalent"; there are two HHGE per diploid human genome.

  5. Film-screen digital radiography

    International Nuclear Information System (INIS)

    Schwenker, R.P.; Eger, H.

    1985-01-01

    The excellent performance of the digital film-screen system as a receptor for projection radiographic data is discussed. An experimental system for obtaining high quality digital radiographic data by laser scanning radiographic films is described. This system is being used to evaluate the clinical utility of various digital image processing algorithms. Future plans include an investigation of quantitative analysis of projection radiographic data. Digital data obtained by film scanning can be used with digital image archiving and communications systems. (author)

  6. The Use of Central Pathology Review With Digital Slide Scanning in Advanced-stage Mycosis Fungoides and Sézary Syndrome: A Multi-institutional and International Pathology Study.

    Science.gov (United States)

    Gru, Alejandro A; Kim, Jinah; Pulitzer, Melissa; Guitart, Joan; Battistella, Maxime; Wood, Gary S; Cerroni, Lorenzo; Kempf, Werner; Willemze, Rein; Pawade, Joya; Querfeld, Christiane; Schaffer, Andras; Pincus, Laura; Tetzlaff, Michael; Duvic, Madeleine; Scarisbrick, Julia; Porcu, Pierluigi; Mangold, Aaron R; DiCaudo, David J; Shinohara, Michi; Hong, Eric K; Horton, Bethany; Kim, Youn H

    2018-06-01

    This pathology PILOT study aims to define the role and feasibility of centralized pathology review in a cohort of 75 patients from different centers in the United States and Europe using digital slide scanning. The pathologic material from 75 patients who had been diagnosed with mycosis fungoides/Sézary syndrome and were clinically staged as IIb or above was retrieved from 11 participating centers. Each pathology reviewer was provided with the pathologic diagnosis (by the referring pathologist), and the following list of histopathologic criteria (presence or absence) from the initial report: epidermotropism, folliculotropism (FT), large cell transformation, syringotropism, and granulomas. Patients with advance stage were selected for this study as this is a population where there is significant variability in the diagnosis of pathologic prognostic and predictive biomarkers. The slides were digitally scanned with an Aperio scanner and consensus review of cases occurred when major or minor discrepancies between the referral diagnosis and central pathology review occurred. Among the 75 cases, 70 (93.3%) had a final consensus diagnosis between the 3 central review pathologists. The overall agreement between the consensus review and the referring pathologist was 60%. The overall agreement was also higher between the reviewers and consensus review, compared with the referring pathologist and consensus. 65.3% of cases had some type of discrepancy (major or minor) between the outside and consensus review. Major discrepancies were seen in 34 of 73 cases (46.6%; 73 cases indicated a yes or no response). Minor discrepancies were seen in 32 of 75 (42.7%) of cases. Most of the major discrepancies were accounted by a difference in interpretation in the presence or absence of large cell transformation or FT. Most minor discrepancies were explained by a different interpretation in the expression of CD30. We found digital slide scanning to be a beneficial, reliable, and practical

  7. Digital breast tomosynthesis: observer performance of clustered microcalcification detection on breast phantom images acquired with an experimental system using variable scan angles, angular increments, and number of projection views.

    Science.gov (United States)

    Chan, Heang-Ping; Goodsitt, Mitchell M; Helvie, Mark A; Zelakiewicz, Scott; Schmitz, Andrea; Noroozian, Mitra; Paramagul, Chintana; Roubidoux, Marilyn A; Nees, Alexis V; Neal, Colleen H; Carson, Paul; Lu, Yao; Hadjiiski, Lubomir; Wei, Jun

    2014-12-01

    To investigate the dependence of microcalcification cluster detectability on tomographic scan angle, angular increment, and number of projection views acquired at digital breast tomosynthesis ( DBT digital breast tomosynthesis ). A prototype DBT digital breast tomosynthesis system operated in step-and-shoot mode was used to image breast phantoms. Four 5-cm-thick phantoms embedded with 81 simulated microcalcification clusters of three speck sizes (subtle, medium, and obvious) were imaged by using a rhodium target and rhodium filter with 29 kV, 50 mAs, and seven acquisition protocols. Fixed angular increments were used in four protocols (denoted as scan angle, angular increment, and number of projection views, respectively: 16°, 1°, and 17; 24°, 3°, and nine; 30°, 3°, and 11; and 60°, 3°, and 21), and variable increments were used in three (40°, variable, and 13; 40°, variable, and 15; and 60°, variable, and 21). The reconstructed DBT digital breast tomosynthesis images were interpreted by six radiologists who located the microcalcification clusters and rated their conspicuity. The mean sensitivity for detection of subtle clusters ranged from 80% (22.5 of 28) to 96% (26.8 of 28) for the seven DBT digital breast tomosynthesis protocols; the highest sensitivity was achieved with the 16°, 1°, and 17 protocol (96%), but the difference was significant only for the 60°, 3°, and 21 protocol (80%, P .99). The conspicuity of subtle and medium clusters with the 16°, 1°, and 17 protocol was rated higher than those with other protocols; the differences were significant for subtle clusters with the 24°, 3°, and nine protocol and for medium clusters with 24°, 3°, and nine; 30°, 3°, and 11; 60°, 3° and 21; and 60°, variable, and 21 protocols (P tomosynthesis provided higher sensitivity and conspicuity than wide-angle DBT digital breast tomosynthesis for subtle microcalcification clusters. © RSNA, 2014.

  8. 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 ...

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

    OpenAIRE

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

    2013-01-01

    In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three kno...

  10. A reference gene set for sex pheromone biosynthesis and degradation genes from the diamondback moth, Plutella xylostella, based on genome and transcriptome digital gene expression analyses.

    Science.gov (United States)

    He, Peng; Zhang, Yun-Fei; Hong, Duan-Yang; Wang, Jun; Wang, Xing-Liang; Zuo, Ling-Hua; Tang, Xian-Fu; Xu, Wei-Ming; He, Ming

    2017-03-01

    Female moths synthesize species-specific sex pheromone components and release them to attract male moths, which depend on precise sex pheromone chemosensory system to locate females. Two types of genes involved in the sex pheromone biosynthesis and degradation pathways play essential roles in this important moth behavior. To understand the function of genes in the sex pheromone pathway, this study investigated the genome-wide and digital gene expression of sex pheromone biosynthesis and degradation genes in various adult tissues in the diamondback moth (DBM), Plutella xylostella, which is a notorious vegetable pest worldwide. A massive transcriptome data (at least 39.04 Gb) was generated by sequencing 6 adult tissues including male antennae, female antennae, heads, legs, abdomen and female pheromone glands from DBM by using Illumina 4000 next-generation sequencing and mapping to a published DBM genome. Bioinformatics analysis yielded a total of 89,332 unigenes among which 87 transcripts were putatively related to seven gene families in the sex pheromone biosynthesis pathway. Among these, seven [two desaturases (DES), three fatty acyl-CoA reductases (FAR) one acetyltransferase (ACT) and one alcohol dehydrogenase (AD)] were mainly expressed in the pheromone glands with likely function in the three essential sex pheromone biosynthesis steps: desaturation, reduction, and esterification. We also identified 210 odorant-degradation related genes (including sex pheromone-degradation related genes) from seven major enzyme groups. Among these genes, 100 genes are new identified and two aldehyde oxidases (AOXs), one aldehyde dehydrogenase (ALDH), five carboxyl/cholinesterases (CCEs), five UDP-glycosyltransferases (UGTs), eight cytochrome P450 (CYP) and three glutathione S-transferases (GSTs) displayed more robust expression in the antennae, and thus are proposed to participate in the degradation of sex pheromone components and plant volatiles. To date, this is the most

  11. A comparison of digital gene expression profiling and methyl DNA immunoprecipitation as methods for gene discovery in honeybee (Apis mellifera behavioural genomic analyses.

    Directory of Open Access Journals (Sweden)

    Cui Guan

    Full Text Available The honey bee has a well-organized system of division of labour among workers. Workers typically progress through a series of discrete behavioural castes as they age, and this has become an important case study for exploring how dynamic changes in gene expression can influence behaviour. Here we applied both digital gene expression analysis and methyl DNA immunoprecipitation analysis to nurse, forager and reverted nurse bees (nurses that have returned to the nursing state after a period spent foraging from the same colony in order to compare the outcomes of these different forms of genomic analysis. A total of 874 and 710 significantly differentially expressed genes were identified in forager/nurse and reverted nurse/forager comparisons respectively. Of these, 229 genes exhibited reversed directions of gene expression differences between the forager/nurse and reverted nurse/forager comparisons. Using methyl-DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq we identified 366 and 442 significantly differentially methylated genes in forager/nurse and reverted nurse/forager comparisons respectively. Of these, 165 genes were identified as differentially methylated in both comparisons. However, very few genes were identified as both differentially expressed and differentially methylated in our comparisons of nurses and foragers. These findings confirm that changes in both gene expression and DNA methylation are involved in the nurse and forager behavioural castes, but the different analytical methods reveal quite distinct sets of candidate genes.

  12. Renal scan

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003790.htm Renal scan To use the sharing features on this ... anaphylaxis . Alternative Names Renogram; Kidney scan Images Kidney anatomy Kidney - blood and urine flow References Chernecky CC, ...

  13. CT Scan

    Science.gov (United States)

    ... disease, lung nodules and liver masses Monitor the effectiveness of certain treatments, such as cancer treatment Detect ... scan done in a hospital or an outpatient facility. CT scans are painless and, with newer machines, ...

  14. What Is the Best Way to Contour Lung Tumors on PET Scans? Multiobserver Validation of a Gradient-Based Method Using a NSCLC Digital PET Phantom

    International Nuclear Information System (INIS)

    Werner-Wasik, Maria; Nelson, Arden D.; Choi, Walter; Arai, Yoshio; Faulhaber, Peter F.; Kang, Patrick; Almeida, Fabio D.; Xiao, Ying; Ohri, Nitin; Brockway, Kristin D.; Piper, Jonathan W.; Nelson, Aaron S.

    2012-01-01

    Purpose: To evaluate the accuracy and consistency of a gradient-based positron emission tomography (PET) segmentation method, GRADIENT, compared with manual (MANUAL) and constant threshold (THRESHOLD) methods. Methods and Materials: Contouring accuracy was evaluated with sphere phantoms and clinically realistic Monte Carlo PET phantoms of the thorax. The sphere phantoms were 10–37 mm in diameter and were acquired at five institutions emulating clinical conditions. One institution also acquired a sphere phantom with multiple source-to-background ratios of 2:1, 5:1, 10:1, 20:1, and 70:1. One observer segmented (contoured) each sphere with GRADIENT and THRESHOLD from 25% to 50% at 5% increments. Subsequently, seven physicians segmented 31 lesions (7–264 mL) from 25 digital thorax phantoms using GRADIENT, THRESHOLD, and MANUAL. Results: For spheres 20 mm (p < 0.065) and <20 mm (p < 0.015). For digital thorax phantoms, GRADIENT was the most accurate (p < 0.01), with a mean absolute % error in volume of 10.99% (11.9% SD), followed by 25% THRESHOLD at 17.5% (29.4% SD), and MANUAL at 19.5% (17.2% SD). GRADIENT had the least systematic bias, with a mean % error in volume of –0.05% (16.2% SD) compared with 25% THRESHOLD at –2.1% (34.2% SD) and MANUAL at –16.3% (20.2% SD; p value <0.01). Interobserver variability was reduced using GRADIENT compared with both 25% THRESHOLD and MANUAL (p value <0.01, Levene’s test). Conclusion: GRADIENT was the most accurate and consistent technique for target volume contouring. GRADIENT was also the most robust for varying imaging conditions. GRADIENT has the potential to play an important role for tumor delineation in radiation therapy planning and response assessment.

  15. What Is the Best Way to Contour Lung Tumors on PET Scans? Multiobserver Validation of a Gradient-Based Method Using a NSCLC Digital PET Phantom

    Energy Technology Data Exchange (ETDEWEB)

    Werner-Wasik, Maria, E-mail: Maria.Werner-wasik@jeffersonhospital.org [Department of Radiation Oncology, Thomas Jefferson University Hospital, Philadelphia, PA (United States); Nelson, Arden D. [MIM Software Inc., Cleveland, OH (United States); Choi, Walter [Department of Radiation Oncology, UPMC Health Systems, Pittsburgh, PA (United States); Arai, Yoshio [Department of Radiation Oncology, Beth Israel Medical Center, New York, NY (Israel); Faulhaber, Peter F. [University Hospitals Case Medical Center, Cleveland, OH (United States); Kang, Patrick [Department of Radiology, Beth Israel Medical Center, New York, NY (Israel); Almeida, Fabio D. [Division of Nuclear Medicine, University of Arizona Health Sciences Center, Tucson, AZ (United States); Xiao, Ying; Ohri, Nitin [Department of Radiation Oncology, Thomas Jefferson University Hospital, Philadelphia, PA (United States); Brockway, Kristin D.; Piper, Jonathan W.; Nelson, Aaron S. [MIM Software Inc., Cleveland, OH (United States)

    2012-03-01

    Purpose: To evaluate the accuracy and consistency of a gradient-based positron emission tomography (PET) segmentation method, GRADIENT, compared with manual (MANUAL) and constant threshold (THRESHOLD) methods. Methods and Materials: Contouring accuracy was evaluated with sphere phantoms and clinically realistic Monte Carlo PET phantoms of the thorax. The sphere phantoms were 10-37 mm in diameter and were acquired at five institutions emulating clinical conditions. One institution also acquired a sphere phantom with multiple source-to-background ratios of 2:1, 5:1, 10:1, 20:1, and 70:1. One observer segmented (contoured) each sphere with GRADIENT and THRESHOLD from 25% to 50% at 5% increments. Subsequently, seven physicians segmented 31 lesions (7-264 mL) from 25 digital thorax phantoms using GRADIENT, THRESHOLD, and MANUAL. Results: For spheres <20 mm in diameter, GRADIENT was the most accurate with a mean absolute % error in diameter of 8.15% (10.2% SD) compared with 49.2% (51.1% SD) for 45% THRESHOLD (p < 0.005). For larger spheres, the methods were statistically equivalent. For varying source-to-background ratios, GRADIENT was the most accurate for spheres >20 mm (p < 0.065) and <20 mm (p < 0.015). For digital thorax phantoms, GRADIENT was the most accurate (p < 0.01), with a mean absolute % error in volume of 10.99% (11.9% SD), followed by 25% THRESHOLD at 17.5% (29.4% SD), and MANUAL at 19.5% (17.2% SD). GRADIENT had the least systematic bias, with a mean % error in volume of -0.05% (16.2% SD) compared with 25% THRESHOLD at -2.1% (34.2% SD) and MANUAL at -16.3% (20.2% SD; p value <0.01). Interobserver variability was reduced using GRADIENT compared with both 25% THRESHOLD and MANUAL (p value <0.01, Levene's test). Conclusion: GRADIENT was the most accurate and consistent technique for target volume contouring. GRADIENT was also the most robust for varying imaging conditions. GRADIENT has the potential to play an important role for tumor delineation in

  16. Genome-wide linkage scan for maximum and length-dependent knee muscle strength in young men: significant evidence for linkage at chromosome 14q24.3.

    Science.gov (United States)

    De Mars, G; Windelinckx, A; Huygens, W; Peeters, M W; Beunen, G P; Aerssens, J; Vlietinck, R; Thomis, M A I

    2008-05-01

    Maintenance of high muscular fitness is positively related to bone health, functionality in daily life and increasing insulin sensitivity, and negatively related to falls and fractures, morbidity and mortality. Heritability of muscle strength phenotypes ranges between 31% and 95%, but little is known about the identity of the genes underlying this complex trait. As a first attempt, this genome-wide linkage study aimed to identify chromosomal regions linked to muscle and bone cross-sectional area, isometric knee flexion and extension torque, and torque-length relationship for knee flexors and extensors. In total, 283 informative male siblings (17-36 years old), belonging to 105 families, were used to conduct a genome-wide SNP-based multipoint linkage analysis. The strongest evidence for linkage was found for the torque-length relationship of the knee flexors at 14q24.3 (LOD = 4.09; p<10(-5)). Suggestive evidence for linkage was found at 14q32.2 (LOD = 3.00; P = 0.005) for muscle and bone cross-sectional area, at 2p24.2 (LOD = 2.57; p = 0.01) for isometric knee torque at 30 degrees flexion, at 1q21.3, 2p23.3 and 18q11.2 (LOD = 2.33, 2.69 and 2.21; p<10(-4) for all) for the torque-length relationship of the knee extensors and at 18p11.31 (LOD = 2.39; p = 0.0004) for muscle-mass adjusted isometric knee extension torque. We conclude that many small contributing genes rather than a few important genes are involved in causing variation in different underlying phenotypes of muscle strength. Furthermore, some overlap in promising genomic regions were identified among different strength phenotypes.

  17. Future approaches to digital systems

    International Nuclear Information System (INIS)

    Woodrough, R.E.; Beckmann, E.; Jenkins, D.; Belcher, D.

    1984-01-01

    The introduction of the first digital imaging systems has led to the concept of a totally digital imaging department - the 'filmless department'. This concept and its associated network system for digital departments are briefly considered. A transducer system of scanned projection radiography with solid state detectors used in digital chest imaging is described. The principles of this transducer system are applicable to other forms of digital radiography. (U.K.)

  18. Simulating single-phase and two-phase non-Newtonian fluid flow of a digital rock scanned at high resolution

    Science.gov (United States)

    Tembely, Moussa; Alsumaiti, Ali M.; Jouini, Mohamed S.; Rahimov, Khurshed; Dolatabadi, Ali

    2017-11-01

    Most of the digital rock physics (DRP) simulations focus on Newtonian fluids and overlook the detailed description of rock-fluid interaction. A better understanding of multiphase non-Newtonian fluid flow at pore-scale is crucial for optimizing enhanced oil recovery (EOR). The Darcy scale properties of reservoir rocks such as the capillary pressure curves and the relative permeability are controlled by the pore-scale behavior of the multiphase flow. In the present work, a volume of fluid (VOF) method coupled with an adaptive meshing technique is used to perform the pore-scale simulation on a 3D X-ray micro-tomography (CT) images of rock samples. The numerical model is based on the resolution of the Navier-Stokes equations along with a phase fraction equation incorporating the dynamics contact model. The simulations of a single phase flow for the absolute permeability showed a good agreement with the literature benchmark. Subsequently, the code is used to simulate a two-phase flow consisting of a polymer solution, displaying a shear-thinning power law viscosity. The simulations enable to access the impact of the consistency factor (K), the behavior index (n), along with the two contact angles (advancing and receding) on the relative permeability.

  19. Genome-wide association scan identifies a risk locus for preeclampsia on 2q14, near the inhibin, beta B gene.

    Directory of Open Access Journals (Sweden)

    Matthew P Johnson

    Full Text Available Elucidating the genetic architecture of preeclampsia is a major goal in obstetric medicine. We have performed a genome-wide association study (GWAS for preeclampsia in unrelated Australian individuals of Caucasian ancestry using the Illumina OmniExpress-12 BeadChip to successfully genotype 648,175 SNPs in 538 preeclampsia cases and 540 normal pregnancy controls. Two SNP associations (rs7579169, p = 3.58×10(-7, OR = 1.57; rs12711941, p = 4.26×10(-7, OR = 1.56 satisfied our genome-wide significance threshold (modified Bonferroni p0.92. We attempted to provide evidence of a putative regulatory role for these SNPs using bioinformatic analyses and found that they all reside within regions of low sequence conservation and/or low complexity, suggesting functional importance is low. We also explored the mRNA expression in decidua of genes ±500 kb of INHBB and found a nominally significant correlation between a transcript encoded by the EPB41L5 gene, ∼250 kb centromeric to INHBB, and preeclampsia (p = 0.03. We were unable to replicate the associations shown by the significant GWAS SNPs in case-control cohorts from Norway and Finland, leading us to conclude that it is more likely that these SNPs are in LD with as yet unidentified causal variant(s.

  20. Digital Materia

    OpenAIRE

    Lindgren, Marcus; Richey, Emma

    2014-01-01

    Med tankar från pedagogen Montessori och filosoferna Platon och Baudrillard har detta arbete behandlat frågor om datorn och dess betydelse för en grafiker. Frågeställningen formulerades efter hand och lydde tillslut: ”Hur kan materia te sig i digital form?” Forskningen resulterade i en hypotes för hur digital materia skulle födas i datorn: genom att blanda två uppsättningar av data, såsom två genuppsättningar tillsammans skapar en ny organism. Under produktionen utvecklades därmed en metod fö...

  1. Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni.

    Directory of Open Access Journals (Sweden)

    Jacob A Tennessen

    Full Text Available New strategies to combat the global scourge of schistosomiasis may be revealed by increased understanding of the mechanisms by which the obligate snail host can resist the schistosome parasite. However, few molecular markers linked to resistance have been identified and characterized in snails.Here we test six independent genetic loci for their influence on resistance to Schistosoma mansoni strain PR1 in the 13-16-R1 strain of the snail Biomphalaria glabrata. We first identify a genomic region, RADres, showing the highest differentiation between susceptible and resistant inbred lines among 1611 informative restriction-site associated DNA (RAD markers, and show that it significantly influences resistance in an independent set of 439 outbred snails. The additive effect of each RADres resistance allele is 2-fold, similar to that of the previously identified resistance gene sod1. The data fit a model in which both loci contribute independently and additively to resistance, such that the odds of infection in homozygotes for the resistance alleles at both loci (13% infected is 16-fold lower than the odds of infection in snails without any resistance alleles (70% infected. Genome-wide linkage disequilibrium is high, with both sod1 and RADres residing on haplotype blocks >2 Mb, and with other markers in each block also showing significant effects on resistance; thus the causal genes within these blocks remain to be demonstrated. Other candidate loci had no effect on resistance, including the Guadeloupe Resistance Complex and three genes (aif, infPhox, and prx1 with immunological roles and expression patterns tied to resistance, which must therefore be trans-regulated.The loci RADres and sod1 both have strong effects on resistance to S. mansoni. Future approaches to control schistosomiasis may benefit from further efforts to characterize and harness this natural genetic variation.

  2. Cooperative scans

    NARCIS (Netherlands)

    M. Zukowski (Marcin); P.A. Boncz (Peter); M.L. Kersten (Martin)

    2004-01-01

    textabstractData mining, information retrieval and other application areas exhibit a query load with multiple concurrent queries touching a large fraction of a relation. This leads to individual query plans based on a table scan or large index scan. The implementation of this access path in most

  3. A digital transducer and digital microphone using an optical technique

    Science.gov (United States)

    Ghelmansarai, F. A.

    1996-09-01

    A transducer is devised to measure pressure, displacements or angles by optical means. This transducer delivers a digital output without relying on interferometry techniques or analogue-to-digital converters. This device is based on an optical scanner and an optical detector. An inter-digital photoconductive detector (IDPC) is employed that delivers a series of pulses, whose number depends on the scan length. A pre-objective scanning configuration is used that allows for the possibility of a flat image plane. The optical scanner provides scanning of IDPC and the generated scan length is proportional to the measurand.

  4. Fast transient digitizer

    International Nuclear Information System (INIS)

    Villa, F.

    1982-01-01

    Method and apparatus for sequentially scanning a plurality of target elements with an electron scanning beam modulated in accordance with variations in a high-frequency analog signal to provide discrete analog signal samples representative of successive portions of the analog signal; coupling the discrete analog signal samples from each of the target elements to a different one of a plurality of high speed storage devices; converting the discrete analog signal samples to equivalent digital signals; and storing the digital signals in a digital memory unit for subsequent measurement or display

  5. Genome-wide linkage scan to identify loci associated with type 2 diabetes and blood lipid phenotypes in the Sikh Diabetes Study.

    Directory of Open Access Journals (Sweden)

    Dharambir K Sanghera

    Full Text Available In this investigation, we have carried out an autosomal genome-wide linkage analysis to map genes associated with type 2 diabetes (T2D and five quantitative traits of blood lipids including total cholesterol, high-density lipoprotein (HDL cholesterol, low-density lipoprotein (LDL cholesterol, very low-density lipoprotein (VLDL cholesterol, and triglycerides in a unique family-based cohort from the Sikh Diabetes Study (SDS. A total of 870 individuals (526 male/344 female from 321 families were successfully genotyped using 398 polymorphic microsatellite markers with an average spacing of 9.26 cM on the autosomes. Results of non-parametric multipoint linkage analysis using S(all statistics (implemented in Merlin did not reveal any chromosomal region to be significantly associated with T2D in this Sikh cohort. However, linkage analysis for lipid traits using QTL-ALL analysis revealed promising linkage signals with p≤0.005 for total cholesterol, LDL cholesterol, and HDL cholesterol at chromosomes 5p15, 9q21, 10p11, 10q21, and 22q13. The most significant signal (p = 0.0011 occurred at 10q21.2 for HDL cholesterol. We also observed linkage signals for total cholesterol at 22q13.32 (p = 0.0016 and 5p15.33 (p = 0.0031 and for LDL cholesterol at 10p11.23 (p = 0.0045. Interestingly, some of linkage regions identified in this Sikh population coincide with plausible candidate genes reported in recent genome-wide association and meta-analysis studies for lipid traits. Our study provides the first evidence of linkage for loci associated with quantitative lipid traits at four chromosomal regions in this Asian Indian population from Punjab. More detailed examination of these regions with more informative genotyping, sequencing, and functional studies should lead to rapid detection of novel targets of therapeutic importance.

  6. Radionuclide scanning

    International Nuclear Information System (INIS)

    Shapiro, B.

    1986-01-01

    Radionuclide scanning is the production of images of normal and diseased tissues and organs by means of the gamma-ray emissions from radiopharmaceutical agents having specific distributions in the body. The gamma rays are detected at the body surface by a variety of instruments that convert the invisible rays into visible patterns representing the distribution of the radionuclide in the body. The patterns, or images, obtained can be interpreted to provide or to aid diagnoses, to follow the course of disease, and to monitor the management of various illnesses. Scanning is a sensitive technique, but its specificity may be low when interpreted alone. To be used most successfully, radionuclide scanning must be interpreted in conjunction with other techniques, such as bone radiographs with bone scans, chest radiographs with lung scans, and ultrasonic studies with thyroid scans. Interpretation is also enhanced by providing pertinent clinical information because the distribution of radiopharmaceutical agents can be altered by drugs and by various procedures besides physiologic and pathologic conditions. Discussion of the patient with the radionuclide scanning specialist prior to the study and review of the results with that specialist after the study are beneficial

  7. A genome-wide scan reveals important roles of DNA methylation in human longevity by regulating age-related disease genes.

    Directory of Open Access Journals (Sweden)

    Fu-Hui Xiao

    Full Text Available It is recognized that genetic factors contribute to human longevity. Besides the hypothesis of existence of longevity genes, another suggests that a lower frequency of risk alleles decreases the incidence of age-related diseases in the long-lived people. However, the latter finds no support from recent genetic studies. Considering the crucial role of epigenetic modification in gene regulation, we then hypothesize that suppressing disease-related genes in longevity individuals is likely achieved by epigenetic modification, e.g. DNA methylation. To test this hypothesis, we investigated the genome-wide methylation profile in 4 Chinese female centenarians and 4 middle-aged controls using methyl-DNA immunoprecipitation sequencing. 626 differentially methylated regions (DMRs were observed between both groups. Interestingly, genes with these DMRs were enriched in age-related diseases, including type-2 diabetes, cardiovascular disease, stroke and Alzheimer's disease. This pattern remains rather stable after including methylomes of two white individuals. Further analyses suggest that the observed DMRs likely have functional roles in regulating disease-associated gene expressions, with some genes [e.g. caspase 3 (CASP3] being down-regulated whereas the others [i.e. interleukin 1 receptor, type 2 (IL1R2] up-regulated. Therefore, our study suggests that suppressing the disease-related genes via epigenetic modification is an important contributor to human longevity.

  8. A genome-wide scan for autoimmune thyroiditis in the Old Order Amish: replication of genetic linkage on chromosome 5q11.2-q14.3.

    Science.gov (United States)

    Allen, Elsie M; Hsueh, Wen-Chi; Sabra, Mona M; Pollin, Toni I; Ladenson, Paul W; Silver, Kristi D; Mitchell, Braxton D; Shuldiner, Alan R

    2003-03-01

    Autoimmune thyroiditis (AITD) is a common disorder characterized by circulating antibodies to epitopes of thyroid tissue and hypothyroidism (Hashimoto's thyroiditis or AITD-hypothyroidism), although many subjects with AITD are euthyroid. Current evidence suggests that AITD is familial and polygenic. We studied AITD in a homogeneous founder Caucasian population, the Old Order Amish of Lancaster County, Pennsylvania. We found autoimmune thyroiditis, defined by the presence of circulating antimicrosomal antibodies, to be relatively common in the Amish, with a prevalence of 22.7%. The prevalence of AITD-hypothyroidism was 9.2%. We performed a genome-wide linkage analysis with 373 short tandem repeat markers in 445 subjects from 29 families. We observed suggestive evidence of linkage of AITD to a locus on chromosome 5q11.2-q14.3 (LOD, 2.30; P = 0.0006 at 94 cM; closest marker, D5S428), a region that was previously reported to be linked to AITD-hypothyroidism in a Japanese study. AITD-hypothyroidism showed a more modest linkage peak to the same region (LOD, 1.46; P = 0.005). Possible linkage (nominal P Amish.

  9. Genome-wide scan identifies variant in TNFSF13 associated with serum IgM in a healthy Chinese male population.

    Directory of Open Access Journals (Sweden)

    Ming Yang

    Full Text Available IgM provides a first line of defense during microbial infections. Serum IgM levels are detected routinely in clinical practice. And IgM is a genetically complex trait. We conducted a two-stage genome-wide association study (GWAS to identify genetic variants affecting serum IgM levels in a Chinese population of 3495, including 1999 unrelated subjects in the first stage and 1496 independent individuals in the second stage. Our data show that a common single nucleotide polymorphism (SNP, rs11552708 located in the TNFSF13 gene was significantly associated with IgM levels (p = 5.00×10(-7 in first stage, p = 1.34×10(-3 in second stage, and p = 4.22×10(-9 when combined. Besides, smoking was identified to be associated with IgM levels in both stages (P0.05. It is suggested that TNFSF13 may be a susceptibility gene affecting serum IgM levels in Chinese male population.

  10. Digital broadcasting

    International Nuclear Information System (INIS)

    Park, Ji Hyeong

    1999-06-01

    This book contains twelve chapters, which deals with digitization of broadcast signal such as digital open, digitization of video signal and sound signal digitization of broadcasting equipment like DTPP and digital VTR, digitization of equipment to transmit such as digital STL, digital FPU and digital SNG, digitization of transmit about digital TV transmit and radio transmit, digital broadcasting system on necessity and advantage, digital broadcasting system abroad and Korea, digital broadcasting of outline, advantage of digital TV, ripple effect of digital broadcasting and consideration of digital broadcasting, ground wave digital broadcasting of DVB-T in Europe DTV in U.S.A and ISDB-T in Japan, HDTV broadcasting, satellite broadcasting, digital TV broadcasting in Korea, digital radio broadcasting and new broadcasting service.

  11. Radiographic film digitizing devices

    International Nuclear Information System (INIS)

    McFee, W.H.

    1988-01-01

    Until recently, all film digitizing devices for use with teleradiology or picture archiving and communication systems used a video camera to capture an image of the radiograph for subsequent digitization. The development of film digitizers that use a laser beam to scan the film represents a significant advancement in digital technology, resulting in improved image quality compared with video scanners. This paper discusses differences in resolution, efficiency, reliability, and the cost between these two types of devices. The results of a modified receiver operating characteristic comparison study of a video scanner and a laser scanner manufactured by the same company are also discussed

  12. Electronically-Scanned Pressure Sensors

    Science.gov (United States)

    Coe, C. F.; Parra, G. T.; Kauffman, R. C.

    1984-01-01

    Sensors not pneumatically switched. Electronic pressure-transducer scanning system constructed in modular form. Pressure transducer modules and analog to digital converter module small enough to fit within cavities of average-sized wind-tunnel models. All switching done electronically. Temperature controlled environment maintained within sensor modules so accuracy maintained while ambient temperature varies.

  13. Scanning table

    CERN Multimedia

    1960-01-01

    Before the invention of wire chambers, particles tracks were analysed on scanning tables like this one. Today, the process is electronic and much faster. Bubble chamber film - currently available - (links can be found below) was used for this analysis of the particle tracks.

  14. 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.

  15. Digital radiography in NDT applications

    International Nuclear Information System (INIS)

    Deprins, E.

    2004-01-01

    A lot of film radiography could be replaced by today's technologies in the field of digital radiography. Only few of these applications have indeed replaced film. The choice to go digital depends on cost, quality requirement, workflow and throughput. Digital images offer a lot of advantages in terms of image manipulation and workflow. But despite the many advantages, a lot of considerations are needed before someone can decide to convert his organization from conventional to digital radiography. This paper gives an overview of all different modalities that can be used in digital radiography with today's technologies, together with the experiences of the pioneers of digital radiography. Film Scanning, Computed Radiography and Digital Radiography by using of different kinds of flat panel detectors all have their specific application fields and customers. What is the status of the technology today, which advantages brings digital radiography, and which are the limitations radiographers have to consider when replacing film by digital systems. (author)

  16. Scanning holograms

    International Nuclear Information System (INIS)

    Natali, S.

    1984-01-01

    This chapter reports on the scanning of 1000 holograms taken in HOBC at CERN. Each hologram is triggered by an interaction in the chamber, the primary particles being pions at 340 GeV/c. The aim of the experiment is the study of charm production. The holograms, recorded on 50 mm film with the ''in line'' technique, can be analyzed by shining a parallel expanded laser beam through the film, obtaining immediately above it the real image of the chamber which can then be scanned and measured with a technique half way between emulsions and bubble chambers. The results indicate that holograms can be analyzed as quickly and reliably as in other visual techniques and that to them is open the same order of magnitude of large scale experiments

  17. Bone scans

    International Nuclear Information System (INIS)

    Hetherington, V.J.

    1989-01-01

    Oftentimes, in managing podiatric complaints, clinical and conventional radiographic techniques are insufficient in determining a patient's problem. This is especially true in the early stages of bone infection. Bone scanning or imaging can provide additional information in the diagnosis of the disorder. However, bone scans are not specific and must be correlated with clinical, radiographic, and laboratory evaluation. In other words, bone scanning does not provide the diagnosis but is an important bit of information aiding in the process of diagnosis. The more useful radionuclides in skeletal imaging are technetium phosphate complexes and gallium citrate. These compounds are administered intravenously and are detected at specific time intervals postinjection by a rectilinear scanner with minification is used and the entire skeleton can be imaged from head to toe. Minification allows visualization of the entire skeleton in a single image. A gamma camera can concentrate on an isolated area. However, it requires multiple views to complete the whole skeletal image. Recent advances have allowed computer augmentation of the data received from radionucleotide imaging. The purpose of this chapter is to present the current radionuclides clinically useful in podiatric patients

  18. The digital Emily project: achieving a photorealistic digital actor.

    Science.gov (United States)

    Alexander, Oleg; Rogers, Mike; Lambeth, William; Chiang, Jen-Yuan; Ma, Wan-Chun; Wang, Chuan-Chang; Debevec, Paul

    2010-01-01

    The Digital Emily Project uses advanced face scanning, character rigging, performance capture, and compositing to achieve one of the world's first photorealistic digital facial performances. The project scanned the geometry and reflectance of actress Emily O'Brien's face in 33 poses, showing different emotions, gaze directions, and lip formations in a light stage. These high-resolution scans-accurate to skin pores and fine wrinkles-became the basis for building a blendshape-based facial-animation rig whose expressions closely matched the scans. The blendshape rig drove displacement maps to add dynamic surface detail. A video-based facial animation system animated the face according to the performance in a reference video, and the digital face was tracked onto the video's motion and rendered under the same illumination. The result was a realistic 3D digital facial performance credited as one of the first to cross the "uncanny valley" between animated and fully human performances.

  19. A meta-analysis of genome-wide association scans identifies IL18RAP, PTPN2, TAGAP, and PUS10 as shared risk loci for Crohn's disease and celiac disease.

    Directory of Open Access Journals (Sweden)

    Eleonora A M Festen

    2011-01-01

    Full Text Available Crohn's disease (CD and celiac disease (CelD are chronic intestinal inflammatory diseases, involving genetic and environmental factors in their pathogenesis. The two diseases can co-occur within families, and studies suggest that CelD patients have a higher risk to develop CD than the general population. These observations suggest that CD and CelD may share common genetic risk loci. Two such shared loci, IL18RAP and PTPN2, have already been identified independently in these two diseases. The aim of our study was to explicitly identify shared risk loci for these diseases by combining results from genome-wide association study (GWAS datasets of CD and CelD. Specifically, GWAS results from CelD (768 cases, 1,422 controls and CD (3,230 cases, 4,829 controls were combined in a meta-analysis. Nine independent regions had nominal association p-value <1.0 x 10⁻⁵ in this meta-analysis and showed evidence of association to the individual diseases in the original scans (p-value < 1 x 10⁻² in CelD and < 1 x 10⁻³ in CD. These include the two previously reported shared loci, IL18RAP and PTPN2, with p-values of 3.37 x 10⁻⁸ and 6.39 x 10⁻⁹, respectively, in the meta-analysis. The other seven had not been reported as shared loci and thus were tested in additional CelD (3,149 cases and 4,714 controls and CD (1,835 cases and 1,669 controls cohorts. Two of these loci, TAGAP and PUS10, showed significant evidence of replication (Bonferroni corrected p-values <0.0071 in the combined CelD and CD replication cohorts and were firmly established as shared risk loci of genome-wide significance, with overall combined p-values of 1.55 x 10⁻¹⁰ and 1.38 x 10⁻¹¹ respectively. Through a meta-analysis of GWAS data from CD and CelD, we have identified four shared risk loci: PTPN2, IL18RAP, TAGAP, and PUS10. The combined analysis of the two datasets provided the power, lacking in the individual GWAS for single diseases, to detect shared loci with a

  20. Digital Raster Graphics (DRG) Lambert

    Data.gov (United States)

    Kansas Data Access and Support Center — The Digital Raster Graphic-Lambert (DRG-Lam) is a raster image of a scanned USGS topographic map with the collar information clipped out, georeferenced to the...

  1. Image processing techniques for digital orthophotoquad production

    Science.gov (United States)

    Hood, Joy J.; Ladner, L. J.; Champion, Richard A.

    1989-01-01

    Orthophotographs have long been recognized for their value as supplements or alternatives to standard maps. Recent trends towards digital cartography have resulted in efforts by the US Geological Survey to develop a digital orthophotoquad production system. Digital image files were created by scanning color infrared photographs on a microdensitometer. Rectification techniques were applied to remove tile and relief displacement, thereby creating digital orthophotos. Image mosaicking software was then used to join the rectified images, producing digital orthophotos in quadrangle format.

  2. Image quality in digital radiography

    International Nuclear Information System (INIS)

    Kuhn, H.

    1986-01-01

    The contribution deals with the potentials of digital radiography and critically evaluates the advantages of drawbacks of the image intensifier-tv-digital system; digitalisation of the X-ray film and scanning of luminescent storage foils. The evaluation is done in comparison with the image quality of the traditional, large-size X-ray picture. (orig.) [de

  3. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  4. Head CT scan

    Science.gov (United States)

    ... scan - orbits; CT scan - sinuses; Computed tomography - cranial; CAT scan - brain ... head size in children Changes in thinking or behavior Fainting Headache, when you have certain other signs ...

  5. Digital radiology. Clinical experience

    Energy Technology Data Exchange (ETDEWEB)

    Stacul, F; Smathers, R L

    1985-01-01

    The authors report the experience achieved ad the Stanford University (USA) with a digital radiography system which allows the digitization of the film and of the images collected with photostimulable phophors. The phophor is essentially an intensifying screen where a latent image is stored after exposure to X-rays and is extracted by a laser scanning. The images collected with the digitized film and with the phophor (chest, breast, bone) have been analyzed. The digitized film offers potential diagnostic advantages over the conventional film, because of the contrast manipulation and many other processing options. The possibility to recover the information of overexposed films appears very attractive. The photostimulable phophors allow to get good quality images, with a consistent reduction of dose and costs. These plates offer the possibility, in the next future, to replace the conventional screen-film systems.

  6. Double-polarizating scanning radiometer

    International Nuclear Information System (INIS)

    Mishev, D.N.; Nazyrski, T.G.

    1986-01-01

    The double-polarizating single-channel scanning radiometer comprises the following serial connected parts: a scanning double-polarizating aerial, a block for polarization separation, a radiometer receiver, an analog-to-digit converter and an information flow forming block. The low frequency input of the radiometer receiver is connected with a control block, which is also connected with a first bus of a microprocessor, the second bus of which is connected with the A-D converter. The control input of the scanning double-polarizating aerial is connected with the first microprocessor bus. The control inputs of the block for polarization separation are linked by an electronic switch with the output of the forming block, the input of which is connected to the first input of the control block. The control inputs of the block for polarization separation are connected with the second and the third input of the information flow forming block. 2 cls

  7. Intraoral scan bodies in implant dentistry: A systematic review.

    Science.gov (United States)

    Mizumoto, Ryan M; Yilmaz, Burak

    2018-04-05

    Intraoral scan body (ISB) design is highly variable and its role in the digital workflow and accuracy of digital impressions is not well understood. The purpose of this systematic review was to determine the relevant reports pertaining to ISBs with regard to design and accuracy and to describe their evolution and role in the digital dentistry workflow. Special attention was placed on their key features in relation to intraoral scanning technology and the digitization process. A MEDLINE/PubMed search was performed to identify relevant reports pertaining to ISB usage in dentistry. This search included but was not limited to scan body features and design, scan body accuracy, and scan body techniques and the role of ISBs in computer-aided design and computer-aided manufacturing (CAD-CAM) processes. Commercially available scan bodies were examined, and a patient situation was shown highlighting the use of ISBs in the digital workflow. Deficiencies in the reports were found regarding various scan body topics, including ISB features/design, accuracy, and the role of ISBs in CAD-CAM processes. ISBs are complex implant-positioning-transfer devices that play an essential role in the digital workflow and fabrication of accurately fitting implant-supported restorations. With scanner technology rapidly evolving and becoming more widespread, future studies are needed and should be directed toward all parts of the digital workflow when using ISBs. By understanding the basic components of ISBs and how they relate to digital scanning and CAD-CAM technology, more emphasis may be placed on their importance and usage in the digital workflow to ensure accurate transfer of implant position to the virtual and analog definitive cast. Efforts should be made by clinicians to identify an optimal ISB design in relation to the specific intraoral scanning technology being used. Copyright © 2017 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights

  8. Digital Culture and Digital Library

    Directory of Open Access Journals (Sweden)

    Yalçın Yalçınkaya

    2016-12-01

    Full Text Available In this study; digital culture and digital library which have a vital connection with each other are examined together. The content of the research consists of the interaction of culture, information, digital culture, intellectual technologies, and digital library concepts. The study is an entry work to integrity of digital culture and digital library theories and aims to expand the symmetry. The purpose of the study is to emphasize the relation between the digital culture and digital library theories acting intersection of the subjects that are examined. Also the perspective of the study is based on examining the literature and analytical evaluation in both studies (digital culture and digital library. Within this context, the methodology of the study is essentially descriptive and has an attribute for the transmission and synthesis of distributed findings produced in the field of the research. According to the findings of the study results, digital culture is an inclusive term that describes the effects of intellectual technologies in the field of information and communication. Information becomes energy and the spectrum of the information is expanding in the vertical rise through the digital culture. In this context, the digital library appears as a new living space of a new environment. In essence, the digital library is information-oriented; has intellectual technology support and digital platform; is in a digital format; combines information resources and tools in relationship/communication/cooperation by connectedness, and also it is the dynamic face of the digital culture in time and space independence. Resolved with the study is that the digital libraries are active and effective in the formation of global knowing and/or mass wisdom in the process of digital culture.

  9. The boundary-scan handbook

    CERN Document Server

    Parker, Kenneth P

    2016-01-01

    Aimed at electronics industry professionals, this 4th edition of the Boundary Scan Handbook describes recent changes to the IEEE1149.1 Standard Test Access Port and Boundary-Scan Architecture. This updated edition features new chapters on the possible effects of the changes on the work of the practicing test engineers and the new 1149.8.1 standard. Anyone needing to understand the basics of boundary scan and its practical industrial implementation will need this book. Provides an overview of the recent changes to the 1149.1 standard and the effect of the changes on the work of test engineers;   Explains the new IEEE 1149.8.1 subsidiary standard and applications;   Describes the latest updates on the supplementary IEEE testing standards. In particular, addresses: IEEE Std 1149.1                      Digital Boundary-Scan IEEE Std 1149.4                      Analog Boundary-Scan IEEE Std 1149.6                      Advanced I/O Testing IEEE Std 1149.8.1           �...

  10. Digital mammography; Mamografia digital

    Energy Technology Data Exchange (ETDEWEB)

    Chevalier, M.; Torres, R.

    2010-07-01

    Mammography represents one of the most demanding radiographic applications, simultaneously requiring excellent contrast sensitivity, high spatial resolution, and wide dynamic range. Film/screen is the most widely extended image receptor in mammography due to both its high spatial resolution and contrast. The film/screen limitations are related with its narrow latitude, structural noise and that is at the same time the medium for the image acquisition, storage and presentation. Several digital detector made with different technologies can overcome these difficulties. Here, these technologies as well as their main advantages and disadvantages are analyzed. Also it is discussed its impact on the mammography examinations, mainly on the breast screening programs. (Author).

  11. Brain PET scan

    Science.gov (United States)

    ... results on a PET scan. Blood sugar or insulin levels may affect the test results in people with diabetes . PET scans may be done along with a CT scan. This combination scan is called a PET/CT. Alternative Names Brain positron emission tomography; PET scan - brain References Chernecky ...

  12. Digital Tectonics

    DEFF Research Database (Denmark)

    Christiansen, Karl; Borup, Ruben; Søndergaard, Asbjørn

    2014-01-01

    Digital Tectonics treats the architectonical possibilities in digital generation of form and production. The publication is the first volume of a series, in which aspects of the strategic focus areas of the Aarhus School of Architecture will be disseminated.......Digital Tectonics treats the architectonical possibilities in digital generation of form and production. The publication is the first volume of a series, in which aspects of the strategic focus areas of the Aarhus School of Architecture will be disseminated....

  13. Digital squares

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Kim, Chul E

    1988-01-01

    Digital squares are defined and their geometric properties characterized. A linear time algorithm is presented that considers a convex digital region and determines whether or not it is a digital square. The algorithm also determines the range of the values of the parameter set of its preimages....... The analysis involves transforming the boundary of a digital region into parameter space of slope and y-intercept...

  14. Digital skrivedidaktik

    DEFF Research Database (Denmark)

    Digital skrivedidaktik består af to dele. Første del præsenterer teori om skrivekompetence og digital skrivning. Digital skrivning er karakteriseret ved at tekster skrives på computer og med digitale værktøjer, hvilket ændrer skrivningens traditionelle praksis, produkt og processer. Hvad er digital...... om elevens skriveproces) og Blogskrivning (der styrker eleverne i at bruge blogs i undervisningen)....

  15. Digital Genome-Wide ncRNA Expression, Including SnoRNAs, across 11 Human Tissues Using PolyA-Neutral Amplification

    Science.gov (United States)

    Castle, John C.; Armour, Christopher D.; Löwer, Martin; Haynor, David; Biery, Matthew; Bouzek, Heather; Chen, Ronghua; Jackson, Stuart; Johnson, Jason M.; Rohl, Carol A.; Raymond, Christopher K.

    2010-01-01

    Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available. PMID:20668672

  16. Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification.

    Directory of Open Access Journals (Sweden)

    John C Castle

    Full Text Available Non-coding RNAs (ncRNAs are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6 is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available.

  17. Using Digital 3D Scanning to Create “Artifictions” of the Passenger Pigeon and Harelip Sucker, Two Extinct Species in Eastern North America: The Future Examines the Past

    Directory of Open Access Journals (Sweden)

    Bruce L. Manzano

    2015-12-01

    Full Text Available The Virtual Curation Laboratory at Virginia Commonwealth University created 3D representations of digital morphological models, termed “artifictions,” of several bone elements from two extinct animals, the passenger pigeon (Ectopistes migratorius Linnaeus Columbidae and the harelip sucker (Moxostoma lacerum Jordan and Brayton Catostomidae. Procuring recent comparative reference skeletons these species is extremely difficult. The creation of artifictions, 3D printed replicas of skeletal remains, aims to help researchers become familiar with the bones of harelip sucker and passenger pigeon to facilitate morphological identification of remains of these species within archaeological assemblages. Here, we discuss the two species, the techniques used to create digital topological models of individual skeletal elements, and the obstacles encountered regarding 3D printed artifictions in zooarchaeology.

  18. Digital Citizenship

    Science.gov (United States)

    Isman, Aytekin; Canan Gungoren, Ozlem

    2014-01-01

    Era in which we live is known and referred as digital age.In this age technology is rapidly changed and developed. In light of these technological advances in 21st century, schools have the responsibility of training "digital citizen" as well as a good citizen. Digital citizens must have extensive skills, knowledge, Internet and …

  19. Heart PET scan

    Science.gov (United States)

    ... nuclear medicine scan; Heart positron emission tomography; Myocardial PET scan ... A PET scan requires a small amount of radioactive material (tracer). This tracer is given through a vein (IV), ...

  20. Precision digital control systems

    Science.gov (United States)

    Vyskub, V. G.; Rozov, B. S.; Savelev, V. I.

    This book is concerned with the characteristics of digital control systems of great accuracy. A classification of such systems is considered along with aspects of stabilization, programmable control applications, digital tracking systems and servomechanisms, and precision systems for the control of a scanning laser beam. Other topics explored are related to systems of proportional control, linear devices and methods for increasing precision, approaches for further decreasing the response time in the case of high-speed operation, possibilities for the implementation of a logical control law, and methods for the study of precision digital control systems. A description is presented of precision automatic control systems which make use of electronic computers, taking into account the existing possibilities for an employment of computers in automatic control systems, approaches and studies required for including a computer in such control systems, and an analysis of the structure of automatic control systems with computers. Attention is also given to functional blocks in the considered systems.

  1. Digital health and perioperative care.

    Science.gov (United States)

    Fotis, Theofanis

    2017-06-01

    According to the U.S. Food and Drug Administration 'the broad scope of digital health includes categories such as mobile health (mHealth), health information technology (IT), wearable devices, telehealth and telemedicine, and personalised medicine, and is used by providers and other stakeholders in their efforts to reduce inefficiencies, improve access, reduce costs, increase quality, and make medicine more personalised for patients (FDA 2016). More recently, Paul Sonier, a digital health strategist and founder of the Linkedin digital health group with more than 40,000 members, defined digital health as 'the convergence of the digital and genomic revolutions with health, healthcare, living, and society' (storyofdigitalhealth.com 2016). Copyright the Association for Perioperative Practice.

  2. Digital subtraktion

    DEFF Research Database (Denmark)

    Mussmann, Bo Redder

    2004-01-01

    Digital subtraktion er en metode til at fjerne uønskede oplysninger i et røntgenbillede. Subtraktionsteknikken bruges primært i forbindelse med angiografi hvor man kun er interesseret i at se selve karret. Derfor er digital subtraktion i daglig tale synonymt med DSA eller DVI – hhv. Digital...... Subtraction Angiography eller Digital Vascular Imaging. Benævnelserne er to røntgenfirmaers navn for den samme teknik. Digital subtraktion kræver speciel software, samt at apparaturet kan eksponere i serier....

  3. Digital preservation

    CERN Document Server

    Deegan, Marilyn

    2013-01-01

    Digital preservation is an issue of huge importance to the library and information profession right now. With the widescale adoption of the internet and the rise of the world wide web, the world has been overwhelmed by digital information. Digital data is being produced on a massive scale by individuals and institutions: some of it is born, lives and dies only in digital form, and it is the potential death of this data, with its impact on the preservation of culture, that is the concern of this book. So how can information professionals try to remedy this? Digital preservation is a complex iss

  4. Digital Resource Use and Non‐Use in the Humanities and Social Sciences Academic Settings is Multifaceted. A review of: Harley, Diane. “Why Study Users? An Environmental Scan of Use and Users of Digital Resources in Humanities and Social Sciences Undergraduate Education.” First Monday 12.1 (Jan. 2007. 7 May 2007 .

    Directory of Open Access Journals (Sweden)

    Lotta Haglund

    2007-06-01

    Full Text Available Objective – (1 To map the digital resources available to undergraduate educators in the humanities and the social sciences, (2 to survey faculty about their use of digital resources, and (3 to examine how understanding use and users can benefit the integration of resources into teaching.Design – A mixed‐methods approach, which included a survey, conducting discussion groups, and in‐depth interviews.Setting – Academic institutions in the United States.Subjects – (1 “Various stakeholders”; (2 31 instructors from three institutions, and 4500 full‐time and part‐time faculty and graduate students (at California public research universities, liberal arts colleges and community colleges; and (3 13 digital resource providers and two other stakeholders, and 16 site owners or user researchers.Methods – (1 A literature review, combined with discussions with various stakeholders. (2 Four sessions of discussion groups with 31 instructors from three institutions formed the basis for developing a faculty surveyi nstrument. The survey was distributed both on paper and online. (3 Collection of data on cost and collaborative development strategies, in‐depth interviews with 13 digital resource providers and two other stakeholders, combined with a two day workshop with 16 experts, both on the subject of online educational resources.Main results – (1 Concerning the humanities and social sciences digital resource landscape, the main results of the literature study were the conclusions that the field of online education studies is complicated by a lack of common vocabulary, definitions, and analyses; and that different stakeholder interests and agendas also influence the understanding of how digital resources are used. With the help of discussion groups, an attempt at creating a typology for digital resources available to undergraduates was made, looking at type of resource, origin, and typeo f role of the provider or site owner. From the

  5. USGS 24k Digital Raster Graphic (DRG) Metadata

    Data.gov (United States)

    Minnesota Department of Natural Resources — Metadata for the scanned USGS 24k Topograpic Map Series (also known as 24k Digital Raster Graphic). Each scanned map is represented by a polygon in the layer and the...

  6. Digital radiography using scintillating screens

    International Nuclear Information System (INIS)

    Salvini, E.

    1988-01-01

    This paper briefly describes the technical features of a digital radiographic system based on the principle of scanning laser stimulated luminescence. Such aspects as the physics of the stimulable phosphor detector are dealt with, and image acquisition, processing, and hard-copy output. Automatic analysis of pixel histograms is described, in a qualitative way, together with contrast modifications and spatial filtering. Physical image characteristics are reported. The overall performance of digital radiography is examined, together with the current requirements and its eventual developments

  7. Digital Natives or Digital Tribes?

    Science.gov (United States)

    Watson, Ian Robert

    2013-01-01

    This research builds upon the discourse surrounding digital natives. A literature review into the digital native phenomena was undertaken and found that researchers are beginning to identify the digital native as not one cohesive group but of individuals influenced by other factors. Primary research by means of questionnaire survey of technologies…

  8. Gamma scanning equipment for nuclear safeguards

    International Nuclear Information System (INIS)

    De Grandi, G.; Stanchi, L.

    1975-01-01

    Many reasons justify the use of gamma techniques in the field of nuclear safeguards. The paper describes electronic equipment for gamma-scanning of non-irradiated fuel elements. The control of the operation is completely digital and driven by a minicomputer and gives more accurate results in respect of an analog chain which has been successfully used in fuel element manufacturing plants

  9. Intraoral scanning systems - a current overview.

    Science.gov (United States)

    Zimmermann, M; Mehl, A; Mörmann, W H; Reich, S

    2015-01-01

    There is no doubt today about the possibilities and potential of digital impression-taking with the aid of intraoral optical impression systems, and the past few years have seen a considerable increase in the range of optical intraoral scanners available on the market. On the strength of numerous innovations and a wider range of indications in orthodontics and implantology, intraoral scanning systems appear to be a highly promising development for the future. Digital impression-taking with intraoral scanners has already shown itself in some respects to be clearly superior to conventional impression- taking. Particularly worthy of mention is the versatile integration of digital impressions into diagnostic and treatment concepts to provide a customizable healthcare solution for the patient. It remains exciting to look forward to future developments that will allow us to observe digital impression-taking--as with other digital applications already established in everyday life--becoming firmly established in the routine of dentistry and dental technology. This article presents an overview of the benefits and limitations of digital impression-taking using intraoral scanning systems, and includes a summary of all the relevant intraoral scanners available on the market at present.

  10. Digital radiography of the chest

    International Nuclear Information System (INIS)

    Sakurai, Kenji; Hachiya, Junichi; Korenaga, Tateo; Nitatori, Toshiaki; Miyasaka, Yasuo; Furuya, Yoshiro

    1984-01-01

    Initial clinical experience in digital chest radiography utilizing photostimulable phosphor and scanning laser stimulated luminescence was reported. Image quality of conventional film/screen radiography and digital radiography was compared in 30 normal cases. Reflecting wide dynamic range of the system, improved image quality was confirmed in all 30 cases, particularly in visibility of various mediastinal structures and pulmonary vessels. High sensor sensitivity of the system enabled digital radiography to reduce radiation dose requirement significantly. Diagnostically acceptable chest images were obtained with approximately 1/5 of routine dose for conventional radiography without significant image quality degradation. Some artifact created by digital processing were mostly overcome by a routine use of simultaneous display of two different types of image processing and therefore was not an actual drawback from diagnostic standpoint. Further technical advancement of the system to be seen for digital storage, retrieval and tranceference of images. (author)

  11. Digital mammography

    International Nuclear Information System (INIS)

    Bick, Ulrich; Diekmann, Felix

    2010-01-01

    This state-of-the-art reference book provides in-depth coverage of all aspects of digital mammography, including detector technology, image processing, computer-aided diagnosis, soft-copy reading, digital workflow, and PACS. Specific advantages and disadvantages of digital mammography in comparison to screen-film mammography are thoroughly discussed. By including authors from both North America and Europe, the book is able to outline variations in the use, acceptance, and quality assurance of digital mammography between the different countries and screening programs. Advanced imaging techniques and future developments such as contrast mammography and digital breast tomosynthesis are also covered in detail. All of the chapters are written by internationally recognized experts and contain numerous high-quality illustrations. This book will be of great interest both to clinicians who already use or are transitioning to digital mammography and to basic scientists working in the field. (orig.)

  12. Digital Insights

    DEFF Research Database (Denmark)

    Knudsen, Gry Høngsmark

    , by incorporating media as both channel, frame, and apparatus for advertising response, the dissertation brings into attention that more aspects than the text-reader relationship influence ad response. Finally, the dissertation proposes the assemblage approach for exploring big data in consumer culture research...... and practices with digital media, when they meet and interpret advertising. Through studies of advertising response on YouTube and experiments with consumers’ response to digitally manipulated images, the dissertation shows how digital media practices facilitate polysemic and socially embedded advertising......This dissertation forwards the theory of digital consumer-response as a perspective to examine how digital media practices influence consumers’ response to advertising. Digital consumer-response is a development of advertising theory that encompasses how consumers employ their knowledge...

  13. Digital Signage

    OpenAIRE

    Fischer, Karl Peter

    2011-01-01

    Digital Signage for in-store advertising at gas stations/retail stores in Germany: A field study Digital Signage networks provide a novel means of advertising with the advantage of easily changeable and highly customizable animated content. Despite the potential and increasing use of these media empirical research is scarce. In a field study at 8 gas stations (with integrated convenience stores) we studied the effect of digital signage advertising on sales for different products and servi...

  14. Sports Digitalization

    DEFF Research Database (Denmark)

    Xiao, Xiao; Hedman, Jonas; Tan, Felix Ter Chian

    2017-01-01

    evolution, as digital technologies are increasingly entrenched in a wide range of sporting activities and for applications beyond mere performance enhancement. Despite such trends, research on sports digitalization in the IS discipline is surprisingly still nascent. This paper aims at establishing...... a discourse on sports digitalization within the discipline. Toward this, we first provide an understanding of the institutional characteristics of the sports industry, establishing its theoretical importance and relevance in our discipline; second, we reveal the latest trends of digitalization in the sports...

  15. Digital printing

    Science.gov (United States)

    Sobotka, Werner K.

    1997-02-01

    Digital printing is described as a tool to replace conventional printing machines completely. Still this goal was not reached until now with any of the digital printing technologies to be described in the paper. Productivity and costs are still the main parameters and are not really solved until now. Quality in digital printing is no problem anymore. Definition of digital printing is to transfer digital datas directly on the paper surface. This step can be carried out directly or with the use of an intermediate image carrier. Keywords in digital printing are: computer- to-press; erasable image carrier; image carrier with memory. Digital printing is also the logical development of the new digital area as it is pointed out in Nicholas Negropotes book 'Being Digital' and also the answer to networking and Internet technologies. Creating images text and color in one country and publishing the datas in another country or continent is the main advantage. Printing on demand another big advantage and last but not least personalization the last big advantage. Costs and being able to coop with this new world of prepress technology is the biggest disadvantage. Therefore the very optimistic growth rates for the next few years are really nonexistent. The development of complete new markets is too slow and the replacing of old markets is too small.

  16. Special raster scanning for reduction of charging effects in scanning electron microscopy.

    Science.gov (United States)

    Suzuki, Kazuhiko; Oho, Eisaku

    2014-01-01

    A special raster scanning (SRS) method for reduction of charging effects is developed for the field of SEM. Both a conventional fast scan (horizontal direction) and an unusual scan (vertical direction) are adopted for acquiring raw data consisting of many sub-images. These data are converted to a proper SEM image using digital image processing techniques. About sharpness of the image and reduction of charging effects, the SRS is compared with the conventional fast scan (with frame-averaging) and the conventional slow scan. Experimental results show the effectiveness of SRS images. By a successful combination of the proposed scanning method and low accelerating voltage (LV)-SEMs, it is expected that higher-quality SEM images can be more easily acquired by the considerable reduction of charging effects, while maintaining the resolution. © 2013 Wiley Periodicals, Inc.

  17. Digital Audiobooks

    DEFF Research Database (Denmark)

    Have, Iben; Pedersen, Birgitte Stougaard

    Audiobooks are rapidly gaining popularity with widely accessible digital downloading and streaming services. The paper is framing how the digital audiobook expands and changes the target groups for book publications and how it as an everyday activity is creating new reading experiences, places...

  18. Digital TMI

    Science.gov (United States)

    Rios, Joseph

    2012-01-01

    Presenting the current status of the Digital TMI project to visiting members of the FAA Command Center. Digital TMI is an effort to store national-level traffic management initiatives in a standards-compliant manner. Work is funded by the FAA.

  19. Determination of the spatial structure of vegetation on the repository of the mine “Fryderyk” in Tarnowskie Góry, based on airborne laser scanning from the ISOK project and digital orthophotomaps

    Directory of Open Access Journals (Sweden)

    Szostak Marta

    2015-06-01

    Full Text Available The purpose of this study was to determine the spatial structure of vegetation on the repository of the mine “Fryderyk” in Tarnowskie Góry. Tested area was located in the Upper Silesian Industrial Region (a large industrial region in Poland. It was a unique refuge habitat – Natura2000; PLH240008. The main aspect of this elaboration was to investigate the possible use of geotechniques and generally available geodata for mapping LULC changes and determining the spatial structure of vegetation. The presented study focuses on the analysis of a spatial structure of vegetation in the research area. This exploration was based on aerial images and orthophotomaps from 1947, 1998, 2003, 2009, 2011 and airborne laser scanning data (2011, ISOK project. Forest succession changes which occurred between 1947 and 2011 were analysed. The selected features of vegetation overgrowing spoil heap “Fryderyk” was determined.

  20. Digital displacements

    DEFF Research Database (Denmark)

    Pors, Anja Svejgaard

    2014-01-01

    In recent years digital reforms are being introduced in the municipal landscape of Denmark. The reforms address the interaction between citizen and local authority. The aim is, that by 2015 at least 80 per cent of all correspondence between citizens and public authority will be transmitted through...... digital interface. However, the transformation of citizen services from traditional face-to-face interaction to digital self-service gives rise to new practices; some citizens need support to be able to manage self-service through digital tools. A mixture of support and teaching, named co......-service, is a new task in public administration, where street level bureaucrats assist citizens in using the new digital solutions. The paper is based on a case study conducted primarily in a citizen service centre in Copenhagen, Denmark. Based on ethnography the paper gives an empirical account of the ongoing...

  1. Digitized mammograms

    International Nuclear Information System (INIS)

    Bruneton, J.N.; Balu-Maestro, C.; Rogopoulos, A.; Chauvel, C.; Geoffray, A.

    1988-01-01

    Two observers conducted a blind evaluation of 100 mammography files, including 47 malignant cases. Films were read both before and after image digitization at 50 μm and 100 μm with the FilmDRSII. Digitization permitted better analysis of the normal anatomic structures and moderately improved diagnostic sensitivity. Searches for microcalcifications before and after digitization at 100 μm and 50 μm showed better analysis of anatomic structures after digitization (especially for solitary microcalcifications). The diagnostic benefit, with discovery of clustered microcalcifications, was more limited (one case at 100 μm, nine cases at 50 μm). Recognition of microcalcifications was clearly improved in dense breasts, which can benefit from reinterpretation after digitization at 50 μm rather 100μm

  2. New Snail Mail Scanning Service

    CERN Multimedia

    2012-01-01

    Modernisation does not stop at the CERN postal service (GS/PS). “With more and more digitisation and the prevalence of e-mail throughout the site, we were hoping to provide more timely delivery of letters and make further saving in resources”, said Tueri Datta, head of GS/PS.   Instead of the standard delivery to your P.O. box, the CERN postal service will digitally scan all letters and books up to 100 pages on reception. These scans will subsequently be sent via e-mail to the corresponding recipient as PDF (Portable Data Format - you will need to install “Acrobat Reader” on your PC). Express mail will be handled with priority. Users without a valid CERN mailbox can register at mail.scan.service@cern.ch in order to have their letters read to them via the phone line (we are currently investigating whether we can use the voices of the last five DGs).   This service will start on 1st April 2012 on the Meyrin site and will gradually replace th...

  3. Radiopharmaceutical scanning agents

    International Nuclear Information System (INIS)

    1976-01-01

    This invention is directed to dispersions useful in preparing radiopharmaceutical scanning agents, to technetium labelled dispersions, to methods for preparing such dispersions and to their use as scanning agents

  4. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Scan and Uptake Thyroid scan and uptake uses small amounts of radioactive materials called radiotracers, a special ... is a branch of medical imaging that uses small amounts of radioactive material to diagnose and determine ...

  5. Nuclear Heart Scan

    Science.gov (United States)

    ... Home / Nuclear Heart Scan Nuclear Heart Scan Also known as Nuclear Stress Test , ... Learn More Connect With Us Contact Us Directly Policies Privacy Policy Freedom of Information Act (FOIA) Accessibility ...

  6. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... of page What will I experience during and after the procedure? Most thyroid scan and thyroid uptake ... you otherwise, you may resume your normal activities after your nuclear medicine scan. If any special instructions ...

  7. RBC nuclear scan

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003835.htm RBC nuclear scan To use the sharing features on this page, please enable JavaScript. An RBC nuclear scan uses small amounts of radioactive material to ...

  8. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  9. Digital Ethics/Going Digital.

    Science.gov (United States)

    Wilson, Bradley

    1996-01-01

    Finds that the recent National Press Photographers Association code of ethics can serve as a model for any photography staff. Discusses how digital imaging is becoming commonplace in classrooms, due to decreasing costs and easier software. Explains digital terminology. Concludes that time saved in the darkroom and at the printer is now spent on…

  10. Scanning gamma camera

    International Nuclear Information System (INIS)

    Engdahl, L.W.; Batter, J.F. Jr.; Stout, K.J.

    1977-01-01

    A scanning system for a gamma camera providing for the overlapping of adjacent scan paths is described. A collimator mask having tapered edges provides for a graduated reduction in intensity of radiation received by a detector thereof, the reduction in intensity being graduated in a direction normal to the scanning path to provide a blending of images of adjacent scan paths. 31 claims, 15 figures

  11. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  12. Digital radiography

    International Nuclear Information System (INIS)

    Coulomb, M.; Dal Soglio, S.; Pittet-Barbier, L.; Ranchoup, Y.; Thony, F.; Ferretti, G.; Robert, F.

    1992-01-01

    Digital projection radiography may replace conventional radiography some day, provided it can meet several requirements: equal or better diagnostic effectiveness of the screen-film systems; reasonable image cost; real improvement in the productivity of the Departments of Imaging. All digital radiographic systems include an X-ray source, an image acquisition and formatting sub-system, a display and manipulation sub-system, and archiving subsystem and a laser editing system, preferably shared by other sources of digital images. Three digitization processes are available: digitization of the radiographic film, digital fluorography and phospholuminescent detectors with memory. The advantages of digital fluoroscopy are appealing: real-time image acquisition, suppression of cassettes; but its disadvantages are far from negligible: it cannot be applied to bedside radiography, the field of examination is limited, and the wide-field spatial resolution is poor. Phospholuminescent detectors with memory have great advantages: they can be used for bedside radiographs and on all the common radiographic systems; spatial resolution is satisfactory; its current disadvantages are considerable. These two systems, have common properties making up the entire philosophy of digital radiology and specific features that must guide our choice according to the application. Digital fluorography is best applied in pediatric radiology. However, evaluation works have showed that it was applicable with sufficient quality to many indications of general radiology in which a fluoroscopic control and fast acquisition of the images are essential; the time gained on the examination may be considerable, as well as the savings on film. Detectors with memory are required for bedside radiographs, in osteoarticular and thoracic radiology, in all cases of traumatic emergency and in the resuscitation and intensive care departments

  13. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  14. Becoming digital

    DEFF Research Database (Denmark)

    Pors, Anja Svejgaard

    2015-01-01

    . An ethnographic account of how digital reforms are implemented in practice shows how street-level bureaucrat’s classic tasks such as specialized casework are being reconfigured into educational tasks that promote the idea of “becoming digital”. In the paper, the author argues that the work of “becoming digital....... Originality/value: The study contributes to ethnographic research in public administration by combining two separate subfields, e-government and street-level bureaucracy, to discern recent transformations in public service delivery. In the digital era, tasks, control and equality are distributed in ways...

  15. Digital Humanities

    DEFF Research Database (Denmark)

    Brügger, Niels

    2016-01-01

    , and preserving material to study, as an object of study in its own right, as an analytical tool, or for collaborating, and for disseminating results. The term "digital humanities" was coined around 2001, and gained currency within academia in the following years. However, computers had been used within......Digital humanities is an umbrella term for theories, methodologies, and practices related to humanities scholarship that use the digital computer as an integrated and essential part of its research and teaching activities. The computer can be used for establishing, finding, collecting...

  16. Digital Snaps

    DEFF Research Database (Denmark)

    Sandbye, Mette; Larsen, Jonas

    . Distance as the New Punctum / Mikko Villi -- pt. II. FAMILY ALBUMS IN TRANSITION -- ch. 4. How Digital Technologies Do Family Snaps, Only Better / Gillian Rose -- ch. 5. Friendship Photography: Memory, Mobility and Social Networking / Joanne Garde-Hansen -- ch. 6. Play, Process and Materiality in Japanese...... -- ch. 9. Retouch Yourself: The Pleasures and Politics of Digital Cosmetic Surgery / Tanya Sheehan -- ch. 10. Virtual Selves: Art and Digital Autobiography / Louise Wolthers -- ch. 11. Mobile-Media Photography: New Modes of Engagement / Michael Shanks and Connie Svabo....

  17. Digital electronics

    CERN Document Server

    Morris, John

    2013-01-01

    An essential companion to John C Morris's 'Analogue Electronics', this clear and accessible text is designed for electronics students, teachers and enthusiasts who already have a basic understanding of electronics, and who wish to develop their knowledge of digital techniques and applications. Employing a discovery-based approach, the author covers fundamental theory before going on to develop an appreciation of logic networks, integrated circuit applications and analogue-digital conversion. A section on digital fault finding and useful ic data sheets completes th

  18. Digital Leadership

    DEFF Research Database (Denmark)

    Zupancic, Tadeja; Verbeke, Johan; Achten, Henri

    2016-01-01

    Leadership is an important quality in organisations. Leadership is needed to introduce change and innovation. In our opinion, in architectural and design practices, the role of leadership has not yet been sufficiently studied, especially when it comes to the role of digital tools and media....... With this paper we intend to initiate a discussion in the eCAADe community to reflect and develop ideas in order to develop digital leadership skills amongst the membership. This paper introduces some important aspects, which may be valuable to look into when developing digital leadership skills....

  19. Digital radiography

    International Nuclear Information System (INIS)

    Zani, M.L.

    2002-01-01

    X-ray radiography is a very common technique used to check the homogeneity of a material or the inside of a mechanical part. Generally the radiation that goes through the material to check, produced an image on a sensitized film. This method requires time because the film needs to be developed, digital radiography has no longer this inconvenient. In digital radiography the film is replaced by digital data and can be processed as any computer file. This new technique is promising but its main inconvenient is that today its resolution is not so good as that of film radiography. (A.C.)

  20. Digital radiography

    International Nuclear Information System (INIS)

    Kusano, Shoichi

    1993-01-01

    Firstly, from an historic point of view, fundamental concepts on digital imaging were reviewed to provide a foundation for discussion of digital radiography. Secondly, this review summarized the results of ongoing research in computed radiography that replaces the conventional film-screen system with a photo-stimulable phosphor plate; and thirdly, image quality, radiation protection, and image processing techniques were discussed with emphasis on picture archiving and communication system environment as our final goal. Finally, future expansion of digital radiography was described based on the present utilization of computed tomography at the National Defense Medical College Hospital. (author) 60 refs

  1. Digital Dentistry — Digital Impression and CAD/CAM System Applications

    Directory of Open Access Journals (Sweden)

    Gabor Alin-Gabriel

    2017-03-01

    Full Text Available Digital imprint and computer-aided design/computer-aided manufacture (CAD/CAM systems offer several benefits compared to traditional techniques. The use of a CAD/CAM system to scan preparations and generate restorations in-office, removes a second appointment for the patient. The existence of precision benefits in using complete systems and chairside scanning systems, has been proven. CAD/CAM restorations have a good longevity and meet the accepted clinical parameters. New digital impression methods are presently accessible, and before long, the long-awaited goal of sparing patients of one the most unpleasant practices in clinical dentistry, acquiring dental impressions, will be exchanged by intraoral digital scanning. CAD/CAM systems existing nowadays, can feed data through accurate digital scans created from plaster models, straight to manufacturing systems that can shape ceramic or resin restorations with no requirement of a physical copy of the prepared, adjacent, and antagonist teeth.

  2. Digital image analysis of NDT radiographs

    International Nuclear Information System (INIS)

    Graeme, W.A. Jr.; Eizember, A.C.; Douglass, J.

    1989-01-01

    Prior to the introduction of Charge Coupled Device (CCD) detectors the majority of image analysis performed on NDT radiographic images was done visually in the analog domain. While some film digitization was being performed, the process was often unable to capture all the usable information on the radiograph or was too time consuming. CCD technology now provides a method to digitize radiographic film images without losing the useful information captured in the original radiograph in a timely process. Incorporating that technology into a complete digital radiographic workstation allows analog radiographic information to be processed, providing additional information to the radiographer. Once in the digital domain, that data can be stored, and fused with radioscopic and other forms of digital data. The result is more productive analysis and management of radiographic inspection data. The principal function of the NDT Scan IV digital radiography system is the digitization, enhancement and storage of radiographic images

  3. Dexter: Data Extractor for scanned graphs

    Science.gov (United States)

    Demleitner, Markus

    2011-12-01

    The NASA Astrophysics Data System (ADS) now holds 1.3 million scanned pages, containing numerous plots and figures for which the original data sets are lost or inaccessible. The availability of scans of the figures can significantly ease the regeneration of the data sets. For this purpose, the ADS has developed Dexter, a Java applet that supports the user in this process. Dexter's basic functionality is to let the user manually digitize a plot by marking points and defining the coordinate transformation from the logical to the physical coordinate system. Advanced features include automatic identification of axes, tracing lines and finding points matching a template.

  4. Digital fabrication

    CERN Document Server

    2012-01-01

    The Winter 2012 (vol. 14 no. 3) issue of the Nexus Network Journal features seven original papers dedicated to the theme “Digital Fabrication”. Digital fabrication is changing architecture in fundamental ways in every phase, from concept to artifact. Projects growing out of research in digital fabrication are dependent on software that is entirely surface-oriented in its underlying mathematics. Decisions made during design, prototyping, fabrication and assembly rely on codes, scripts, parameters, operating systems and software, creating the need for teams with multidisciplinary expertise and different skills, from IT to architecture, design, material engineering, and mathematics, among others The papers grew out of a Lisbon symposium hosted by the ISCTE-Instituto Universitario de Lisboa entitled “Digital Fabrication – A State of the Art”. The issue is completed with four other research papers which address different mathematical instruments applied to architecture, including geometric tracing system...

  5. Digital Relationships

    DEFF Research Database (Denmark)

    Ledborg Hansen, Richard

    -­rich information and highly interesting communication are sky-­high and rising. With a continuous increase in digitized communication follows a decrease in face-­to-­face encounters and our ability to engage in inter-­personal relationships are suffering for it (Davis, 2013). The behavior described in this paper......-­‐Jones, 2011) for increases in effectiveness and efficiency we indiscriminately embrace digital communication and digitized information dissemination with enthusiasm – at the risk of ignoring the potentially dark side of technology. However, technology also holds a promise for better understanding precisely...... for the same reasons – that the growing amount of digitized communication “out there” represents data waiting to be sifted, analyzed and decoded. In this paper “Facebook behavior” refers to a particular behavior characterized by presenting your self and representations of selected self in the hope of getting...

  6. Digital Discretion

    DEFF Research Database (Denmark)

    Busch, Peter Andre; Zinner Henriksen, Helle

    2018-01-01

    discretion is suggested to reduce this footprint by influencing or replacing their discretionary practices using ICT. What is less researched is whether digital discretion can cause changes in public policy outcomes, and under what conditions such changes can occur. Using the concept of public service values......This study reviews 44 peer-reviewed articles on digital discretion published in the period from 1998 to January 2017. Street-level bureaucrats have traditionally had a wide ability to exercise discretion stirring debate since they can add their personal footprint on public policies. Digital......, we suggest that digital discretion can strengthen ethical and democratic values but weaken professional and relational values. Furthermore, we conclude that contextual factors such as considerations made by policy makers on the macro-level and the degree of professionalization of street...

  7. Programmable Digital Controller

    Science.gov (United States)

    Wassick, Gregory J.

    2012-01-01

    An existing three-channel analog servo loop controller has been redesigned for piezoelectric-transducer-based (PZT-based) etalon control applications to a digital servo loop controller. This change offers several improvements over the previous analog controller, including software control over proportional-integral-derivative (PID) parameters, inclusion of other data of interest such as temperature and pressure in the control laws, improved ability to compensate for PZT hysteresis and mechanical mount fluctuations, ability to provide pre-programmed scanning and stepping routines, improved user interface, expanded data acquisition, and reduced size, weight, and power.

  8. A fluorescence scanning electron microscope

    International Nuclear Information System (INIS)

    Kanemaru, Takaaki; Hirata, Kazuho; Takasu, Shin-ichi; Isobe, Shin-ichiro; Mizuki, Keiji; Mataka, Shuntaro; Nakamura, Kei-ichiro

    2009-01-01

    Fluorescence techniques are widely used in biological research to examine molecular localization, while electron microscopy can provide unique ultrastructural information. To date, correlative images from both fluorescence and electron microscopy have been obtained separately using two different instruments, i.e. a fluorescence microscope (FM) and an electron microscope (EM). In the current study, a scanning electron microscope (SEM) (JEOL JXA8600 M) was combined with a fluorescence digital camera microscope unit and this hybrid instrument was named a fluorescence SEM (FL-SEM). In the labeling of FL-SEM samples, both Fluolid, which is an organic EL dye, and Alexa Fluor, were employed. We successfully demonstrated that the FL-SEM is a simple and practical tool for correlative fluorescence and electron microscopy.

  9. Digital Collections, Digital Libraries & the Digitization of Cultural Heritage Information.

    Science.gov (United States)

    Lynch, Clifford

    2002-01-01

    Discusses digital collections and digital libraries. Topics include broadband availability; digital rights protection; content, both non-profit and commercial; digitization of cultural content; sustainability; metadata harvesting protocol; infrastructure; authorship; linking multiple resources; data mining; digitization of reference works;…

  10. Frequency characteristics of the laser film digitizer

    International Nuclear Information System (INIS)

    Ishimitsu, Y.; Taira, R.K.; Huang, H.K.

    1988-01-01

    The frequency characteristics of the laser film digitizer in the parallel and in the perpendicular scan direction are different. Because of this difference, moire pattern artifacts may appear in the digitized image. The authors found that this phenomenon is due to the frequency transfer characteristics of the various components in the laser film digitizer. From this observation, they derive a relationship between the spatial frequency content of the original image and the laser beam spot size based on the concept of image contrast. This relationship can be utilized to avoid the appearance of the moire pattern in the digitized image

  11. Tomographic scanning apparatus with ionization detector means

    International Nuclear Information System (INIS)

    1981-01-01

    This patent specification describes a tomographic scanning apparatus using a fan beam and digital output signal. Particular reference is made to the gas-pressurized ionization detector chamber, consisting of an array of side-by-side elongate ionization detection cells, the principal axis of each of the said cells being oriented along a radius extending towards the radiation source, and connection means for applying potentials across the cells for taking their output signals. (U.K.)

  12. digital natives and digital immigrants

    OpenAIRE

    Cardina, Bruno; Francisco, Jerónimo; Reis, Pedro; trad. Silva, Fátima

    2011-01-01

    This article focuses on the generational gaps in school learning. Initially, we have tried to provide the framework in relation to the term digital native in order to understand the key aspects of the generation born after the advent and the global use of the Internet. They were found to be “multitasking” people, linked to technology and connectivity, as opposed to digital immigrants, born in an earlier period and seeking to adapt to the technological world. We also present some r...

  13. Atomized scan strategy for high definition for VR application

    Science.gov (United States)

    Huang, Shuping; Ran, Feng; Ji, Yuan; Chen, Wendong

    2017-10-01

    Silicon-based OLED (Organic Light Emitting Display) microdisplay technology begins to attract people's attention in the emerging VR and AR devices. The high display frame refresh rate is an important solution to alleviate the dizziness in VR applications. Traditional display circuit drivers use the analog method or the digital PWM method that follow the serial scan order from the first pixel to the last pixel by using the shift registers. This paper proposes a novel atomized scan strategy based on the digital fractal scan strategy using the pseudo-random scan order. It can be used to realize the high frame refresh rate with the moderate pixel clock frequency in the high definition OLED microdisplay. The linearity of the gray level is also improved compared with the Z fractal scan strategy.

  14. Curve Digitizer – A software for multiple curves digitizing

    Directory of Open Access Journals (Sweden)

    Florentin ŞPERLEA

    2010-06-01

    Full Text Available The Curve Digitizer is software that extracts data from an image file representing a graphicand returns them as pairs of numbers which can then be used for further analysis and applications.Numbers can be read on a computer screen stored in files or copied on paper. The final result is adata set that can be used with other tools such as MSEXCEL. Curve Digitizer provides a useful toolfor any researcher or engineer interested in quantifying the data displayed graphically. The image filecan be obtained by scanning a document

  15. Lung PET scan

    Science.gov (United States)

    ... Chest PET scan; Lung positron emission tomography; PET - chest; PET - lung; PET - tumor imaging; ... Grainger & Allison's Diagnostic Radiology: A Textbook of Medical Imaging . 6th ed. Philadelphia, ...

  16. Scanning of bone metastases

    International Nuclear Information System (INIS)

    Robillard, J.

    1977-01-01

    The Centers against cancer of Caen, Angers, Montpellier, Strasbourg and 'the Curie Foundation' have confronted their experience in detection of bone metastases by total body scanning. From the investigation by this procedure, of 1,467 patients with cancer, it results: the confrontation between radio and scanning shows a rate of false positive and false negative identical to the literature ones; the countage scanning allows to reduce the number of false positive; scanning allows to direct bone biopsy and to improve efficiency of histological examination [fr

  17. Digital evidence

    Directory of Open Access Journals (Sweden)

    Lukić Tatjana

    2012-01-01

    Full Text Available Although computer makes human activities faster and easier, innovating and creating new forms of work and other kinds of activities, it also influenced the criminal activity. The development of information technology directly affects the development of computer forensics without which, it can not even imagine the discovering and proving the computer offences and apprehending the perpetrator. Information technology and computer forensic allows us to detect and prove the crimes committed by computer and capture the perpetrators. Computer forensics is a type of forensics which can be defined as a process of collecting, preserving, analyzing and presenting digital evidence in court proceedings. Bearing in mind, that combat against crime, in which computers appear as an asset or object of the offense, requires knowledge of digital evidence as well as specific rules and procedures, the author in this article specifically addresses the issues of digital evidence, forensic (computer investigation, specific rules and procedures for detecting, fixing and collecting digital evidence and use of this type of evidence in criminal proceedings. The author also delas with international standards regarding digital evidence and cyber-space investigation.

  18. Digital watermark

    Directory of Open Access Journals (Sweden)

    Jasna Maver

    2000-01-01

    Full Text Available The huge amount of multimedia contents available on the World-Wide-Web is beginning to raise the question of their protection. Digital watermarking is a technique which can serve various purposes, including intellectual property protection, authentication and integrity verification, as well as visible or invisible content labelling of multimedia content. Due to the diversity of digital watermarking applicability, there are many different techniques, which can be categorised according to different criteria. A digital watermark can be categorised as visible or invisible and as robust or fragile. In contrast to the visible watermark where a visible pattern or image is embedded into the original image, the invisible watermark does not change the visual appearance of the image. The existence of such a watermark can be determined only through a watermark ex¬traction or detection algorithm. The robust watermark is used for copyright protection, while the fragile watermark is designed for authentication and integrity verification of multimedia content. A watermark must be detectable or extractable to be useful. In some watermarking schemes, a watermark can be extracted in its exact form, in other cases, we can detect only whether a specific given watermarking signal is present in an image. Digital libraries, through which cultural institutions will make multimedia contents available, should support a wide range of service models for intellectual property protection, where digital watermarking may play an important role.

  19. Digital Creativity

    DEFF Research Database (Denmark)

    Petersson Brooks, Eva; Brooks, Anthony Lewis

    2014-01-01

    This paper reports on a study exploring the outcomes from children’s play with technology in early childhood learning practices. The paper addresses questions related to how digital technology can foster creativity in early childhood learning environments. It consists of an analysis of children......’s interaction with the KidSmart furniture focusing on digital creativity potentials and play values suggested by the technology. The study applied a qualitative approach and included125 children (aged three to five), 10 pedagogues, and two librarians. The results suggests that educators should sensitively...... consider intervening when children are interacting with technology, and rather put emphasize into the integration of the technology into the environment and to the curriculum in order to shape playful structures for children’s digital creativity....

  20. Digital radiography

    International Nuclear Information System (INIS)

    Rath, M.; Lissner, J.; Rienmueller, R.; Haendle, J.; Siemens A.G., Erlangen

    1984-01-01

    Using a prototype of an electronic, universal examination unit equipped with a special X-ray TV installation, spotfilm exposures and digital angiographies with high spatial resolution and wide-range contrast could be made in the clinic for the first time. With transvenous contrast medium injection, the clinical results of digital angiography show excellent image quality in the region of the carotids and renal arteries as well as the arteries of the extremities. The electronic series exposures have an image quality almost comparable to the quality obtained with cutfilm changers in conventional angiography. There are certain limitations due to the input field of 25 cm X-ray image intensified used. In respect of the digital angiography imaging technique, the electronic universal unit is fully suitable for clinical application. (orig.) [de

  1. Enterprise Implementation of Digital Pathology: Feasibility, Challenges, and Opportunities.

    Science.gov (United States)

    Hartman, D J; Pantanowitz, L; McHugh, J S; Piccoli, A L; OLeary, M J; Lauro, G R

    2017-10-01

    Digital pathology is becoming technically possible to implement for routine pathology work. At our institution, we have been using digital pathology for second opinion intraoperative consultations for over 10 years. Herein, we describe our experience in converting to a digital pathology platform for primary pathology diagnosis. We implemented an incremental rollout for digital pathology on subspecialty benches, beginning with cases that contained small amounts of tissue (biopsy specimens). We successfully scanned over 40,000 slides through our digital pathology system. Several lessons (both challenges and opportunities) were learned through this implementation. A successful conversion to digital pathology requires pre-imaging adjustments, integrated software and post-imaging evaluations.

  2. Introduction of the digitization software GDgraph

    International Nuclear Information System (INIS)

    Chen Guochang; Jin Yongli; Wang Jimin

    2015-01-01

    The evaluators and experimenters always desire to have full and latest experimental data sets. However, the data are often published as figures without any numerical values for some publications or journals. Furthermore, the quality of figures is not always good enough, especially for some figures scanned from the hard copy of old publications. On the other hand, the researchers would like to retrieve the data directly from EXFOR database. Digitization of figures is only one method to obtain the numerical data and correlative uncertainty, when there are only figures available from publications. Therefore we need a digitization tool to fit the requirements from evaluation, measurement and EXFOR compilation in CNDC. Before 2000, there have no common software to digitize experimental and evaluated data. And the quality of digitization results can not fit the requirements of evaluation and measurement using the traditional coordinate paper or rule. The end of twenty century, the PC was developed so quickly that to develop a software for digitization purpose become possible. Since 1997, CNDC devotes to design and develop a software for digitization. Four years later, the first version of digitization software GDGraph was developed using VC++ and released in CNDC. Although, the functions of the 1 st version of GDGraph is fit the basic requirements of digitization only, in which can digitize one group data excluding data error, BMP image format only, and it can not randomly delete digitizing data points. However, it obtains higher quality digitizing results and efficiency than the traditional method

  3. High resolution RGB color line scan camera

    Science.gov (United States)

    Lynch, Theodore E.; Huettig, Fred

    1998-04-01

    A color line scan camera family which is available with either 6000, 8000 or 10000 pixels/color channel, utilizes off-the-shelf lenses, interfaces with currently available frame grabbers, includes on-board pixel by pixel offset correction, and is configurable and controllable via RS232 serial port for computer controlled or stand alone operation is described in this paper. This line scan camera is based on an available 8000 element monochrome line scan camera designed by AOA for OEM use. The new color version includes improvements such as better packaging and additional user features which make the camera easier to use. The heart of the camera is a tri-linear CCD sensor with on-chip color balancing for maximum accuracy and pinned photodiodes for low lag response. Each color channel is digitized to 12 bits and all three channels are multiplexed together so that the resulting camera output video is either a 12 or 8 bit data stream at a rate of up to 24Megpixels/sec. Conversion from 12 to 8 bit, or user-defined gamma, is accomplished by on board user-defined video look up tables. The camera has two user-selectable operating modes; lows speed, high sensitivity mode or high speed, reduced sensitivity mode. The intended uses of the camera include industrial inspection, digital archiving, document scanning, and graphic arts applications.

  4. Digital photogrammetry

    CERN Document Server

    Egels, Yves

    2003-01-01

    Photogrammetry is the use of photography for surveying primarily and is used for the production of maps from aerial photographs. Along with remote sensing, it represents the primary means of generating data for Geographic Information Systems (GIS). As technology develops, it is becoming easier to gain access to it. The cost of digital photogrammetric workstations are falling quickly and these new tools are therefore becoming accessible to more and more users. Digital Photogrammetry is particularly useful as a text for graduate students in geomantic and is also suitable for people with a good basic scientific knowledge who need to understand photogrammetry, and who wish to use the book as a reference.

  5. Digital Marketing

    OpenAIRE

    Jerry Wind; Vijay Mahajan

    2002-01-01

    The digital revolution has shaken marketing to its core with consumers being offered greater price transparency and often even the chance to dictate the price. What does pricing mean in a world in which customers propose their own prices (as at priceline.com) or buyers and sellers haggle independently in auctions (as at e-Bay)? The most significant changes in the digital marketing show the emergence of 'cyber consumers', the cyber business-to-business world and the changing reality of an incr...

  6. Digital "X"

    DEFF Research Database (Denmark)

    Baiyere, Abayomi; Grover, Varun; Gupta, Alok

    2017-01-01

    Interest in using digital before existing research concepts seem to be on the rise in the IS field. This panel is positioned to explore what value lies in labelling our research as digital “x” as opposed to the well established IT “x” (where “x” can be strategy, infrastructure, innovation, artifa...... between this stream of research and existing research. Central among the expected output of the panel is the advancement of suggestions for future research and the critical pitfalls to avoid in doing so....

  7. Digital Radiography

    Science.gov (United States)

    1986-01-01

    System One, a digital radiography system, incorporates a reusable image medium (RIM) which retains an image. No film is needed; the RIM is read with a laser scanner, and the information is used to produce a digital image on an image processor. The image is stored on an optical disc. System allows the radiologist to "dial away" unwanted images to compare views on three screens. It is compatible with existing equipment and cost efficient. It was commercialized by a Stanford researcher from energy selective technology developed under a NASA grant.

  8. Digital filters

    CERN Document Server

    Hamming, Richard W

    1997-01-01

    Digital signals occur in an increasing number of applications: in telephone communications; in radio, television, and stereo sound systems; and in spacecraft transmissions, to name just a few. This introductory text examines digital filtering, the processes of smoothing, predicting, differentiating, integrating, and separating signals, as well as the removal of noise from a signal. The processes bear particular relevance to computer applications, one of the focuses of this book.Readers will find Hamming's analysis accessible and engaging, in recognition of the fact that many people with the s

  9. Digital voltmeter

    International Nuclear Information System (INIS)

    Yohannes Kamadi; Soekarno.

    1976-01-01

    The electrical voltage measuring equipment with digital display has been made. This equipment uses four digits display with single polarity measurement and integrating system. Pulses from the oscillator will be counted and converted to the staircase voltages, and compared to the voltage measured. When the balance is already achieved, the pulse will appear at the comparator circuit. This pulse will be used to trigger univibrator circuit. The univibrator output is used as signal for stopping the counting, and when reading time T already stops, the counting system will be reset. (authors)

  10. Digital communication

    CERN Document Server

    Das, Apurba

    2010-01-01

    ""Digital Communications"" presents the theory and application of the philosophy of Digital Communication systems in a unique but lucid form. This book inserts equal importance to the theory and application aspect of the subject whereby the authors selected a wide class of problems. The Salient features of the book are: the foundation of Fourier series, Transform and wavelets are introduces in a unique way but in lucid language; the application area is rich and resemblance to the present trend of research, as we are attached with those areas professionally; a CD is included which contains code

  11. Digital literacies

    CERN Document Server

    Hockly, Nicky; Pegrum, Mark

    2014-01-01

    Dramatic shifts in our communication landscape have made it crucial for language teaching to go beyond print literacy and encompass the digital literacies which are increasingly central to learners' personal, social, educational and professional lives. By situating these digital literacies within a clear theoretical framework, this book provides educators and students alike with not just the background for a deeper understanding of these key 21st-century skills, but also the rationale for integrating these skills into classroom practice. This is the first methodology book to address not jus

  12. Model PET Scan Activity

    Science.gov (United States)

    Strunk, Amber; Gazdovich, Jennifer; Redouté, Oriane; Reverte, Juan Manuel; Shelley, Samantha; Todorova, Vesela

    2018-05-01

    This paper provides a brief introduction to antimatter and how it, along with other modern physics topics, is utilized in positron emission tomography (PET) scans. It further describes a hands-on activity for students to help them gain an understanding of how PET scans assist in detecting cancer. Modern physics topics provide an exciting way to introduce students to current applications of physics.

  13. Scanning laser Doppler vibrometry

    DEFF Research Database (Denmark)

    Brøns, Marie; Thomsen, Jon Juel

    With a Scanning Laser Doppler Vibrometer (SLDV) a vibrating surface is automatically scanned over predefined grid points, and data processed for displaying vibration properties like mode shapes, natural frequencies, damping ratios, and operational deflection shapes. Our SLDV – a PSV-500H from...

  14. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available Toggle navigation Test/Treatment Patient Type Screening/Wellness Disease/Condition Safety En Español More Info Images/Videos About Us News Physician Resources Professions Site Index A-Z Thyroid Scan and Uptake Thyroid scan and uptake uses ...

  15. The new scanning nuclear microprobe in Uppsala

    International Nuclear Information System (INIS)

    Sunde, T.; Nystroem, J.; Lindh, U.

    1991-01-01

    During 1989/90 a scanning microprobe, developed for 2-4 MeV protons and submicron resolution, is being installed at the EN-tandem accelerator at the The Svedberg Laboratory, Uppsala University, Sweden. The probe-forming units (object diaphragm, aperture diaphragm and triplet of spark-eroded quadrupoles), the scanning unit of current-controlled ferrite cores and a current digitizer are of Oxford design. The other parts are commercial products or are constructed by ourselves. The latter includes the equipment for optical alignment by interference, a feedback-controlled magnetic beam steerer and stabiliser, a fast beam deflector, specially designed mechanical vibration reducers and dedicated AT expansion cards for scanning control and data acquisition. (orig.)

  16. Transverse section scanning mechanism

    International Nuclear Information System (INIS)

    Doherty, E.J.

    1978-01-01

    Apparatus is described for scanning a transverse, radionuclide scan-field using an array of focussed collimators. The collimators are movable tangentially on rails, driven by a single motor via a coupled screw. The collimators are also movable in a radial direction on rails driven by a step motor via coupled screws and bevel gears. Adjacent bevel gears rotate in opposite directions so adjacent collimators move in radially opposite directions. In use, the focal point of each collimator scans at least half of the scan-field, e.g. a human head located in the central aperture, and the electrical outputs of detectors associated with each collimator are used to determine the distribution of radioactive emission intensity at a number of points in the scan-field. (author)

  17. LIDAR COMBINED SCANNING UNIT

    Directory of Open Access Journals (Sweden)

    V. V. Elizarov

    2016-11-01

    Full Text Available Subject of Research. The results of lidar combined scanning unit development for locating leaks of hydrocarbons are presented The unit enables to perform high-speed scanning of the investigated space in wide and narrow angle fields. Method. Scanning in a wide angular field is produced by one-line scanning path by means of the movable aluminum mirror with a frequency of 20Hz and amplitude of 20 degrees of swing. Narrowband scanning is performed along a spiral path by the deflector. The deflection of the beam is done by rotation of the optical wedges forming part of the deflector at an angle of ±50. The control function of the scanning node is performed by a specialized software product written in C# programming language. Main Results. This scanning unit allows scanning the investigated area at a distance of 50-100 m with spatial resolution at the level of 3 cm. The positioning accuracy of the laser beam in space is 15'. The developed scanning unit gives the possibility to browse the entire investigated area for the time not more than 1 ms at a rotation frequency of each wedge from 50 to 200 Hz. The problem of unambiguous definition of the beam geographical coordinates in space is solved at the software level according to the rotation angles of the mirrors and optical wedges. Lidar system coordinates are determined by means of GPS. Practical Relevance. Development results open the possibility for increasing the spatial resolution of scanning systems of a wide range of lidars and can provide high positioning accuracy of the laser beam in space.

  18. [Constructing 3-dimensional colorized digital dental model assisted by digital photography].

    Science.gov (United States)

    Ye, Hong-qiang; Liu, Yu-shu; Liu, Yun-song; Ning, Jing; Zhao, Yi-jiao; Zhou, Yong-sheng

    2016-02-18

    To explore a method of constructing universal 3-dimensional (3D) colorized digital dental model which can be displayed and edited in common 3D software (such as Geomagic series), in order to improve the visual effect of digital dental model in 3D software. The morphological data of teeth and gingivae were obtained by intra-oral scanning system (3Shape TRIOS), constructing 3D digital dental models. The 3D digital dental models were exported as STL files. Meanwhile, referring to the accredited photography guide of American Academy of Cosmetic Dentistry (AACD), five selected digital photographs of patients'teeth and gingivae were taken by digital single lens reflex camera (DSLR) with the same exposure parameters (except occlusal views) to capture the color data. In Geomagic Studio 2013, after STL file of 3D digital dental model being imported, digital photographs were projected on 3D digital dental model with corresponding position and angle. The junctions of different photos were carefully trimmed to get continuous and natural color transitions. Then the 3D colorized digital dental model was constructed, which was exported as OBJ file or WRP file which was a special file for software of Geomagic series. For the purpose of evaluating the visual effect of the 3D colorized digital model, a rating scale on color simulation effect in views of patients'evaluation was used. Sixteen patients were recruited and their scores on colored and non-colored digital dental models were recorded. The data were analyzed using McNemar-Bowker test in SPSS 20. Universal 3D colorized digital dental model with better color simulation was constructed based on intra-oral scanning and digital photography. For clinical application, the 3D colorized digital dental models, combined with 3D face images, were introduced into 3D smile design of aesthetic rehabilitation, which could improve the patients' cognition for the esthetic digital design and virtual prosthetic effect. Universal 3D colorized

  19. Digital delicacies

    OpenAIRE

    Holley, Rose

    2001-01-01

    This presentation outlines the purpose and work of the newly appointed Digital Projects Librarian at the University of Auckland. It gives a brief overview of what digitisation is, the benefits, the stages of a digitisation project and also samples of interesting international digitisation projects and new University of Auckland Library Digitisation projects.

  20. Digital Forensics

    Science.gov (United States)

    Harron, Jason; Langdon, John; Gonzalez, Jennifer; Cater, Scott

    2017-01-01

    The term forensic science may evoke thoughts of blood-spatter analysis, DNA testing, and identifying molds, spores, and larvae. A growing part of this field, however, is that of digital forensics, involving techniques with clear connections to math and physics. This article describes a five-part project involving smartphones and the investigation…

  1. Digital Disruption

    DEFF Research Database (Denmark)

    Rosenstand, Claus Andreas Foss

    det digitale domæne ud over det niveau, der kendetegner den nuværende debat, så præsenteres der ny viden om digital disruption. Som noget nyt udlægges Clayton Christens teori om disruptiv innovation med et særligt fokus på små organisationers mulighed for eksponentiel vækst. Specielt udfoldes...... forholdet mellem disruption og den stadig accelererende digitale udvikling i konturerne til ny teoridannelse om digital disruption. Bogens undertitel ”faretruende og fascinerende forandringer” peger på, at der er behov for en nuanceret debat om digital disruption i modsætning til den tone, der er slået an i...... videre kalder et ”disruption-råd”. Faktisk er rådet skrevet ind i 2016 regeringsgrundlaget for VLK-regeringen. Disruption af organisationer er ikke et nyt fænomen; men hastigheden, hvormed det sker, er stadig accelererende. Årsagen er den globale mega-trend: Digitalisering. Og derfor er specielt digital...

  2. Digital books.

    Science.gov (United States)

    Wink, Diane M

    2011-01-01

    In this bimonthly series, the author examines how nurse educators can use the Internet and Web-based computer technologies such as search, communication, and collaborative writing tools; social networking and social bookmarking sites; virtual worlds; and Web-based teaching and learning programs. This article describes digital books.

  3. Digital forvaltning

    DEFF Research Database (Denmark)

    Remmen, Arne; Larsen, Torben; Mosgaard, Mette

    2004-01-01

    Større effektivitet, bedre service og mere demokrai er blot nogle af forventningerne til indførelse af digital forveltning i kommunerne. Kapitlet giver bland andet svar på spørgsmålene : Hvordan lever kommunerne op hertil i dagligdagen? hvilke virkemidler anvender de? Hvilke barrierer har der været...

  4. Digital Methods

    NARCIS (Netherlands)

    Rogers, R.

    2013-01-01

    In Digital Methods, Richard Rogers proposes a methodological outlook for social and cultural scholarly research on the Web that seeks to move Internet research beyond the study of online culture. It is not a toolkit for Internet research, or operating instructions for a software package; it deals

  5. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  6. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  7. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  8. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  9. Digital Beamforming Scatterometer

    Science.gov (United States)

    Rincon, Rafael F.; Vega, Manuel; Kman, Luko; Buenfil, Manuel; Geist, Alessandro; Hillard, Larry; Racette, Paul

    2009-01-01

    feeds for vertical and horizontal polarization. System upgrades to dual polarization are currently under way. The DBSAR processor is a reconfigurable data acquisition and processor system capable of real-time, high-speed data processing. DBSAR uses an FPGA-based architecture to implement digitally down-conversion, in-phase and quadrature (I/Q) demodulation, and subsequent radar specific algorithms. The core of the processor board consists of an analog-to-digital (AID) section, three Altera Stratix field programmable gate arrays (FPGAs), an ARM microcontroller, several memory devices, and an Ethernet interface. The processor also interfaces with a navigation board consisting of a GPS and a MEMS gyro. The processor has been configured to operate in scatterometer, Synthetic Aperture Radar (SAR), and altimeter modes. All the modes are based on digital beamforming which is a digital process that generates the far-field beam patterns at various scan angles from voltages sampled in the antenna array. This technique allows steering the received beam and controlling its beam-width and side-lobe. Several beamforming techniques can be implemented each characterized by unique strengths and weaknesses, and each applicable to different measurement scenarios. In Scatterometer mode, the radar is capable to.generate a wide beam or scan a narrow beam on transmit, and to steer the received beam on processing while controlling its beamwidth and side-lobe level. Table I lists some important radar characteristics

  10. Laser Scanning in Forests

    Directory of Open Access Journals (Sweden)

    Håkan Olsson

    2012-09-01

    Full Text Available The introduction of Airborne Laser Scanning (ALS to forests has been revolutionary during the last decade. This development was facilitated by combining earlier ranging lidar discoveries [1–5], with experience obtained from full-waveform ranging radar [6,7] to new airborne laser scanning systems which had components such as a GNSS receiver (Global Navigation Satellite System, IMU (Inertial Measurement Unit and a scanning mechanism. Since the first commercial ALS in 1994, new ALS-based forest inventory approaches have been reported feasible for operational activities [8–12]. ALS is currently operationally applied for stand level forest inventories, for example, in Nordic countries. In Finland alone, the adoption of ALS for forest data collection has led to an annual savings of around 20 M€/year, and the work is mainly done by companies instead of governmental organizations. In spite of the long implementation times and there being a limited tradition of making changes in the forest sector, laser scanning was commercially and operationally applied after about only one decade of research. When analyzing high-ranked journal papers from ISI Web of Science, the topic of laser scanning of forests has been the driving force for the whole laser scanning research society over the last decade. Thus, the topic “laser scanning in forests” has provided a significant industrial, societal and scientific impact. [...

  11. Bone scan in pediatrics

    International Nuclear Information System (INIS)

    Gordon, I.; Peters, A.M.

    1987-01-01

    In 1984, a survey carried out in 21 countries in Europe showed that bone scintigraphy comprised 16% of all paediatric radioisotope scans. Although the value of bone scans in paediatrics is potentially great, their quality varies greatly, and poor-quality images are giving this valuable technique a bad reputation. The handling of children requires a sensitive staff and the provision of a few simple inexpensive items of distraction. Attempting simply to scan a child between two adult patients in a busy general department is a recipe for an unhappy, uncooperative child with the probable result of poor images. The intravenous injection of isotope should be given adjacent to the gamma camera room, unless dynamic scans are required, so that the child does not associate the camera with the injection. This injection is best carried out by someone competent in paediatric venipunture; the entire procedure should be explained to the child and parent, who should remain with child throughout. It is naive to think that silence makes for a cooperative child. The sensitivity of bone-seeking radioisotope tracers and the marked improvement in gamma camera resolution has allowed the bone scanning to become an integrated technique in the assessment of children suspected of suffering from pathological bone conditions. The tracer most commonly used for routine bone scanning is 99m Tc diphosphonate (MDP); other isotopes used include 99m Tc colloid for bone marrow scans and 67 Ga citrate and 111 In white blood cells ( 111 In WBC) for investigation of inflammatory/infective lesions

  12. MutScan: fast detection and visualization of target mutations by scanning FASTQ data.

    Science.gov (United States)

    Chen, Shifu; Huang, Tanxiao; Wen, Tiexiang; Li, Hong; Xu, Mingyan; Gu, Jia

    2018-01-22

    Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering, which may cause miss-detection of key mutations with low frequencies. Variant validation is also indicated for key mutations detected by bioinformatics pipelines. Typically, this process can be executed using alignment visualization tools such as IGV or GenomeBrowse. However, these tools are too heavy and therefore unsuitable for validating mutations in ultra-deep sequencing data. We developed MutScan to address problems of sensitive detection and efficient validation for target mutations. MutScan involves highly optimized string-searching algorithms, which can scan input FASTQ files to grab all reads that support target mutations. The collected supporting reads for each target mutation will be piled up and visualized using web technologies such as HTML and JavaScript. Algorithms such as rolling hash and bloom filter are applied to accelerate scanning and make MutScan applicable to detect or visualize target mutations in a very fast way. MutScan is a tool for the detection and visualization of target mutations by only scanning FASTQ raw data directly. Compared to conventional pipelines, this offers a very high performance, executing about 20 times faster, and offering maximal sensitivity since it can grab mutations with even one single supporting read. MutScan visualizes detected mutations by generating interactive pile-ups using web technologies. These can serve to validate target mutations, thus avoiding false positives. Furthermore, MutScan can visualize all mutation records in a VCF file to HTML pages for cloud-friendly VCF validation. MutScan is an open source tool available at GitHub: https://github.com/OpenGene/MutScan.

  13. Full cycle rapid scan EPR deconvolution algorithm.

    Science.gov (United States)

    Tseytlin, Mark

    2017-08-01

    Rapid scan electron paramagnetic resonance (RS EPR) is a continuous-wave (CW) method that combines narrowband excitation and broadband detection. Sinusoidal magnetic field scans that span the entire EPR spectrum cause electron spin excitations twice during the scan period. Periodic transient RS signals are digitized and time-averaged. Deconvolution of absorption spectrum from the measured full-cycle signal is an ill-posed problem that does not have a stable solution because the magnetic field passes the same EPR line twice per sinusoidal scan during up- and down-field passages. As a result, RS signals consist of two contributions that need to be separated and postprocessed individually. Deconvolution of either of the contributions is a well-posed problem that has a stable solution. The current version of the RS EPR algorithm solves the separation problem by cutting the full-scan signal into two half-period pieces. This imposes a constraint on the experiment; the EPR signal must completely decay by the end of each half-scan in order to not be truncated. The constraint limits the maximum scan frequency and, therefore, the RS signal-to-noise gain. Faster scans permit the use of higher excitation powers without saturating the spin system, translating into a higher EPR sensitivity. A stable, full-scan algorithm is described in this paper that does not require truncation of the periodic response. This algorithm utilizes the additive property of linear systems: the response to a sum of two inputs is equal the sum of responses to each of the inputs separately. Based on this property, the mathematical model for CW RS EPR can be replaced by that of a sum of two independent full-cycle pulsed field-modulated experiments. In each of these experiments, the excitation power equals to zero during either up- or down-field scan. The full-cycle algorithm permits approaching the upper theoretical scan frequency limit; the transient spin system response must decay within the scan

  14. Genomic Signatures of Reinforcement

    Directory of Open Access Journals (Sweden)

    Austin G. Garner

    2018-04-01

    Full Text Available Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.

  15. Genomic Signatures of Reinforcement

    Science.gov (United States)

    Goulet, Benjamin E.

    2018-01-01

    Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved. PMID:29614048

  16. A simple method of digitizing analog scintigrams for quantification and digital archiving

    International Nuclear Information System (INIS)

    Schramm, M.; Kaempfer, B.; Wolf, H.; Clausen, M.; Wendhausen, H.; Henze, E.

    1993-01-01

    This study was undertaken to evaluate a quick, reliable and cheap method of digitizing analog scintigrams. 40 whole-body bone scintigrams were obtained simultaneously in analog and genuine digital format. The analog scans on X-ray film were then digitized seecondarily by three different methods: 300 dpi flatbed scanning, high-resolution camera scanning and camcorder recording. A simple exposure approach using a light box, a cheap camcorder, a PC and image grabber hard- and software proved to be optimal. Visual interpretation showed no differences in clinical findings when comparing the analog images with their secondarily digitized counterparts. To test the possibility of quantification, 126 equivalent ROIs were drawn both in the genuine digital and the secondarily digitized images. Comparing the ROI count to whole-body count percentage of the corresponding ROIs showed the correlation to be linear. The evaluation of phantom studies showed the linear correlation to be true within a wide activity range. Thus, secondary digitalization of analog scintigrams is an easy, cheap and reliable method of archiving images and allows secondary digital quantification. (orig.) [de

  17. [A simple method of digitizing analog scintigrams for quantification and digital archiving].

    Science.gov (United States)

    Schramm, M; Kämpfer, B; Wolf, H; Clausen, M; Wendhausen, H; Henze, E

    1993-02-01

    This study was undertaken to evaluate a quick, reliable and cheap method of digitizing analog scintigrams. 40 whole-body bone scintigrams were obtained simultaneously in analog and genuine digital format. The analog scans on x-ray film were then digitized secondarily by three different methods: 300 dpi flat-bed scanning, high-resolution camera scanning and camcorder recording. A simple exposure approach using a light box, a cheap camcorder, a PC and image grabber hard- and software proved to be optimal. Visual interpretation showed no differences in clinical findings when comparing the analog images with their secondarily digitized counterparts. To test the possibility of quantification, 126 equivalent ROIs were drawn both in the genuine digital and the secondarily digitized images. Comparing the ROI count to whole-body count percentage of the corresponding ROIs showed the correlation to be linear. The evaluation of phantom studies showed the linear correlation to be true within a wide activity range. Thus, secondary digitalization of analog scintigrams is an easy, cheap and reliable method of archiving images and allows secondary digital quantification.

  18. Poaching Museum Collections using Digital 3D Technologies

    Directory of Open Access Journals (Sweden)

    Sarah Younan

    2015-12-01

    Full Text Available This paper investigates the creative engagement with digital 3D models of museum artefacts and gives insight into new uses of museum collections enabled by digital scanning, editing and 3D printing technologies. Digital 3D models of museum artefacts are malleable and increasingly easy to use. Additionally, freely available 3D software has made 3D scanning, editing and manufacturing possible for non-specialists. These technologies allow users to create new artworks through the creation and transformation of digital replicas of museum artefacts. Examples of creative works, taken from two case studies that involve the creative use of digital reproductions of museum artefacts are presented in this paper. These projects are illustrative of a larger trend: the digital ‘poaching’ of heritage artefacts. This paper examines how digital 3D technologies can foster creative forms of museum engagement, democratise access to museum collections and engage users with personal forms of museum experience.

  19. The along track scanning radiometer for ERS-1 - Scan geometry and data simulation

    Science.gov (United States)

    Prata, A. J. Fred; Cechet, Robert P.; Barton, Ian J.; Llewellyn-Jones, David T.

    1990-01-01

    The first European remote-sensing satellite (ERS-1), due to be launched in 1990, will carry the along track scanning radiometer (ATSR), which has been specifically designed to give accurate satellite measurements of sea surface temperature (SST). Details of the novel scanning technique used by the ATSR are given, and data from the NOAA-9 AVHRR instrument are used to simulate raw ATSR imagery. Because of the high precision of the onboard blackbodies, the active cooling of the detectors, 12-b digitization, and dual-angle capability, the ATSR promises to achieve higher-accuracy satellite-derived SSTs than are currently available.

  20. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... for a thyroid scan is 30 minutes or less. Thyroid Uptake You will be given radioactive iodine ( ... for each thyroid uptake is five minutes or less. top of page What will I experience during ...

  1. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... evaluate changes in the gland following medication use, surgery, radiotherapy or chemotherapy top of page How should ... such as an x-ray or CT scan, surgeries or treatments using iodinated contrast material within the ...

  2. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... abnormal was found, and should not be a cause of concern for you. If you had an ... abnormal was found, and should not be a cause of concern for you. Actual scanning time for ...

  3. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    1981-01-01

    Details are given of a tomographic scanning apparatus, with particular reference to a multiplexer slip ring means for receiving output from the detectors and enabling interfeed to the image reconstruction station. (U.K.)

  4. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    1981-01-01

    Details are presented of a tomographic scanning apparatus, its rotational assembly, and the control and circuit elements, with particular reference to the amplifier and multiplexing circuits enabling detector signal calibration. (U.K.)

  5. Pediatric CT Scans

    Science.gov (United States)

    The Radiation Epidemiology Branch and collaborators have initiated a retrospective cohort study to evaluate the relationship between radiation exposure from CT scans conducted during childhood and adolescence and the subsequent development of cancer.

  6. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... which are encased in metal and plastic and most often shaped like a box, attached to a ... will I experience during and after the procedure? Most thyroid scan and thyroid uptake procedures are painless. ...

  7. Heart CT scan

    Science.gov (United States)

    ... make to decrease the risk of heart disease. Risks Risks of CT scans include: Being exposed to ... urac.org). URAC's accreditation program is an independent audit to verify that A.D.A.M. follows ...

  8. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... eat for several hours before your exam because eating can affect the accuracy of the uptake measurement. ... often unattainable using other imaging procedures. For many diseases, nuclear medicine scans yield the most useful information ...

  9. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... A thyroid scan is a type of nuclear medicine imaging. The radioactive iodine uptake test (RAIU) is ... thyroid function, but does not involve imaging. Nuclear medicine is a branch of medical imaging that uses ...

  10. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... that help physicians diagnose and evaluate medical conditions. These imaging scans use radioactive materials called radiopharmaceuticals or ... or had thyroid cancer. A physician may perform these imaging tests to: determine if the gland is ...

  11. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Because nuclear medicine procedures are able to pinpoint molecular activity within the body, they offer the potential ... or imaging device that produces pictures and provides molecular information. The thyroid scan and thyroid uptake provide ...

  12. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Actual scanning time for each thyroid uptake is five minutes or less. top of page What will ... diagnostic procedures have been used for more than five decades, and there are no known long-term ...

  13. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... top of page Additional Information and Resources RTAnswers.org Radiation Therapy for Head and Neck Cancer top ... Scan and Uptake Sponsored by Please note RadiologyInfo.org is not a medical facility. Please contact your ...

  14. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... often unattainable using other imaging procedures. For many diseases, nuclear medicine scans yield the most useful information needed to make a diagnosis or to determine appropriate treatment, if any. Nuclear medicine is less expensive and ...

  15. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... the gamma camera and single-photon emission-computed tomography (SPECT). The gamma camera, also called a scintillation ... high as with other imaging techniques, such as CT or MRI. However, nuclear medicine scans are more ...

  16. Scanning Auger Electron Microscope

    Data.gov (United States)

    Federal Laboratory Consortium — A JEOL model 7830F field emission source, scanning Auger microscope.Specifications / Capabilities:Ultra-high vacuum (UHV), electron gun range from 0.1 kV to 25 kV,...

  17. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... as an overactive thyroid gland, a condition called hyperthyroidism , cancer or other growths assess the nature of ... an x-ray or CT scan, surgeries or treatments using iodinated contrast material within the last two ...

  18. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... painless. However, during the thyroid scan, you may feel uncomfortable when lying completely still with your head ... When the radiotracer is given intravenously, you will feel a slight pin prick when the needle is ...

  19. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... energy. top of page What are some common uses of the procedure? The thyroid scan is used ... community, you can search the ACR-accredited facilities database . This website does not provide cost information. The ...

  20. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... scan and thyroid uptake provide information about the structure and function of the thyroid. The thyroid is ... computer, create pictures offering details on both the structure and function of organs and tissues in your ...

  1. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... found, and should not be a cause of concern for you. If you had an intravenous line ... found, and should not be a cause of concern for you. Actual scanning time for each thyroid ...

  2. Body CT (CAT Scan)

    Science.gov (United States)

    ... a CT scan can be reformatted in multiple planes, and can even generate three-dimensional images. These ... other medical conditions and whether you have a history of heart disease, asthma, diabetes, kidney disease or ...

  3. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... the gland following medication use, surgery, radiotherapy or chemotherapy top of page How should I prepare? You ... You will receive specific instructions based on the type of scan you are undergoing. top of page ...

  4. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Uptake? A thyroid scan is a type of nuclear medicine imaging. The radioactive iodine uptake test (RAIU) ... of thyroid function, but does not involve imaging. Nuclear medicine is a branch of medical imaging that ...

  5. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    1981-01-01

    This patent specification describes a tomographic scanning apparatus, with particular reference to the adjustable fan beam and its collimator system, together with the facility for taking a conventional x-radiograph without moving the patient. (U.K.)

  6. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... exam of any medications you are taking, including vitamins and herbal supplements. You should also inform them ... of scan you are undergoing. top of page What does the equipment look like? The special camera ...

  7. The Scanning Optical Microscope.

    Science.gov (United States)

    Sheppard, C. J. R.

    1978-01-01

    Describes the principle of the scanning optical microscope and explains its advantages over the conventional microscope in the improvement of resolution and contrast, as well as the possibility of producing a picture from optical harmonies generated within the specimen.

  8. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... the gland following medication use, surgery, radiotherapy or chemotherapy top of page How should I prepare? You ... but is often performed on hospitalized patients as well. Thyroid Scan You will be positioned on an ...

  9. Soft control of scanning probe microscope with high flexibility.

    Science.gov (United States)

    Liu, Zhenghui; Guo, Yuzheng; Zhang, Zhaohui; Zhu, Xing

    2007-01-01

    Most commercial scanning probe microscopes have multiple embedded digital microprocessors and utilize complex software for system control, which is not easily obtained or modified by researchers wishing to perform novel and special applications. In this paper, we present a simple and flexible control solution that just depends on software running on a single-processor personal computer with real-time Linux operating system to carry out all the control tasks including negative feedback, tip moving, data processing and user interface. In this way, we fully exploit the potential of a personal computer in calculating and programming, enabling us to manipulate the scanning probe as required without any special digital control circuits and related technical know-how. This solution has been successfully applied to a homemade ultrahigh vacuum scanning tunneling microscope and a multiprobe scanning tunneling microscope.

  10. Digital Humanities and networked digital media

    DEFF Research Database (Denmark)

    Finnemann, Niels Ole

    2014-01-01

    This article discusses digital humanities and the growing diversity of digital media, digital materials and digital methods. The first section describes the humanities computing tradition formed around the interpretation of computation as a rule-based process connected to a concept of digital...... materials centred on the digitisation of non-digital, finite works, corpora and oeuvres. The second section discusses “the big tent” of contemporary digital humanities. It is argued that there can be no unifying interpretation of digital humanities above the level of studying digital materials with the help...... of software-supported methods. This is so, in part, because of the complexity of the world and, in part, because digital media remain open to the projection of new epistemologies onto the functional architecture of these media. The third section discusses the heterogeneous character of digital materials...

  11. Becoming digital

    DEFF Research Database (Denmark)

    Pors, Anja Svejgaard

    2015-01-01

    government, and draws on empirical material generated through observations, field notes, interviews and policy documents. The material is documenting how service is performed by frontline agents in the ‘bureaucratic encounter’ with citizens, who needs assistance to use digital self-service in order to apply...... online for a public benefit. Findings: The paper shows that e-government technology changes the mode of professionalism in citizen service from service to support. The paper gives an empirical account of recent Danish digital reforms and shows how the reforms both enable and constrain the work...... of ‘becoming digital’ by frontline agents. Overall the street-level bureaucrat’s classical tasks such as specialized casework are being displaced into promoting and educational tasks. An implication of this is blurred distinctions between professional skills and personal competences of the frontline agent...

  12. Digital resources

    Directory of Open Access Journals (Sweden)

    Redazione Reti Medievali (a cura di

    2005-12-01

    Full Text Available Bibliotheca Latinitatis Mediaevalis (circa VII sec. - XIV sec. IntraText Digital Library [01/06] Corpus Scriptorum Latinorum. A digital library of Latin literature by David Camden [01/06] Fonti disponibili online concernenti la vita religiosa medievale Rete Vitae Religiosae Mediaevalis Studia Conectens [01/06] Fuentes del Medievo Hispanico Instituto de Historia, Consejo Superior de Investigaciones Científicas [01/06] Latin Literature Forum Romanum [01/06] Ludovico Antonio Muratori, Dissertazioni sopra le antichità italiane, 1751 Biblioteca dei Classici Italiani di Giuseppe Bonghi [01/06] Medieval Latin The Latin Library [01/06] Médiévales Presses Universitaires de Vincennes - Revues.org [01/06] Regesta imperii Deutsche Kommission für die Bearbeitung der Regesta Imperii e.V. [01/06] Suda On Line Byzantine Lexicography [01/06

  13. Digital teenagers

    Directory of Open Access Journals (Sweden)

    Rafael Conde Melguizo

    2011-12-01

    Full Text Available Espín, Manuel (Coord.(2011 Adolescentes Digitales.  Revista Estudios de Juventud, Nº 92. Marzo 2011. INJUVE, Madrid."Adolescentes digitales" se nos muestra como una obra que pretende explorar desde distintos puntos de vista la realidad de la generación conocida como “nativos digitales” (Prensky, la generación actual de adolescentes que ha crecido con internet y el mundo digital como su entorno normal de socialización.

  14. Digital Flora

    OpenAIRE

    Bunnell, Katie

    2007-01-01

    This research is concerned with developing a new business model for flexible small scale ceramic production that exploits the customisation capabilities of digital manufacturing technologies and the market potential and global connectivity of the world wide web. It is arguably of particular relevance to regional economic development in remote areas (Amin, Tomaney, Sabel) such as Cornwall where there is a culture of high quality small scale production, limited market and manufacturing opportun...

  15. A fast DSP-based calorimeter hit scanning system

    International Nuclear Information System (INIS)

    Sekikawa, S.; Arai, I.; Suzuki, A.; Watanabe, A.; Marlow, D.R.; Mindas, C.R.; Wixted, R.L.

    1997-01-01

    A custom made digital signal processor (DSP) based system has been developed to scan calorimeter hits read by a 32-channel FASTBUS waveform recorder board. The scanner system identifies hit calorimeter elements by surveying their discriminated outputs. This information is used to generate a list of addresses, which guides the read-out process. The system is described and measurements of the scan times are given. (orig.)

  16. A Color Raster Scanning System for Digitizing Cartographic Data.

    Science.gov (United States)

    1979-11-01

    adequate mechanical bond but did not fully fill the joint, and was subsequently filled by hand welding. As a result of the hand welding used to close the...Preprocessor faults. The functions callable by this routine are: Transfer calibration parameters. This subtest ships the A/D contents to the 8/32 as the 4

  17. Routine digital pathology workflow: The Catania experience

    Directory of Open Access Journals (Sweden)

    Filippo Fraggetta

    2017-01-01

    Full Text Available Introduction: Successful implementation of whole slide imaging (WSI for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. Methods: All (100% permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Results: Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Conclusion: Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory.

  18. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  19. Digital citizens Digital nations: the next agenda

    NARCIS (Netherlands)

    A.W. (Bert) Mulder; M.W. (Martijn) Hartog

    2015-01-01

    DIGITAL CITIZENS CREATE A DIGITAL NATION Citizens will play the lead role as they – in the next phase of the information society – collectively create a digital nation. Personal adoption of information and communication technology will create a digital infrastructure that supports individual and

  20. Viral RNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis

    International Nuclear Information System (INIS)

    Kolakofsky, Daniel; Le Mercier, Philippe; Iseni, Frederic; Garcin, Dominique

    2004-01-01

    mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in that the genome RNA is embedded in an N protein assembly (the nucleocapsid) and the viral RNA polymerase does not dissociate from the template after release of each mRNA, but rather scans the genome RNA for the next gene-start site. A revised model for NNV RNA synthesis is presented, in which RNA polymerase scanning plays a prominent role. Polymerase scanning of the template is known to occur as the viral transcriptase negotiates gene junctions without falling off the template

  1. 1:100k Digital Raster Graphic - Collars Removed

    Data.gov (United States)

    Minnesota Department of Natural Resources — A digital raster graphic (DRG) is a scanned image of an U.S. Geological Survey (USGS) standard series topographic map, including all map collar information. The...

  2. Digital Raster Graphics (DRG) UTM NAD 83 Clipped

    Data.gov (United States)

    Kansas Data Access and Support Center — The Digital Raster Graphic (DRG) is a raster image of a scanned USGS topographic map including the collar information, georeferenced to the UTM grid. For display...

  3. Digital Raster Graphics (DRG) UTM NAD 27 Clipped

    Data.gov (United States)

    Kansas Data Access and Support Center — The Digital Raster Graphic (DRG) is a raster image of a scanned USGS topographic map including the collar information, georeferenced to the UTM grid. For display...

  4. Digital Raster Graphics (DRG) UTM NAD 83 County

    Data.gov (United States)

    Kansas Data Access and Support Center — The Digital Raster Graphic (DRG) is a raster image of a scanned USGS topographic map including the collar information, georeferenced to the UTM grid and tiled by...

  5. Fast-scan, beam-profile monitor

    International Nuclear Information System (INIS)

    Waugh, A.F.

    1977-01-01

    A minimodular, data-acquisition system can be used to rapidly interrogate a 45-point matrix of beam-current sampling targets over the 3- x 12-in. rectangular, output beam cross section of a 50-A, neutral-beam ion source. This system, operating at a throughput rate of 12 μs per channel, can make several complete scans during the 10- to 25-ms-duration beam pulse. Data obtained are available in both analog and digital form. The analog signal is used to create an immediately interpretable CRT display of the beam-current density profile that shows how well the source is aimed. The digital data are held in buffer memory until transfer to a minicomputer for software processing and plotting

  6. Scanning and georeferencing historical USGS quadrangles

    Science.gov (United States)

    Fishburn, Kristin A.; Davis, Larry R.; Allord, Gregory J.

    2017-06-23

    The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the Historical Topographic Map Collection in 2011, is to provide access to a digital repository of USGS topographic maps that is available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of traditional topographic maps, and, prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic process. The next generation of topographic maps, US Topo, is being released by the USGS in digital form, and newer technologies make it possible to also deliver historical maps in the same electronic format that is more publicly accessible.

  7. Natural History Specimen Digitization: Challenges and Concerns

    Directory of Open Access Journals (Sweden)

    Ana Vollmar

    2010-10-01

    Full Text Available A survey on the challenges and concerns invovled with digitizing natural history specimens was circulated to curators, collections managers, and administrators in the natural history community in the Spring of 2009, with over 200 responses received. The overwhelming barrier to digitizing collections was a lack of funding, based on a limited number of sources, leaving institutions mostly responsible for providing the necessary support. The uneven digitization landscape leads to a patchy accumulation of records at varying qualities, and based on different priorities, ulitimately influencing the data's fitness for use. The survey also found that although the kind of specimens found in collections and their storage can be quite varible, there are many similar challenges when digitizing including imaging, automated text scanning and parsing, geo-referencing, etc. Thus, better communication between domains could foster knowledge on digitization leading to efficiencies that could be disseminated through documentation of best practices and training.

  8. Preoperative bone scans

    International Nuclear Information System (INIS)

    Charkes, N.D.; Malmud, L.S.; Caswell, T.; Goldman, L.; Hall, J.; Lauby, V.; Lightfoot, W.; Maier, W.; Rosemond, G.

    1975-01-01

    Strontium nitrate Sr-87m bone scans were made preoperatively in a group of women with suspected breast cancer, 35 of whom subsequently underwent radical mastectomy. In 3 of the 35 (9 percent), the scans were abnormal despite the absence of clinical or roentgenographic evidence of metastatic disease. All three patients had extensive axillary lymph node involvement by tumor, and went on to have additional bone metastases, from which one died. Roentgenograms failed to detect the metastases in all three. Occult bone metastases account in part for the failure of radical mastectomy to cure some patients with breast cancer. It is recommended that all candidates for radical mastectomy have a preoperative bone scan. (U.S.)

  9. Frequency scanning microstrip antennas

    DEFF Research Database (Denmark)

    Danielsen, Magnus; Jørgensen, Rolf

    1979-01-01

    The principles of using radiating microstrip resonators as elements in a frequency scanning antenna array are described. The resonators are cascade-coupled. This gives a scan of the main lobe due to the phase-shift in the resonator in addition to that created by the transmission line phase......-shift. Experimental results inX-band, in good agreement with the theory, show that it is possible to scan the main lobe an angle ofpm30degby a variation of the frequencypm300MHz, and where the 3 dB beamwidth is less than10deg. The directivity was 14.7 dB, while the gain was 8.1 dB. The efficiency might be improved...

  10. Digital fluorimeter

    International Nuclear Information System (INIS)

    Mello, H.A. de.

    1980-11-01

    The specifications of a digital fluorimeter. That with adequated analytical techniques permits to determine trace amounts of fluorescents materials in samples, are described. The fluorimeter is of the reflection type, and uses fluorescents lamps for the excitation and an optical system which is connected to a photomultiplyer machine and permits the measurement of the light intensity. In the case of IEN (Instituto de Engenharia Nuclear) the equipment is used for to determine the uranium content in sample materials to be exported. The precision of the instrument is about + - 1% in the scale of 0.1 which is the normally one used in the current researchs. (E.G.) [pt

  11. Digital entrepreneurship

    DEFF Research Database (Denmark)

    Brem, Alexander; Richter, Chris; Kraus, Sascha

    2017-01-01

    comprising guided interviews with 14 companies from Germany, Austria and Switzerland provides detailed insights into different aspects of the sharing economy phenomenon. Our results make a direct contribution to sharing economy research, especially regarding the new business models of start-ups. Here, we...... find a clear difference between the relevance of economic and social orientation. The latter appears to be in higher demand among customers than entrepreneurs. The increasingly digitalized environment has led to a changed living situation characterized by urbanity, openness to new solutions, changed...

  12. Focus: Digital

    DEFF Research Database (Denmark)

    Technology has been an all-important and defining element within the arts throughout the 20th century, and it has fundamentally changed the ways in which we produce and consume music. With this Focus we investigate the latest developments in the digital domain – and their pervasiveness and rapid...... production and reception of contemporary music and sound art. With ‘Digital’ we present four composers' very different answers to how technology impact their work. To Juliana Hodkinson it has become an integral part of her sonic writing. Rudiger Meyer analyses the relationships between art and design and how...

  13. One bacterial cell, one complete genome.

    Directory of Open Access Journals (Sweden)

    Tanja Woyke

    2010-04-01

    Full Text Available While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA. Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs, indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  14. One Bacterial Cell, One Complete Genome

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos; Clum, Alicia; Copeland, Alex; Schackwitz, Wendy; Lapidus, Alla; Wu, Dongying; McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.; Bristow, James; Cheng, Jan-Fang

    2010-04-26

    While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  15. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    Abele, M.

    1983-01-01

    A computerized tomographic scanning apparatus suitable for diagnosis and for improving target identification in stereotactic neurosurgery is described. It consists of a base, a source of penetrating energy, a detector which produces scanning signals and detector positioning means. A frame with top and bottom arms secures the detector and source to the top and bottom arms respectively. A drive mechanism rotates the frame about an axis along which the frame may also be moved. Finally, the detector may be moved relative to the bottom arm in a direction contrary to the rotation of the frame. (U.K.)

  16. Scanning the phenomenological MSSM

    CERN Document Server

    Wuerzinger, Jonas

    2017-01-01

    A framework to perform scans in the 19-dimensional phenomenological MSSM is developed and used to re-evaluate the ATLAS experiments' sensitivity to R-parity-conserving supersymmetry with LHC Run 2 data ($\\sqrt{s}=13$ TeV), using results from 14 separate ATLAS searches. We perform a $\\tilde{t}_1$ dedicated scan, only considering models with $m_{\\tilde{t}_1}<1$ TeV, while allowing both a neutralino ($\\tilde{\\chi}_1^0$) and a sneutrino ($\\tilde{\

  17. Calibration of scanning Lidar

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Courtney, Michael

    This report describes the tests carried out on a scanning lidar at the DTU Test Station for large wind turbines, Høvsøre. The tests were divided in two parts. In the first part, the purpose was to obtain wind speed calibrations at two heights against two cup anemometers mounted on a mast. Additio......This report describes the tests carried out on a scanning lidar at the DTU Test Station for large wind turbines, Høvsøre. The tests were divided in two parts. In the first part, the purpose was to obtain wind speed calibrations at two heights against two cup anemometers mounted on a mast...

  18. Adaptive Optical Scanning Holography

    Science.gov (United States)

    Tsang, P. W. M.; Poon, Ting-Chung; Liu, J.-P.

    2016-01-01

    Optical Scanning Holography (OSH) is a powerful technique that employs a single-pixel sensor and a row-by-row scanning mechanism to capture the hologram of a wide-view, three-dimensional object. However, the time required to acquire a hologram with OSH is rather lengthy. In this paper, we propose an enhanced framework, which is referred to as Adaptive OSH (AOSH), to shorten the holographic recording process. We have demonstrated that the AOSH method is capable of decreasing the acquisition time by up to an order of magnitude, while preserving the content of the hologram favorably. PMID:26916866

  19. Digital Position Encoding Of Galvanometer Scanner In A Laser Microscope

    Science.gov (United States)

    Liljeborg, Anders

    1988-09-01

    An account is given of a realization of a feedback method to digitize the analog position signal from a moving iron galvanometer. It is employed in a confocal scanning laser microscope for generating digital images. The photometric sampling has to be closely coupled to the position of a mirror that scans a focused laser beam across a microscope specimen. Pictures with low geometric distortion are obtained up to the size 1024 x 1024 pixels.

  20. Digital Humanities

    DEFF Research Database (Denmark)

    Nielsen, Hans Jørn

    2015-01-01

    overgangen fra trykkekultur til digital kultur. For det første problemstillingen omkring digitalisering af litterær kulturarv med fokus på kodning og tagging af teksten samt organisering i hypertekststrukturer. For det andet reorganiseringen af det digitale dokument i dataelementer og database. For det......Artiklen præsenterer først nogle generelle problemstillinger omkring Digital Humanities (DH) med det formål at undersøge dem nærmere i relation til konkrete eksempler på forskellige digitaliseringsmåder og ændringer i dokumentproduktion. I en nærmere afgrænsning vælger artiklen den tendens i DH......, der betragter DH som forbundet med "making" og "building" af digitale objekter og former. Dette kan også karakteriseres som DH som praktisk-produktiv vending. Artiklen har valgt tre typer af digitalisering. De er valgt ud fra, at de skal repræsentere forskellige måder at håndtere digitaliseringen på...

  1. Scanning the Heavens

    Science.gov (United States)

    Hayes, Brian

    1994-12-01

    Gleaning further clues to the structure of the universe will require larger data samples. To that end, a major new survey of the skies called the Sloan Digital Star Survey (SDSS), is in preparation. It will catalog some 50 million galaxies and about 70 million stars. A new 2.5 meter telescope to be erected at Apache Point Observatory in New Mexico will be dedicated to the survey. The telescope is not the key innovation that will make the survey possible. The crucial factor is the technology for digitally recording large numbers of images and spectra and for automating the analysis, recognition, and classification of those images and spectra. The methods to be used are discussed.

  2. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... process that regulates the rate at which the body converts food to energy. top of page What are some common uses of the procedure? The thyroid scan is used to determine the size, shape and position of the thyroid gland. The ...

  3. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available Toggle navigation Test/Treatment Patient Type Screening/Wellness Disease/Condition Safety En Español More Info Images/Videos About Us News Physician Resources Professions Site Index A-Z Thyroid Scan and Uptake ...

  4. Dialogue scanning measuring systems

    International Nuclear Information System (INIS)

    Borodyuk, V.P.; Shkundenkov, V.N.

    1985-01-01

    The main developments of scanning measuring systems intended for mass precision processsing of films in nuclear physics problems and in related fields are reviewed. A special attention is paid to the problem of creation of dialogue systems which permit to simlify the development of control computer software

  5. Scanning electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cox, B. [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada)

    1970-05-15

    The JSM-11 scanning electron microscope at CRNL has been used extensively for topographical studies of oxidized metals, fracture surfaces, entomological and biological specimens. A non-dispersive X-ray attachment permits the microanalysis of the surface features. Techniques for the production of electron channeling patterns have been developed. (author)

  6. Scanning tunneling microscopy

    International Nuclear Information System (INIS)

    Binnig, G.; Rohrer, H.

    1983-01-01

    Based on vacuum tunneling, a novel type of microscope, the scanning tunneling microscope (STM) was developed. It has an unprecedented resolution in real space on an atomic scale. The authors review the important technical features, illustrate the power of the STM for surface topographies and discuss its potential in other areas of science and technology. (Auth.)

  7. Bone scan in rheumatology

    International Nuclear Information System (INIS)

    Morales G, R.; Cano P, R.; Mendoza P, R.

    1993-01-01

    In this chapter a revision is made concerning different uses of bone scan in rheumatic diseases. These include reflex sympathetic dystrophy, osteomyelitis, spondyloarthropaties, metabolic bone diseases, avascular bone necrosis and bone injuries due to sports. There is as well some comments concerning pediatric pathology and orthopedics. (authors). 19 refs., 9 figs

  8. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... information. The thyroid scan and thyroid uptake provide information about the structure and function of the thyroid. The thyroid is a gland in the neck that controls metabolism , a chemical process that regulates the rate at which the body ...

  9. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    1981-01-01

    Details are given of a tomographic scanning apparatus, with particular reference to the means of adjusting the apparent gain of the signal processing means for receiving output signals from the detectors, to compensate for drift in the gain characteristics, including means for passing a reference signal. (U.K.)

  10. Stabilized radiographic scanning agent

    International Nuclear Information System (INIS)

    Fawzi, M.B.

    1979-01-01

    A stable composition useful in preparation of technetium-99m-based radiographic scanning agents has been developed. The composition contains a stabilizing amount of gentisate stabilizer selected from gentisic acid and its soluble pharmaceutically-acceptable salts and esthers. (E.G.)

  11. Scanning electron microscope

    International Nuclear Information System (INIS)

    Anon.

    1980-01-01

    The principle underlying the design of the scanning electron microscope (SEM), the design and functioning of SEM are described. Its applications in the areas of microcircuitry and materials science are outlined. The development of SEM in India is reviewed. (M.G.B.)

  12. Radiographic scanning agent

    International Nuclear Information System (INIS)

    Tofe, A.J.

    1976-01-01

    A stable radiographic scanning agent on a sup(99m)Tc basis has been developed. The substance contains a pertechnetate reduction agent, tin(II)-chloride, chromium(II)-chloride, or iron(II)-sulphate, as well as an organospecific carrier and ascorbic acid or a pharmacologically admissible salt or ester of ascorbic acid. (VJ) [de

  13. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... you: have had any tests, such as an x-ray or CT scan, surgeries or treatments using iodinated ... page How does the procedure work? With ordinary x-ray examinations, an image is made by passing x- ...

  14. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... for a thyroid scan is 30 minutes or less. Thyroid Uptake You will be given radioactive iodine (I-123 or I-131) in liquid or capsule form to swallow. The thyroid uptake will begin several hours to 24 hours later. Often, two separate uptake ...

  15. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... an x-ray or CT scan, surgeries or treatments using iodinated contrast material within the last two months. are taking medications or ingesting other substances that contain iodine , including kelp, seaweed, cough syrups, multivitamins or heart medications. have any ...

  16. Knowledge Organisation Systems in North American Digital Library Collections

    Science.gov (United States)

    Shiri, Ali; Chase-Kruszewski, Sarah

    2009-01-01

    Purpose: The purpose of this paper is to report an investigation into the types of knowledge organisation systems (KOSs) utilised in North American digital library collections. Design/methodology/approach: The paper identifies, analyses and deep scans online North American hosted digital libraries. It reviews the literature related to the…

  17. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  18. GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

    Science.gov (United States)

    Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

    2013-04-10

    Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. 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...

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

    Science.gov (United States)

    2012-06-01

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

  1. Genome scanning for identification of resistance gene analogs (RGAs)

    African Journals Online (AJOL)

    Disease resistance in plants is a desirable economic trait. Many disease resistance genes from various plants have been cloned so far. The gene products of some of these can be distinguished by the presence of an N terminal nucleotide binding site and a C-terminal stretch of leucine-rich repeats. Oligonucleotides already ...

  2. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  3. Digital radiography

    DEFF Research Database (Denmark)

    Precht, H; Gerke, O; Rosendahl, K

    2012-01-01

    BACKGROUND: New developments in processing of digital radiographs (DR), including multi-frequency processing (MFP), allow optimization of image quality and radiation dose. This is particularly promising in children as they are believed to be more sensitive to ionizing radiation than adults....... OBJECTIVE: To examine whether the use of MFP software reduces the radiation dose without compromising quality at DR of the femur in 5-year-old-equivalent anthropomorphic and technical phantoms. MATERIALS AND METHODS: A total of 110 images of an anthropomorphic phantom were imaged on a DR system (Canon DR...... with CXDI-50 C detector and MLT[S] software) and analyzed by three pediatric radiologists using Visual Grading Analysis. In addition, 3,500 images taken of a technical contrast-detail phantom (CDRAD 2.0) provide an objective image-quality assessment. RESULTS: Optimal image-quality was maintained at a dose...

  4. Fokus: Digital

    DEFF Research Database (Denmark)

    2014-01-01

    i det digitale domæne – udviklinger, der foregår hastigt og er gennemgribende, og som derfor kræver et nærmere blik på forholdet mellem kunsten og teknologien. Komponistens forståelse af sin metier udfordres – samtidig med at befæstede ideer om kunstværket møder modstand fra nye mediemæssige...... sammenhænge og fra forandrede distributionsformer. Dette betyder ændrede betingelser for både produktion og reception af kunstmusik og lydkunst. Med Digital tager vi udgangspunkt i fire komponisters meget forskellige bud på hvordan teknologien spiller en rolle i arbejdet. Juliana Hodkinson beskriver hvordan...

  5. The Squiggle: A Digital Musical Instrument

    OpenAIRE

    Sheehan, Brian

    2004-01-01

    This paper discusses some of the issues pertaining to thedesign of digital musical instruments that are to effectively fillthe role of traditional instruments (i.e. those based on physicalsound production mechanisms). The design andimplementation of a musical instrument that addresses some ofthese issues, using scanned synthesis coupled to a "smart"physical system, is described.

  6. Digital Photography--a Question of Ethics.

    Science.gov (United States)

    Meltzer, Bonnie

    1996-01-01

    Discusses reasons for computer manipulation of photographs and the need to educate students about the ethics involving digital scanning. Focuses on ownership, copyrights, reasons for changing a photograph, reader-interpretation, and the context in which the photograph is used. Suggests a photo illustration project to teach students about these…

  7. Development and validation of novel digitalized cervicography system

    Science.gov (United States)

    Kim, Soo-Nyung; Kim, Yun Hwan; Nam, Kye-Hyun; Lee, Seon-Kyung; Lee, Tae Sung; Choi, Ho-Sun; Han, Sei-Jun

    2016-01-01

    Objective Digital cervicography systems would be expected to reduce the costs of film cervicography, and provide the opportunity for "telemedicine-based" screening. We aimed to develop web-based digital cervicography system, and validate it compared with conventional film cervicography. Methods A hundred cases from five centers were prospectively included, and cervical images (analogue, digitalized by scanning analogue, and digital) were taken separately using both analogue (Cerviscope) and digital camera (Dr. Cervicam) in each patient. Nine specialists evaluated the three kinds of images of each case with time interval between evaluations of each image. To validate novel digitalized system, we analyzed intra-observer variance among evaluation results of three kinds of images. Results Sixty-three cases were finally analyzed after excluding technically defective cases that cannot be evaluable on analogue images. The generalized kappa for analogue versus digital image was 0.83, for analogue versus scanned image 0.72, and for digital versus scanned image was 0.71; all were in excellent consensus. Conclusion Digitalized cervicography system can be substituted for the film cervicography very reliably, and can be used as a promising telemedicine tool for cervical cancer screening. PMID:27200314

  8. Enhancer Identification through Comparative Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Visel, Axel; Bristow, James; Pennacchio, Len A.

    2006-10-01

    With the availability of genomic sequence from numerousvertebrates, a paradigm shift has occurred in the identification ofdistant-acting gene regulatory elements. In contrast to traditionalgene-centric studies in which investigators randomly scanned genomicfragments that flank genes of interest in functional assays, the modernapproach begins electronically with publicly available comparativesequence datasets that provide investigators with prioritized lists ofputative functional sequences based on their evolutionary conservation.However, although a large number of tools and resources are nowavailable, application of comparative genomic approaches remains far fromtrivial. In particular, it requires users to dynamically consider thespecies and methods for comparison depending on the specific biologicalquestion under investigation. While there is currently no single generalrule to this end, it is clear that when applied appropriately,comparative genomic approaches exponentially increase our power ingenerating biological hypotheses for subsequent experimentaltesting.

  9. Image analysis and machine learning in digital pathology: Challenges and opportunities.

    Science.gov (United States)

    Madabhushi, Anant; Lee, George

    2016-10-01

    With the rise in whole slide scanner technology, large numbers of tissue slides are being scanned and represented and archived digitally. While digital pathology has substantial implications for telepathology, second opinions, and education there are also huge research opportunities in image computing with this new source of "big data". It is well known that there is fundamental prognostic data embedded in pathology images. The ability to mine "sub-visual" image features from digital pathology slide images, features that may not be visually discernible by a pathologist, offers the opportunity for better quantitative modeling of disease appearance and hence possibly improved prediction of disease aggressiveness and patient outcome. However the compelling opportunities in precision medicine offered by big digital pathology data come with their own set of computational challenges. Image analysis and computer assisted detection and diagnosis tools previously developed in the context of radiographic images are woefully inadequate to deal with the data density in high resolution digitized whole slide images. Additionally there has been recent substantial interest in combining and fusing radiologic imaging and proteomics and genomics based measurements with features extracted from digital pathology images for better prognostic prediction of disease aggressiveness and patient outcome. Again there is a paucity of powerful tools for combining disease specific features that manifest across multiple different length scales. The purpose of this review is to discuss developments in computational image analysis tools for predictive modeling of digital pathology images from a detection, segmentation, feature extraction, and tissue classification perspective. We discuss the emergence of new handcrafted feature approaches for improved predictive modeling of tissue appearance and also review the emergence of deep learning schemes for both object detection and tissue classification

  10. Digital work in a digitally challenged organization

    NARCIS (Netherlands)

    Davison, R.M.; Ou, Carol

    Digitally literate employees are accustomed to having free access to digital media technologies. However, some organizations enact information technology (IT) governance structures that explicitly proscribe access to these technologies, resulting in considerable tension between employees and the

  11. Scanning probe microscopy

    International Nuclear Information System (INIS)

    Mainsbridge, B.

    1994-01-01

    In late 1959, Richard Feynman observed that manoeuvring atoms was something that could be done in principle but has not been done, 'because we are too big'. In 1982, the scanning tunnelling microscope (STM) was invented and is now a central tool for the construction of nanoscale devices in what was known as molecular engineering, and now, nanotechnology. The principles of the microscope are outlined and references are made to other scanning devices which have evolved from the original invention. The method of employment of the STM as a machine tool is described and references are made to current speculations on applications of the instrument in nanotechnology. A short bibliography on this topic is included. 27 refs., 7 figs

  12. Scanning probe microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mainsbridge, B [Murdoch Univ., WA (Australia). School of Mathematical and Physical Sciences

    1994-12-31

    In late 1959, Richard Feynman observed that manoeuvring atoms was something that could be done in principle but has not been done, `because we are too big`. In 1982, the scanning tunnelling microscope (STM) was invented and is now a central tool for the construction of nanoscale devices in what was known as molecular engineering, and now, nanotechnology. The principles of the microscope are outlined and references are made to other scanning devices which have evolved from the original invention. The method of employment of the STM as a machine tool is described and references are made to current speculations on applications of the instrument in nanotechnology. A short bibliography on this topic is included. 27 refs., 7 figs.

  13. 67Ga lung scan

    International Nuclear Information System (INIS)

    Niden, A.H.; Mishkin, F.S.; Khurana, M.M.L.; Pick, R.

    1977-01-01

    Twenty-three patients with clinical signs of pulmonary embolic disease and lung infiltrates were studied to determine the value of gallium citrate 67 Ga lung scan in differentiating embolic from inflammatory lung disease. In 11 patients without angiographically proved embolism, only seven had corresponding ventilation-perfusion defects compatible with inflammatory disease. In seven of these 11 patients, the 67 Ga concentration indicated inflammatory disease. In the 12 patients with angiographically proved embolic disease, six had corresponding ventilation-perfusion defects compatible with inflammatory disease. None had an accumulation of 67 Ga in the area of pulmonary infiltrate. Thus, ventilation-perfusion lung scans are of limited value when lung infiltrates are present. In contrast, the accumulation of 67 Ga in the lung indicates an inflammatory process. Gallium imaging can help select those patients with lung infiltrates who need angiography

  14. Horizon Scanning for Pharmaceuticals

    DEFF Research Database (Denmark)

    Lepage-Nefkens, Isabelle; Douw, Karla; Mantjes, GertJan

    for a joint horizon scanning system (HSS).  We propose to create a central “horizon scanning unit” to perform the joint HS activities (a newly established unit, an existing HS unit, or a third party commissioned and financed by the collaborating countries). The unit will be responsible for the identification...... and filtration of new and emerging pharmaceutical products. It will maintain and update the HS database, organise company pipeline meetings, and disseminate the HSS’s outputs.  The HS unit works closely together with the designated national HS experts in each collaborating country. The national HS experts...... will collect country-specific information, liaise between the central HS unit and country-specific clinical and other experts, coordinate the national prioritization process (to select products for early assessment), and communicate the output of the HSS to national decision makers.  The outputs of the joint...

  15. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Multichannel scanning spectrophotometer

    International Nuclear Information System (INIS)

    Lagutin, A.F.

    1979-01-01

    A spectrophotometer designed in the Crimea astrophysical observatory is described. The spectrophotometer is intended for the installation at the telescope to measure energy distribution in the star spectra in the 3100-8550 A range. The device is made according to the scheme with a fixed diffraction lattice. The choice of the optical kinematic scheme is explained. The main design elements are shown. Some singularities of the scanning drive kinematics are considered. The device performance is given

  17. Scanning drop sensor

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jian; Xiang, Chengxiang; Gregoire, John

    2017-05-09

    Electrochemical experiments are performed on a collection of samples by suspending a drop of electrolyte solution between an electrochemical experiment probe and one of the samples that serves as a test sample. During the electrochemical experiment, the electrolyte solution is added to the drop and an output solution is removed from the drop. The probe and collection of samples can be moved relative to one another so the probe can be scanned across the samples.

  18. Scanning drop sensor

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jian; Xiang, Chengxiang; Gregoire, John M.; Shinde, Aniketa A.; Guevarra, Dan W.; Jones, Ryan J.; Marcin, Martin R.; Mitrovic, Slobodan

    2017-05-09

    Electrochemical or electrochemical and photochemical experiments are performed on a collection of samples by suspending a drop of electrolyte solution between an electrochemical experiment probe and one of the samples that serves as a test sample. During the electrochemical experiment, the electrolyte solution is added to the drop and an output solution is removed from the drop. The probe and collection of samples can be moved relative to one another so the probe can be scanned across the samples.

  19. IMEF gamma scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Baek, Sang Yeol; Park, Dae Kyu; Ahn, Sang Bok; Ju, Yong Sun; Jeon, Yong Bum

    1997-06-01

    The gamma scanning system which is installed in IMEF is the equipment obtaining the gamma ray spectrum from irradiated fuels. This equipment could afford the useful data relating spent fuels like as burn-up measurements. We describe the specifications of the equipment and its accessories, and also described its operation procedure so that an operator can use this report as the operation procedure. (author). 1 tab., 11 figs., 11 refs.

  20. IMEF gamma scanning system

    International Nuclear Information System (INIS)

    Baek, Sang Yeol; Park, Dae Kyu; Ahn, Sang Bok; Ju, Yong Sun; Jeon, Yong Bum.

    1997-06-01

    The gamma scanning system which is installed in IMEF is the equipment obtaining the gamma ray spectrum from irradiated fuels. This equipment could afford the useful data relating spent fuels like as burn-up measurements. We describe the specifications of the equipment and its accessories, and also described its operation procedure so that an operator can use this report as the operation procedure. (author). 1 tab., 11 figs., 11 refs

  1. Scanning unit for collectrons

    International Nuclear Information System (INIS)

    Plaige, Yves.

    1976-01-01

    This invention concerns a measurement scanning assembly for collectron type detectors. It is used in measuring the neutron flux in nuclear reactors. As the number of these detectors in a reactor can be very great, they are not usually all connected permanently to the measuring facility but rather in turn by means of a scanning device which carries out, as it were, multiplexing between all the collectrons and the input of a single measuring system. The object of the invention is a scanning assembly which is of relative simplicity through an original organisation. Specifically, according to this organisation, the collectrons outputs are grouped together in bunches, each of these bunches being processed by a multiplexing sub-assembly belonging to a first stage, the different outputs of these multiplexing subassemblies of this first stage being grouped together yet again in bunches processed by multiplexors forming a new stage and so forth. Further, this structure is specially adapted for use with collectrons by utilising a current amplifier at each multiplexing level so that from one end to the other of the multiplexing system, the commutations are carried out on currents and not on voltages [fr

  2. Forensic Scanning Electron Microscope

    Science.gov (United States)

    Keeley, R. H.

    1983-03-01

    The scanning electron microscope equipped with an x-ray spectrometer is a versatile instrument which has many uses in the investigation of crime and preparation of scientific evidence for the courts. Major applications include microscopy and analysis of very small fragments of paint, glass and other materials which may link an individual with a scene of crime, identification of firearms residues and examination of questioned documents. Although simultaneous observation and chemical analysis of the sample is the most important feature of the instrument, other modes of operation such as cathodoluminescence spectrometry, backscattered electron imaging and direct x-ray excitation are also exploited. Marks on two bullets or cartridge cases can be compared directly by sequential scanning with a single beam or electronic linkage of two instruments. Particles of primer residue deposited on the skin and clothing when a gun is fired can be collected on adhesive tape and identified by their morphology and elemental composition. It is also possible to differentiate between the primer residues of different types of ammunition. Bullets may be identified from the small fragments left behind as they pass through the body tissues. In the examination of questioned documents the scanning electron microscope is used to establish the order in which two intersecting ink lines were written and to detect traces of chemical markers added to the security inks on official documents.

  3. Accuracy of Digital Impressions and Fitness of Single Crowns Based on Digital Impressions

    Science.gov (United States)

    Yang, Xin; Lv, Pin; Liu, Yihong; Si, Wenjie; Feng, Hailan

    2015-01-01

    In this study, the accuracy (precision and trueness) of digital impressions and the fitness of single crowns manufactured based on digital impressions were evaluated. #14-17 epoxy resin dentitions were made, while full-crown preparations of extracted natural teeth were embedded at #16. (1) To assess precision, deviations among repeated scan models made by intraoral scanner TRIOS and MHT and model scanner D700 and inEos were calculated through best-fit algorithm and three-dimensional (3D) comparison. Root mean square (RMS) and color-coded difference images were offered. (2) To assess trueness, micro computed tomography (micro-CT) was used to get the reference model (REF). Deviations between REF and repeated scan models (from (1)) were calculated. (3) To assess fitness, single crowns were manufactured based on TRIOS, MHT, D700 and inEos scan models. The adhesive gaps were evaluated under stereomicroscope after cross-sectioned. Digital impressions showed lower precision and better trueness. Except for MHT, the means of RMS for precision were lower than 10 μm. Digital impressions showed better internal fitness. Fitness of single crowns based on digital impressions was up to clinical standard. Digital impressions could be an alternative method for single crowns manufacturing. PMID:28793417

  4. Accuracy of Digital Impressions and Fitness of Single Crowns Based on Digital Impressions

    Directory of Open Access Journals (Sweden)

    Xin Yang

    2015-06-01

    Full Text Available In this study, the accuracy (precision and trueness of digital impressions and the fitness of single crowns manufactured based on digital impressions were evaluated. #14-17 epoxy resin dentitions were made, while full-crown preparations of extracted natural teeth were embedded at #16. (1 To assess precision, deviations among repeated scan models made by intraoral scanner TRIOS and MHT and model scanner D700 and inEos were calculated through best-fit algorithm and three-dimensional (3D comparison. Root mean square (RMS and color-coded difference images were offered. (2 To assess trueness, micro computed tomography (micro-CT was used to get the reference model (REF. Deviations between REF and repeated scan models (from (1 were calculated. (3 To assess fitness, single crowns were manufactured based on TRIOS, MHT, D700 and inEos scan models. The adhesive gaps were evaluated under stereomicroscope after cross-sectioned. Digital impressions showed lower precision and better trueness. Except for MHT, the means of RMS for precision were lower than 10 μm. Digital impressions showed better internal fitness. Fitness of single crowns based on digital impressions was up to clinical standard. Digital impressions could be an alternative method for single crowns manufacturing.

  5. USNA DIGITAL FORENSICS LAB

    Data.gov (United States)

    Federal Laboratory Consortium — To enable Digital Forensics and Computer Security research and educational opportunities across majors and departments. Lab MissionEstablish and maintain a Digital...

  6. The Prosthetic Workflow in the Digital Era

    Directory of Open Access Journals (Sweden)

    Lidia Tordiglione

    2016-01-01

    Full Text Available The purpose of this retrospective study was to clinically evaluate the benefits of adopting a full digital workflow for the implementation of fixed prosthetic restorations on natural teeth. To evaluate the effectiveness of these protocols, treatment plans were drawn up for 15 patients requiring rehabilitation of one or more natural teeth. All the dental impressions were taken using a Planmeca PlanScan® (Planmeca OY, Helsinki, Finland intraoral scanner, which provided digital casts on which the restorations were digitally designed using Exocad® (Exocad GmbH, Germany, 2010 software and fabricated by CAM processing on 5-axis milling machines. A total of 28 single crowns were made from monolithic zirconia, 12 vestibular veneers from lithium disilicate, and 4 three-quarter vestibular veneers with palatal extension. While the restorations were applied, the authors could clinically appreciate the excellent match between the digitally produced prosthetic design and the cemented prostheses, which never required any occlusal or proximal adjustment. Out of all the restorations applied, only one exhibited premature failure and was replaced with no other complications or need for further scanning. From the clinical experience gained using a full digital workflow, the authors can confirm that these work processes enable the fabrication of clinically reliable restorations, with all the benefits that digital methods bring to the dentist, the dental laboratory, and the patient.

  7. Can We Teach Digital Natives Digital Literacy?

    Science.gov (United States)

    Ng, Wan

    2012-01-01

    In recent years, there has been much debate about the concept of digital natives, in particular the differences between the digital natives' knowledge and adoption of digital technologies in informal versus formal educational contexts. This paper investigates the knowledge about educational technologies of a group of undergraduate students…

  8. Digital radiographic techniques in the analysis of paintings

    International Nuclear Information System (INIS)

    James, A.E. Jr.; Gibbs, S.J.; James, A.E. III; Pickens, D.R.; Sloan, M.; Price, R.R.; Erickson, J.J.

    1985-01-01

    In this chapter the authors use the term digital radiography to mean any method of radiographic image production in which the silver halide-based film is replaced by an electronic sensor for production of an image. There are essentially three types of digital radiographic systems available at present, but others will be developed. These differ primarily in the method of image production and the rapidity with which images can be produced. The three methods discussed are digital fluoroscopy, scanned projection radiography, and the scanned point source radiography. Each has certain characteristics which, if properly utilized, will allow improved x-ray analysis of paintings

  9. A Technique for Digital Impression and Bite Registration for a Single Edentulous Arch.

    Science.gov (United States)

    Fang, Yiqin; Fang, Jing-Huan; Jeong, Seung-Mi; Choi, Byung-Ho

    2018-03-09

    Few studies have reported the application of digital technology for the process of impression and interocclusal recordings in edentulous patients. This article describes a digitizing system for generating digital edentulous models with a jaw relationship by taking direct digital impressions and a virtual bite registration using intraoral digital scanning. A specialized scan retractor was used to make digital impressions of edentulous jaws in patients' mouths using an intraoral scanner. Virtual bite registration was obtained with optical scanning of the buccal surfaces of both jaws at the occlusal vertical dimension. The registration was then used as a reference for aligning both jaws. Digital edentulous models that include the jaw relationship would be clinically beneficial for the fabrication of complete dentures in edentulous patients. © 2018 by the American College of Prosthodontists.

  10. 3D Digital Smile Design With a Mobile Phone and Intraoral Optical Scanner.

    Science.gov (United States)

    Daher, René; Ardu, Stefano; Vjero, Osela; Krejci, Ivo

    2018-06-01

    Extraoral facial scanning using a mobile phone has emerged as a viable, cost-effective option for certain applications not requiring high precision, such as patient education and 3-dimensional (3D) digital smile design. This technological development is particularly promising for general practitioners (GPs) who may not be able to invest in expensive,complex digital impressioning devices. This article describes and illustrates a relatively simple and accessible workflow that avails digital 3D facial scanning benefits to GPs.

  11. Digital produktion

    DEFF Research Database (Denmark)

    Bogen sætter fokus på digital produktion, som er en stærk læringsform, der faciliterer elevernes læreprocesser og kvalificerer elevernes faglige læringsresultater. Det sker når lærerne udarbejder didaktiske rammedesign, hvor eleverne arbejder selvstændigt inden for dette rammedesign, og hvor mål og...... procesevaluering stilladserer elevernes faglige proces. I digitale produktionsprocesser arbejder eleverne iterativt, de udvikler ejerskab til produktionen og fastholder selv deres læreprocesser. It’s multimodalitet, elevernes kollaborative tilgange, videndeling mellem eleverne og elevernes uformelle lege- og...... elevernes digitale produktion er lærernes didaktiske rammesætning og stilladserende tilgange. Her lægger lærerne op til, at eleverne som didaktiske designere i relation til rammesætningen skal organisere og planlægge deres læreprocesser, inddrages i målsætning, evaluering og valg af digitale ressourcer...

  12. Digital dannelse

    DEFF Research Database (Denmark)

    Bundsgaard, Jeppe

    2012-01-01

    I al vores iver efter at få presset nogle flere digitale dimser ind i skolen, er vi i fare for at glemme hvad det er vi skal med disse dimser. Der er store forventninger til at de kan gøre det lettere at være lærer (og dermed billigere), og det kan det måske. Men der er jo også et dannelsesspørgs......I al vores iver efter at få presset nogle flere digitale dimser ind i skolen, er vi i fare for at glemme hvad det er vi skal med disse dimser. Der er store forventninger til at de kan gøre det lettere at være lærer (og dermed billigere), og det kan det måske. Men der er jo også et...... dannelsesspørgsmål knyttet til it. Hvad er egentlig digital dannelse? Og hvad betyder det for danskfaget?...

  13. Digital forensics digital evidence in criminal investigations

    CERN Document Server

    Marshall, Angus McKenzie

    2009-01-01

    The vast majority of modern criminal investigations involve some element of digital evidence, from mobile phones, computers, CCTV and other devices. Digital Forensics: Digital Evidence in Criminal Investigations provides the reader with a better understanding of how digital evidence complements "traditional" scientific evidence and examines how it can be used more effectively and efficiently in a range of investigations. Taking a new approach to the topic, this book presents digital evidence as an adjunct to other types of evidence and discusses how it can be deployed effectively in s

  14. Digital subtraction angiography in patients with central vertigo

    International Nuclear Information System (INIS)

    Inamori, Toru; Takayasu, Yukio; Umetani, Yoshio; Taruoka, Akinori.

    1985-01-01

    Digital subtraction angiography (DSA) is a recently developed non-invasive intravenous angiography which has become possible through real time digital subtraction of x-ray transmission data from an image intensifier and television system. The output signals of the image intensifier-television camera system are digitized by an analog-digital converter. The digital information, 512x512 pixels and 9 bits deep, is fed into the image processing assembly after logarithmic amplification, where 2-8 frames are added and subtracted from mask images for the final digital images. Intravenous digital subtraction angiography was performed in 21 patients with intractable dizzy spells of central origin resistant to treatment. These patients showed some signs of CNS disturbance, although there were no significant findings on CT scans. Surprisingly, findings were abnormal in 14 of 21 patients (66.7%). DSA is, therefore, considered to be an important aid in the diagnosis of vertigo of the central type. (J.P.N.)

  15. Cost analysis of operating an all-digital radiology department

    International Nuclear Information System (INIS)

    Arenson, R.L.; Soshadri, S.B.; DeSimone, D.; Hiss, S.S.

    1988-01-01

    Using the current film system as a baseline, this study analyzes the cost of digital acquisition, transmission, archiving, and display of all images generated in our department. Two approaches are considered: (1) conventional x-ray films are digitized with a laser scanning film digitizer; (2) images are captured with a direct digital receptor and no film is created. In both approaches, images from digital modalities are acquired directly from the scanners. The cost of equipment and its maintenance, film, supplies, storage space, operations, personnel, and so forth are analyzed for all approaches. The annual cost of operating the film system is $2.5 million. The estimated annual cost is $2.3 million for the first digital approach, $1.8 million for the second. This analysis demonstrates that these digital approaches can be cost-effective, viable alternatives to film-bases systems

  16. Metrological large range scanning probe microscope

    International Nuclear Information System (INIS)

    Dai Gaoliang; Pohlenz, Frank; Danzebrink, Hans-Ulrich; Xu Min; Hasche, Klaus; Wilkening, Guenter

    2004-01-01

    We describe a metrological large range scanning probe microscope (LR-SPM) with an Abbe error free design and direct interferometric position measurement capability, aimed at versatile traceable topographic measurements that require nanometer accuracy. A dual-stage positioning system was designed to achieve both a large measurement range and a high measurement speed. This dual-stage system consists of a commercially available stage, referred to as nanomeasuring machine (NMM), with a motion range of 25 mmx25 mmx5 mm along x, y, and z axes, and a compact z-axis piezoelectric positioning stage (compact z stage) with an extension range of 2 μm. The metrological LR-SPM described here senses the surface using a stationary fixed scanning force microscope (SFM) head working in contact mode. During operation, lateral scanning of the sample is performed solely by the NMM. Whereas the z motion, controlled by the SFM signal, is carried out by a combination of the NMM and the compact z stage. In this case the compact z stage, with its high mechanical resonance frequency (greater than 20 kHz), is responsible for the rapid motion while the NMM simultaneously makes slower movements over a larger motion range. To reduce the Abbe offset to a minimum the SFM tip is located at the intersection of three interferometer measurement beams orientated in x, y, and z directions. To improve real time performance two high-end digital signal processing (DSP) systems are used for NMM positioning and SFM servocontrol. Comprehensive DSP firmware and Windows XP-based software are implemented, providing a flexible and user-friendly interface. The instrument is able to perform large area imaging or profile scanning directly without stitching small scanned images. Several measurements on different samples such as flatness standards, nanostep height standards, roughness standards as well as sharp nanoedge samples and 1D gratings demonstrate the outstanding metrological capabilities of the instrument

  17. Digital platforms as enablers for digital transformation

    DEFF Research Database (Denmark)

    Hossain, Mokter; Lassen, Astrid Heidemann

    transformation is crucial. This study aims at exploring how organizations are driven towards transformation in various ways to embrace digital platforms for ideas, technologies, and knowledge. It shows the opportunities and challenges digital platforms bring in organizations. It also highlights underlying......Digital platforms offer new ways for organizations to collaborate with the external environment for ideas, technologies, and knowledge. They provide new possibilities and competence but they also bring new challenges for organizations. Understanding the role of these platforms in digital...... mechanisms and potential outcomes of various digital platforms. The contribution of the submission is valuable for scholars to understand and further explore this area. It provides insight for practitioners to capture value through digital platforms and accelerate the pace of organizations’ digital...

  18. Automatic Ultrasound Scanning

    DEFF Research Database (Denmark)

    Moshavegh, Ramin

    on the user adjustments on the scanner interface to optimize the scan settings. This explains the huge interest in the subject of this PhD project entitled “AUTOMATIC ULTRASOUND SCANNING”. The key goals of the project have been to develop automated techniques to minimize the unnecessary settings...... on the scanners, and to improve the computer-aided diagnosis (CAD) in ultrasound by introducing new quantitative measures. Thus, four major issues concerning automation of the medical ultrasound are addressed in this PhD project. They touch upon gain adjustments in ultrasound, automatic synthetic aperture image...

  19. Radiographic scanning agent

    International Nuclear Information System (INIS)

    Bevan, J.A.

    1983-01-01

    This invention relates to radiodiagnostic agents and more particularly to a composition and method for preparing a highly effective technetium-99m-based bone scanning agent. One deficiency of x-ray examination is the inability of that technique to detect skeletal metastases in their incipient stages. It has been discovered that the methanehydroxydiphosphonate bone mineral-seeking agent is unique in that it provides the dual benefits of sharp radiographic imaging and excellent lesion detection when used with technetium-99m. This agent can also be used with technetium-99m for detecting soft tissue calcification in the manner of the inorganic phosphate radiodiagnostic agents

  20. Spinal CT scan, 1

    International Nuclear Information System (INIS)

    Nakagawa, Hiroshi

    1982-01-01

    Methods of CT of the cervical and thoracic spines were explained, and normal CT pictures of them were described. Spinal CT was evaluated in comparison with other methods in various spinal diseases. Plain CT revealed stenosis due to spondylosis or ossification of posterior longitudinal ligament and hernia of intervertebral disc. CT took an important role in the diagnosis of spinal cord tumors with calcification and destruction of the bone. CT scan in combination with other methods was also useful for the diagnosis of spinal injuries, congenital anomalies and infections. (Ueda, J.)