WorldWideScience

Sample records for landmark genome scanning

  1. Arterial tree tracking from anatomical landmarks in magnetic resonance angiography scans

    Science.gov (United States)

    O'Neil, Alison; Beveridge, Erin; Houston, Graeme; McCormick, Lynne; Poole, Ian

    2014-03-01

    This paper reports on arterial tree tracking in fourteen Contrast Enhanced MRA volumetric scans, given the positions of a predefined set of vascular landmarks, by using the A* algorithm to find the optimal path for each vessel based on voxel intensity and a learnt vascular probability atlas. The algorithm is intended for use in conjunction with an automatic landmark detection step, to enable fully automatic arterial tree tracking. The scan is filtered to give two further images using the top-hat transform with 4mm and 8mm cubic structuring elements. Vessels are then tracked independently on the scan in which the vessel of interest is best enhanced, as determined from knowledge of typical vessel diameter and surrounding structures. A vascular probability atlas modelling expected vessel location and orientation is constructed by non-rigidly registering the training scans to the test scan using a 3D thin plate spline to match landmark correspondences, and employing kernel density estimation with the ground truth center line points to form a probability density distribution. Threshold estimation by histogram analysis is used to segment background from vessel intensities. The A* algorithm is run using a linear cost function constructed from the threshold and the vascular atlas prior. Tracking results are presented for all major arteries excluding those in the upper limbs. An improvement was observed when tracking was informed by contextual information, with particular benefit for peripheral vessels.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ritter, M.

    2007-04-27

    This thesis presents a new strategy and a spatial method for the geometric calibration of 3D measurement devices at the micro-range, based on spatial reference structures with nanometersized landmarks (nanomarkers). The new method was successfully applied for the 3D calibration of scanning probe microscopes (SPM) and confocal laser scanning microscopes (CLSM). Moreover, the spatial method was also used for the photogrammetric self-calibration of scanning electron microscopes (SEM). In order to implement the calibration strategy to all scanning microscopes used, the landmark-based principle of reference points often applied at land survey or at close-range applications has been transferred to the nano- and micro-range in the form of nanomarker. In order to function as a support to the nanomarkers, slope-shaped step pyramids have been developed and fabricated by focused ion beam (FIB) induced metal deposition. These FIB produced 3D microstructures have been sized to embrace most of the measurement volume of the scanning microscopes. Additionally, their special design allows the homogenous distribution of the nanomarkers. The nanomarkers were applied onto the support and the plateaus of the slope-step pyramids by FIB etching (milling) as landmarks with as little as several hundreds of nanometers in diameter. The nanomarkers are either of point-, or ring-shaped design. They are optimized so that they can be spatially measured by SPM and CLSM, and, imaged and photogrammetrically analyzed on the basis of SEM data. The centre of the each nanomarker serves as reference point in the measurement data or images. By applying image processing routines, the image (2D) or object (3D) coordinates of each nanomarker has been determined with subpixel accuracy. The correlative analysis of the SPM, CLSM and photogrammetric SEM measurement data after 3D calibration resulted in mean residues in the measured coordinates of as little as 13 nm. Without the coupling factors the mean residues are up to 6 times higher. By taking into account the orthogonality of the measurement coordinate axes when performing a 3D calibration, a comparative and quantitative analysis of 3D scanning microscopy has been made possible. (orig.)

  3. Genome-based peptide fingerprint scanning

    OpenAIRE

    Giddings, Michael C.; Shah, Atul A.; Gesteland, Ray; Moore, Barry

    2002-01-01

    We have implemented a method that identifies the genomic origins of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. Unlike previously reported techniques, this method requires no predefined ORF or protein annotations. Fixed-size windows along the genome sequence are scored by an equation accounting for the number of matching peptides, the number of missed enzymatic cleavages in each peptide, the number ...

  4. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    Science.gov (United States)

    ... Research 2012 July 2012 Genome-Wide Scan Reveals Mutation Associated with Melanoma A team of international researchers ... Institute, and other funding organizations discovered a rare mutation in the microphthalmia-associated transcription factor (MITF) gene. ...

  5. A note on generalized Genome Scan Meta-Analysis statistics

    OpenAIRE

    Feng Anne C; Koziol James A

    2005-01-01

    Abstract Background Wise et al. introduced a rank-based statistical technique for meta-analysis of genome scans, the Genome Scan Meta-Analysis (GSMA) method. Levinson et al. recently described two generalizations of the GSMA statistic: (i) a weighted version of the GSMA statistic, so that different studies could be ascribed different weights for analysis; and (ii) an order statistic approach, reflecting the fact that a GSMA statistic can be computed for each chromosomal region or bin width ac...

  6. Microarray Analysis: Genome-scale hypothesis scanning

    OpenAIRE

    Gibson, Greg

    2003-01-01

    Microarrays can survey genome-wide expression patterns. Not only can these gene expression profiles be used to identify a few genes of interest, they are now being creatively applied for hypothesis generation and testing

  7. Genome-wide scan for loci of Asperger syndrome.

    Science.gov (United States)

    Ylisaukko-oja, T; Nieminen-von Wendt, T; Kempas, E; Sarenius, S; Varilo, T; von Wendt, L; Peltonen, L; Järvelä, I

    2004-02-01

    Asperger syndrome (AS), characterised by inadequate social interaction, lack of empathy and a dependence of routines and rituals, is classified as belonging to the autism spectrum disorders (DSM-IV and ICD-10). Although the prevalence of AS has been estimated to range from 0.3 up to 48.4 per 10 000, the phenotype still remains relatively unrecognised by clinicians. Several reports, including the original description by Hans Asperger (1944), have suggested that AS has a strong genetic component. Here, we have performed a genome-wide scan on Finnish families ascertained for AS with a strictly defined phenotype. In the initial scan, Z(max)>1.5 was observed on nine chromosomal regions, 1q21-22, 3p14-24, 3q25-27, 4p14, 4q32, 6p25, 6q16, 13q31-33 and 18p11. In the fine mapping stage, the highest two-point LOD scores were observed on chromosomes 1q21-22 (D1S484, Z(max dom)=3.58), 3p14-24 (D3S2432, Z(max dom)=2.50) and 13q31-33 (D13S793, Z(max dom)=1.59). The loci on 1q21-22 and 3p14-24 overlap with previously published autism susceptibility loci, and the loci on 1q21-22 and 13q31-33 overlap with the reported schizophrenia susceptibility loci. The present study is the first genome-wide screen in AS and therefore replication data sets are needed to evaluate further the significance of the AS-loci identified here. PMID:14966474

  8. 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.

  9. Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part I: Methods and Power Analysis

    OpenAIRE

    Levinson, Douglas F.; Levinson, Matthew D.; Segurado, Ricardo; Lewis, Cathryn M

    2003-01-01

    This is the first of three articles on a meta-analysis of genome scans of schizophrenia (SCZ) and bipolar disorder (BPD) that uses the rank-based genome scan meta-analysis (GSMA) method. Here we used simulation to determine the power of GSMA to detect linkage and to identify thresholds of significance. We simulated replicates resembling the SCZ data set (20 scans; 1,208 pedigrees) and two BPD data sets using very narrow (9 scans; 347 pedigrees) and narrow (14 scans; 512 pedigrees) diagnoses. ...

  10. A Fast Implementation of a Scan Statistic for Identifying Chromosomal Patterns of Genome Wide Association Studies

    OpenAIRE

    Yan V. Sun; Jacobsen, Douglas M.; Turner, Stephen T; BOERWINKLE, Eric; Kardia, Sharon L. R.

    2009-01-01

    In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and...

  11. Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part II: Schizophrenia

    OpenAIRE

    Lewis, Cathryn M; Levinson, Douglas F.; Wise, Lesley H.; Delisi, Lynn E.; Straub, Richard E.; Hovatta, Iiris; Williams, Nigel M; Schwab, Sibylle G.; Pulver, Ann E.; Faraone, Stephen V.; Brzustowicz, Linda M.; Kaufmann, Charles A.; Garver, David L.; Gurling, Hugh M. D.; Lindholm, Eva

    2003-01-01

    Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across stu...

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

    Science.gov (United States)

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

    2010-09-01

    Genome scans have been used in the studies of ecological speciation to find genomic regions ('outlier loci') showing reduced gene flow between divergent populations/species. High-throughput sequencing ('454') offers new opportunities in this field via transcriptome sequencing. Divergent ecotypes of the marine gastropod Littorina saxatilis represent a good example of incipient ecological speciation. We performed a 454-based genome scan between H and M ecotypes of L. saxatilis from the British Isles using cDNA of pooled individuals. Allele frequencies were calculated for 2454 single nucleotide polymorphisms (SNPs), within 572 contigs, and 7% of loci were detected as outliers. Functional annotation of the contigs containing outlier SNPs showed that they included shell matrix and muscle proteins (lithostathine, mucin, titin), proteins involved in energetic metabolism (arginine kinase, NADH dehydrogenase) and reverse transcriptases. Follow-up investigations into these proteins and unannotated outliers will be a promising route in the study of ecological speciation in L. saxatilis. PMID:20695960

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

    Directory of Open Access Journals (Sweden)

    Wiuf Carsten

    2009-07-01

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

  14. Landmarks in Hybrid Planning

    Directory of Open Access Journals (Sweden)

    Mohamed Elkawkagy

    2013-11-01

    Full Text Available Although planning techniques achieved a significant progress during recent years, solving many planning problem still difficult even for modern planners. In this paper, we will adopt landmark concept to hybrid planning setting - a method that combines reasoning about procedural knowledge and causalities. Land-marks are a well-known concept in the realm of classical planning. Recently, they have been adapted to hierarchical approaches. Such landmarks can be extracted in a pre-processing step from a declarative hierarchical planning domain and problem description. It was shown how this technique allows for a considerable reduction of the search space by eliminating futile plan development options before the actual planning. Therefore, we will present a new approach to in¬tegrate landmark pre-processing technique in the context of hierarchical planning with landmark technique in the classical planning. This integration allows to incorporate the ability of using extracted landmark tasks from hierarchical domain knowledge in the form of HTN and using landmark literals from classical planning. To this end, we will construct a transformation technique to transform the hybrid planning domain into a classical domain model. The method¬ologies in this paper have been implemented successfully, and we will present some experimental results that give evidence for the consid-erable performance increase gained through planning system.

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

    DEFF Research Database (Denmark)

    Panagiotou, Orestis A; Travis, Ruth C

    2014-01-01

    BACKGROUND: No single-nucleotide polymorphisms (SNPs) specific for aggressive prostate cancer have been identified in genome-wide association studies (GWAS). OBJECTIVE: To test if SNPs associated with other traits may also affect the risk of aggressive prostate cancer. DESIGN, SETTING, AND PARTICIPANTS: SNPs implicated in any phenotype other than prostate cancer (p?10(-7)) were identified through the catalog of published GWAS and tested in 2891 aggressive prostate cancer cases and 4592 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). The 40 most significant SNPs were followed up in 4872 aggressive prostate cancer cases and 24 534 controls from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Odds ratios (ORs) and 95% confidence intervals (CIs) for aggressive prostate cancer were estimated. RESULTS AND LIMITATIONS: A total of 4666 SNPs were evaluated by the BPC3. Two signals were seen in regions already reported for prostate cancer risk. rs7014346 at 8q24.21 was marginally associated with aggressive prostate cancer in the BPC3 trial (p=1.6×10(-6)), whereas after meta-analysis by PRACTICAL the summary OR was 1.21 (95% CI 1.16-1.27; p=3.22×10(-18)). rs9900242 at 17q24.3 was also marginally associated with aggressive disease in the meta-analysis (OR 0.90, 95% CI 0.86-0.94; p=2.5×10(-6)). Neither of these SNPs remained statistically significant when conditioning on correlated known prostate cancer SNPs. The meta-analysis by BPC3 and PRACTICAL identified a third promising signal, marked by rs16844874 at 2q34, independent of known prostate cancer loci (OR 1.12, 95% CI 1.06-1.19; p=4.67×10(-5)); it has been shown that SNPs correlated with this signal affect glycine concentrations. The main limitation is the heterogeneity in the definition of aggressive prostate cancer between BPC3 and PRACTICAL. CONCLUSIONS: We did not identify new SNPs for aggressive prostate cancer. However, rs16844874 may provide preliminary genetic evidence on the role of the glycine pathway in prostate cancer etiology. PATIENT SUMMARY: We evaluated whether genetic variants associated with several traits are linked to the risk of aggressive prostate cancer. No new such variants were identified.

  16. BasemapLandmarks_CEMETERY

    Vermont Center for Geographic Information — The BasemapLandmarks_CEMETERY point layer contains cemeteries in the state of Vermont. The data is based on VTrans Town Highway Maps. Some points have been moved to...

  17. Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan

    Science.gov (United States)

    Dickson, Peter A.; Montgomery, Grant W.; Henders, Anjali; Campbell, Megan J.; Martin, Nicholas G.; James, Michael R.

    2005-01-01

    Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA–DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, despite their inherent instability during DNA replication, and the obvious challenge that this presents to WGA techniques. Here, we aimed to assess the applicability of MDA in STR genotyping by conducting a genome-wide scan of 768 STR markers for MDAs of 15 high quality genomic DNAs. We found that MDA genotyping call and accuracy rates were only marginally lower than for genomic DNA. Pooling of three replicate MDAs resulted in a small increase in both call rate and genotyping accuracy. We identified 34 STRs (4.4% of total markers) of which five essentially failed with MDA samples, and 29 of which showed elevated genotyping failures/discrepancies in the MDAs. We emphasise the importance of DNA and MDA quality checks, and the use of appropriate controls to identify problematic STR markers. PMID:16055919

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

    International Nuclear Information System (INIS)

    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)

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

    OpenAIRE

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

    1998-01-01

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

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

    OpenAIRE

    Jahanshad, Neda; Rajagopalan, Priya; Hua, Xue; Hibar, Derrek P.; Nir, Talia M.; Weiner, Michael W.; Medland, Sarah E.; Montgomery, Grant W.; Hansell, Narelle K.; Mcmahon, Katie L.; Zubicaray, Greig I.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.; Weiner, Michael

    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 s...

  1. Genome-wide association scan for five major dimensions of personality

    OpenAIRE

    Terracciano, Antonio; Sanna, Serena; Uda, Manuela; Deiana, Barbara; Usala, Gianluca; Busonero, Fabio; Maschio, Andrea; Scally, Matthew; Patriciu, Nicholas; Chen, Wei-Min; Distel, Marijn A.; Slagboom, Eline P.; Boomsma, Dorret I.; Villafuerte, Sandra; ?liwerska, El?bieta

    2008-01-01

    Personality traits are summarized by five broad dimensions with pervasive influences on major life outcomes, strong links to psychiatric disorders, and clear heritable components. To identify genetic variants associated with each of the five dimensions of personality we performed a genome wide association (GWA) scan of 3,972 individuals from a genetically isolated population within Sardinia, Italy. Based on analyses of 362,129 single nucleotide polymorphisms (SNPs) we found several strong sig...

  2. Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing.

    Science.gov (United States)

    Paris, Margot; Despres, Laurence

    2012-04-01

    AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier detection with 454 sequencing of AFLP fragments to obtain sequences from outlier loci. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant and Bti-susceptible A. aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetic algorithms. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences, and the 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin-binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis. PMID:22348648

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

    Science.gov (United States)

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

    2014-03-01

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

  4. City of Chicago Landmarks

    Science.gov (United States)

    The city of Chicago has many hundreds of wonderful architectural landmarks and this helpful website is a great resource for anyone with an interest in such matters. On the site, visitors can start by checking out the Landmarks Tours to get started. There over a dozen tours here, including Mansions Tour, Art Deco Tour, and Pre-Fire Chicago Tour. Moving on, visitors may also wish to look over the Architects area. Here they will encounter some of the usual suspects (Frank Lloyd Wright, Louis Sullivan, etc.) and learn about some lesser-known architects, such as Solon S. Beman and William W. Boyington, who designed the wonderful entrance to Rosehill Cemetery. The Style Guide offers a great primer for those who'd like to know more about two dozen architectural styles, including Craftsman, International, and Tudor Revival. Finally, the site also includes a Listings area, complete with information about all of the buildings on the city's official landmarks list.

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

    OpenAIRE

    Bhatia, Gaurav; Tandon, Arti; 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.

    2013-01-01

    We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations, and conclude that any selection in African Americans since admixture is sufficiently weak that it falls below the threshold of our power to detect it using a large sample size. These results stand in contrast to the findings of a recent stu...

  6. A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data

    OpenAIRE

    Wang, Zhen; Chen, Qiang; Yang, Yumei; Yang, Hongjie; He, Pengfei; Zhang, Zhe; Chen, Zhenliang; Liao, Rongrong; Tu, Yingying; Zhang, Xiangzhe; Wang, Qishan; Pan, Yuchun

    2014-01-01

    Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, genome-wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome-wide scale. Surveying for selection footprints across porcine genomes can be quite valuable for reve...

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

    DEFF Research Database (Denmark)

    Sylvester-Hvid, C.; Nielsen, Morten

    2004-01-01

    An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. 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-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201-12). Foreach HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 2 6 months after the genome was established), we have tested the majority 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.

  8. Genome-wide linkage and association scans for pulse pressure in Chinese twins

    DEFF Research Database (Denmark)

    Zhang, Dongfeng; Pang, Zengchang

    2012-01-01

    Elevated pulse pressure (PP) is associated with cardiovascular disorders and mortality in various populations. The genetic influence on PP has been confirmed by heritability estimates using related individuals. Recently, efforts have been made by mapping genes that are linked to the phenotype. We report the results of our gene mapping studies conducted in the Chinese population in mainland China. The genome-wide linkage and association scans were carried out on 63 middle-aged dizygotic twin pairs using high-density markers. The linkage analysis identified three significant linkage peaks (all with a single point P

  9. Genome-wide Association Scan for Childhood Caries Implicates Novel Genes

    OpenAIRE

    Shaffer, J. R.; Wang, X.; Feingold, E.; Lee, M.; Begum, F.; Weeks, D. E.; Cuenco, K. T.; Barmada, M. M.; Wendell, S. K.; Crosslin, D. R.; Laurie, C. C.; Doheny, K. F.; Pugh, E. W.; Zhang, Q.; Feenstra, B.

    2011-01-01

    Dental caries is the most common chronic disease in children and a major public health concern due to its increasing incidence, serious health and social co-morbidities, and socio-demographic disparities in disease burden. We performed the first genome-wide association scan for dental caries to identify associated genetic loci and nominate candidate genes affecting tooth decay in 1305 US children ages 3-12 yrs. Affection status was defined as 1 or more primary teeth with evidence of decay bas...

  10. Ordered Landmarks in Planning

    CERN Document Server

    Hoffmann, J; Sebastia, L; 10.1613/jair.1492

    2011-01-01

    Many known planning tasks have inherent constraints concerning the best order in which to achieve the goals. A number of research efforts have been made to detect such constraints and to use them for guiding search, in the hope of speeding up the planning process. We go beyond the previous approaches by considering ordering constraints not only over the (top-level) goals, but also over the sub-goals that will necessarily arise during planning. Landmarks are facts that must be true at some point in every valid solution plan. We extend Koehler and Hoffmann's definition of reasonable orders between top level goals to the more general case of landmarks. We show how landmarks can be found, how their reasonable orders can be approximated, and how this information can be used to decompose a given planning task into several smaller sub-tasks. Our methodology is completely domain- and planner-independent. The implementation demonstrates that the approach can yield significant runtime performance improvements when used...

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

    OpenAIRE

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

    2005-01-01

    Abstract In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA). Using the 7-cM microsatellite map, nonparametric multipoint linkage analyses were performed separately on each of the four simulated populations independently to determine p-values. The genome of each population was divided into 20-cM bin regions, and each bin was rank-ordered based on the most significa...

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

    Directory of Open Access Journals (Sweden)

    Regan Kelly R

    2010-05-01

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

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

    Directory of Open Access Journals (Sweden)

    Gasser Thomas

    2007-07-01

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

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

    OpenAIRE

    David Jean-Philippe; Tetreau Guillaume; Paris Margot; Bonin Aurélie; Després Laurence

    2009-01-01

    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 conductin...

  15. National Historic Chemical Landmarks

    Science.gov (United States)

    The American Chemical Society (ACS) displays the key roles chemists played in "expanding the frontiers of knowledge, advancing medicine and industry, and creating products from aspirin to zippers" at this website. Users can find clear summaries and images of the places, discoveries, and achievements that have been designated landmarks by ACS members and an international committee. Within many of the biographies, educators can find links to teaching guides and activities. Individuals that know of an unrecognized important element of the chemical heritage can learn how to nominate the site, artifact, or collection.

  16. Whole-genome scan for guttural pouch tympany in Arabian and German warmblood horses.

    Science.gov (United States)

    Zeitz, A; Spötter, A; Blazyczek, I; Diesterbeck, U; Ohnesorge, B; Deegen, E; Distl, O

    2009-12-01

    Equine guttural pouch tympany (GPT) is a hereditary disease in foals of several breeds, including thoroughbreds, Arabian, Quarter and warmblood horses. We performed a whole-genome scan for GPT in 143 horses from five Arabian and five German warmblood families and genotyped 257 microsatellites. Chromosome-wide significant linkage was detected on ECA2 and ECA15 using multipoint non-parametric linkage analyses. Analyses stratified by sex revealed chromosome-wide significant linkage on ECA2 for fillies and chromosome-wide significant linkage on ECA15 for colts. For Arabian colts, the quantitative trait locus (QTL) on ECA15 was genome-wide significant. Haplotypes including two to four microsatellites within the QTL on ECA2 and 15 in fillies and colts, respectively, were significantly associated with GPT for both breeds. Thus, our analysis indicated sex-specific QTL, a fact which is in agreement with a two- to fourfold higher incidence of GPT in females. This is the first report of QTL for equine GPT and a first step towards identifying genes responsible for GPT. PMID:19703122

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

    Science.gov (United States)

    Logean, Antoine; Rognan, Didier

    2002-04-01

    A new computational method (EpiDock) is proposed for predicting peptide binding to class I MHC proteins, from the amino acid sequence of any protein of immunological interest. Starting from the primary structure of the target protein, individual three-dimensional structures of all possible MHC-peptide (8-, 9- and 10-mers) complexes are obtained by homology modelling. A free energy scoring function (Fresno) is then used to predict the absolute binding free energy of all possible peptides to the class I MHC restriction protein. Assuming that immunodominant epitopes are usually found among the top MHC binders, the method can thus be applied to predict the location of immunogenic peptides on the sequence of the protein target. When applied to the prediction of HLA-A*0201-restricted T-cell epitopes from the Hepatitis B virus, EpiDock was able to recover 92% of known high affinity binders and 80% of known epitopes within a filtered subset of all possible nonapeptides corresponding to about one tenth of the full theoretical list. The proposed method is fully automated and fast enough to scan a viral genome in less than an hour on a parallel computing architecture. As it requires very few starting experimental data, EpiDock can be used: (i) to predict potential T-cell epitopes from viral genomes (ii) to roughly predict still unknown peptide binding motifs for novel class I MHC alleles. PMID:12400854

  18. 75 FR 69120 - National Natural Landmark Designations

    Science.gov (United States)

    2010-11-10

    ...currently lists 586 National Natural Landmarks nationwide. Of the...private parties. National Natural Landmark designation is not...activity, and does not imply a right of public access. However...use implications. National Natural Landmark preservation is...

  19. Comparative genome scan detects host-related divergent selection in the grasshopper Hesperotettix viridis.

    Science.gov (United States)

    Apple, Jennifer L; Grace, Tony; Joern, Anthony; St Amand, Paul; Wisely, Samantha M

    2010-09-01

    In this study, we used a comparative genome scan to examine patterns of population differentiation with respect to host plant use in Hesperotettix viridis, a Nearctic oligophagous grasshopper locally specialized on various Asteraceae including Solidago, Gutierrezia, and Ericameria. We identified amplified fragment length polymorphism (AFLP) loci with significantly elevated F(ST) (outlier loci) in multiple different-host and same-host comparisons of populations while controlling for geographic distance. By comparing the number and identities of outlier loci in different-host vs. same-host comparisons, we found evidence of host plant-related divergent selection for some population comparisons (Solidago- vs. Gutierrezia-feeders), while other comparisons (Ericameria- vs. Gutierrezia-feeders) failed to demonstrate a strong role for host association in population differentiation. In comparisons of Solidago- vs. Gutierrezia-feeding populations, a relatively high number of outlier loci observed repeatedly in different-host comparisons (35% of all outliers and 2.7% of all 625 AFLP loci) indicated a significant role for host-related selection in contributing to overall genomic differentiation in this grasshopper. Mitochondrial DNA sequence data revealed a star-shaped phylogeny with no host- or geography-related structure, low nucleotide diversity, and high haplotype diversity, suggesting a recent population expansion. mtDNA data do not suggest a long period of isolation in separate glacial refugia but are instead more compatible with a single glacial refugium and more recent divergence in host use. Our study adds to research documenting heterogeneity in differentiation across the genome as a consequence of divergent natural selection, a phenomenon that may occur as part of the process of ecological speciation. PMID:20735740

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

    Science.gov (United States)

    Webb, Bradley T; van den Oord, Edwin; Akkari, Anthony; Wilton, Steve; Ly, Tina; Duff, Rachael; Barnes, Kathleen C; Carlsen, Karin; Gerritsen, Jorrit; Lenney, Warren; Silverman, Michael; Sly, Peter; Sundy, John; Tsanakas, John; von Berg, Andrea; Whyte, Moira; Blumenthal, Malcolm; Vestbo, Jorgen; Middleton, Lefkos; Helms, Peter J; Anderson, Wayne H; Pillai, Sreekumar G

    2007-03-01

    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 > or = 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, and D8S2324, respectively. The results from chromosomes 1 and 3 replicate previous reports of linkage. We also replicate linkage to 5q with peak LODs of 1.96 (SPT(per)) and 1.77 (IgE) at or near marker D5S1480. Our results provide further evidence implicating chromosomes 1, 3, and 5q. The current report 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. PMID:17103228

  1. Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

    Science.gov (United States)

    Bigham, Abigail; Bauchet, Marc; Pinto, Dalila; Mao, Xianyun; Akey, Joshua M.; Mei, Rui; Scherer, Stephen W.; Julian, Colleen G.; Wilson, Megan J.; López Herráez, David; Brutsaert, Tom; Parra, Esteban J.; Moore, Lorna G.; Shriver, Mark D.

    2010-01-01

    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 studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude. PMID:20838600

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

    Science.gov (United States)

    Bigham, Abigail; Bauchet, Marc; Pinto, Dalila; Mao, Xianyun; Akey, Joshua M; Mei, Rui; Scherer, Stephen W; Julian, Colleen G; Wilson, Megan J; López Herráez, David; Brutsaert, Tom; Parra, Esteban J; Moore, Lorna G; Shriver, Mark D

    2010-09-01

    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 studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude. PMID:20838600

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

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E

    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, and D8S2324, respectively. The results from chromosomes 1 and 3 replicate previous reports of linkage. We also replicate linkage to 5q with peak LODs of 1.96 (SPT(per)) and 1.77 (IgE) at or near marker D5S1480. Our results provide further evidence implicating chromosomes 1, 3, and 5q. The current report 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.

  4. Genome-wide association scan for five major dimensions of personality

    Science.gov (United States)

    Terracciano, Antonio; Sanna, Serena; Uda, Manuela; Deiana, Barbara; Usala, Gianluca; Busonero, Fabio; Maschio, Andrea; Scally, Matthew; Patriciu, Nicholas; Chen, Wei-Min; Distel, Marijn A; Slagboom, Eline P; Boomsma, Dorret I; Villafuerte, Sandra; ?liwerska, El?bieta; Burmeister, Margit; Amin, Najaf; Janssens, A. Cecile J.W.; van Duijn, Cornelia M.; Schlessinger, David; Abecasis, Gonçalo R.; Costa, Paul T.

    2008-01-01

    Personality traits are summarized by five broad dimensions with pervasive influences on major life outcomes, strong links to psychiatric disorders, and clear heritable components. To identify genetic variants associated with each of the five dimensions of personality we performed a genome wide association (GWA) scan of 3,972 individuals from a genetically isolated population within Sardinia, Italy. Based on analyses of 362,129 single nucleotide polymorphisms (SNPs) we found several strong signals within or near genes previously implicated in psychiatric disorders. They include the association of Neuroticism with SNAP25 (rs362584, P = 5 × 10?5), Extraversion with BDNF and two cadherin genes (CDH13 and CDH23; Ps < 5 × 10?5), Openness with CNTNAP2 (rs10251794, P = 3 × 10?5), Agreeableness with CLOCK (rs6832769, P = 9 × 10?6), and Conscientiousness with DYRK1A (rs2835731, P = 3 × 10?5). Effect sizes were small (less than 1% of variance), and most failed to replicate in the follow-up independent samples (N up to 3,903), though the association between Agreeableness and CLOCK was supported in two of three replication samples (overall P = 2 × 10?5). We infer that a large number of loci may influence personality traits and disorders, requiring larger sample sizes for the GWA approach to identify significant genetic variants. PMID:18957941

  5. Whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux.

    Science.gov (United States)

    Cordell, Heather J; Darlay, Rebecca; Charoen, Pimphen; Stewart, Aisling; Gullett, Ambrose M; Lambert, Heather J; Malcolm, Sue; Feather, Sally A; Goodship, Timothy H J; Woolf, Adrian S; Kenda, Rajko B; Goodship, Judith A

    2010-01-01

    Primary vesicoureteric reflux accounts for approximately 10% of kidney failure requiring dialysis or transplantation, and sibling studies suggest a large genetic component. Here, we report a whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux and reflux nephropathy. We used linkage and family-based association approaches to analyze 320 white families (661 affected individuals, generally from families with two affected siblings) from two populations (United Kingdom and Slovenian). We found modest evidence of linkage but no clear overlap with previous studies. We tested for but did not detect association with six candidate genes (AGTR2, HNF1B, PAX2, RET, ROBO2, and UPK3A). Family-based analysis detected associations with one single-nucleotide polymorphism (SNP) in the UK families, with three SNPs in the Slovenian families, and with three SNPs in the combined families. A case-control analysis detected associations with three additional SNPs. The results of this study, which is the largest to date investigating the genetics of reflux, suggest that major loci may not exist for this common renal tract malformation within European populations. PMID:19959718

  6. Landmarks GIScience for intelligent services

    CERN Document Server

    Richter, Kai-Florian

    2014-01-01

    This book covers the latest research on landmarks in GIS, including practical applications. It addresses perceptual and cognitive aspects of natural and artificial cognitive systems, computational aspects with respect to identifying or selecting landmarks for various purposes, and communication aspects of human-computer interaction for spatial information provision. Concise and organized, the book equips readers to handle complex conceptual aspects of trying to define and formally model these situations. The book provides a thorough review of the cognitive, conceptual, computational and commun

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

    Science.gov (United States)

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

    2013-01-01

    Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection. PMID:23237097

  8. 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 genome sequence and MITE characterization to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.

  9. 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.

  10. A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data.

    Science.gov (United States)

    Wang, Zhen; Chen, Qiang; Yang, Yumei; Yang, Hongjie; He, Pengfei; Zhang, Zhe; Chen, Zhenliang; Liao, Rongrong; Tu, Yingying; Zhang, Xiangzhe; Wang, Qishan; Pan, Yuchun

    2014-12-01

    Pigs have experienced dramatic selection due to domestication, which has led to many different phenotypes when compared to their wild counterparts, especially in the last several decades. Currently, genome-wide scans in both cattle and humans showing positive selection footprints have been investigated. However, few studies have focused on porcine selection footprints, particularly on a genome-wide scale. Surveying for selection footprints across porcine genomes can be quite valuable for revealing the genetic mechanisms of phenotypic diversity. Here, we employed a medium sequencing depth (5-20x/site per individual, on average) approach called genotyping by genome reducing and sequencing (GGRS) to detect genome-wide selection signatures of two domestic pig breeds (Yorkshire and Landrace) that have been under intensive selection for traits of muscle development, growth and behavior. The relative extended haplotype homozygosity test, which identifies selection signatures by measuring the characteristics of haplotypes' frequency distribution within a single population, was also applied to identify potential positively selected regions. As a result, signatures of positive selection were found in each breed. However, most selection signatures were population specific and related to genomic regions containing genes for biological categories including brain development, metabolism, growth and olfaction. Furthermore, the result of the gene set enrichment analysis indicated that selected regions of the two breeds presented a different over-representation of genes in the Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathways. Our results revealed a genome-wide map of selection footprints in pigs and may help us better understand the mechanisms of selection in pig breeding. PMID:25327778

  11. Genome-Wide Linkage Scan in Gullah-Speaking African American Families With Type 2 Diabetes

    Science.gov (United States)

    Sale, Michèle M.; Lu, Lingyi; Spruill, Ida J.; Fernandes, Jyotika K.; Lok, Kerry H.; Divers, Jasmin; Langefeld, Carl D.; Garvey, W. Timothy

    2009-01-01

    OBJECTIVE—The Gullah-speaking African American population from the Sea Islands of South Carolina is characterized by a low degree of European admixture and high rates of type 2 diabetes and diabetic complications. Affected relative pairs with type 2 diabetes were recruited through the Sea Islands Genetic African American Registry (Project SuGAR). RESEARCH DESIGN AND METHODS—We conducted a genome-wide linkage scan, genotyping 5,974 single nucleotide polymorphisms in 471 affected subjects and 50 unaffected relatives from 197 pedigrees. Data were analyzed using a multipoint engine for rapid likelihood inference and ordered subsets analyses (OSAs) for age at type 2 diabetes diagnosis, waist circumference, waist-to-hip ratio, and BMI. We searched for heterogeneity and interactions using a conditional logistic regression likelihood approach. RESULTS—Linkage peaks on chromosome 14 at 123–124 cM were detected for type 2 diabetes (logarithm of odds [LOD] 2.10) and for the subset with later age at type 2 diabetes diagnosis (maximum LOD 4.05). Two linkage peaks on chromosome 7 were detected at 44–45 cM for type 2 diabetes (LOD 1.18) and at 78 cM for type 2 diabetes (LOD 1.64) and the subset with earlier age at type 2 diabetes diagnosis (maximum LOD 3.93). The chromosome 14 locus and a peak on 7p at 29.5 cM were identified as important in the multilocus model. Other regions that provided modest evidence for linkage included chromosome 1 at 167.5 cM (LOD 1.51) and chromosome 3 at 121.0 cM (LOD 1.61). CONCLUSIONS—This study revealed a novel type 2 diabetes locus in an African American population on 14q that appears to reduce age of disease onset and confirmed two loci on chromosome 7. PMID:18835935

  12. Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan

    OpenAIRE

    Dickson, Peter A.; Montgomery, Grant W.; Henders, Anjali; Campbell, Megan J.; Martin, Nicholas G.; James, Michael R.

    2005-01-01

    Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA–DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, desp...

  13. Testing groups of genomic locations for enrichment in disease loci using linkage scan data: A method for hypothesis testing

    Directory of Open Access Journals (Sweden)

    Avramopoulos Dimitrios

    2006-06-01

    Full Text Available Abstract Genes for complex disorders have proven hard to find using linkage analysis. The results rarely reach the desired level of significance and researchers often have failed to replicate positive findings. There is, however, a wealth of information from other scientific approaches which enables the formation of hypotheses on groups of genes or genomic regions likely to be enriched in disease loci. Examples include genes belonging to specific pathways or producing proteins interacting with known risk factors, genes that show altered expression levels in patients or even the group of top scoring locations in a linkage study. We show here that this hypothesis of enrichment for disease loci can be tested using genome-wide linkage data, provided that these data are independent from the data used to generate the hypothesis. Our method is based on the fact that non-parametric linkage analyses are expected to show increased scores at each one of the disease loci, although this increase might not rise above the noise of stochastic variation. By using a summary statistic and calculating its empirical significance, we show that enrichment hypotheses can be tested with power higher than the power of the linkage scan data to identify individual loci. Via simulated linkage scans for a number of different models, we gain insight in the interpretation of genome scan results and test the power of our proposed method. We present an application of the method to real data from a late-onset Alzheimer's disease linkage scan as a proof of principle.

  14. 3D facial landmarks : Inter-operator variability of manual annotation

    DEFF Research Database (Denmark)

    Fagertun, Jens; Harder, Stine

    2014-01-01

    BACKGROUND: Manual annotation of landmarks is a known source of variance, which exist in all fields of medical imaging, influencing the accuracy and interpretation of the results. However, the variability of human facial landmarks is only sparsely addressed in the current literature as opposed to e.g. the research fields of orthodontics and cephalometrics. We present a full facial 3D annotation procedure and a sparse set of manually annotated landmarks, in effort to reduce operator time and minimize the variance. METHOD: Facial scans from 36 voluntary unrelated blood donors from the Danish Blood Donor Study was randomly chosen. Six operators twice manually annotated 73 anatomical and pseudo-landmarks, using a three-step scheme producing a dense point correspondence map. We analyzed both the intra- and inter-operator variability, using mixed-model ANOVA. We then compared four sparse sets of landmarks in order to construct a dense correspondence map of the 3D scans with a minimum point variance. RESULTS: The anatomical landmarks of the eye were associated with the lowest variance, particularly the center of the pupils. Whereas points of the jaw and eyebrows have the highest variation. We see marginal variability in regards to intra-operator and portraits. Using a sparse set of landmarks (n=14), that capture the whole face, the dense point mean variance was reduced from 1.92 to 0.54 mm. CONCLUSION: The inter-operator variability was primarily associated with particular landmarks, where more leniently landmarks had the highest variability. The variables embedded in the portray and the reliability of a trained operator did only have marginal influence on the variability. Further, using 14 of the annotated landmarks we were able to reduced the variability and create a dense correspondences mesh to capture all facial features.

  15. 3D facial landmarks: Inter-operator variability of manual annotation

    DEFF Research Database (Denmark)

    Fagertun, Jens; Harder, Stine

    2014-01-01

    Background Manual annotation of landmarks is a known source of variance, which exist in all fields of medical imaging, influencing the accuracy and interpretation of the results. However, the variability of human facial landmarks is only sparsely addressed in the current literature as opposed to e.g. the research fields of orthodontics and cephalometrics. We present a full facial 3D annotation procedure and a sparse set of manually annotated landmarks, in effort to reduce operator time and minimize the variance. Method Facial scans from 36 voluntary unrelated blood donors from the Danish Blood Donor Study was randomly chosen. Six operators twice manually annotated 73 anatomical and pseudo-landmarks, using a three-step scheme producing a dense point correspondence map. We analyzed both the intra- and inter-operator variability, using mixed-model ANOVA. We then compared four sparse sets of landmarks in order to construct a dense correspondence map of the 3D scans with a minimum point variance. Results The anatomical landmarks of the eye were associated with the lowest variance, particularly the center of the pupils. Whereas points of the jaw and eyebrows have the highest variation. We see marginal variability in regards to intra-operator and portraits. Using a sparse set of landmarks (n=14), that capture the whole face, the dense point mean variance was reduced from 1.92 to 0.54 mm. Conclusion The inter-operator variability was primarily associated with particular landmarks, where more leniently landmarks had the highest variability. The variables embedded in the portray and the reliability of a trained operator did only have marginal influence on the variability. Further, using 14 of the annotated landmarks we were able to reduced the variability and create a dense correspondences mesh to capture all facial features.

  16. 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.

  17. Reproducibility of imaging skull anatomic landmarks utilizing three-dimensional computed tomography

    International Nuclear Information System (INIS)

    The study investigated the reproducibility of locating specific anatomic landmarks, utilizing computed tomography (CT), for the purpose of assigning accurate coordinates on the skull. Three-dimensional (3-D) CT data, obtained by scanning a dry adult skull, were processed using a multi-planar reconstruction (MPR) system. Each landmark was identified five times by the same technician, and the average distances between points identifying the same landmark were calculated. The 15 landmarks studied were the infra-orbital foramina, the external auditory meatus, the foramina rotundum, the foramina ovale, the optic canals, anterior crinoid processes, anterior nasal spine, crista galli, and the sella turcica. Three additional artificial markers placed in occlusal dental splints were also examined. The crinoid processes were identified with the highest degree of accuracy. The crista galli and optic canals were also located with reproducible results. The standard deviation calculated from the fine attempts to locate the artificial markers was smaller than that calculated from attempts to identify any of the landmarks. This implies that coordinates on the craniofacial bones should be defined using artificial markers rather than bony landmarks. Artificial markers placed in occlusal dental splints easily can be applied clinically. Complicated facial bone contours should be analyzed mathematically. In clinical setting, these points were found to be reproducible in 15 bony landmarks d to be reproducible in 15 bony landmarks on the skull. (N.K.)

  18. An Evaluation of Cellular Neural Networks for the Automatic Identification of Cephalometric Landmarks on Digital Images

    Directory of Open Access Journals (Sweden)

    Rosalia Leonardi

    2009-01-01

    Full Text Available Several efforts have been made to completely automate cephalometric analysis by automatic landmark search. However, accuracy obtained was worse than manual identification in every study. The analogue-to-digital conversion of X-ray has been claimed to be the main problem. Therefore the aim of this investigation was to evaluate the accuracy of the Cellular Neural Networks approach for automatic location of cephalometric landmarks on softcopy of direct digital cephalometric X-rays. Forty-one, direct-digital lateral cephalometric radiographs were obtained by a Siemens Orthophos DS Ceph and were used in this study and 10 landmarks (N, A Point, Ba, Po, Pt, B Point, Pg, PM, UIE, LIE were the object of automatic landmark identification. The mean errors and standard deviations from the best estimate of cephalometric points were calculated for each landmark. Differences in the mean errors of automatic and manual landmarking were compared with a 1-way analysis of variance. The analyses indicated that the differences were very small, and they were found at most within 0.59?mm. Furthermore, only few of these differences were statistically significant, but differences were so small to be in most instances clinically meaningless. Therefore the use of X-ray files with respect to scanned X-ray improved landmark accuracy of automatic detection. Investigations on softcopy of digital cephalometric X-rays, to search more landmarks in order to enable a complete automatic cephalometric analysis, are strongly encouraged.

  19. Distance Landmarks Revisited for Road Graphs

    OpenAIRE

    Ma, Shuai; Feng, Kaiyu; Wang, Haixun; Li, Jianxin; Huai, Jinpeng

    2014-01-01

    Computing shortest distances is one of the fundamental problems on graphs, and remains a {\\em challenging} task today. {\\em Distance} {\\em landmarks} have been recently studied for shortest distance queries with an auxiliary data structure, referred to as {\\em landmark} {\\em covers}. This paper studies how to apply distance landmarks for fast {\\em exact} shortest distance query answering on large road graphs. However, the {\\em direct} application of distance landmarks is {\\e...

  20. 3D facial landmark detection under large yaw and expression variations.

    Science.gov (United States)

    Perakis, Panagiotis; Passalis, Georgios; Theoharis, Theoharis; Kakadiaris, Ioannis A

    2013-07-01

    A 3D landmark detection method for 3D facial scans is presented and thoroughly evaluated. The main contribution of the presented method is the automatic and pose-invariant detection of landmarks on 3D facial scans under large yaw variations (that often result in missing facial data), and its robustness against large facial expressions. Three-dimensional information is exploited by using 3D local shape descriptors to extract candidate landmark points. The shape descriptors include the shape index, a continuous map of principal curvature values of a 3D object's surface, and spin images, local descriptors of the object's 3D point distribution. The candidate landmarks are identified and labeled by matching them with a Facial Landmark Model (FLM) of facial anatomical landmarks. The presented method is extensively evaluated against a variety of 3D facial databases and achieves state-of-the-art accuracy (4.5-6.3 mm mean landmark localization error), considerably outperforming previous methods, even when tested with the most challenging data. PMID:23681986

  1. Frontal sinus depth at four landmarks in breeds of dog typically affected by sinonasal aspergillosis.

    Science.gov (United States)

    Burrow, R; McCarroll, D; Baker, M; Darby, P; McConnell, F; Cripps, P

    2012-01-01

    The objective of this study was to assess whether the frontal sinuses in dogs with aspergillosis and of breeds typically affected by this condition were deeper at a more caudal location. CT scans of the head performed at the Small Animal Teaching Hospital, University of Liverpool, between April 2007 and March 2009 for dogs diagnosed with aspergillosis (group 1) and unaffected dogs of similar breeds (group 2) were selected for study. Sinus depth was measured at four standardised locations from reconstructed images of these CT scans. Data were compared for differences in sinus depth between groups and between landmarks. No significant difference was found between measurements within individual dogs or for each of the various landmarks between groups. Difference in depth of the sinuses between landmarks was significant (P<0.001). Sinus depth was significantly greater at the more caudal landmarks and was shallowest at the previously recommended landmark for sinus entry. In 54 per cent of dogs, the frontal sinus depth measured less than or equal to 2 cm at one or more of the landmarks. Sinus entry at the deepest point will reduce the risk of accidentally damaging underlying structures. This may be approximately 1 cm caudal, in breeds of dog that typically develop aspergillosis, to a previously suggested landmark. PMID:22016511

  2. A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon.

    Science.gov (United States)

    Reddy, Umesh K; Abburi, Lavanya; Abburi, Venkata Lakshmi; Saminathan, Thangasamy; Cantrell, Robert; Vajja, Venkata Gopinath; Reddy, Rishi; Tomason, Yan R; Levi, Amnon; Wehner, Todd C; Nimmakayala, Padma

    2015-01-01

    Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5' untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness. PMID:25425675

  3. A pose-independent method for 3D face landmark formalization.

    Science.gov (United States)

    Vezzetti, Enrico; Moos, Sandro; Marcolin, Federica; Stola, Vincenzo

    2012-12-01

    Recently, 3D landmark extraction has been widely researched and experimented in medical field, for both corrective and aesthetic purposes. Automation of these procedures on three-dimensional face renderings is something desirable for the specialists who work in this field. In this work we propose a new method for accurate landmark localization on facial scans. The method relies on geometrical descriptors, such as curvatures and Shape Index, for computing candidate and initial points, and on a statistical model based on Procrustes Analysis and Principal Component Analysis, which is fitted to candidate points, for extracting the final landmarks. The elaborated method is independent on face pose. PMID:22939737

  4. Information content in genome-wide scans: concordance between patterns of genetic differentiation and linkage mapping associations

    Directory of Open Access Journals (Sweden)

    Law Andrew

    2011-01-01

    Full Text Available Abstract Background Scanning the genome with high density SNP markers has become a standard approach for identifying regions of the genome showing substantial between-population genetic differentiation, and thus evidence of diversifying selection. Such regions may contain genes of large phenotypic effect. However, few studies have attempted to address the power or efficacy of such an approach. Results In this study, the patterns of allele frequency differences between two cattle breeds based on the Bovine HapMap study were compared with statistical evidence for QTL based on a linkage mapping study of an experimental population formed by a cross between the same breeds. Concordance between the two datasets was seen for chromosomes carrying QTL with strong statistical support, such as BTA5 and BTA18, which carry genes associated with coat color. For these chromosomes, there was a correspondence between the strength of the QTL signal along the chromosome and the degree of genetic differentiation between breeds. However, such an association was not seen in a broader comparison that also included chromosomes carrying QTL with lower significance levels. In addition, other chromosomal regions with substantial QTL effects did not include markers showing extreme between-breed genetic differentiation. Furthermore, the overall consistency between the two studies was weak, with low genome-wide correlation between the statistical values obtained in the linkage mapping study and between-breed genetic differentiation from the HapMap study. Conclusions These results suggest that genomic diversity scans are capable of detecting regions associated with qualitative traits but may be limited in their power to detect regions associated with quantitative phenotypic differences between populations, which may depend on the marker resolution of the study and the level of LD in the populations under investigation.

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

    OpenAIRE

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

    1998-01-01

    Genetic factors influence the development of type II diabetes mellitus, but genetic loci for the most common forms of diabetes have not been identified. A genomic scan was conducted to identify loci linked to diabetes and body-mass index (BMI) in Pima Indians, a Native American population with a high prevalence of type II diabetes. Among 264 nuclear families containing 966 siblings, 516 autosomal markers with a median distance between adjacent markers of 6.4 cM were genotyped. Variance-compon...

  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

    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. A genome scan for parent-of-origin linkage effects in alcoholism

    OpenAIRE

    Wang Ke-Sheng; Mt, Greenwood Celia; Liu Xiao-Qing; Paterson Andrew D

    2005-01-01

    Abstract Background Alcoholism is a complex disease in which genomic imprinting may play an important role in its susceptibility. Objective To conduct a genome-wide search for loci that may have strong parent-of-origin linkage effects in alcoholism; to compare the linkage results between the microsatellites and the two single-nucleotide polymorphism (SNP) platforms. Methods Nonparametric linkage analyses were performed using ALLEGRO with the three sets of markers provided by the Genetic Analy...

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

    Directory of Open Access Journals (Sweden)

    Prasad Aparna

    2010-03-01

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

  9. Combined Genome Scans for Body Stature in 6,602 European Twins: Evidence for Common Caucasian Loci

    Science.gov (United States)

    Perola, Markus; Sammalisto, Sampo; Hiekkalinna, Tero; Martin, Nick G; Visscher, Peter M; Montgomery, Grant W; Benyamin, Beben; Harris, Jennifer R; Boomsma, Dorret; Willemsen, Gonneke; Hottenga, Jouke-Jan; Christensen, Kaare; Kyvik, Kirsten Ohm; Sørensen, Thorkild I. A; Pedersen, Nancy L; Magnusson, Patrik K. E; Spector, Tim D; Widen, Elisabeth; Silventoinen, Karri; Kaprio, Jaakko; Palotie, Aarno; Peltonen, Leena

    2007-01-01

    Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locus (QTL) analysis of one of the most heritable human complex traits, adult stature (body height) using genome-wide scans performed for 3,817 families (8,450 individuals) derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom with an approximate ten-centimorgan microsatellite marker map. The marker maps for different studies differed and they were 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 was 81% for stature in the pooled dataset. We found evidence for a major QTL for human stature on 8q21.3 (multipoint logarithm of the odds 3.28), and suggestive evidence for loci on Chromosomes X, 7, and 20. Some evidence of sex heterogeneity was found, however, no obvious female-specific QTLs emerged. 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 loci (http://www.genomeutwin.org/stature_gene_map.htm). PMID:17559308

  10. A genome-wide scan for breast cancer risk haplotypes among African American women.

    Science.gov (United States)

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

    2013-01-01

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

  11. Mapping of quantitative trait loci for blood pressure and cardiac mass in the rat by genome scanning of recombinant inbred strains.

    OpenAIRE

    PRAVENEC, M; Gauguier, D; Schott, JJ; Buard, J.; Kren, V; Bila, V; Szpirer, C.; SZPIRER, J; Wang, JM; Huang, H.

    1995-01-01

    In the HXB and BXH recombinant inbred strains derived from the spontaneously hypertensive rat and the normotensive Brown Norway rat, we determined the strain distribution patterns of 500 genetic markers to scan the rodent genome for quantitative trait loci regulating cardiac mass and blood pressure. The markers spanned approximately 1,139 cM of the genome and were tested for correlations with left ventricular mass adjusted for body weight, and with systolic, diastolic, and mean arterial press...

  12. Sequence-tagged connectors: A sequence approach to mapping and scanning the human genome

    OpenAIRE

    Mahairas, Gregory G.; Wallace, James C.; Smith, Kim; Swartzell, Steven; Holzman, Ted; Keller, Andrew; Shaker, Ron; Furlong, Jeff; Young, Janet; Zhao, Shaying; Adams, Mark D.; Hood, Leroy

    1999-01-01

    The sequence-tagged connector (STC) strategy proposes to generate sequence tags densely scattered (every 3.3 kilobases) across the human genome by arraying 450,000 bacterial artificial chromosomes (BACs) with randomly cleaved inserts, sequencing both ends of each, and preparing a restriction enzyme fingerprint of each. The STC resource, containing end sequences, fingerprints, and arrayed BACs, creates a map where the interrelationships of the individual BAC clones are resolved through their S...

  13. Genome Scan for Tourette Disorder in Affected-Sibling-Pair and Multigenerational Families

    OpenAIRE

    2006-01-01

    Tourette disorder (TD) is a neuropsychiatric disorder with a complex mode of inheritance and is characterized by multiple waxing and waning motor and phonic tics. This article reports the results of the largest genetic linkage study yet undertaken for TD. The sample analyzed includes 238 nuclear families yielding 304 “independent” sibling pairs and 18 separate multigenerational families, for a total of 2,040 individuals. A whole-genome screen with the use of 390 microsatellite markers was...

  14. 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. PMID:25183526

  15. [Genome-wide scan reveals the molecular mechanisms of functional differentiation of Myotis lucifugus and Pteropus vampyrus].

    Science.gov (United States)

    Zeng, Yan-Ni; Shen, Yong-Yi; Zhang, Ya-Ping

    2013-06-01

    The physiological and behavioral differences between Myotis lucifugus and Pteropus vampyrus should be attributed to molecular mechanisms and deserve intensive investigation. We conducted genome-wide scan for coding sequences from the orthologue genes of seven mammalian species. Selection analyses were carried out by setting the branches leading to Myotis lucifugus and Pteropus vampyrus as foreground branches, respectively. Enrichment analyses were conducted for positively selected genes. Our results indicated that more genes exhibited positive selection in Myotis lucifugus than that in Pteropus vampyrus. The positively selected genes of the two species were enriched in different functions. The differences between Myotis lucifugus and Pteropus vampyrus represented their differentiation in biological functions, especially the functions of immunity, motor ability, energetic metabolism and sensory organ development. PMID:23775999

  16. A genome-wide scan for type 1 diabetes susceptibility genes in nuclear families with multiple affected siblings in Finland

    Directory of Open Access Journals (Sweden)

    Cordell Heather J

    2007-12-01

    Full Text Available Abstract Background A genome-wide search for genes that predispose to type 1 diabetes using linkage analysis was performed using 900 microsatellite markers in 70 nuclear families with affected siblings from Finland, a population expected to be more genetically homogeneous than others, and having the highest incidence of type 1 diabetes in the world and, yet, the highest proportion in Europe of cases (10% carrying neither of the highest risk HLA haplotypes that include DR3 or DR4 alleles. Results In addition to the evidence of linkage to the HLA region on 6p21 (nominal p = 4.0 × 10-6, significant evidence of linkage in other chromosome regions was not detected with a single-locus analysis. The two-locus analysis conditional on the HLA gave a maximum lod score (MLS of 3.1 (nominal p = 2 × 10-4 on chromosome 9p13 under an additive model; MLS of 2.1 (nominal p = 6.1 × 10-3 on chromosome 17p12 and MLS of 2.5 (nominal p = 2.9 × 10-3 on chromosome 18p11 under a general model. Conclusion Our genome scan data confirmed the primary contribution of the HLA genes also in the high-risk Finnish population, and suggest that non-HLA genes also contribute to the familial clustering of type 1 diabetes in Finland.

  17. Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm.

    Science.gov (United States)

    Patocchi, A; Walser, M; Tartarini, S; Broggini, G A L; Gennari, F; Sansavini, S; Gessler, C

    2005-08-01

    For all known major apple scab resistance genes except Vr, molecular markers have been published. However, the precise position of some of these genes, in the apple genome, remains to be identified. Knowledge about the relative position of apple scab resistance genes is necessary to preliminarily evaluate the probability of success of their pyramidization. Pyramidization of different resistance genes into the same genotype is a reliable way to create cultivars with durable apple scab resistance. Applying the genome scanning approach (GSA), we identified the linkage group of the scab resistance gene Vm, derived from Malus micromalus, and we found a new molecular marker tightly associated with the gene. The simple sequence repeat Hi07h02, previously mapped on linkage group 17, cosegregates with the Vm gene (no recombinants in the 95 plants tested). The already published sequence-characterized amplified region Vm marker OPB12(687) was found to be linked at about 5 cM from the resistance gene and, therefore, this marker also maps on linkage group 17 of apple. This is the first report of the discovery of a major apple scab resistance gene on linkage group 17. The advantages of using GSA for the identification of molecular markers for qualitative traits are discussed. PMID:16094431

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

    Science.gov (United States)

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

    2014-10-01

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas. PMID:25242497

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

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Bustamente, Carlos

    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 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.

  20. 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.

  1. 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

  2. Genome-wide association Scan of dental caries in the permanent dentition

    Directory of Open Access Journals (Sweden)

    Wang Xiaojing

    2012-12-01

    Full Text Available Abstract Background Over 90% of adults aged 20 years or older with permanent teeth have suffered from dental caries leading to pain, infection, or even tooth loss. Although caries prevalence has decreased over the past decade, there are still about 23% of dentate adults who have untreated carious lesions in the US. Dental caries is a complex disorder affected by both individual susceptibility and environmental factors. Approximately 35-55% of caries phenotypic variation in the permanent dentition is attributable to genes, though few specific caries genes have been identified. Therefore, we conducted the first genome-wide association study (GWAS to identify genes affecting susceptibility to caries in adults. Methods Five independent cohorts were included in this study, totaling more than 7000 participants. For each participant, dental caries was assessed and genetic markers (single nucleotide polymorphisms, SNPs were genotyped or imputed across the entire genome. Due to the heterogeneity among the five cohorts regarding age, genotyping platform, quality of dental caries assessment, and study design, we first conducted genome-wide association (GWA analyses on each of the five independent cohorts separately. We then performed three meta-analyses to combine results for: (i the comparatively younger, Appalachian cohorts (N?=?1483 with well-assessed caries phenotype, (ii the comparatively older, non-Appalachian cohorts (N?=?5960 with inferior caries phenotypes, and (iii all five cohorts (N?=?7443. Top ranking genetic loci within and across meta-analyses were scrutinized for biologically plausible roles on caries. Results Different sets of genes were nominated across the three meta-analyses, especially between the younger and older age cohorts. In general, we identified several suggestive loci (P-value???10E-05 within or near genes with plausible biological roles for dental caries, including RPS6KA2 and PTK2B, involved in p38-depenedent MAPK signaling, and RHOU and FZD1, involved in the Wnt signaling cascade. Both of these pathways have been implicated in dental caries. ADMTS3 and ISL1 are involved in tooth development, and TLR2 is involved in immune response to oral pathogens. Conclusions As the first GWAS for dental caries in adults, this study nominated several novel caries genes for future study, which may lead to better understanding of cariogenesis, and ultimately, to improved disease predictions, prevention, and/or treatment.

  3. A genome-wide scan in affected sibling pairs with idiopathic recurrent miscarriage suggests genetic linkage

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, H S

    2011-01-01

    Previously, siblings of patients with idiopathic recurrent miscarriage (IRM) have been shown to have a higher risk of miscarriage. This study comprises two parts: (i) an epidemiological part, in which we introduce data on the frequency of miscarriage among 268 siblings of 244 patients with IRM and (ii) a genetic part presenting data from a genome-wide linkage study of 38 affected sibling pairs with IRM. All IRM patients (probands) had experienced three or more miscarriages and affected siblings two or more miscarriages. The sibling pairs were genotyped by the Affymetrix GeneChip 50K XbaI platform and non-parametric linkage analysis was performed via the software package Merlin. We find that siblings of IRM patients exhibit a higher frequency of miscarriage than population controls regardless of age at the time of pregnancy. We identify chromosomal regions with LOD scores between 2.5 and 3.0 in subgroups of affected sibling pairs. Maximum LOD scores were identified in four occurrences: for rs10514716 (3p14.2) when analyzing sister-pairs only; for rs10511668 (9p22.1) and rs341048 (11q13.4) when only analyzing families where the probands have had four or more miscarriages; and for rs10485275 (6q16.3) when analyzing one sibling pair from each family only. We identify no founder mutations. Concluding, our results imply that IRM patients and their siblings share factors which increase the risk of miscarriage. In this first genome-wide linkage study of affected sibling pairs with IRM, we identify regions on chromosomes 3, 6, 9 and 11 which warrant further investigation in order to elucidate their putative roles in the genesis of IRM.

  4. 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.

  5. A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait

    DEFF Research Database (Denmark)

    Sahana, Goutam; Kadlecová, Veronika

    2013-01-01

    Feed conversion ratio (FCR) is an economically important trait in pigs and feed accounts for a significant proportion of the costs involved in pig production. In this study we used a high density SNP chip panel, Porcine SNP60 BeadChip, to identify association between FCR and SNP markers and to study the genetic architecture of the trait. After quality control, a total of 30,847 SNPs that could be mapped to the 18 porcine autosomes (SSC) following the pig genome assembly 10.2, were used in the analyses. Deregressed estimated breeding value was used as the response variable. A total of 3,071 Duroc pigs had both FCR data and genotype data. The linkage disequilibrium (r2) between adjacent markers was 0.56. Two association mapping approaches were used: linear mixed model (LMM) based on single locus regression analysis and a Bayesian variable selection approach (BVS). A total of 79 significant (p < 0.0001) SNP associations on six chromosomes were identified by LMM analyses. Out of these, ten SNPs crossed the genome-wide significance threshold. These ten SNPs were all located on the chromosomes 4 and 14. In the BVS analysis, a total of 44 SNPs located on 12 chromosomes had posterior probability more than or equal to 0.05, i.e. Bayes factor ? 10. Thirteen SNPs were identified both by LMM and BVS. These 13 SNPs were located on four chromosomes 4, 7, 8 and 14. Hypoxia inducible factor 1, alpha subunit inhibitor (HIF1AN) and Ladybird homeobox 1 (LBX1) are two possible candidate genes affecting FCR on chromosomes 4 and 14, respectively. The study provides a list of SNPs associated with FCR and also offers valuable information on the genetic architecture and candidate genes for this trait

  6. Autonomous Robot Navigation based on Visual Landmarks

    DEFF Research Database (Denmark)

    Livatino, Salvatore

    The use of landmarks for robot navigation is a popular alternative to having a geometrical model of the environment through which to navigate and monitor self-localization. If the landmarks are defined as special visual structures already in the environment then we have the possibility of fully autonomous navigation and self-localization using automatically selected landmarks. The thesis investigates autonomous robot navigation and proposes a new method which benefits from the potential of the visual sensor to provide accuracy and reliability to the navigation process while relying on naturally available environment features (natural landmarks). The goal is also to integrate techniques and algorithms (also related to other research field) in the same navigation system, in order to improve localization performance and system autonomy. The proposed localization strategy is based on a continuous update of the estimated robot position while the robot is moving. In order to make the system autonomous, both acquisition and observation of landmarks have to be carried out automatically. The thesis consequently proposes a method for learning and navigation of a working environment and it explores automatic acquisition and recognition of visual landmarks. In particular, a two-phase procedure is proposed: first phase is for an automatic acquisition of visual-landmarks, second phase is for estimating robot position during navigation (based on the acquired landmarks). The feasibility and applicability of the proposed method is based on a system with a simple setup. The novelty and potentiality, are in combining algorithms for panoramic view-synthesis, attention selection, stereo reconstruction, triangulation, optimal triplet selection, and image-based rendering. Experiments demonstrate that the system can automatically learn and store visual landmarks, and later recognize these landmarks from arbitrary positions and thus estimate robot position and heading.

  7. 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.

  8. Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D

    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 population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. RESULTS: High genetic diversity (? = 2.4 × 10(-4)), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, 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 drug-resistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. CONCLUSIONS: The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines.

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

    DEFF Research Database (Denmark)

    Ocholla, Harold; Preston, Mark D

    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 population genetics approaches to investigate genetic diversity and population structure and identify loci under selection. RESULTS: ?High genetic diversity (? = 2.4 × 10(-4)), moderately high multiplicity of infection (2.7), and low linkage disequilibrium (500-bp) were observed in Chikhwawa District, Malawi, 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 drug-resistance loci, including pfcrt, pfdhps, pfmdr1, and pfgch1. CONCLUSIONS: ?The sequence variations observed at drug-resistance loci reflect differences in each country's historical use of antimalarial drugs and may be useful in formulating local malaria treatment guidelines.

  10. Orbit and attitude state recoveries from Landmark data

    Science.gov (United States)

    Fuchs, A. F.; Velez, C. E.; Goad, C. C.

    1975-01-01

    The navigation of earth-referenced satellites with imaging data rather than, or in addition to, conventional radio tracking and attitude sensor telemetry is gaining increased popularity. Driving forces include a trend towards spacecraft autonomy, a need for timely and highly accurate gridding information, and a growing awareness of the presence of high quality navigation information contained in such data. This paper describes the techniques used and the results obtained in an experiment to determine the orbit and attitude state of the geosynchronous SMS-1 spacecraft from Landmark observations extracted from earth images generated by the on-board Visible and Infrared Spin-Scan Radiometer (VISSR).

  11. 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.

  12. The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations.

    Science.gov (United States)

    Vaughn, Justin N; Nelson, Randall L; Song, Qijian; Cregan, Perry B; Li, Zenglu

    2014-11-01

    Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean's unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ?100% and ?33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ?6×10(-5) per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean's nutrient portfolio. PMID:25246241

  13. Deviation of landmarks in accordance with methods of establishing reference planes in three-dimensional facial CT evaluation

    International Nuclear Information System (INIS)

    This study aimed to investigate the deviation of landmarks from horizontal or midsagittal reference planes according to the methods of establishing reference planes. Computed tomography (CT) scans of 18 patients who received orthodontic and orthognathic surgical treatment were reviewed. Each CT scan was reconstructed by three methods for establishing three orthogonal reference planes (namely, the horizontal, midsagittal, and coronal reference planes). The horizontal (bilateral porions and bilateral orbitales) and midsagittal (crista galli, nasion, prechiasmatic point, opisthion, and anterior nasal spine) landmarks were identified on each CT scan. Vertical deviation of the horizontal landmarks and horizontal deviation of the midsagittal landmarks were measured. The porion and orbitale, which were not involved in establishing the horizontal reference plane, were found to deviate vertically from the horizontal reference plane in the three methods. The midsagittal landmarks, which were not used for the midsagittal reference plane, deviated horizontally from the midsagittal reference plane in the three methods. In a three-dimensional facial analysis, the vertical and horizontal deviations of the landmarks from the horizontal and midsagittal reference planes could vary depending on the methods of establishing reference planes.

  14. Deviation of landmarks in accordance with methods of establishing reference planes in three-dimensional facial CT evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Kaeng Won; Yoon, Suk Ja; Kang, Byung Cheol; Kook, Min Suk; Lee, Jae Seo [School of Dentistry, Dental Science Research Institute, Chonnam National University, Gwangju (Korea, Republic of); Kim, Young Hee [Dept. of Oral and Maxillofacial Radiology, Hallym University Sacred Heart Hospital, Anyang (Korea, Republic of); Palomo, Juan Martin [Dept. of Orthodontics, School of Dental Medicine, Case Western Reserve University, Cleveland (Korea, Republic of)

    2014-09-15

    This study aimed to investigate the deviation of landmarks from horizontal or midsagittal reference planes according to the methods of establishing reference planes. Computed tomography (CT) scans of 18 patients who received orthodontic and orthognathic surgical treatment were reviewed. Each CT scan was reconstructed by three methods for establishing three orthogonal reference planes (namely, the horizontal, midsagittal, and coronal reference planes). The horizontal (bilateral porions and bilateral orbitales) and midsagittal (crista galli, nasion, prechiasmatic point, opisthion, and anterior nasal spine) landmarks were identified on each CT scan. Vertical deviation of the horizontal landmarks and horizontal deviation of the midsagittal landmarks were measured. The porion and orbitale, which were not involved in establishing the horizontal reference plane, were found to deviate vertically from the horizontal reference plane in the three methods. The midsagittal landmarks, which were not used for the midsagittal reference plane, deviated horizontally from the midsagittal reference plane in the three methods. In a three-dimensional facial analysis, the vertical and horizontal deviations of the landmarks from the horizontal and midsagittal reference planes could vary depending on the methods of establishing reference planes.

  15. A genome-wide scan in families with maturity-onset diabetes of the young : evidence for further genetic heterogeneity

    DEFF Research Database (Denmark)

    Frayling, Timothy M; Lindgren, Cecilia M

    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 to chromosomes 6 (nonparametric linkage [NPL]score 2.12 at 71 cM) and 10 (NPL score 1.88 at 169-175 cM), and to chromosomes 3 (heterogeneity LOD [HLOD] score 1.27 at 124 cM) and 5 (HLOD score 1.22 at 175 cM) in 14 more strictly defined families. Our results provide evidence for further heterogeneity in MODY.

  16. Genome-wide scan identifies a quantitative trait locus at 4p15.3 for serum urate.

    Science.gov (United States)

    Cummings, Nik; Dyer, Thomas D; Kotea, Navaratnam; Kowlessur, Sudhir; Chitson, Pierrot; Zimmet, Paul; Blangero, John; Jowett, Jeremy B M

    2010-11-01

    Elevated serum urate levels lead to gout and are associated with hypertension, metabolic syndrome, type 2 diabetes and cardiovascular diseases. The purpose of this study was to identify evidence for genetic linkage with serum urate and to determine whether variation within positional candidate genes is associated with serum urate levels in a non-European population. Genetic linkage analysis and single nucleotide polymorphism (SNP) genotyping was performed in a large family pedigree cohort from Mauritius. We assessed associations between serum urate levels and 97 SNPs in a positional candidate gene, SLC2A9. A genome-wide scan identified a new region with evidence for linkage for serum urate at 4p15.3. SNP genotyping identified significant association between six SNP variants in SLC2A9 and serum urate levels. Allelic and gender-based effects were noted for several SNPs. Significant correlations were also observed between serum urate levels and individual components of metabolic syndrome. Our study results implicate genetic variation in SLC2A9 in influencing levels of serum urate over a broad range of values in a large Mauritian family cohort. PMID:20588307

  17. Automatic landmarking for building biological shape models

    OpenAIRE

    Hicks, Y.; Marshall, D.; Martin, R. R.; Rosin, P. L.; Bayer, M. M.; Manning, D. G.

    2002-01-01

    We present a new method for automatic landmark extraction from the contours of biological specimens. Our ultimate goal is to enable automatic identification of biological specimens in photographs and drawings held in a database. We propose to use active appearance models for visual indexing of both photographs and drawings. Automatic landmark extraction will assist us in building the models. We describe the results of using our method on drawings and photographs of examples of diatoms, and pr...

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

    Science.gov (United States)

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

    2015-04-01

    Genome-wide association studies are routinely used to identify genomic regions associated with traits of interest. However, this ignores an important class of genomic associations, that of epistatic interactions. A genome-wide interaction analysis between single nucleotide polymorphisms (SNPs) using highly dense markers can detect epistatic interactions, but is a difficult task due to multiple testing and computational demand. However, It is important for revealing complex trait heredity. This study considers analytical methods that detect statistical interactions between pairs of loci. We investigated a three-stage modelling procedure: (i) a model without the SNP to estimate the variance components; (ii) a model with the SNP using variance component estimates from (i), thus avoiding iteration; and (iii) using the significant SNPs from (ii) for genome-wide epistasis analysis. We fitted these three-stage models to field data for growth and ultrasound measures for subcutaneous fat thickness in Brahman cattle. The study demonstrated the usefulness of modelling epistasis in the analysis of complex traits as it revealed extra sources of genetic variation and identified potential candidate genes affecting the concentration of insulin-like growth factor-1 and ultrasound scan measure of fat depth traits. Information about epistasis can add to our understanding of the complex genetic networks that form the fundamental basis of biological systems. PMID:25754883

  19. Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program

    OpenAIRE

    Curtis, Ellison R.; Hunt Steven C; Wilk Jemma B; Laramie Jason M; Chakravarti Aravinda; Boerwinkle Eric; Myers Richard H

    2006-01-01

    Abstract Background Elevated resting heart rate has been shown in multiple studies to be a strong predictor of cardiovascular disease. Previous family studies have shown a significant heritable component to heart rate with several groups conducting genomic linkage scans to identify quantitative trait loci. Methods We performed a genome-wide linkage scan to identify quantitative trait loci influencing resting heart rate among 3,282 Caucasians and 3,989 African-Americans in three independent ne...

  20. Ultrasound of the elbow: A systematic approach using bony landmarks

    International Nuclear Information System (INIS)

    The use of bony landmarks can be helpful in performing an ultrasound study of the elbow. We discuss bony landmarks that can be used for evaluation of the common extensor tendon, ulnar collateral ligament and common flexor tendon, coronoid and olecranon fossa, ulnar nerve, and biceps tendon. We discuss bony landmarks for each of these structures.

  1. Automated landmark-guided deformable image registration

    Science.gov (United States)

    Kearney, Vasant; Chen, Susie; Gu, Xuejun; Chiu, Tsuicheng; Liu, Honghuan; Jiang, Lan; Wang, Jing; Yordy, John; Nedzi, Lucien; Mao, Weihua

    2015-01-01

    The purpose of this work is to develop an automated landmark-guided deformable image registration (LDIR) algorithm between the planning CT and daily cone-beam CT (CBCT) with low image quality. This method uses an automated landmark generation algorithm in conjunction with a local small volume gradient matching search engine to map corresponding landmarks between the CBCT and the planning CT. The landmarks act as stabilizing control points in the following Demons deformable image registration. LDIR is implemented on graphics processing units (GPUs) for parallel computation to achieve ultra fast calculation. The accuracy of the LDIR algorithm has been evaluated on a synthetic case in the presence of different noise levels and data of six head and neck cancer patients. The results indicate that LDIR performed better than rigid registration, Demons, and intensity corrected Demons for all similarity metrics used. In conclusion, LDIR achieves high accuracy in the presence of multimodality intensity mismatch and CBCT noise contamination, while simultaneously preserving high computational efficiency.

  2. Landmark papers on photorefractive nonlinear optics

    CERN Document Server

    Yeh, Pochi

    1995-01-01

    This book, intended for students, researchers and engineers, is a collection of classic papers on photorefractive nonlinear optics. Included are landmark papers on fundamental photorefractive phenomena, two-wave mixing, four-wave mixing, phase conjugators and resonators, material growth and physics, and applications in image processing, optical storage and optical computing.

  3. Automated landmark-guided deformable image registration.

    Science.gov (United States)

    Kearney, Vasant; Chen, Susie; Gu, Xuejun; Chiu, Tsuicheng; Liu, Honghuan; Jiang, Lan; Wang, Jing; Yordy, John; Nedzi, Lucien; Mao, Weihua

    2015-01-01

    The purpose of this work is to develop an automated landmark-guided deformable image registration (LDIR) algorithm between the planning CT and daily cone-beam CT (CBCT) with low image quality. This method uses an automated landmark generation algorithm in conjunction with a local small volume gradient matching search engine to map corresponding landmarks between the CBCT and the planning CT. The landmarks act as stabilizing control points in the following Demons deformable image registration. LDIR is implemented on graphics processing units (GPUs) for parallel computation to achieve ultra fast calculation. The accuracy of the LDIR algorithm has been evaluated on a synthetic case in the presence of different noise levels and data of six head and neck cancer patients. The results indicate that LDIR performed better than rigid registration, Demons, and intensity corrected Demons for all similarity metrics used. In conclusion, LDIR achieves high accuracy in the presence of multimodality intensity mismatch and CBCT noise contamination, while simultaneously preserving high computational efficiency. PMID:25479095

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    Age-related hearing impairment (ARHI), or presbycusis, is a very common multifactorial disorder. Despite the knowledge that genetics play an important role in the etiology of human ARHI as revealed by heritability studies, to date, its precise genetic determinants remain elusive. Here we report the results of a cross-sectional family-based genetic study employing audiometric data. By using principal component analysis, we were able to reduce the dimensionality of this multivariate phenotype while capturing most of the variation and retaining biologically important features of the audiograms. We conducted a genome-wide association as well as a linkage scan with high-density SNP microarrays. Because of the presence of genetic population substructure, association testing was stratified after which evidence was combined by meta-analysis. No association signals reaching genome-wide significance were detected. Linkage analysis identified a linkage peak on 8q24.13-q24.22 for a trait correlated to audiogram shape. The signal reached genome-wide significance, as assessed by simulations. This finding represents the first locus for an ARHI trait Udgivelsesdato: 2008/9/12

  5. A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle.

    Science.gov (United States)

    Wu, Yang; Fan, Huizhong; Jing, Shengyun; Xia, Jiangwei; Chen, Yan; Zhang, Lupei; Gao, Xue; Li, Junya; Gao, Huijiang; Ren, Hongyan

    2015-06-01

    Copy number variations (CNVs) have recently been identified as promising sources of genetic variation, complementary to single nucleotide polymorphisms (SNPs). As a result, detection of CNVs has attracted a great deal of attention. In this study, we performed genome-wide CNV detection using Illumina Bovine HD BeadChip (770k) data on 792 Simmental cattle. A total of 263 CNV regions (CNVRs) were identified, which included 137 losses, 102 gains and 24 regions classified as both loss and gain, covering 35.48 Mb (1.41%) of the bovine genome. The length of these CNVRs ranged from 10.18 kb to 1.76 Mb, with an average length of 134.78 kb and a median length of 61.95 kb. In 136 of these regions, a total of 313 genes were identified related to biological functions such as transmembrane activity and olfactory transduction activity. To validate the results, we performed quantitative PCR to detect nine randomly selected CNVRs and successfully confirmed seven (77.6%) of them. Our results present a map of cattle CNVs derived from high-density SNP data, which expands the current CNV map of the cattle genome and provides useful information for investigation of genomic structural variation in cattle. PMID:25917301

  6. The behavioural relevance of landmark texture for honeybee homing

    Directory of Open Access Journals (Sweden)

    LauraDittmar

    2011-04-01

    Full Text Available Honeybees visually pinpoint the location of a food source using landmarks. Studies on the role of visual memories have suggested that bees approach the goal by finding a close match between their current view and a memorized view of the goal location. The most relevant landmark features for this matching process seem to be their retinal positions, the size as defined by their edges, and their colour. Recently, we showed that honeybees can use landmarks that are statically camouflaged, suggesting that motion cues are relevant as well. Currently it is unclear how bees weight these different landmark features when accomplishing navigational tasks, and whether this depends on their saliency. Since natural objects are often distinguished by their texture, we investigate the behavioural relevance and the interplay of the spatial configuration and the texture of landmarks. We show that landmark texture is a feature that bees memorise, and being given the opportunity to identify landmarks by their texture improves the bees’ navigational performance. Landmark texture is weighted more strongly than landmark configuration when it provides the bees with positional information and when the texture is salient. In the vicinity of the landmark honeybees changed their flight behaviour according to its texture.

  7. Genome Scanning for Interspecific Differentiation Between Two Closely Related Oak Species [Quercus robur L. and Q. petraea (Matt.) Liebl.

    OpenAIRE

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

    2004-01-01

    Interspecific differentiation values (GST) between two closely related oak species (Quercus petraea and Q. robur) were compiled across different studies with the aim to explore the distribution of differentiation at the genome level. The study was based on a total set of 389 markers (isozymes, AFLPs, SCARs, microsatellites, and SNPs) for which allelic frequencies were estimated in pairs of populations sampled throughout the sympatric distribution of the two species. The overall distribution o...

  8. A genome-wide "pleiotropy scan'' does not identify new susceptibility loci for estrogen receptor negative breast cancer

    OpenAIRE

    Campa, Daniele; Barrdahl, Myrto; Tsilidis, Konstantinos K.; Severi, Gianluca; Diver, W. Ryan; Siddiq, Afshan; Chanock, Stephen; Hoover, Robert N.; Ziegler, Regina G.; Berg, Christine D.; Buys, Saundra S.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick R.; Le Marchand, Loic

    2014-01-01

    Approximately 15-30% of all breast cancer tumors are estrogen receptor negative (ER-). Compared with ER- positive (ER+) disease they have an earlier age at onset and worse prognosis. Despite the vast number of risk variants identified for numerous cancer types, only seven loci have been unambiguously identified for ER- negative breast cancer. With the aim of identifying new susceptibility SNPs for this disease we performed a pleiotropic genome-wide association study (GWAS). We selected 3079 S...

  9. A Genome-Wide “Pleiotropy Scan” Does Not Identify New Susceptibility Loci for Estrogen Receptor Negative Breast Cancer

    OpenAIRE

    Campa, Daniele; Barrdahl, Myrto; Tsilidis, Konstantinos K.; Severi, Gianluca; Diver, W. Ryan; Siddiq, Afshan; Chanock, Stephen; Hoover, Robert N.; Ziegler, Regina G.; Berg, Christine D.; Buys, Saundra S.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick R.; Le Marchand, Loi?c

    2014-01-01

    Approximately 15–30% of all breast cancer tumors are estrogen receptor negative (ER?). Compared with ER-positive (ER+) disease they have an earlier age at onset and worse prognosis. Despite the vast number of risk variants identified for numerous cancer types, only seven loci have been unambiguously identified for ER-negative breast cancer. With the aim of identifying new susceptibility SNPs for this disease we performed a pleiotropic genome-wide association study (GWAS). We selected 3079...

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

    OpenAIRE

    Scherer Stephen W; Pinto Dalila; Tango Toshiro; Takahashi Kunihiko; Nishiyama Takeshi; Takami Satoshi; Kishino Hirohisa

    2011-01-01

    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 ...

  11. Combined Genome Scans for Body Stature in 6,602 European Twins: Evidence for Common Caucasian Loci

    OpenAIRE

    Perola, M.; Sammalisto, S.; Hiekkalinna, T.; Martin, N. G.; Visscher, P. M.; Montgomery, Gw; Benyamin, B.; Harris, J. R.; Boomsma, D. I.; Willemsen, G.; Hottenga, J. J.; Christensen, K.; Kyvik, K.; Sorensen, T. I. A.; Pedersen, N. L.

    2007-01-01

    Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait l...

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

    Science.gov (United States)

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

    2014-10-01

    Developmental dyslexia (DD) is a complex heritable disorder with unexpected difficulty in learning to read and spell despite adequate intelligence, education, environment, and normal senses. We performed genome-wide screening for copy number variations (CNVs) in 10 large Indian dyslexic families using Affymetrix Genome-Wide Human SNP Array 6.0. Results revealed the complex genomic rearrangements due to one non-contiguous deletion and five contiguous micro duplications and micro deletions at 17q21.31 region in three dyslexic families. CNVs in this region harbor the genes KIAA1267, LRRC37A, ARL17A/B, NSFP1, and NSF. The CNVs in case 1 and case 2 at this locus were found to be in homozygous state and case 3 was a de novo CNV. These CNVs were found with at least one CNV having a common break and end points in the parents. This cluster of genes containing NSF is implicated in learning, cognition, and memory, though not formally associated with dyslexia. Molecular network analysis of these and other dyslexia related module genes suggests NSF and other genes to be associated with cellular/vesicular membrane fusion and synaptic transmission. Thus, we suggest that NSF in this cluster would be the nearest gene responsible for the learning disability phenotype. PMID:25139666

  13. The accuracy of image registration for the brain and the nasopharynx using external anatomical landmarks

    International Nuclear Information System (INIS)

    We investigated the accuracy of 3D image registration using markers that are repeatedly applied to external anatomical landmarks on the head. The purpose of this study is to establish a lower limit of the errors that would occur in, for instance, MRI-SPECT matching, which in some situations can only be achieved using external landmarks. Marker matching was compared with (single-modality) volume matching for 20 MRI scans. The results were compared with a published expression for the target registration error (TRE) which gives the 3D distribution of the mismatch between both scans. It was found that the main error source is reapplying the external markers on the anatomical landmarks. The published expression describes the relative distribution of the TRE in space well, but tends to underestimate the actual registration error. This deviation is due to anisotropy in the error distribution of the marker position (errors in the direction perpendicular to the skin surface are in general much smaller than errors in other directions). A simulation of marker matching with anisotropy in the errors confirmed this finding. With four reapplied markers, the TRE is 6 mm or smaller in most regions of the head. (author)

  14. Detection of natural landmarks through multiscale opponent features

    OpenAIRE

    Todt, Eduardo; Torras Geni?s, Carme

    2000-01-01

    This work presents a landmark detection system for the walking robot operating in unknown unstructured outdoor environments. Most landmark detection approaches are not adequate for this application, since they rely on either structured information or a priori knowledge about the landmarks. Instead, the proposed system makes use of visual saliency concepts stemming from studies of animal and human perception. Thus, biologically inspired opponent features (in color and orientation) are searched...

  15. Concurrent map building and localization with landmark validation

    OpenAIRE

    Andrade Cetto, Juan; Sanfeliu Cortés, Alberto

    2002-01-01

    This communication addresses the issue of concurrent map building and localization (CML) for a mobile robot in an unknown environment. The proposed solution extends over previous contributions in that the environment must not be static, nor the landmarks be uniquely identifiable. To this aim we introduce a map model that includes not only the robot and landmark locations in a reference frame, but also a model for landmark quality assessment. Convergence of the map covariance is preserved in t...

  16. Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function

    Science.gov (United States)

    Puffenberger, Erik G.; Hu-Lince, Diane; Parod, Jennifer M.; Craig, David W.; Dobrin, Seth E.; Conway, Andrew R.; Donarum, Elizabeth A.; Strauss, Kevin A.; Dunckley, Travis; Cardenas, Javier F.; Melmed, Kara R.; Wright, Courtney A.; Liang, Winnie; Stafford, Phillip; Flynn, C. Robert; Morton, D. Holmes; Stephan, Dietrich A.

    2004-01-01

    We have identified a lethal phenotype characterized by sudden infant death (from cardiac and respiratory arrest) with dysgenesis of the testes in males [Online Mendelian Inheritance in Man (OMIM) accession no. 608800]. Twenty-one affected individuals with this autosomal recessive syndrome were ascertained in nine separate sibships among the Old Order Amish. High-density single-nucleotide polymorphism (SNP) genotyping arrays containing 11,555 single-nucleotide polymorphisms evenly distributed across the human genome were used to map the disease locus. A genome-wide autozygosity scan localized the disease gene to a 3.6-Mb interval on chromosome 6q22.1-q22.31. This interval contained 27 genes, including two testis-specific Y-like genes (TSPYL and TSPYL4) of unknown function. Sequence analysis of the TSPYL gene in affected individuals identified a homozygous frameshift mutation (457_458insG) at codon 153, resulting in truncation of translation at codon 169. Truncation leads to loss of a peptide domain with strong homology to the nucleosome assembly protein family. GFP-fusion expression constructs were constructed and illustrated loss of nuclear localization of truncated TSPYL, suggesting loss of a nuclear localization patch in addition to loss of the nucleosome assembly domain. These results shed light on the pathogenesis of a disorder of sexual differentiation and brainstem-mediated sudden death, as well as give insight into a mechanism of transcriptional regulation. PMID:15273283

  17. Active shape models incorporating isolated landmarks for medical image annotation

    Science.gov (United States)

    Norajitra, Tobias; Meinzer, Hans-Peter; Stieltjes, Bram; Maier-Hein, Klaus H.

    2014-03-01

    Apart from their robustness in anatomic surface segmentation, purely surface based 3D Active Shape Models lack the ability to automatically detect and annotate non-surface key points of interest. However, annotation of anatomic landmarks is desirable, as it yields additional anatomic and functional information. Moreover, landmark detection might help to further improve accuracy during ASM segmentation. We present an extension of surface-based 3D Active Shape Models incorporating isolated non-surface landmarks. Positions of isolated and surface landmarks are modeled conjoint within a point distribution model (PDM). Isolated landmark appearance is described by a set of haar-like features, supporting local landmark detection on the PDM estimates using a kNN-Classi er. Landmark detection was evaluated in a leave-one-out cross validation on a reference dataset comprising 45 CT volumes of the human liver after shape space projection. Depending on the anatomical landmark to be detected, our experiments have shown in about 1/4 up to more than 1/2 of all test cases a signi cant improvement in detection accuracy compared to the position estimates delivered by the PDM. Our results encourage further research with regard to the combination of shape priors and machine learning for landmark detection within the Active Shape Model Framework.

  18. Landmark experiments in twentieth-century physics

    CERN Document Server

    Trigg, George L

    2011-01-01

    Physics is very much an experimental science, but too often, students at the undergraduate level are not exposed to the reality of experimental physics ? i.e., what was done in a given experiment, why it was done, the background of physics against which the experiment was carried out and the changes in theory and knowledge that resulted. In this hook, the author helps to remedy the situation by presenting a variety of ""landmark"" experiments that have brought about significant alterations in our ideas about some aspect of nature. Among these scientific milestones are discoveries about the wa

  19. Single-Copy Nuclear Gene Primers for Streptanthus and Other Brassicaceae from Genomic Scans, Published Data, and ESTs

    Directory of Open Access Journals (Sweden)

    N. Ivalú Cacho

    2013-07-01

    Full Text Available Premise of the study: We report 11 primer sets for nine single-copy nuclear genes in Streptanthus and other Thelypodieae (Brassicaceae and their utility at tribal-level and species-level phylogenetics in this poorly resolved group. Methods and Results: We selected regions based on a cross-referenced matrix of previous studies and public Brassica expressed sequence tags. To design primers, we used alignments of low-depth-coverage Illumina sequencing of genomic DNA for two species of Brassica mapped onto Arabidopsis thaliana. We report several primer combinations for five regions that consistently amplified a single band and yielded high-quality sequences for at least 70% of the species assayed, and for four additional regions whose utility might be clade specific. Conclusions: Our primers will be useful in improving resolution at shallow depths across the Thelypodieae, and likely in other Brassicaceae.

  20. A genome-wide scan in affected sib-pairs with idiopathic recurrent miscarriage suggests genetic linkage

    DEFF Research Database (Denmark)

    Kolte, Astrid Marie; Nielsen, Henriette Svarre

    2011-01-01

    Previously, siblings of patients with idiopathic recurrent miscarriage (IRM) have been shown to have a higher risk of miscarriage. This study comprises two parts: (i) an epidemiological part, in which we introduce data on the frequency of miscarriage among 268 siblings of 244 patients with IRM and (ii) a genetic part presenting data from a genome-wide linkage study of 38 affected sibling pairs with IRM. All IRM patients (probands) had experienced three or more miscarriages and affected siblings two or more miscarriages. The sibling pairs were genotyped by the Affymetrix GeneChip 50K XbaI platform and non-parametric linkage analysis was performed via the software package Merlin. We find that siblings of IRM patients exhibit a higher frequency of miscarriage than population controls regardless of age at the time of pregnancy. We identify chromosomal regions with LOD scores between 2.5 and 3.0 in subgroups of affected sibling pairs. Maximum LOD scores were identified in four occurrences: for rs10514716 (3p14.2) when analyzing sister-pairs only; for rs10511668 (9p22.1) and rs341048 (11q13.4) when only analyzing families where the probands have had four or more miscarriages; and for rs10485275 (6q16.3) when analyzing one sibling pair from each family only. We identify no founder mutations. Concluding, our results imply that IRM patients and their siblings share factors which increase the risk of miscarriage. In this first genome-wide linkage study of affected sibling pairs with IRM, we identify regions on chromosomes 3, 6, 9 and 11 which warrant further investigation in order to elucidate their putative roles in the genesis of IRM.

  1. Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds

    DEFF Research Database (Denmark)

    Gregersen, Vivi R; Conley, Lene N

    2012-01-01

    BACKGROUND: Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole). The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. RESULTS: Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL), 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 micro gram/g). In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. CONCLUSIONS: Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.

  2. Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds

    Directory of Open Access Journals (Sweden)

    Gregersen Vivi R

    2012-01-01

    Full Text Available Abstract Background Boar taint is the undesirable smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone and skatole (3-methyl-indole. The steroid androstenone is a sex pheromone produced in the testis of the boars. Skatole is produced from tryptophan by bacteria in the intestine of the pigs. In many countries pigs are castrated as piglets to avoid boar taint, however, this is undesirable for animal welfare reasons. Genetic variations affecting the level of boar taint have previously been demonstrated in many breeds. In the study presented in this paper, markers and haplotypes, which can be applied to DNA-based selection schemes in order to reduce or eliminate the boar taint problem, are identified. Results Approximately 30,000 SNPs segregating in 923 boars from three Danish breeds; Duroc, Landrace, and Yorkshire, were used to conduct genome wide association studies of boar taint compounds. At 46 suggestive quantitative trait loci (QTL, 25 haplotypes and three single markers with effects were identified. Furthermore, 40% of the haplotypes mapped to previously identified regions. Haplotypes were also analysed for effects of slaughter weight and meat content. The most promising haplotype was identified on Sus scrofa chromosome 1. The gain in fixed effect of having this haplotype on level of androstenone in Landrace was identified to be high (1.279 ?g/g. In addition, this haplotype explained 16.8% of the phenotypic variation within the trait. The haplotype was identified around the gene CYB5A which is known to have an indirect impact on the amount of androstenone. In addition to CYB5A, the genes SRD5A2, LOC100518755, and CYP21A2 are candidate genes for other haplotypes affecting androstenone, whereas, candidate genes for the indolic compounds were identified to be SULT1A1 and CYP2E1. Conclusions Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed.

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

    Science.gov (United States)

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

    2011-04-01

    Outlier detection methods were used to scan the genome of the boreal conifer black spruce (Picea mariana [Mill.] B.S.P.) for gene single-nucleotide polymorphisms (SNPs) potentially involved in adaptations to temperature and precipitation variations. The scan involved 583 SNPs from 313 genes potentially playing adaptive roles. Differentiation estimates among population groups defined following variation in temperature and precipitation were moderately high for adaptive quantitative characters such as the timing of budset or tree height (Q(ST) = 0.189-0.314). Average differentiation estimates for gene SNPs were null, with F(ST) values of 0.005 and 0.006, respectively, among temperature and precipitation population groups. Using two detection approaches, a total of 26 SNPs from 25 genes distributed among 11 of the 12 linkage groups of black spruce were detected as outliers with F(ST) as high as 0.078. Nearly half of the outlier SNPs were located in exons and half of those were nonsynonymous. The functional annotations of genes carrying outlier SNPs and regression analyses between the frequencies of these SNPs and climatic variables supported their implication in adaptive processes. Several genes carrying outlier SNPs belonged to gene families previously found to harbour outlier SNPs in a reproductively isolated but largely sympatric congeneric species, suggesting differential subfunctionalization of gene duplicates. Selection coefficient estimates (S) were moderate but well above the magnitude of drift (>1/N(e)), indicating that the signature of natural selection could be detected at the nucleotide level despite the recent establishment of these populations during the Holocene. PMID:21375634

  4. A new method to validate thoracic CT-CT deformable image registration using auto-segmented 3D anatomical landmarks

    DEFF Research Database (Denmark)

    Nielsen, Martin S; Østergaard, Lasse R

    2015-01-01

    BACKGROUND: Deformable image registrations are prone to errors in aligning reliable anatomically features. Consequently, identification of registration inaccuracies is important. Particularly thoracic three-dimensional (3D) computed tomography (CT)-CT image registration is challenging due to lack of contrast in lung tissue. This study aims for validation of thoracic CT-CT image registration using auto-segmented anatomically landmarks. MATERIAL AND METHODS: Five lymphoma patients were CT scanned three times within a period of 18 months, with the initial CT defined as the reference scan. For each patient the two successive CT scans were registered to the reference CT using three different image registration algorithms (Demons, B-spline and Affine). The image registrations were evaluated using auto-segmented anatomical landmarks (bronchial branch points) and Dice Similarity Coefficients (DSC). Deviation of corresponding bronchial landmarks were used to quantify inaccuracies in respect of both misalignment and geometric location within lungs. RESULTS: The median bronchial branch point deviations were 1.6, 1.1 and 4.2 (mm) for the three tested algorithms (Demons, B-spline and Affine). The maximum deviations (> 15 mm) were found within both Demons and B-spline image registrations. In the upper part of the lungs the median deviation of 1.7 (mm) was significantly different (p 15 mm in both Demons and B-spline deformable algorithms.

  5. Visual Homing in the Absence of Feature-Based Landmark Information

    Science.gov (United States)

    Gillner, Sabine; Weiss, Anja M.; Mallot, Hanspeter A.

    2008-01-01

    Despite that fact that landmarks play a prominent role in human navigation, experimental evidence on how landmarks are selected and defined by human navigators remains elusive. Indeed, the concept of a "landmark" is itself not entirely clear. In everyday language, the term landmark refers to salient, distinguishable, and usually nameable objects,…

  6. A high-density genome scan detects evidence for a bipolar-disorder susceptibility locus on 13q32 and other potential loci on 1q32 and 18p11.2

    OpenAIRE

    Detera-Wadleigh, Sevilla D; Badner, Judith A; BERRETTINI, WADE H.; Yoshikawa, Takeo; Goldin, Lynn R.; Turner, Gordon; Rollins, Denise Y.; Moses, Tracy; Sanders, Alan R.; Karkera, Jayaprakash D.; Esterling, Lisa E.; Zeng, Jin; Ferraro, Thomas N.; Guroff, Juliet J.; Kazuba, Diane

    1999-01-01

    Bipolar disorder is a severe mental illness characterized by mood swings of elation and depression. Family, twin, and adoption studies suggest a complex genetic etiology that may involve multiple susceptibility genes and an environmental component. To identify chromosomal loci contributing to vulnerability, we have conducted a genome-wide scan on ?396 individuals from 22 multiplex pedigrees by using 607 microsatellite markers. Multipoint nonparametric analysis detected the strongest evidenc...

  7. Automatic Evaluation of Landmarks for Image-Based Navigation Update

    Directory of Open Access Journals (Sweden)

    Stefan Lang

    2009-01-01

    Full Text Available The successful mission of an autonomous airborne system like an unmanned aerial vehicle (UAV strongly depends on its accurate navigation. While GPS is not always available and pose estimation based solely on Inertial Measurement Unit (IMU drifts, image-based navigation may become a cheap and robust additional pose measurement device. For the actual navigation update a landmark-based approach is used. It is essential that the used landmarks are well chosen. Therefore we introduce an approach for evaluating landmarks in terms of the matching distance, which is the maximum misplacement in the position of the landmark that can be corrected. We validate the evaluations with our 3D reconstruction system working on data captured from a helicopter.

  8. Automated Landmark Identification for Human Cortical Surface-Based Registration

    OpenAIRE

    Anticevic, Alan; Repovs, Grega; Dierker, Donna; Harwell, John; Coalson, Tim; Barch, Deanna M.; Essen, David C.

    2011-01-01

    Volume-based registration (VBR) is the predominant method used in human neuroimaging to compensate for individual variability. However, surface-based registration (SBR) techniques have an inherent advantage over VBR because they respect the topology of the convoluted cortical sheet. There is evidence that existing SBR methods indeed confer a registration advantage over affine VBR. Landmark-SBR constrains registration using explicit landmarks to represent corresponding geographical locations o...

  9. Detection of point landmarks in multidimensional tensor data?

    Science.gov (United States)

    Ruiz-Alzola, J.; Kikinis, R.; Westin, C.-F.

    2015-01-01

    This paper describes a unified approach to the detection of point landmarks—whose neighborhoods convey discriminant information—including multidimensional scalar, vector, and higher-order tensor data. The method is based on the interpretation of generalized correlation matrices derived from the gradient of tensor functions, a probabilistic interpretation of point landmarks, and the application of tensor algebra. Results on both synthetic and real tensor data are presented.

  10. Automatic Evaluation of Landmarks for Image-Based Navigation Update

    OpenAIRE

    Stefan Lang; Michael Kirchhof

    2009-01-01

    The successful mission of an autonomous airborne system like an unmanned aerial vehicle (UAV) strongly depends on its accurate navigation. While GPS is not always available and pose estimation based solely on Inertial Measurement Unit (IMU) drifts, image-based navigation may become a cheap and robust additional pose measurement device. For the actual navigation update a landmark-based approach is used. It is essential that the used landmarks are well chosen. Therefore we introduce an approach...

  11. Some historical landmarks in nuclear and radiochemistry

    International Nuclear Information System (INIS)

    The study of conduction of electricity through evacuated tubes led to the discovery of cathode rays by Plucker in 1858. No outstanding results were produced in the study of these rays until 1895-1896 when incisive minds of Roentgen and Thomson led, respectively, to the Nobel prize winning discoveries of x-rays and electron. Fortutious linking of phosphorescence with x-ray emission led Becquerel to discover uranic rays and his colleagues M. Curie an P. Curie to their research on radiation phenomenon. A gigantic forward wave of human knowledge ensued from these discoveries. The postulation of nuclear atom by Rutherford was an important landmark in this forward movement. Rutherford and Soddy postulated that the spontaneous emission of radiations (? and ?) by atoms is accompanied by chemical changes. Subsequent studies by Rutherford and his colleagues in England, Curie-Joliot team in France, Fermi et al. in Italy and Hahn et al. in Germany established transmutation of atomic nuclei by nuclear radiations (? and n). This article is an attempt to pay a humble tribute to the pioneers who opened the gates to the world of nuclear sciences. (author). 135 refs., 1 fig

  12. Measure of Landmark Semantic Salience through Geosocial Data Streams

    Directory of Open Access Journals (Sweden)

    Teriitutea Quesnot

    2014-12-01

    Full Text Available Research in the area of spatial cognition demonstrated that references to landmarks are essential in the communication and the interpretation of wayfinding instructions for human being. In order to detect landmarks, a model for the assessment of their salience has been previously developed by Raubal and Winter. According to their model, landmark salience is divided into three categories: visual, structural, and semantic. Several solutions have been proposed to automatically detect landmarks on the basis of these categories. Due to a lack of relevant data, semantic salience has been frequently reduced to objects’ historical and cultural significance. Social dimension (i.e., the way an object is practiced and recognized by a person or a group of people is systematically excluded from the measure of landmark semantic salience even though it represents an important component. Since the advent of mobile Internet and smartphones, the production of geolocated content from social web platforms—also described as geosocial data—became commonplace. Actually, these data allow us to have a better understanding of the local geographic knowledge. Therefore, we argue that geosocial data, especially Social Location Sharing datasets, represent a reliable source of information to precisely measure landmark semantic salience in urban area.

  13. CT scan

    Science.gov (United States)

    A computed tomography (CT) scan is an imaging method that uses x-rays to create pictures of cross-sections of the body. Related tests include: Abdominal CT scan Cranial CT scan Lumbosacral spine CT scan ...

  14. 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-type KRAS resulted in the inhibition of cell growth and suppression of p44/42 MAP kinase and AKT activity. Conclusion Our study highlights the utility of DGS for identification of copy-number alterations. Using DGS, we identified KRAS as a gene that is amplified in human gastric cancer. We demonstrated that gene amplification likely forms the molecular basis of overactivation of KRAS in gastric cancer. Additional studies using a larger cohort of gastric cancer specimens are required to determine the diagnostic and therapeutic implications of KRAS amplification and overexpression.

  15. Discriminative BoW framework for mobile landmark recognition.

    Science.gov (United States)

    Chen, Tao; Yap, Kim-Hui

    2014-05-01

    This paper proposes a new soft bag-of-words (BoW) method for mobile landmark recognition based on discriminative learning of image patches. Conventional BoW methods often consider the patches/regions in the images as equally important for learning. Amongst the few existing works that consider the discriminative information of the patches, they mainly focus on selecting the representative patches for training, and discard the others. This binary hard selection approach results in underutilization of the information available, as some discarded patches may still contain useful discriminative information. Further, not all the selected patches will contribute equally to the learning process. In view of this, this paper presents a new discriminative soft BoW approach for mobile landmark recognition. The main contribution of the method is that the representative and discriminative information of the landmark is learned at three levels: patches, images, and codewords. The patch discriminative information for each landmark is first learned and incorporated through vector quantization to generate soft BoW histograms. Coupled with the learned representative information of the images and codewords, these histograms are used to train an ensemble of classifiers using fuzzy support vector machine. Experimental results on two different datasets show that the proposed method is effective in mobile landmark recognition. PMID:23846513

  16. Somaclonal variation and comparison to mutation induced by X-rays in rice (Oryza sativa L.) by using rice landmarker

    International Nuclear Information System (INIS)

    By using rice DNA clones of landmarker set 1, set 2 and new set, RFLP analysis was carried out in plants of cv. Tsugaruotome and cv. Mutsuhomare which were derived from 300 Gy of X-ray-irradiated seeds. In the three landmarker sets were consisted of 106 genomic DNA clones and 235 cDNA clones. Each cultivar has five plants which showed polymorphism. It is considered that the occurrence of some mutation of gene concerned with DNA repairing because certain plants showed polymorphism by many landmarkers as probes. Activity of retrotransposon such as Tos17 and alteration of methylation pattern were not observed on any plants derived from X-ray-irradiated seeds. On the other hand, in plants regenerated from cultured calli, it was found the movement of Tos17 to certain area of hot spot and alteration of methylation pattern. Furthermore, it has been reported that amplification of repeated DNA segment which was not observed in the mutation induced by X-rays. Thus, on plant breeding the somaclonal variation may be more useful than the mutation induced by X-rays

  17. CT Scan (CAT Scan)

    Science.gov (United States)

    This patient education program explains the benefits and risks of Computed Axial Tomography, CAT scan or CT scan, and describes the procedure for the test. This is a MedlinePlus Interactive Health Tutorial from the National Library of Medicine, designed and developed by the Patient Education Institute. NOTE: The tutorial requires a special Flash plug-in, version 4 or above. If you do not have Flash, you will be prompted to obtain a free download of the software before you start the tutorial. You will also need an Acrobat Reader, available as a free download, in order to view the Reference Summary.

  18. Adaptive Landmark-Based Navigation System Using Learning Techniques

    DEFF Research Database (Denmark)

    Zeidan, Bassel; Dasgupta, Sakyasingha

    2014-01-01

    The goal-directed navigational ability of animals is an essential prerequisite for them to survive. They can learn to navigate to a distal goal in a complex environment. During this long-distance navigation, they exploit environmental features, like landmarks, to guide them towards their goal. Inspired by this, we develop an adaptive landmark-based navigation system based on sequential reinforcement learning. In addition, correlation-based learning is also integrated into the system to improve learning performance. The proposed system has been applied to simulated simple wheeled and more complex hexapod robots. As a result, it allows the robots to successfully learn to navigate to distal goals in complex environments.

  19. Combining Speedup techniques based on Landmarks and Containers

    Directory of Open Access Journals (Sweden)

    R. KALPANA

    2010-09-01

    Full Text Available The Dijkstra’s algorithm [1] , which is applied in many real world problems like mobile routing, road maps, railway networks, etc,. is used to find the shortest path between source and destination. There are many techniques available to speedup the algorithm while guaranteeing the optimality of the solution. The main focus of the work is to implement landmark technique and Containers separately and compare the results with random graphs and planar graphs. The combined speedup technique which is based on landmarks and containers were also experimented with random graphs and planar graphs to improvethe speedup of the shortest path queries.

  20. Landmarks or panoramas: what do navigating ants attend to for guidance?

    OpenAIRE

    Beugnon Guy; Wystrach Antoine; Cheng Ken

    2011-01-01

    Abstract Background Insects are known to rely on terrestrial landmarks for navigation. Landmarks are used to chart a route or pinpoint a goal. The distant panorama, however, is often thought not to guide navigation directly during a familiar journey, but to act as a contextual cue that primes the correct memory of the landmarks. Results We provided Melophorus bagoti ants with a huge artificial landmark located right near the nest entrance to find out whether navigating ants focus on such a pr...

  1. 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 ...

  2. Evolving a Multiagent System for Landmark-based Robot Navigation

    OpenAIRE

    Ambastha, Madhur; Busquets, Didac; Lopez Mantaras, Ramon; Sierra, Carles

    2005-01-01

    In this article, we build upon a multiagent architecture for landmark-based navigation in unknown environments. In this architecture, each of the agents in the navigation system has a bidding function that is controlled by a set of parameters. We show here the good results obtained by an evolutionary approach that tunes the parameter set values for two navigation tasks.

  3. An Adaptive Algorithm for Finding Frequent Sets in Landmark Windows

    DEFF Research Database (Denmark)

    Dang, Xuan-Hong; Ong, Kok-Leong

    2012-01-01

    We consider a CPU constrained environment for finding approximation of frequent sets in data streams using the landmark window. Our algorithm can detect overload situations, i.e., breaching the CPU capacity, and sheds data in the stream to “keep up”. This is done within a controlled error threshold by exploiting the Chernoff-bound. Empirical evaluation of the algorithm confirms the feasibility.

  4. On-line SLAM using clustered landmarks with omnidirectional vision

    Scientific Electronic Library Online (English)

    Jun, Okamoto Jr.; Vitor Campanholo, Guizilini.

    2010-12-01

    Full Text Available The problem of SLAM (simultaneous localization and mapping) is a fundamental problem in autonomous robotics. It arises when a robot must create a map of the regions it has navigated while localizing itself on it, using results from one step to increase precision in another by eliminating errors inhe [...] rent to the sensors. One common solution consists of establishing landmarks in the environment which are used as reference points for absolute localization estimates and form a sparse map that is iteratively refined as more information is obtained. This paper introduces a method of landmark selection and clustering in omnidirectional images for on-line SLAM, using the SIFT algorithm for initial feature extraction and assuming no prior knowledge of the environment. Visual sensors are an attractive way of collecting information from the environment, but tend to create an excessive amount of landmarks that are individually prone to false matches due to image noise and object similarities. By clustering several features in single objects, our approach eliminates landmarks that do not consistently represent the environment, decreasing computational cost and increasing the reliability of information incorporated. Tests conducted in real navigational situations show a significant improvement in performance without loss of quality.

  5. Robust discriminative tracking via landmark-based label propagation.

    Science.gov (United States)

    Wu, Yuwei; Pei, Mingtao; Yang, Min; Yuan, Junsong; Jia, Yunde

    2015-05-01

    The appearance of an object could be continuously changing during tracking, thereby being not independent identically distributed. A good discriminative tracker often needs a large number of training samples to fit the underlying data distribution, which is impractical for visual tracking. In this paper, we present a new discriminative tracker via landmark-based label propagation (LLP) that is nonparametric and makes no specific assumption about the sample distribution. With an undirected graph representation of samples, the LLP locally approximates the soft label of each sample by a linear combination of labels on its nearby landmarks. It is able to effectively propagate a limited amount of initial labels to a large amount of unlabeled samples. To this end, we introduce a local landmarks approximation method to compute the cross-similarity matrix between the whole data and landmarks. Moreover, a soft label prediction function incorporating the graph Laplacian regularizer is used to diffuse the known labels to all the unlabeled vertices in the graph, which explicitly considers the local geometrical structure of all samples. Tracking is then carried out within a Bayesian inference framework, where the soft label prediction value is used to construct the observation model. Both qualitative and quantitative evaluations on the benchmark data set containing 51 challenging image sequences demonstrate that the proposed algorithm outperforms the state-of-the-art methods. PMID:25706637

  6. Automatic facial expression recognition based on features extracted from tracking of facial landmarks

    Science.gov (United States)

    Ghimire, Deepak; Lee, Joonwhoan

    2014-01-01

    In this paper, we present a fully automatic facial expression recognition system using support vector machines, with geometric features extracted from the tracking of facial landmarks. Facial landmark initialization and tracking is performed by using an elastic bunch graph matching algorithm. The facial expression recognition is performed based on the features extracted from the tracking of not only individual landmarks, but also pair of landmarks. The recognition accuracy on the Extended Kohn-Kanade (CK+) database shows that our proposed set of features produces better results, because it utilizes time-varying graph information, as well as the motion of individual facial landmarks.

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

    OpenAIRE

    Simino, Jeannette; Shi, Gang; Kume, Rezart; Schwander, Karen; Province, Michael A.; Gu, C Charles; Kardia, Sharon; Chakravarti, Aravinda; Ehret, Georg Benedikt; Olshen, Richard A; Turner, Stephen T; Ho, Low-Tone; ZHU, XIAOFENG; Jaquish, Cashell; Paltoo, Dina

    2011-01-01

    A preliminary genome-wide linkage analysis of blood pressure in the Family Blood Pressure Program (FBPP) was reported previously. We harnessed the power and ethnic diversity of the final pooled FBPP dataset to identify novel loci for blood pressure thereby enhancing localization of genes containing less common variants with large effects on blood pressure levels and hypertension.

  8. A genome-wide linkage scan identifies multiple chromosomal regions influencing serum lipid levels in the population on the Samoan islands* s?

    OpenAIRE

    Åberg, Karolina; Dai, Feng; Sun, Guangyun; Keighley, Ember; INDUGULA, SUBBA RAO; Bausserman, Linda; VIALI, SATUPAITEA; TUITELE, JOHN; Deka, Ranjan; Weeks, Daniel E; McGarvey, Stephen T.

    2008-01-01

    Abnormal lipid levels are important risk factors for cardiovascular diseases. We conducted genome-wide variance component linkage analyses to search for loci influencing total cholesterol (TC), LDL, HDL and triglyceride in families residing in American Samoa and Samoa as well as in a combined sample from the two polities. We adjusted the traits for a number of environmental covariates, ...

  9. Reliability of a coordinate system based on anatomical landmarks of the maxillofacial skeleton. An evaluation method for three-dimensional images obtained by cone-beam computed tomography

    International Nuclear Information System (INIS)

    We propose a method for evaluating the reliability of a coordinate system based on maxillofacial skeletal landmarks and use it to assess two coordinate systems. Scatter plots and 95% confidence ellipses of an objective landmark were defined as an index for demonstrating the stability of the coordinate system. A head phantom was positioned horizontally in reference to the Frankfurt horizontal and occlusal planes and subsequently scanned once in each position using cone-beam computed tomography. On the three-dimensional images created with a volume-rendering procedure, six dentists twice set two different coordinate systems: coordinate system 1 was defined by the nasion, sella, and basion, and coordinate system 2 was based on the left orbitale, bilateral porions, and basion. The menton was assigned as an objective landmark. The scatter plot and 95% ellipse of the menton indicated the high-level reliability of coordinate system 2. The patterns with the two coordinate systems were similar between data obtained in different head positions. The method presented here may be effective for evaluating the reliability (reproducibility) of coordinate systems based on skeletal landmarks. (author)

  10. Landmarks or panoramas: what do navigating ants attend to for guidance?

    Directory of Open Access Journals (Sweden)

    Beugnon Guy

    2011-08-01

    Full Text Available Abstract Background Insects are known to rely on terrestrial landmarks for navigation. Landmarks are used to chart a route or pinpoint a goal. The distant panorama, however, is often thought not to guide navigation directly during a familiar journey, but to act as a contextual cue that primes the correct memory of the landmarks. Results We provided Melophorus bagoti ants with a huge artificial landmark located right near the nest entrance to find out whether navigating ants focus on such a prominent visual landmark for homing guidance. When the landmark was displaced by small or large distances, ant routes were affected differently. Certain behaviours appeared inconsistent with the hypothesis that guidance was based on the landmark only. Instead, comparisons of panoramic images recorded on the field, encompassing both landmark and distal panorama, could explain most aspects of the ant behaviours. Conclusion Ants navigating along a familiar route do not focus on obvious landmarks or filter out distal panoramic cues, but appear to be guided by cues covering a large area of their panoramic visual field, including both landmarks and distal panorama. Using panoramic views seems an appropriate strategy to cope with the complexity of natural scenes and the poor resolution of insects' eyes. The ability to isolate landmarks from the rest of a scene may be beyond the capacity of animals that do not possess a dedicated object-perception visual stream like primates.

  11. Multifunction Digital Research Scanning System

    International Nuclear Information System (INIS)

    The multifunction digital research scanning system is a modularly constructed organ visualization system. The design objective of this system is quantification of organ visualization data, i.e. ?Ci/g. It is a high-speed (500 cm/min), 14-crystal, digital rectilinear scanner built as a special-purpose hard-wired computer. The two synchronous detector heads, one beneath and one above the scantable, each consisting of a linear array of seven, 3-in. x 2-in. NaI(Tl) crystals, each crystal having its own focused collimator. Each 7-detector array can be independently moved in the vertical direction. The exact position of the detectors is known at all times by the use of an absolute 13-bit shaft angle encoder along the longitudinal axis of the scantable and a programmable SloSyn motor across the table. Anatomical landmarks may be programmed into the system and automatically recognized when the detector passes over these points. The scan field is 198 cm long by 62 cm wide with a position resolution of 0.14 cm. The primary scan motion is along the longitudinal axis of the table and the detectors are indexed across the table. The scan image is built up seven lines at a time, allowing the total scanfield to be visualized with each pass of the detectors. Each crystal has its own 8-bit or 12-bit counter with buffer storage. A single fast pulse-height analyser (200 nsec. random pulse-pair resolution) is used for all 14 crystals using a time-sharing 'cueing' technique. The major compharing 'cueing' technique. The major components of the system consist of the mechanical scanning frame and position encoders; radiation detectors, coincidence circuitry and nuclear instrumentation; counters and buffer storage; anatomical landmark recognition section; arithmetic section; program control logic; system control logic; output control logic and the output devices. At present, the output devices consist of digital cathode-ray tubes, a storage scope, an IBM l/O writer and a Kennedy incremental read-write magnetic tape recorder. This system has been designed to perform a variety of quantitative clinical procedures. These studies include iso-sensitivity scanning, dual radionuclide scanning, whole-body and linear profile counting, positron scanning and dynamic function studies. (author)

  12. Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins

    OpenAIRE

    Phair, Robert D.; Scaffidi, Paola; Elbi, Cem; Vecerova?, Jaromi?ra; Dey, Anup; Ozato, Keiko; Brown, David T.; Hager, Gordon; Bustin, Michael; Misteli, Tom

    2004-01-01

    Genome structure and gene expression depend on a multitude of chromatin-binding proteins. The binding properties of these proteins to native chromatin in intact cells are largely unknown. Here, we describe an approach based on combined in vivo photobleaching microscopy and kinetic modeling to analyze globally the dynamics of binding of chromatin-associated proteins in living cells. We have quantitatively determined basic biophysical properties, such as off rate constants, residence time, and ...

  13. Genetic variants in vitamin D metabolism-related genes and body mass index: Analysis of genome-wide scan data of ?7 000 Chinese women

    OpenAIRE

    Dorjgochoo, Tsogzolmaa; Shi, Jiajun; Gao, Yu-Tang; Long, Jirong; Delahanty, Ryan; Xiang, Yong-Bing; Cai, Qiuyin; Shu, Xiao Ou

    2011-01-01

    Vitamin D deficiency has been consistently associated with obesity. However, it is unclear whether vitamin D deficiency is the cause or consequence of obesity. We investigated this question by evaluating the association between genetic variants in vitamin D metabolism pathway genes and obesity-related traits. Using directly genotyped and imputed data from a genome-wide association (GWA) study of 6,922 women aged 25–70 years, we examined the association of 198 SNPs in vitamin D pathway genes...

  14. Genome-wide scan of job-related exhaustion with three replication studies implicate a susceptibility variant at the UST gene locus

    OpenAIRE

    Sulkava, Sonja; Ollila, Hanna M.; Ahola, Kirsi; Partonen, Timo; Viitasalo, Katriina; Kettunen, Johannes; Lappalainen, Maarit; Kivima?ki, Mika; Vahtera, Jussi; Lindstro?m, Jaana; Ha?rma?, Mikko; Puttonen, Sampsa; Salomaa, Veikko; Paunio, Tiina

    2013-01-01

    Job-related exhaustion is the core dimension of burnout, a work-related stress syndrome that has several negative health consequences. In this study, we explored the molecular genetic background of job-related exhaustion. A genome-wide analysis of job-related exhaustion was performed in the GENMETS subcohort (n = 1256) of the Finnish population-based Health 2000 study. Replication analyses included an analysis of the strongest associations in the rest of the Health 2000 sample (n = 1660 worke...

  15. The Generic Genome Browser: A Building Block for a Model Organism System Database

    OpenAIRE

    Stein, Lincoln D; Mungall, Christopher; Shu, Shengqiang; Caudy, Michael; Mangone, Marco; Day, Allen; Nickerson, Elizabeth; Stajich, Jason E.; Harris, Todd W.; Arva, Adrian; Lewis, Suzanna

    2002-01-01

    The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search ...

  16. Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

    Science.gov (United States)

    Baute, Gregory J; Kane, Nolan C; Grassa, Christopher J; Lai, Zhao; Rieseberg, Loren H

    2015-04-01

    The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study, we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower (Helianthus annuus), a globally important oilseed. To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of H. annuus, as well as two cross-compatible wild relatives, Helianthus argophyllus and Helianthus petiolaris. Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped quantitative trait loci (QTLs), such as branching. Admixture analyses revealed that all the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line. Cumulatively, introgressions cover c. 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes, probably because of the reintroduction of branching. PMID:25641359

  17. The influence of off-screen landmarks on user orientation

    OpenAIRE

    Korda, Amichai

    2014-01-01

    Maps displayed on hand held devices, such as smartphones; provide limited visibility due to their small screen display. In order to overcome display limitations, researchers have developed new techniques that point users to objects and landmarks located off-screen, which is known as an “off-screen interface”. Since this is a new type of map interface, there is little information regarding the effect it has on the user’s perception of the environment and spatial orientation abilities. ...

  18. Locating landmarks on high-dimensional free energy surfaces.

    Science.gov (United States)

    Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark E

    2015-03-17

    Coarse graining of complex systems possessing many degrees of freedom can often be a useful approach for analyzing and understanding key features of these systems in terms of just a few variables. The relevant energy landscape in a coarse-grained description is the free energy surface as a function of the coarse-grained variables, which, despite the dimensional reduction, can still be an object of high dimension. Consequently, navigating and exploring this high-dimensional free energy surface is a nontrivial task. In this paper, we use techniques from multiscale modeling, stochastic optimization, and machine learning to devise a strategy for locating minima and saddle points (termed "landmarks") on a high-dimensional free energy surface "on the fly" and without requiring prior knowledge of or an explicit form for the surface. In addition, we propose a compact graph representation of the landmarks and connections between them, and we show that the graph nodes can be subsequently analyzed and clustered based on key attributes that elucidate important properties of the system. Finally, we show that knowledge of landmark locations allows for the efficient determination of their relative free energies via enhanced sampling techniques. PMID:25737545

  19. Perceptual organization and artificial attention for visual landmarks detection.

    Science.gov (United States)

    Antúnez, Esther; Palomino, Antonio J; Marfil, Rebeca; Bandera, Juan P

    2013-03-01

    In biological vision systems, attention mechanisms are responsible for selecting the relevant information from the sensed field of view, so that the complete scene can be analyzed using a sequence of rapid eye saccades. In recent years, efforts have been made to imitate such attention behavior in artificial vision systems, because it allows optimizing the computational resources as they can be focused on the processing of a set of selected regions. In the framework of mobile robotics navigation, this work proposes an artificial model where attention is deployed at the level of objects (visual landmarks) and where new processes for estimating bottom-up and top-down (target-based) saliency maps are employed. Bottom-up attention is implemented through a hierarchical process, whose final result is the perceptual grouping of the image content. The hierarchical grouping is applied using a Combinatorial Pyramid that represents each level of the hierarchy by a combinatorial map. The process takes into account both image regions (faces in the map) and edges (arcs in the map). Top-down attention searches for previously detected landmarks, enabling their re-detection when the robot presumes that it is revisiting a known location. Landmarks are described by a combinatorial submap; thus, this search is conducted through an error-tolerant submap isomorphism procedure. PMID:23328946

  20. AUTOMATIC DETECTION AND CLASSIFICATION OF RETINAL VASCULAR LANDMARKS

    Directory of Open Access Journals (Sweden)

    Hadi Hamad

    2014-06-01

    Full Text Available The main contribution of this paper is introducing a method to distinguish between different landmarks of the retina: bifurcations and crossings. The methodology may help in differentiating between arteries and veins and is useful in identifying diseases and other special pathologies, too. The method does not need any special skills, thus it can be assimilated to an automatic way for pinpointing landmarks; moreover it gives good responses for very small vessels. A skeletonized representation, taken out from the segmented binary image (obtained through a preprocessing step, is used to identify pixels with three or more neighbors. Then, the junction points are classified into bifurcations or crossovers depending on their geometrical and topological properties such as width, direction and connectivity of the surrounding segments. The proposed approach is applied to the public-domain DRIVE and STARE datasets and compared with the state-of-the-art methods using proper validation parameters. The method was successful in identifying the majority of the landmarks; the average correctly identified bifurcations in both DRIVE and STARE datasets for the recall and precision values are: 95.4% and 87.1% respectively; also for the crossovers, the recall and precision values are: 87.6% and 90.5% respectively; thus outperforming other studies.

  1. Quality-Aware Estimation of Facial Landmarks in Video Sequences

    DEFF Research Database (Denmark)

    Haque, Mohammad Ahsanul; Nasrollahi, Kamal

    2015-01-01

    Face alignment in video is a primitive step for facial image analysis. The accuracy of the alignment greatly depends on the quality of the face image in the video frames and low quality faces are proven to cause erroneous alignment. Thus, this paper proposes a system for quality aware face alignment by using a Supervised Decent Method (SDM) along with a motion based forward extrapolation method. The proposed system first extracts faces from video frames. Then, it employs a face quality assessment technique to measure the face quality. If the face quality is high, the proposed system uses SDM for facial landmark detection. If the face quality is low the proposed system corrects the facial landmarks that are detected by SDM. Depending upon the face velocity in consecutive video frames and face quality measure, two algorithms are proposed for correction of landmarks in low quality faces by using an extrapolation polynomial. Experimental results illustrate the competency of the proposed method while comparing with the state-of-theart methods including an SDM-based method (from CVPR-2013) and a very recent method (from CVPR-2014) that uses parallel cascade of linear regression (Par-CLR).

  2. The post-birthday world: consequences of temporal landmarks for temporal self-appraisal and motivation.

    Science.gov (United States)

    Peetz, Johanna; Wilson, Anne E

    2013-02-01

    Much as physical landmarks help structure our representation of space, temporal landmarks such as birthdays and significant calendar dates structure our perception of time, such that people may organize or categorize their lives into "chunks" separated by these markers. Categories on the temporal landscape may vary depending on what landmarks are salient at a given time. We suggest these landmarks have implications for identity and motivation. The present research examined consequences of salient temporal landmarks for perceptions of the self across time and motivation to pursue successful future selves. Studies 1 and 2 show that temporally extended selves are perceived as less connected to, and more dissimilar from, the current self when an intervening landmark event has been made salient. Study 3 addresses the proposed mechanism, demonstrating that intervening landmarks lead people to categorize pre- and postlandmark selves into separate categories more often than when the same time period contains no salient landmarks. Finally, we examined whether landmark-induced mental contrasting of present state and future desired state could increase goal-pursuit motivation (in an effort to bridge the gap between inferior present and better future states). Studies 4-6 demonstrate that landmark-induced discrepancies between current health and hoped-for future health increased participants' motivation to exercise and increased the likelihood that they acted in line with their future-oriented goals. PMID:23066883

  3. Volumetric Image Guidance Using Carina vs Spine as Registration Landmarks for Conventionally Fractionated Lung Radiotherapy

    International Nuclear Information System (INIS)

    Purpose: To compare the relative accuracy of 2 image guided radiation therapy methods using carina vs spine as landmarks and then to identify which landmark is superior relative to tumor coverage. Methods and Materials: For 98 lung patients, 2596 daily image-guidance cone-beam computed tomography scans were analyzed. Tattoos were used for initial patient alignment; then, spine and carina registrations were performed independently. A separate analysis assessed the adequacy of gross tumor volume, internal target volume, and planning target volume coverage on cone-beam computed tomography using the initial, middle, and final fractions of radiation therapy. Coverage was recorded for primary tumor (T), nodes (N), and combined target (T+N). Three scenarios were compared: tattoos alignment, spine registration, and carina registration. Results: Spine and carina registrations identified setup errors ?5 mm in 35% and 46% of fractions, respectively. The mean vector difference between spine and carina matching had a magnitude of 3.3 mm. Spine and carina improved combined target coverage, compared with tattoos, in 50% and 34% (spine) to 54% and 46% (carina) of the first and final fractions, respectively. Carina matching showed greater combined target coverage in 17% and 23% of fractions for the first and final fractions, respectively; with spine matching, this was only observed in 4% (first) and 6% (final) of fractions. Carina matching provided superior nodes coverage at the endvided superior nodes coverage at the end of radiation compared with spine matching (P=.0006), without compromising primary tumor coverage. Conclusion: Frequent patient setup errors occur in locally advanced lung cancer patients. Spine and carina registrations improved combined target coverage throughout the treatment course, but carina matching provided superior combined target coverage.

  4. Gallium scan

    Science.gov (United States)

    Liver gallium scan; Bony gallium scan ... You will get a radioactive material called gallium injected into your vein. The gallium travels through the bloodstream and collects in the bones and certain organs. Your health care provider will ...

  5. Renal scan

    Science.gov (United States)

    A renal scan is a nuclear medicine exam in which a small amount of radioactive material (radioisotope) is used to ... vary. This article provides a general overview. A renal scan is similar to a renal perfusion scintiscan . It ...

  6. Microarray data mining using landmark gene-guided clustering

    Directory of Open Access Journals (Sweden)

    Cho HyungJun

    2008-02-01

    Full Text Available Abstract Background Clustering is a popular data exploration technique widely used in microarray data analysis. Most conventional clustering algorithms, however, generate only one set of clusters independent of the biological context of the analysis. This is often inadequate to explore data from different biological perspectives and gain new insights. We propose a new clustering model that can generate multiple versions of different clusters from a single dataset, each of which highlights a different aspect of the given dataset. Results By applying our SigCalc algorithm to three yeast Saccharomyces cerevisiae datasets we show two results. First, we show that different sets of clusters can be generated from the same dataset using different sets of landmark genes. Each set of clusters groups genes differently and reveals new biological associations between genes that were not apparent from clustering the original microarray expression data. Second, we show that many of these new found biological associations are common across datasets. These results also provide strong evidence of a link between the choice of landmark genes and the new biological associations found in gene clusters. Conclusion We have used the SigCalc algorithm to project the microarray data onto a completely new subspace whose co-ordinates are genes (called landmark genes, known to belong to a Biological Process. The projected space is not a true vector space in mathematical terms. However, we use the term subspace to refer to one of virtually infinite numbers of projected spaces that our proposed method can produce. By changing the biological process and thus the landmark genes, we can change this subspace. We have shown how clustering on this subspace reveals new, biologically meaningful clusters which were not evident in the clusters generated by conventional methods. The R scripts (source code are freely available under the GPL license. The source code is available [see Additional File 1] as additional material, and the latest version can be obtained at http://www4.ncsu.edu/~pchopra/landmarks.html. The code is under active development to incorporate new clustering methods and analysis. Additional file 1 R source code file Click here for file

  7. Computing Topology Preservation of RBF Transformations for Landmark-Based Image Registration

    OpenAIRE

    Cavoretto, R.; Rossi, A.; Qiao, H.; Quatember, B.; Recheis, W; M. Mayr

    2014-01-01

    In image registration, a proper transformation should be topology preserving. Especially for landmark-based image registration, if the displacement of one landmark is larger enough than those of neighbourhood landmarks, topology violation will be occurred. This paper aim to analyse the topology preservation of some Radial Basis Functions (RBFs) which are used to model deformations in image registration. Mat\\'{e}rn functions are quite common in the statistic literature (see, ...

  8. Diverse Landmark Sampling from Determinantal Point Processes for Scalable Manifold Learning

    OpenAIRE

    Wachinger, Christian; Golland, Polina

    2015-01-01

    High computational costs of manifold learning prohibit its application for large point sets. A common strategy to overcome this problem is to perform dimensionality reduction on selected landmarks and to successively embed the entire dataset with the Nystr\\"om method. The two main challenges that arise are: (i) the landmarks selected in non-Euclidean geometries must result in a low reconstruction error, (ii) the graph constructed from sparsely sampled landmarks must approxim...

  9. Landmark risk prediction of residual life for breast cancer survival.

    Science.gov (United States)

    Parast, Layla; Cai, Tianxi

    2013-09-10

    The importance of developing personalized risk prediction estimates has become increasingly evident in recent years. In general, patient populations may be heterogenous and represent a mixture of different unknown subtypes of disease. When the source of this heterogeneity and resulting subtypes of disease are unknown, accurate prediction of survival may be difficult. However, in certain disease settings, the onset time of an observable short-term event may be highly associated with these unknown subtypes of disease and thus may be useful in predicting long-term survival. One approach to incorporate short-term event information along with baseline markers for the prediction of long-term survival is through a landmark Cox model, which assumes a proportional hazards model for the residual life at a given landmark point. In this paper, we use this modeling framework to develop procedures to assess how a patient's long-term survival trajectory may change over time given good short-term outcome indications along with prognosis on the basis of baseline markers. We first propose time-varying accuracy measures to quantify the predictive performance of landmark prediction rules for residual life and provide resampling-based procedures to make inference about such accuracy measures. Simulation studies show that the proposed procedures perform well in finite samples. Throughout, we illustrate our proposed procedures by using a breast cancer dataset with information on time to metastasis and time to death. In addition to baseline clinical markers available for each patient, a chromosome instability genetic score, denoted by CIN25, is also available for each patient and has been shown to be predictive of survival for various types of cancer. We provide procedures to evaluate the incremental value of CIN25 for the prediction of residual life and examine how the residual life profile changes over time. This allows us to identify an informative landmark point, t(0) , such that accurate risk predictions of the residual life could be made for patients who survive past t(0) without metastasis. PMID:23494768

  10. Análise de agrupamento de diferentes densidades de marcadores no mapeamento genético por varredura genômica / Cluster analysis of different marker densities in genetic mapping using genome scan

    Scientific Electronic Library Online (English)

    Marcelo, Jangarelli; Ricardo Frederico, Euclydes; Cosme Damião, Cruz; Paulo Roberto, Cecon; Antonio Policarpo Souza, Carneiro.

    2010-12-01

    Full Text Available A simulação tem contribuído para o avanço da genômica nas diversas áreas do melhoramento genético. Foram simulados mapeamentos genéticos utilizando diferentes densidades de marcadores para estimar os valores fenotípicos na seleção assistida por marcadores (SAM), em características quantitativas com [...] valores de herdabilidade de 0,10; 0,40; e 0,70. Procedeu-se a análise de agrupamento com os desempenhos fenotípicos, cuja finalidade foi obter estruturas de classificação entre as densidades visando à otimização na detecção de QTL. O sistema de simulação genética (Genesys) foi utilizado para três genomas (cada qual constituído de uma única característica cuja distinção estava no valor da herdabilidade) e para as populações base e inicial. Cada população inicial foi submetida à seleção assistida por marcadores por 20 gerações consecutivas, em que os genitores selecionados acasalavam-se seletivamente entre os melhores e os piores. O mapeamento empregando de média a alta densidade de marcadores assinalou eficiência nos progressos fenotípicos obtidos com a SAM. Menores quantidades de marcadores são requeridas para manter determinado poder de detecção de QTL à medida que se eleva a magnitude da herdabilidade. A análise de agrupamento indicou otimização e correspondência nos incrementos fenotípicos ao admitir as densidades de 4 e 6 cM; 4, 6, 8 e 10 cM; e 6 e 8 cM para as herdabilidades de 0,10; 0,40; e 0,70, respectivamente. Abstract in english Simulation has contributed to the advancement of genomics in the different areas of genetic improvement. Genetic mappings were simulated using different densities of genetic markers to estimate phenotypic values of quantitative traits with heritabilities of 0.10; 0.40 and 0.70 in marker assisted sel [...] ection (MAS). Cluster analysis with phenotypic performances was carried out to generate classification structures among the densities aiming to optimize QTL detection . The genetic simulation system (Genesys) was used to simulate three genomes (each consisting of a single characteristic differing in the heritability value) and the base and original populations. Each initial population was subjected to selection assisted by markers for 20 consecutive generations, in which selected parents mated selectively, between best and worst. The mapping using medium to high marker density showed efficiency in the phenotypic progress obtained with MAS. Smaller marker quantities are required to maintain power of QTL detection with increase in heritability. The cluster analysis indicated optimization and correspondence in phenotypic increases, when allowing the densities of 4 and 6 cM, 4, 6, 8 and 10 cM, and 6 and 8 cM for the heritabilities of 0.10; 0.40 and 0.70, respectively.

  11. Análise de agrupamento de diferentes densidades de marcadores no mapeamento genético por varredura genômica Cluster analysis of different marker densities in genetic mapping using genome scan

    Directory of Open Access Journals (Sweden)

    Marcelo Jangarelli

    2010-12-01

    Full Text Available A simulação tem contribuído para o avanço da genômica nas diversas áreas do melhoramento genético. Foram simulados mapeamentos genéticos utilizando diferentes densidades de marcadores para estimar os valores fenotípicos na seleção assistida por marcadores (SAM, em características quantitativas com valores de herdabilidade de 0,10; 0,40; e 0,70. Procedeu-se a análise de agrupamento com os desempenhos fenotípicos, cuja finalidade foi obter estruturas de classificação entre as densidades visando à otimização na detecção de QTL. O sistema de simulação genética (Genesys foi utilizado para três genomas (cada qual constituído de uma única característica cuja distinção estava no valor da herdabilidade e para as populações base e inicial. Cada população inicial foi submetida à seleção assistida por marcadores por 20 gerações consecutivas, em que os genitores selecionados acasalavam-se seletivamente entre os melhores e os piores. O mapeamento empregando de média a alta densidade de marcadores assinalou eficiência nos progressos fenotípicos obtidos com a SAM. Menores quantidades de marcadores são requeridas para manter determinado poder de detecção de QTL à medida que se eleva a magnitude da herdabilidade. A análise de agrupamento indicou otimização e correspondência nos incrementos fenotípicos ao admitir as densidades de 4 e 6 cM; 4, 6, 8 e 10 cM; e 6 e 8 cM para as herdabilidades de 0,10; 0,40; e 0,70, respectivamente.Simulation has contributed to the advancement of genomics in the different areas of genetic improvement. Genetic mappings were simulated using different densities of genetic markers to estimate phenotypic values of quantitative traits with heritabilities of 0.10; 0.40 and 0.70 in marker assisted selection (MAS. Cluster analysis with phenotypic performances was carried out to generate classification structures among the densities aiming to optimize QTL detection . The genetic simulation system (Genesys was used to simulate three genomes (each consisting of a single characteristic differing in the heritability value and the base and original populations. Each initial population was subjected to selection assisted by markers for 20 consecutive generations, in which selected parents mated selectively, between best and worst. The mapping using medium to high marker density showed efficiency in the phenotypic progress obtained with MAS. Smaller marker quantities are required to maintain power of QTL detection with increase in heritability. The cluster analysis indicated optimization and correspondence in phenotypic increases, when allowing the densities of 4 and 6 cM, 4, 6, 8 and 10 cM, and 6 and 8 cM for the heritabilities of 0.10; 0.40 and 0.70, respectively.

  12. Learned predictiveness training modulates biases towards using boundary or landmark cues during navigation.

    Science.gov (United States)

    Buckley, Matthew G; Smith, Alastair D; Haselgrove, Mark

    2015-06-01

    A number of navigational theories state that learning about landmark information should not interfere with learning about shape information provided by the boundary walls of an environment. A common test of such theories has been to assess whether landmark information will overshadow, or restrict, learning about shape information. Whilst a number of studies have shown that landmarks are not able to overshadow learning about shape information, some have shown that landmarks can, in fact, overshadow learning about shape information. Given the continued importance of theories that grant the shape information that is provided by the boundary of an environment a special status during learning, the experiments presented here were designed to assess whether the relative salience of shape and landmark information could account for the discrepant results of overshadowing studies. In Experiment 1, participants were first trained that either the landmarks within an arena (landmark-relevant), or the shape information provided by the boundary walls of an arena (shape-relevant), were relevant to finding a hidden goal. In a subsequent stage, when novel landmark and shape information were made relevant to finding the hidden goal, landmarks dominated behaviour for those given landmark-relevant training, whereas shape information dominated behaviour for those given shape-relevant training. Experiment 2, which was conducted without prior relevance training, revealed that the landmark cues, unconditionally, dominated behaviour in our task. The results of the present experiments, and the conflicting results from previous overshadowing experiments, are explained in terms of associative models that incorporate an attention variant. PMID:25409751

  13. Relative warps meet cladistics: A contribution to the phylogenetic relationships ofbaleen whales based on landmark analyses of mysticete crania

    Directory of Open Access Journals (Sweden)

    Hampe O Baszio S

    2010-06-01

    Full Text Available During the last few years research on fossil baleen whales experienced a renaissance. Several important fossils weredescribed, and new and extended cladistic analyses were performed, partly including molecular data from living species.Despite the progress in our knowledge of their phylogeny, many questions have still not been resolved. A different attemptto illustrate mysticete relationships is presented here using landmark analyses. For the present analysis, 38 dorsalviews of mysticete skulls and skull reconstructions were scanned and thirteen landmarks were defined. The method usedis the relative warp analysis. This method allows a clustering of elements according to their similarity in shape. The calculatedrelative warps explain main shape variations in the sample. As in parsimony analyses the toothed mysticetes areclearly distinguishable. Representatives of the Aetocetoidea are grouped very closely together and therefore their classificationin this family is strongly supported. The performed analysis shows that the crania of the Balaenidae have developedsimilarities to the cranium of Janjucetus hunderi. The restriction of the Cetotheriidae to a small group of taxa isconfirmed here and includes in this analysis Cetotherium, Mixocetus, Piscobalaena, and Titanocetus with a close relationshipto the living gray whale. The stem-balaenopterids do not show any clear signals in the present analysis. There isno support for a subdivision into further families. The structure of the dorsal cranium of Protororqualus andPraemegaptera is very similar to that of Balaenoptera

  14. Microbial Genomics

    Science.gov (United States)

    Web page with links to microbes in the Joint Genome Institute (JGI) system than have finished genomes and draft genomes. There are also links to JGI home page, genome portal home, and the human genome project.

  15. Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program

    Directory of Open Access Journals (Sweden)

    Ellison R Curtis

    2006-03-01

    Full Text Available Abstract Background Elevated resting heart rate has been shown in multiple studies to be a strong predictor of cardiovascular disease. Previous family studies have shown a significant heritable component to heart rate with several groups conducting genomic linkage scans to identify quantitative trait loci. Methods We performed a genome-wide linkage scan to identify quantitative trait loci influencing resting heart rate among 3,282 Caucasians and 3,989 African-Americans in three independent networks comprising the Family Blood Pressure Program (FBPP using 368 microsatellite markers. Mean heart rate measurements were used in a regression model including covariates for age, body mass index, pack-years, currently drinking alcohol (yes/no, hypertension status and medication usage to create a standardized residual for each gender/ethnic group within each study network. This residual was used in a nonparametric variance component model to generate a LOD score and a corresponding P value for each ethnic group within each study network. P values from each ethnic group and study network were merged using an adjusted Fisher's combining P values method and the resulting P values were converted to LOD scores. The entire analysis was redone after individuals currently taking beta-blocker medication were removed. Results We identified significant evidence of linkage (LOD = 4.62 to chromosome 10 near 142.78 cM in the Caucasian group of HyperGEN. Between race and network groups we identified a LOD score of 1.86 on chromosome 5 (between 39.99 and 45.34 cM in African-Americans in the GENOA network and the same region produced a LOD score of 1.12 among Caucasians within a different network (HyperGEN. Combining all network and race groups we identified a LOD score of 1.92 (P = 0.0013 on chromosome 5p13-14. We assessed heterogeneity for this locus between networks and ethnic groups and found significant evidence for low heterogeneity (P ? 0.05. Conclusion We found replication (LOD > 1 between ethnic groups and between study networks with low heterogeneity on chromosome 5p13-14 suggesting that a gene in this region influences resting heart rate.

  16. Shape representation for efficient landmark-based segmentation in 3-d.

    Science.gov (United States)

    Ibragimov, Bulat; Likar, Boštjan; Pernuš, Franjo; Vrtovec, Tomaž

    2014-04-01

    In this paper, we propose a novel approach to landmark-based shape representation that is based on transportation theory, where landmarks are considered as sources and destinations, all possible landmark connections as roads, and established landmark connections as goods transported via these roads. Landmark connections, which are selectively established, are identified through their statistical properties describing the shape of the object of interest, and indicate the least costly roads for transporting goods from sources to destinations. From such a perspective, we introduce three novel shape representations that are combined with an existing landmark detection algorithm based on game theory. To reduce computational complexity, which results from the extension from 2-D to 3-D segmentation, landmark detection is augmented by a concept known in game theory as strategy dominance. The novel shape representations, game-theoretic landmark detection and strategy dominance are combined into a segmentation framework that was evaluated on 3-D computed tomography images of lumbar vertebrae and femoral heads. The best shape representation yielded symmetric surface distance of 0.75 mm and 1.11 mm, and Dice coefficient of 93.6% and 96.2% for lumbar vertebrae and femoral heads, respectively. By applying strategy dominance, the computational costs were further reduced for up to three times. PMID:24710155

  17. Marking time: selective use of temporal landmarks as barriers between current and future selves.

    Science.gov (United States)

    Peetz, Johanna; Wilson, Anne E

    2014-01-01

    Temporal landmarks such as birthdays and significant calendar dates structure our perception of time. People might highlight temporal landmarks spontaneously in an effort to regulate connections between temporal selves. Five studies demonstrated that landmarks are used spontaneously to induce psychological separation from undesirable temporal selves. Participants were more likely to think of events that fell in between the current and the future self if an imagined future self was negative than if it was positive (Studies 1a, 1b, and 2). Furthermore, when a self-enhancement mindset was activated, participants were more likely to call to mind intervening temporal landmarks to protect themselves from a negative future self than when this mindset was not activated (Study 3). Finally, when psychological separations between the current self and a negative future self were introduced through alternate means, participants no longer selectively used landmarks to separate themselves from this future self (Study 4). PMID:23969622

  18. Software-guided standardization of manual landmark data in medical images.

    Science.gov (United States)

    Prüm, Hermann; Gerigk, Lars; Hintze, Christian; Thieke, Christian; Floca, Ralf

    2011-01-01

    It is crucial to evaluate registration algorithms in order to make them available in clinical practice. Several evaluation strategies have been proposed in the past, and one approach is to evaluate these algorithms with intrinsic anatomical landmarks identified by a health professional. The acquisition and handling of large amounts of these landmark data is a time-consuming task for the health professional, and it is vulnerable to errors and inconsistencies. Additionally, limited access to appropriate tools makes dealing with landmark data considerably more difficult. We introduce a strategy for the acquisition of landmarks for the landmark-based evaluation of registration algorithms and we present an ontology-driven software tool that assists the different partners involved to act according to that strategy. This tool provides the user with intrinsic knowledge of the registration problems, the possibility to conveniently make the acquired data available to further processing, and an easy-to-use graphical interface. PMID:20888204

  19. The use of anatomical landmarks for percutaneous nephrolithotomy

    Directory of Open Access Journals (Sweden)

    Esat Kaan Akbay

    2012-06-01

    Full Text Available Objective: The aim of our study was to describe the external anatomical landmarks and angles as a training guide for urologists in the performance of percutaneous nephrolithotomy (PCNL in the prone position. Materials and Methods: Between 2006 and 2008, 50 patients (including 10 resident cases undergoing PCNL met the study criteria. The inclusion criteria consisted of patients with renal stones scheduled for a lower calyceal puncture PCNL where the number of attempts to access the calyx ? 3, and clear urine was seen draining from the needle. The exclusion criteria consisted of previous ipsilateral kidney surgery, severe hydronephrosis, anomalies of the renal or skeletal systems, BMI>30 kg/m2, upper/middle calyceal puncture and age ?18. Several anatomical landmarks and angles were measured, recorded and analyzed. Results: The mean length of (Pi was 10.1±1.7 cm (range 7-14, (Pe was 9.9±1.7 cm (range 6-13, (a was 11.2±2.8 cm (range 5.5-17, (b was 5.3±2.3 cm (range 1.5-11 cm, (x was 5.1±1.9 cm (range 1-8, (x1 was 3.3±1.7 cm (range 1.5-8.2, (y was 7.1±1.7 cm (range 3.3-11.6, (y1 was 3.8±1.6 cm (range 1-9 and (t was 4.9±1.7 cm (range 3-9. The mean angle for (a was 49±13º (range 30-70º, (b was 41±13º (range 20-70º and (g was 61±13º (range 28-80º. In resident cases, the median number of attempts was 1 (range 1-3, the median overall time for successful access was 7.25 minutes (range 2-12 and the median fl uoroscopy time was 62.5 seconds (range 30-150. Conclusion: A knowledge of these anatomical landmarks and angles may increase the capacity of urologists to repetitively perform the precise task of percutaneous access of the lower calyceal during PCNL.

  20. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-01-01

    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. PMID:19259127

  1. Elections and landmark policies in Tanzania and Uganda

    DEFF Research Database (Denmark)

    Kjær, Anne Mette; Therkildsen, Ole

    2013-01-01

    Much of the relevant literature on Africa downplays the salience of elections for policy-making and implementation. Instead, the importance of factors such as clientelism, ethnicity, organized interest group and donor influence, is emphasized. We argue that, in addition, elections now motivate political elites to focus on policies they perceive to be able to gain votes. This is based on analyses of six landmark decisions made during the last fifteen years in the social, productive and public finance sectors in Tanzania and Uganda. Such policies share a number of key characteristics: they are clearly identifiable with the party in power; citizens country-wide are targeted; and policy implementation aim at immediate, visible results. The influence of elections on policy making and implementation could therefore be more significant in countries where elections are more competitive than in Tanzania and Uganda.

  2. A review of the tragal pointer: anatomy and its importance as a landmark in surgical procedures.

    Science.gov (United States)

    Muhleman, M A; Wartmann, C T; Hage, R; Matusz, P; Shoja, M M; Tubbs, R S; Loukas, M

    2012-05-01

    The tragal pointer has long been used as a surgical landmark for the identification of the facial nerve trunk and the maxillary artery in such procedures as parotidectomy, internal fixation of subcondylar and condylar fractures, mandibular osteotomy, temporomandibular joint arthroplasty, and percutaneous blocks of branches of the trigeminal nerve and pterygopalatine ganglion. Aside from its use as an external landmark, it has also been implicated as a contributor to crease formation in the presence of peripheral arterial disease. This article will review the available literature on the tragal pointer's use as an external landmark. PMID:22648581

  3. 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.

  4. 77 FR 44670 - Information Collection Activities: National Historic Landmarks (NHL) Condition Survey

    Science.gov (United States)

    2012-07-30

    ...regarding the condition of designated landmarks. A questionnaire will be designed and used to collect information...condition data. Regional NPS staff contributed to the design of the questionnaire that is the subject of this request. II....

  5. A class of spline functions for landmark-based image registration

    OpenAIRE

    Rossi, Alessandra; Cavoretto, Roberto; Allasia, Giampietro

    2011-01-01

    A class of spline functions, called Lobachevsky splines, is proposed for landmark-based image registration. Analytic expressions of Lobachevsky splines and some of their properties are given, reasoning in the context of probability theory. Since these functions have simple analytic expressions and compact support, landmark-based transformations can be advantageously defined using them. Numerical results point out accuracy and stability of Lobachevsky splines, comparing them with Gaussians and...

  6. Learning Compact Visual Descriptors for Low Bit Rate Mobile Landmark Search

    OpenAIRE

    Duan, Ling-yu Peking University; Chen, Jie Peking University; Ji, Rongrong Peking University; Huang, Tiejun Peking University; Gao, Wen Peking University

    2013-01-01

    Coming with the ever growing computational power of mobile devices, mobile visual search have undergone an evolution in techniques and applications. A significant trend is low bit rate visual search, where compact visual descriptors are extracted directly over a mobile and delivered as queries rather than raw images to reduce the query transmission latency. In this article, we introduce our work on low bit rate mobile landmark search, in which a compact yet discriminative landmark image descr...

  7. Development of a New Software for Automatic Anatomical landmark Detection in Cephalometric X-ray Images

    Directory of Open Access Journals (Sweden)

    S. Nooranian

    2005-08-01

    Full Text Available Background & Objectives: As a routine clinical procedure in orthodontics, there are many geometrical calcula-tions usually taken place on the lateral x-ray images of the head in order to develop an appropriate treatment plan. This is currently done manually by the expert radiologists and/or orthodontists. It can take an experi-enced orthodontist up to thirty minutes to analyze one x-ray image and the results are still influenced by both subjective and objective errors. Here a new software for automatic anatomical landmark detection in cepha-lometric x-ray images is presented. The software extracts ten commonly used main landmarks. Methods and Materials: In this research, a combination of various image processing techniques including Template Matching, Edge Walking, and Shape Registration is employed to develop an automatic cephalomet-ric landmark detection algorithm within the x-ray images of the head. Ten essential and commonly used landmarks were selected as the target points. Results: The accuracy of the automatic landmark detection algorithm was evaluated with comparing the re-sults obtained by the automatic algorithm to those manually identified by an expert orthodontist on a data base of 10 x-ray images. The statistical analysis showed that 92% of the landmarks were determined accurately within an acceptable region of 4 millimeters from the points an expert had defined.. Conclusions: A MATLAB-based software was developed accordingly to help an orthodontist automatically identify the most commonly used 10 main cephalometric landmarks. The method can be extended for more landmarks in the future.

  8. Learning of landmark stability and instability by hippocampal place cells.

    Science.gov (United States)

    Jeffery, K J

    1998-01-01

    Place cells in the rat hippocampus fire whenever the animal is in a particular location. In a symmetrical environment, their receptive fields (place fields) are oriented by visual cues, and if these are unavailable they are oriented by movement-generated (idiothetic) cues. The present study tested the hypothesis that the cells would learn not to 'trust' a visual cue if the rat experienced it to be unstable (Knierim et al., 1995. Place cells, head direction cells and the learning of landmark stability. J. Neurosci. 15, 1648-1659). In an otherwise symmetrical environment, a visual cue was moved with respect to the idiothetic cues, either in sight or out-of-sight of the rat. When the visual cue was moved out-of-sight of the rat, place fields were initially oriented by this cue in preference to the idiothetic cues. However, if the cue was seen by the rat to be mobile, place fields ceased following the visual cue and became oriented by the idiothetic cues instead. If the cue was not seen to be mobile until the rat had had several days of experience in the environment, then the fields continued to be oriented by the (now visibly mobile) visual cue. It thus appears that the orienting influence of a visual cue on place fields can be either strengthened or weakened relative to the idiothetic cues, depending on the experience of the rat. PMID:9705005

  9. Desert ants benefit from combining visual and olfactory landmarks.

    Science.gov (United States)

    Steck, Kathrin; Hansson, Bill S; Knaden, Markus

    2011-04-15

    The desert ant, Cataglyphis fortis, uses both visual and olfactory cues to guide its return to the nest. The ants use vision-based path integration for long-distance navigation and memorize the visual and olfactory surrounding of the nest to finally locate the entrance. In the present study we investigated how the visual and the olfactory navigation systems interact. In field experiments ants were trained to associate the nest with a visual cue, an olfactory cue or a combination of both cues. We tested ants after one, five and 15 training runs, to investigate whether the ants would make use of the training cues to pinpoint the nest. We found that they were slow to learn the location of the nest when it was specified by just an olfactory or a visual cue. However, the ants focused their nest search after the first training run with the combined cue. Equally experienced ants responded to the individually presented visual or olfactory cues with the same high accuracy as they did to the combined cue. After 15 training runs, the combined cue still evoked an accurate response in the test, whereas the individually presented cues no longer did. Apparently, C. fortis benefit from combining their visual and olfactory navigational tools, because the bimodal sensory input accelerates the acquisition of landmark information. PMID:21430208

  10. Bone scans

    International Nuclear Information System (INIS)

    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

  11. Reliability and reproducibility of three-dimensional cephalometric landmarks using CBCT: a systematic review

    Scientific Electronic Library Online (English)

    Cinthia de Oliveira, LISBOA; Daniele, MASTERSON; Andréa Fonseca Jardim, MOTTA; Alexandre Trindade, MOTTA.

    2015-04-01

    Full Text Available Objective : The aim of this study was to review the reliability and reproducibility of 3D-CBCT (cone beam computed tomography) cephalometric landmark identification. Methods : Electronic databases (Pubmed, Scopus, Web of Science) were searched for papers published from 1998 to October 2014. Specifi [...] c strategies were developed for each database, with the guidance of a librarian. Two reviewers independently analyzed the titles and abstracts for inclusion. The articles that met the inclusion and exclusion criteria were selected for full-text reading, and the selected articles went through methodological quality evaluation. After the exclusion of repeated articles, the titles of the remaining ones were read and 1,328 of them were excluded. The abstracts of 173 articles were read, of which 43 were selected, read in full and submitted to the inclusion and exclusion criteria. Fourteen articles or studies with reliable methodology and reproducibility remained. The data were collected, organized into figures and analyzed for determination of the reliability and reproducibility of the three-dimensional cephalometric landmarks. Results : Overall, the landmarks on the median sagittal line and dental landmarks had the highest reliability, while the landmarks on the condyle, porion and the orbitale presented lower levels of reliability. Point S must be marked in the multiplanar views associated with visualization in 3D reconstruction. Further studies are necessary for evaluating soft tissue landmarks.

  12. Detection and location of 127 anatomical landmarks in diverse CT datasets

    Science.gov (United States)

    Dabbah, Mohammad A.; Murphy, Sean; Pello, Hippolyte; Courbon, Romain; Beveridge, Erin; Wiseman, Stewart; Wyeth, Daniel; Poole, Ian

    2014-03-01

    The automatic detection and localization of anatomical landmarks has wide application, including intra and interpatient registration, study location and navigation, and the targeting of specialized algorithms. In this paper, we demonstrate the automatic detection and localization of 127 anatomically defined landmarks distributed throughout the body, excluding arms. Landmarks are defined on the skeleton, vasculature and major organs. Our approach builds on the classification forests method,1 using this classifier with simple image features which can be efficiently computed. For the training and validation of the method we have used 369 CT volumes on which radiographers and anatomists have marked ground truth (GT) - that is the locations of all defined landmarks occurring in that volume. A particular challenge is to deal with the wide diversity of datasets encountered in radiology practice. These include data from all major scanner manufacturers, different extents covering single and multiple body compartments, truncated cardiac acquisitions, with and without contrast. Cases with stents and catheters are also represented. Validation is by a leave-one-out method, which we show can be efficiently implemented in the context of decision forest methods. Mean location accuracy of detected landmarks is 13.45mm overall; execution time averages 7s per volume on a modern server machine. We also present localization ROC analysis to characterize detection accuracy - that is to decide if a landmark is or is not present in a given dataset.

  13. Characterization of the Arachis (Leguminosae D genome using fluorescence in situ hybridization (FISH chromosome markers and total genome DNA hybridization

    Directory of Open Access Journals (Sweden)

    Germán Robledo

    2008-01-01

    Full Text Available Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH of the 5S and 45S rRNA genes and heterochromatic 4'-6-diamidino-2-phenylindole (DAPI positive bands. We used chromosome landmarks identified by these markers to construct the first Arachis species ideogram in which all the homologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome constitution (D genome of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes.

  14. Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization

    Scientific Electronic Library Online (English)

    Germán, Robledo; Guillermo, Seijo.

    Full Text Available Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH) of the 5S and 45S rRNA genes and heterochromatic 4'-6-diamidino-2-phenylindole (DAPI) positive bands. We used chromosome landmarks identified by these markers to construct the first Arachis spe [...] cies ideogram in which all the homologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome constitution (D genome) of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes.

  15. Thyroid Scan and Uptake

    Science.gov (United States)

    Thyroid Scan and Uptake Play Video Clip (00:03:26) Your Radiologist Explains Thyroid Scan Procedure ...more videos ... the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is a type ...

  16. Self-motivated visual scanning predicts flexible navigation in a virtual environment.

    Science.gov (United States)

    Ploran, Elisabeth J; Bevitt, Jacob; Oshiro, Jaris; Parasuraman, Raja; Thompson, James C

    2014-01-01

    The ability to navigate flexibly (e.g., reorienting oneself based on distal landmarks to reach a learned target from a new position) may rely on visual scanning during both initial experiences with the environment and subsequent test trials. Reliance on visual scanning during navigation harkens back to the concept of vicarious trial and error, a description of the side-to-side head movements made by rats as they explore previously traversed sections of a maze in an attempt to find a reward. In the current study, we examined if visual scanning predicted the extent to which participants would navigate to a learned location in a virtual environment defined by its position relative to distal landmarks. Our results demonstrated a significant positive relationship between the amount of visual scanning and participant accuracy in identifying the trained target location from a new starting position as long as the landmarks within the environment remain consistent with the period of original learning. Our findings indicate that active visual scanning of the environment is a deliberative attentional strategy that supports the formation of spatial representations for flexible navigation. PMID:24427132

  17. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations

    OpenAIRE

    Witherspoon, David J.; Zhang, Yuhua; Xing, Jinchuan; Watkins, W. Scott; Ha, Hongseok; Batzer, Mark A.; Jorde, Lynn B.

    2013-01-01

    Alu retrotransposons are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction libraries. In a single experiment, ME-Scan identifies nearly all AluYb8 and AluYb9 elements, with high sensitivity for both rare and common insertions, in 169 individual...

  18. PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use

    OpenAIRE

    Heidi Vähämaa; Ville R. Koskinen; Waltteri Hosia; Robert Moulder; Nevalainen, Olli S.; Riitta Lahesmaa; Tero Aittokallio; Jussi Salmi

    2011-01-01

    We present a versatile user-friendly software tool, PolyAlign, for the alignment of multiple LC-MS signal maps with the option of manual landmark setting or automated alignment. One of the spectral images is selected as a reference map, and after manually setting the landmarks, the program warps the images using either polynomial or Hermite transformation. The software provides an option for automated landmark finding. The software includes a very fast zoom-in function synchronized between th...

  19. Visual motion-sensitive neurons in the bumblebee brain convey information about landmarks during a navigational task

    OpenAIRE

    Martin Egelhaaf

    2014-01-01

    Bees use visual memories to find the spatial location of previously learnt food sites. Characteristic learning flights help acquiring these memories at newly discovered foraging locations where landmarks - salient objects in the vicinity of the goal location - can play an important role in guiding the animal’s homing behavior. Although behavioral experiments have shown that bees can use a variety of visual cues to distinguish objects as landmarks, the question of how landmark features are e...

  20. Genomic Testing

    Science.gov (United States)

    ... About CDC.gov . Public Health Genomics Share Compartir Genomic Testing Fact Sheet: Identifying Opportunities to Improve Health and Transform Healthcare [PDF 139.91 KB] Genomic Tests by Levels of Evidence Guidelines, Policies and ...

  1. Repeatability and reproducibility of landmarks--a three-dimensional computed tomography study.

    Science.gov (United States)

    Titiz, Irem; Laubinger, Michala; Keller, Thomas; Hertrich, Klaus; Hirschfelder, Ursula

    2012-06-01

    The aim of this study was to investigate the repeatability and reproducibility of the placement of anthropological cephalometric landmarks on three-dimensional computed tomography (3D CT) cranial reconstructions derived from volume data sets. In addition, the influence of the observer's experience on the repeatability of landmark setting was also explored. Twenty patients without any craniofacial deformity (11 females and 9 males; age range 6.1-16 years) were selected retrospectively from CT volume data sets already available from 695 patients of Dental Clinic 3, Orthodontics of Erlangen University Hospital. The CT examination was performed with the SOMATOM Sensation64 (Siemens AG Medical Solutions, Erlangen, Germany). The program VoXim6.1 (IVS Solutions AG, Chemnitz, Germany) was used for 3D reconstruction of the volume data sets. A total of 28 landmarks were examined in the skeleton module of the program VoXim6.1. The randomly sorted data sets were analysed by two orthodontists and two postgraduate students. Each data set was analysed twice by each observer at an interval of 3 weeks. The analysis of variance regarding random effects was used to calculate the intraobserver and interobserver components of standard deviation (SD) of depiction of individual landmarks as measures of repeatability and reproducibility, respectively. Median intraserial SD and interserial SD of 0.46 mm (range: 0.14-2.00 mm) and 0.20 mm (range: 0.02-2.47 mm), respectively, were obtained depending on the landmark and plane. This study included systematic analysis of extreme values (outliers) in the assessment of the quality of measurements obtained. Descriptive statistics revealed qualitative differences in the depiction of different landmarks. The landmarks nasion and infradentale revealed a minor SD in all three spatial coordinates with the smallest SD for infradentale (SD = 0.18 mm) in the transverse plane. However, no systematic trend was identified with regard to the influence of the observer's level of experience affecting the repeatability of landmark positioning. Thus, the repeatability and reproducibility of placements of landmarks with 3D CT were found to be acceptable for a majority of anatomical positions. PMID:21566086

  2. Visual landmark information gains control of the head direction signal at the lateral mammillary nuclei.

    Science.gov (United States)

    Yoder, Ryan M; Peck, James R; Taube, Jeffrey S

    2015-01-28

    The neural representation of directional heading is conveyed by head direction (HD) cells located in an ascending circuit that includes projections from the lateral mammillary nuclei (LMN) to the anterodorsal thalamus (ADN) to the postsubiculum (PoS). The PoS provides return projections to LMN and ADN and is responsible for the landmark control of HD cells in ADN. However, the functional role of the PoS projection to LMN has not been tested. The present study recorded HD cells from LMN after bilateral PoS lesions to determine whether the PoS provides landmark control to LMN HD cells. After the lesion and implantation of electrodes, HD cell activity was recorded while rats navigated within a cylindrical arena containing a single visual landmark or while they navigated between familiar and novel arenas of a dual-chamber apparatus. PoS lesions disrupted the landmark control of HD cells and also disrupted the stability of the preferred firing direction of the cells in darkness. Furthermore, PoS lesions impaired the stable HD cell representation maintained by path integration mechanisms when the rat walked between familiar and novel arenas. These results suggest that visual information first gains control of the HD cell signal in the LMN, presumably via the direct PoS ? LMN projection. This visual landmark information then controls HD cells throughout the HD cell circuit. PMID:25632114

  3. Arm CT scan

    Science.gov (United States)

    CAT scan - arm; Computed axial tomography scan - arm; Computed tomography scan - arm; CT scan - arm ... stopping.) A computer creates separate images of the arm area, called slices. These images can be stored, ...

  4. Domestication genomics: evidence from animals.

    Science.gov (United States)

    Wang, Guo-Dong; Xie, Hai-Bing; Peng, Min-Sheng; Irwin, David; Zhang, Ya-Ping

    2014-02-01

    Animal domestication has far-reaching significance for human society. The sequenced genomes of domesticated animals provide critical resources for understanding the genetic basis of domestication. Various genomic analyses have shed a new light on the mechanism of artificial selection and have allowed the mapping of genes involved in important domestication traits. Here, we summarize the published genomes of domesticated animals that have been generated over the past decade, as well as their origins, from a phylogenomic point of view. This review provides a general description of the genomic features encountered under a two-stage domestication process. We also introduce recent findings for domestication traits based on results from genome-wide association studies and selective-sweep scans for artificially selected genomic regions. Particular attention is paid to issues relating to the costs of domestication and the convergent evolution of genes between domesticated animals and humans. PMID:25384135

  5. Automated planning of MRI scans of knee joints

    Science.gov (United States)

    Bystrov, Daniel; Pekar, Vladimir; Young, Stewart; Dries, Sebastian P. M.; Heese, Harald S.; van Muiswinkel, Arianne M.

    2007-03-01

    A novel and robust method for automatic scan planning of MRI examinations of knee joints is presented. Clinical knee examinations require acquisition of a 'scout' image, in which the operator manually specifies the scan volume orientations (off-centres, angulations, field-of-view) for the subsequent diagnostic scans. This planning task is time-consuming and requires skilled operators. The proposed automated planning system determines orientations for the diagnostic scan by using a set of anatomical landmarks derived by adapting active shape models of the femur, patella and tibia to the acquired scout images. The expert knowledge required to position scan geometries is learned from previous manually planned scans, allowing individual preferences to be taken into account. The system is able to automatically discriminate between left and right knees. This allows to use and merge training data from both left and right knees, and to automatically transform all learned scan geometries to the side for which a plan is required, providing a convenient integration of the automated scan planning system in the clinical routine. Assessment of the method on the basis of 88 images from 31 different individuals, exhibiting strong anatomical and positional variability demonstrates success, robustness and efficiency of all parts of the proposed approach, which thus has the potential to significantly improve the clinical workflow.

  6. Internal jugular vein cannulation: an ultrasound-guided technique versus a landmark-guided technique

    Scientific Electronic Library Online (English)

    Gurkan, Turker; Fatma Nur, Kaya; Alp, Gurbet; Hale, Aksu; Cuneyt, Erdogan; Ahmet, Atlas.

    Full Text Available OBJECTIVES: To compare the landmark-guided technique versus the ultrasound-guided technique for internal jugular vein cannulation in spontaneously breathing patients. METHODS: A total of 380 patients who required internal jugular vein cannulation were randomly assigned to receive internal jugular ve [...] in cannulation using either the landmark- or ultrasound-guided technique in Bursa, Uludag University Faculty of Medicine, between April and November, 2008. Failed catheter placement, risk of complications from placement, risk of failure on first attempt at placement, number of attempts until successful catheterization, time to successful catheterization and the demographics of each patient were recorded. RESULTS: The overall complication rate was higher in the landmark group than in the ultrasound-guided group (p

  7. Landmark Detection via Ann for a Web Based Autonomous Mobile Robot: Sunar

    Directory of Open Access Journals (Sweden)

    Nihat Y?lmaz

    2006-06-01

    Full Text Available In this study, a landmark detection method was developed for finding or position correction of a web based mobile robot designed and implemented for long term and regular scientific purposes. Colored numeric and alphanumeric character sticker in place of other artificial landmarks appropriate for robot is selected to be landmark for understanding of both human and robot. Statistical analysis of captured and segmented image part is used for feature vector extraction. Statistical properties of histogram, projections and image raw data are selectable components of feature vector. The feature vector is tested by previously trained multilayer perceptron feed forward neural network (ANN. For this aim, online programs required for robotic activities, image processing and neural network processes have been developed on web interface of web-robot. In this program, improved software libraries for SUNAR system are employed. Real time results and robot scenes are monitored online on web portal.

  8. EXPLOITING 3D ULTRASOUND FOR FETAL DIAGNOSTIC PURPOSE THROUGH FACIAL LANDMARKING

    Directory of Open Access Journals (Sweden)

    Enrico Vezzetti

    2014-06-01

    Full Text Available In the last decade, three-dimensional landmarking has gained attention for different applications, such as face recognition for both identification of suspects and authentication, facial expression recognition, corrective and aesthetic surgery, syndrome study and diagnosis. This work focuses on the last one by proposing a geometrically-based landmark extraction algorithm aimed at diagnosing syndromes on babies before their birth. Pivotal role in this activity is the support provided by physicians and 3D ultrasound tools for working on real faces. In particular, the landmarking algorithm here proposed only relies on descriptors coming from Differential Geometry (Gaussian, mean, and principal curvatures, derivatives, coefficients of first and second fundamental forms, Shape and Curvedness indexes and is tested on nine facial point clouds referred to nine babies taken by a three-dimensional ultrasound tool at different weeks' gestation. The results obtained, validated with the support of four practitioners, show that the localization is quite accurate. All errors lie in the range between 0 and 3.5 mm and the mean distance for each shell is in the range between 0.6 and 1.6 mm. The landmarks showing the highest errors are the ones belonging to the mouth region. Instead, the most precise landmark is the pronasal, on the nose tip, with a mean distance of 0.55 mm. Relying on current literature, this study is something missing in the state-of-the-art of the field, as present facial studies on 3D ultrasound do not work on automatic landmarking yet.

  9. Genome Research

    Science.gov (United States)

    Genome Research, the Web version of Cold Spring Harbor Laboratory's printed journal, focuses on "genome studies in all species, including genetic and physical mapping, DNA sequencing, genome-based analyses of biological processes, gene discovery, comparative genome analyses, evolution studies, forensics, informatics, statistical and mathematical methods, genome structure and function, and technological innovations and applications." Online issues are available from April 1997; tables of contents and abstracts begin August 1995. The free access period for Genome Research ends December 31, 1998. Genome Research is made available through Stanford University's HighWire Press.

  10. Animals' Use of Landmarks and Metric Information to Reorient: Effects of the Size of the Experimental Space

    Science.gov (United States)

    Sovrano, Valeria Anna; Bisazza, Angelo; Vallortigara, Giorgio

    2005-01-01

    Disoriented children could use geometric information in combination with landmark information to reorient themselves in large but not in small experimental spaces. We tested fish in the same task and found that they were able to conjoin geometric and non-geometric (landmark) information to reorient themselves in both the large and the small space…

  11. Shape Analysis of 3D Head Scan Data for U.S. Respirator Users

    OpenAIRE

    Stephanie Lynch; Viscusi, Dennis J.; Stacey Benson; Slice, Dennis E.; Ziqing Zhuang

    2010-01-01

    In 2003, the National Institute for Occupational Safety and Health (NIOSH) conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D) landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA) was con...

  12. Precision landmark location for machine vision and photogrammetry finding and achieving the maximum possible accuracy

    CERN Document Server

    Gutierrez, José A

    2007-01-01

    Shows the reader how to derive theoretical limits to the precision of landmark identification in electronic imagesMATLAB® package assists the reader with applying theoretical results in real engineering systemsSteps outside the usual earth-sciences and civil-engineering base of photogrammetry to improve animation, medical imaging and robotic vision applications

  13. Application of landmark morphometrics to skulls representing the orders of living mammals

    Directory of Open Access Journals (Sweden)

    Leslie Marcus

    2000-06-01

    Full Text Available Abstract Statistical analyses of geometric morphometric data have been generally restricted to the Euclidean space tangent to curved shape space. This approach is based on the knowledge that such an approximation does not affect statistical and biological conclusions, when differences among specimens' shapes are not too large. We examined the wide variation of shapes within the vertebrate class Mammalia to determine the tangent space approximation by comparing Procrustes distances in Kendall shape space to tangent space distances among 53 mammal skulls and articulated jaws belonging to almost all of the living orders. Previous studies have been restricted to relatively low taxonomic levels, implying a narrower range of shapes. Thirty-five three-dimensional (3D landmarks on the sagittal plane and right side of each specimen were digitized using a MicroScribe 3DX. Procrustes and tangent space distances between all specimens were compared using the program TPSSMALL (Rohlf, 1998b. The correlations between these distances were always greater than 0.99. Lower jaw and brain subsets of the landmarks gave similar results, while the face subset had more scatter, but nearly the same correlation. The 3D shapes, as summarized by the landmarks, were clustered and the dendrogram was compared to a currently hypothesized phylogeny. We also point out that data from landmark morphometrics are as appropriate as morphological and molecular data for cladistic analysis.

  14. The developmental trajectory of intramaze and extramaze landmark biases in spatial navigation: An unexpected journey.

    Science.gov (United States)

    Buckley, Matthew G; Haselgrove, Mark; Smith, Alastair D

    2015-06-01

    Adults learning to navigate to a hidden goal within an enclosed space have been found to prefer information provided by the distal cues of an environment, as opposed to proximal landmarks within the environment. Studies with children, however, have shown that 5- or 7-year-olds do not display any preference toward distal or proximal cues during navigation. This suggests that a bias toward learning about distal cues occurs somewhere between the age of 7 years and adulthood. We recruited 5- to 11-year-old children and an adult sample to explore the developmental profile of this putative change. Across a series of 3 experiments, participants were required to navigate to a hidden goal in a virtual environment, the location of which was signaled by both extramaze and intramaze landmark cues. During testing, these cues were placed into conflict to assess the search preferences of participants. Consistent with previously reported findings, adults were biased toward using extramaze information. However, analysis of the data from children, which incorporated age as a continuous variable, suggested that older children in our sample were, in fact, biased toward using the intramaze landmark in our task. These findings suggest the bias toward using distal cues in spatial navigation, frequently displayed by adults, may be a comparatively late developing trait, and one that could supersede an initial developmental preference for proximal landmarks. (PsycINFO Database Record PMID:25844850

  15. RBC nuclear scan

    Science.gov (United States)

    An RBC nuclear scan uses small amounts of radioactive material to mark (tag) red blood cells (RBCs). Your body is then ... radiation -- it does not give off radiation. Most nuclear scans (including an RBC scan) are not recommended ...

  16. Nuclear Heart Scan

    Science.gov (United States)

    ... from the NHLBI on Twitter. What Is a Nuclear Heart Scan? A nuclear heart scan is a test that provides important ... use it to create pictures of your heart. Nuclear heart scans are used for three main purposes: ...

  17. Lumbar spine CT scan

    Science.gov (United States)

    CAT scan - lumbar spine; Computed axial tomography scan - lumbar spine; Computed tomography scan - lumbar spine; CT - lower back ... Koh DM, Roditi G. Intravascular contrast media for radiology, CT, and MRI. In: Adam A, Dixon AK, ...

  18. 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.

  19. The Genome Sequence of Drosophila melanogaster

    Science.gov (United States)

    Ramanujan, Krishna.

    On Thursday March 23, 2000, a historic milestone was marked as researchers announced they have completed mapping the genome of the fruit fly, Drosophila melanogaster. The achievement, which was announced in a special issue of the journal Science, culminates close to 100 years of research. Drosophila melanogaster is the most complex animal thus far to have its genetic sequence deciphered. The findings have important implications for human medical research and for completing a map of the human genome. Mapping the fruit fly genome has been a broad collaborative effort between academia and industry in several countries. While a foundation was laid by US (Berkeley), European, and Canadian Drosophila Genome Projects, Celera Genomic finished the job over the last year by employing super-computers and state-of-the-art gene-sequencing machines. The techniques learned and used in this last phase of mapping may now be applied to more rapidly decode genes of other organisms, including humans. This week's In The News takes a closer look at this important landmark.

  20. Self-motivated visual scanning predicts flexible navigation in a virtual environment

    OpenAIRE

    Elisabeth Jeannette Ploran; Jacob Bevitt

    2014-01-01

    The ability to navigate flexibly (e.g., reorienting oneself based on distal landmarks to reach a learned target from a new position) may rely on visual scanning during both initial experiences with the environment and subsequent test trials. Reliance on visual scanning during navigation harkens back to the concept of vicarious trial and error, a description of the side-to-side head movements made by rats as they explore previously traversed sections of a maze in an attempt to find a reward. I...

  1. Objectively identifying landmark use and predicting flight trajectories of the homing pigeon using Gaussian processes

    Science.gov (United States)

    Mann, Richard; Freeman, Robin; Osborne, Michael; Garnett, Roman; Armstrong, Chris; Meade, Jessica; Biro, Dora; Guilford, Tim; Roberts, Stephen

    2011-01-01

    Pigeons home along idiosyncratic habitual routes from familiar locations. It has been suggested that memorized visual landmarks underpin this route learning. However, the inability to experimentally alter the landscape on large scales has hindered the discovery of the particular features to which birds attend. Here, we present a method for objectively classifying the most informative regions of animal paths. We apply this method to flight trajectories from homing pigeons to identify probable locations of salient visual landmarks. We construct and apply a Gaussian process model of flight trajectory generation for pigeons trained to home from specific release sites. The model shows increasing predictive power as the birds become familiar with the sites, mirroring the animal's learning process. We subsequently find that the most informative elements of the flight trajectories coincide with landscape features that have previously been suggested as important components of the homing task. PMID:20656739

  2. Landmark clinical trials influencing surgical management of non-invasive and invasive breast cancer.

    Science.gov (United States)

    Julian, Thomas B; Venditti, Charis A; Duggal, Shivani

    2015-01-01

    The surgical management of breast cancer has changed considerably since the use of the Halstedian radical mastectomy early in the 20th century. Over the last 50 years, several landmark clinical trials from the USA and Europe have resulted in a paradigm shift in the management of breast cancer toward less radical forms of surgery with the combined use of multi-modality treatments including systemic chemotherapy, endocrine therapy, and radiotherapy. Advances in such research have established a new worldwide standard of care for breast cancer surgical management and treatment, which has become more patient centric and which places a higher emphasis on cosmesis and improved patient quality of life. In this chapter, we review the landmark clinical trials that have influenced surgical management for non-invasive and invasive breast cancer and that serve to guide current clinical practices to date. PMID:25521007

  3. Development of a landmark recognition system for the posture measurement of mobile robots

    International Nuclear Information System (INIS)

    A landmark recognition system, consisting of retroreflective landmarks, a CCD camera, a strobe unit, an image processing board, and processing software, has been developed to solve the problem of the posture (position and orientation) identification of mobile robots in manufacturing environments. The binary image processing technique instead of gray image technique has been adapted in this system to perform the fast posture measurement of the robots. The experimental results demonstrated real-time measurement capability of this system while maintaining good reliability and reasonable accuracy. A camera calibration technique has been described to reduce the effects of unwanted measurement error sources. The system after camera calibration procedure has demonstrated enhanced performance in terms of error component in posture measurement. (Author)

  4. Exploiting context information to aid landmark detection in SenseCam images

    OpenAIRE

    Blighe, Michael; Le Borgne, Herve?; O Connor, Noel E.; Smeaton, Alan F.; Jones, Gareth J. F.

    2006-01-01

    In this paper, we describe an approach designed to exploit context information in order to aid the detection of landmark images from a large collection of photographs. The photographs were generated using Microsoft’s SenseCam, a device designed to passively record a visual diary and cover a typical day of the user wearing the camera. The proliferation of digital photos along with the associated problems of managing and organising these collections provide the background motivati...

  5. Forebrain development in fetal MRI: evaluation of anatomical landmarks before gestational week 27

    International Nuclear Information System (INIS)

    Forebrain malformations include some of the most severe developmental anomalies and require early diagnosis. The proof of normal or abnormal prosencephalic development may have an influence on further management in the event of a suspected fetal malformation. The purpose of this retrospective study was to evaluate the detectability of anatomical landmarks of forebrain development using in vivo fetal magnetic resonance imaging (MRI) before gestational week (gw) 27. MRI studies of 83 singleton fetuses (gw 16-26, average ±sd: gw 22 ± 2) performed at 1.5 Tesla were assessed. T2-weighted (w) fast spin echo, T1w gradient-echo and diffusion-weighted sequences were screened for the detectability of anatomical landmarks as listed below. The interhemispheric fissure, ocular bulbs, corpus callosum, infundibulum, chiasm, septum pellucidum (SP), profile, and palate were detectable in 95%, 95%, 89%, 87%, 82%, 81%, 78%, 78% of cases. Olfactory tracts were more easily delineated than bulbs and sulci (37% versus 18% and 8%), with significantly higher detection rates in the coronal plane. The pituitary gland could be detected on T1w images in 60% with an increasing diameter with gestational age (p=0.041). The delineation of olfactory tracts (coronal plane), chiasm, SP and pituitary gland were significantly increased after week 21 (p<0.05). Pathologies were found in 28% of cases. This study provides detection rates for anatomical landmarks of forebrain development with fetal MRI beforrebrain development with fetal MRI before gw 27. Several anatomical structures are readily detectable with routine fetal MRI sequences; thus, if these landmarks are not delineable, it should raise the suspicion of a pathology. Recommendations regarding favorable sequences/planes are provided. (orig.)

  6. Landmark-free statistical analysis of the shape of plant leaves.

    Science.gov (United States)

    Laga, Hamid; Kurtek, Sebastian; Srivastava, Anuj; Miklavcic, Stanley J

    2014-12-21

    The shapes of plant leaves are important features to biologists, as they can help in distinguishing plant species, measuring their health, analyzing their growth patterns, and understanding relations between various species. Most of the methods that have been developed in the past focus on comparing the shape of individual leaves using either descriptors or finite sets of landmarks. However, descriptor-based representations are not invertible and thus it is often hard to map descriptor variability into shape variability. On the other hand, landmark-based techniques require automatic detection and registration of the landmarks, which is very challenging in the case of plant leaves that exhibit high variability within and across species. In this paper, we propose a statistical model based on the Squared Root Velocity Function (SRVF) representation and the Riemannian elastic metric of Srivastava et al. (2011) to model the observed continuous variability in the shape of plant leaves. We treat plant species as random variables on a non-linear shape manifold and thus statistical summaries, such as means and covariances, can be computed. One can then study the principal modes of variations and characterize the observed shapes using probability density models, such as Gaussians or Mixture of Gaussians. We demonstrate the usage of such statistical model for (1) efficient classification of individual leaves, (2) the exploration of the space of plant leaf shapes, which is important in the study of population-specific variations, and (3) comparing entire plant species, which is fundamental to the study of evolutionary relationships in plants. Our approach does not require descriptors or landmarks but automatically solves for the optimal registration that aligns a pair of shapes. We evaluate the performance of the proposed framework on publicly available benchmarks such as the Flavia, the Swedish, and the ImageCLEF2011 plant leaf datasets. PMID:25123432

  7. Combination of 2 Three Point Articulators for Preclinical Work Demonstration of Teeth Arrangement and Anatomical Landmarks

    OpenAIRE

    Leoney, A.; Shastry, Y. M.

    2012-01-01

    The combination of 2 three point articulators was done to visualize and appreciate the various teeth setting principles and anatomical landmarks both in occlusion and out of occlusion. In other words this technique would give a simultaneous image of the various teeth arrangement principles at a glance. The various teeth arrangement principles highlighted in this article would be the following: individual tooth arrangement principles of anterior and posterior teeth, arch form, midline, incisiv...

  8. The effect of providing a USB syllabus on resident reading of landmark articles

    OpenAIRE

    Mayy Chahla; Michael Eberlein; Scott Wright

    2010-01-01

    Background: The acquisition of new knowledge is a primary goal of residency training. Retrieving and retaining influential primary and secondary medical literature can be challenging for house officers. We set out to investigate the effect of a Universal Serial Bus (USB) drive loaded with landmark scientific articles on housestaff education in a pilot study. Methods: We created a USB syllabus that contains 187 primary scientific research articles. The electronic syllabus had links to the full...

  9. ACS National Historic Chemical Landmark: Charles Martin Hall's Discovery of the Electrochemical Process for Aluminum

    Science.gov (United States)

    Craig, Norman C.

    1997-11-01

    On September 17, 1997 in Oberlin, OH, Oberlin College and the Cleveland Section of the American Chemical Society hosted a celebration in which Charles Martin Hall's discovery of the electrochemical process for extracting aluminum metal from the ore was designated as a National Historic Chemical Landmark by the ACS. Woodshed laboratory with mannequins of Charles Martin Hall and his sister Julia. Photograph used with permission from Oberlin News-Tribune

  10. LANDMARK-BASED SPEECH RECOGNITION: REPORT OF THE 2004 JOHNS HOPKINS SUMMER WORKSHOP

    OpenAIRE

    Hasegawa-johnson, Mark; Baker, James; Borys, Sarah; Chen, Ken; Coogan, Emily; Greenberg, Steven; Juneja, Amit; Kirchhoff, Katrin; Livescu, Karen; Mohan, Srividya; Muller, Jennifer; Sonmez, Kemal; Wang, Tianyu

    2005-01-01

    Three research prototype speech recognition systems are described, all of which use recently developed methods from artificial intelligence (specifically support vector machines, dynamic Bayesian networks, and maximum entropy classification) in order to implement, in the form of an automatic speech recognizer, current theories of human speech perception and phonology (specifically landmark-based speech perception, nonlinear phonology, and articulatory phonology). All three systems begin with ...

  11. The Jugular Dural Fold—A Helpful Skull Base Landmark to the Cranial Nerves

    OpenAIRE

    Silverstein, Herbert; Willcox, Thomas O.; Rosenberg, Seth I.; Seidman, Michael D.

    1995-01-01

    During a retrosigmoid (or combined retrolabyrinthine-retrosigmoid) approach to the posterior fossa for vestibular neurectomy or removal of small acoustic neuromas, a white dural fold is a consistent landmark to cranial nerves VII through XII. This fold of dura appears as a white linear structure extending from the foramen magnum across the sigmoid sinus, attaching to the posterior aspect of the temporal bone, anterior to the vestibular aqueduct. The name “jugular dural fold” is suggested for ...

  12. Knee joint secondary motion accuracy improved by quaternion-based optimizer with bony landmark constraints.

    Science.gov (United States)

    Wang, Hongsheng; Zheng, Naiqaun Nigel

    2010-12-01

    Skin marker-based motion analysis has been widely used in biomechanical studies and clinical applications. Unfortunately, the accuracy of knee joint secondary motions is largely limited by the nonrigidity nature of human body segments. Numerous studies have investigated the characteristics of soft tissue movement. Utilizing these characteristics, we may improve the accuracy of knee joint motion measurement. An optimizer was developed by incorporating the soft tissue movement patterns at special bony landmarks into constraint functions. Bony landmark constraints were assigned to the skin markers at femur epicondyles, tibial plateau edges, and tibial tuberosity in a motion analysis algorithm by limiting their allowed position space relative to the underlying bone. The rotation matrix was represented by quaternion, and the constrained optimization problem was solved by Fletcher's version of the Levenberg-Marquardt optimization technique. The algorithm was validated by using motion data from both skin-based markers and bone-mounted markers attached to fresh cadavers. By comparing the results with the ground truth bone motion generated from the bone-mounted markers, the new algorithm had a significantly higher accuracy (root-mean-square (RMS) error: 0.7 ± 0.1 deg in axial rotation and 0.4 ± 0.1 deg in varus-valgus) in estimating the knee joint secondary rotations than algorithms without bony landmark constraints (RMS error: 1.7 ± 0.4 deg in axial rotation and 0.7 ± 0.1 deg in varus-valgus). Also, it predicts a more accurate medial-lateral translation (RMS error: 0.4 ± 0.1 mm) than the conventional techniques (RMS error: 1.2 ± 0.2 mm). The new algorithm, using bony landmark constrains, estimates more accurate secondary rotations and medial-lateral translation of the underlying bone. PMID:21142329

  13. Genome-wide scan identifies a copy number variable region at 3p21.1 that influences the TLR9 expression levels in IgA nephropathy patients.

    Science.gov (United States)

    Sallustio, Fabio; Cox, Sharon N; Serino, Grazia; Curci, Claudia; Pesce, Francesco; De Palma, Giuseppe; Papagianni, Aikaterini; Kirmizis, Dimitrios; Falchi, Mario; Schena, Francesco P

    2015-07-01

    Immunoglobulin A nephropathy (IgAN) is a complex multifactorial disease characterized by genetic factors that influence the pathogenesis of the disease. In this context, an intriguing role could be ascribed to copy number variants (CNVs). We performed the whole-genome screening of CNVs in familial IgAN patients, their healthy relatives and healthy subjects (HSs). In the initial screening, we included 217 individuals consisting of 51 biopsy-proven familial IgAN cases and 166 healthy relatives. We identified 148 IgAN-specific aberrations, specifically 105 loss and 43 gain, using a new statistical approach that allowed us to identify aberrations that were concordant across multiple samples. Several CNVs overlapped with regions evidenced by previous genome-wide genetic studies. We focused our attention on a CNV located in chromosome 3, which contains the TLR9 gene and found that IgAN patients characterized by deteriorated renal function carried low copy number of this CNV. Moreover, the TLR9 gene expression was low and significantly correlated with the loss aberration. Conversely, IgAN patients with normal renal function had no aberration and the TLR9 mRNA was expressed at the same level as in HSs. We confirmed our data in another cohort of Greek subjects. In conclusion, here we performed the first genome-wide CNV study in IgAN identifying structural variants that could help the genetic dissection of this complex disease, and pointed out a loss aberration in the chromosome 3, which is responsible for the downregulation of TLR9 expression that, in turn, could contribute to the deterioration of the renal function in IgAN patients. PMID:25293716

  14. Visual motion-sensitive neurons in the bumblebee brain convey information about landmarks during a navigational task

    Directory of Open Access Journals (Sweden)

    Martin Egelhaaf

    2014-09-01

    Full Text Available Bees use visual memories to find the spatial location of previously learnt food sites. Characteristic learning flights help acquiring these memories at newly discovered foraging locations where landmarks - salient objects in the vicinity of the goal location - can play an important role in guiding the animal’s homing behavior. Although behavioral experiments have shown that bees can use a variety of visual cues to distinguish objects as landmarks, the question of how landmark features are encoded by the visual system is still open. Recently, it could be shown that motion cues are sufficient to allow bees localizing their goal using landmarks that can hardly be discriminated from the background texture. Here, we tested the hypothesis that motion sensitive neurons in the bee’s visual pathway provide information about such landmarks during a learning flight and might, thus, play a role for goal localization. We tracked learning flights of free-flying bumblebees (Bombus terrestris in an arena with distinct visual landmarks, reconstructed the visual input during these flights, and replayed ego-perspective movies to tethered bumblebees while recording the activity of direction-selective wide-field neurons in their optic lobe. By comparing neuronal responses during a typical learning flight and targeted modifications of landmark properties in this movie we demonstrate that these objects are indeed represented in the bee’s visual motion pathway. We find that object-induced responses vary little with object texture, which is in agreement with behavioral evidence. These neurons thus convey information about landmark properties that are useful for view-based homing.

  15. Precise visual navigation using multi-stereo vision and landmark matching

    Science.gov (United States)

    Zhu, Zhiwei; Oskiper, Taragay; Samarasekera, Supun; Kumar, Rakesh

    2007-04-01

    Traditional vision-based navigation system often drifts over time during navigation. In this paper, we propose a set of techniques which greatly reduce the long term drift and also improve its robustness to many failure conditions. In our approach, two pairs of stereo cameras are integrated to form a forward/backward multi-stereo camera system. As a result, the Field-Of-View of the system is extended significantly to capture more natural landmarks from the scene. This helps to increase the pose estimation accuracy as well as reduce the failure situations. Secondly, a global landmark matching technique is used to recognize the previously visited locations during navigation. Using the matched landmarks, a pose correction technique is used to eliminate the accumulated navigation drift. Finally, in order to further improve the robustness of the system, measurements from low-cost Inertial Measurement Unit (IMU) and Global Positioning System (GPS) sensors are integrated with the visual odometry in an extended Kalman Filtering framework. Our system is significantly more accurate and robust than previously published techniques (1~5% localization error) over long-distance navigation both indoors and outdoors. Real world experiments on a human worn system show that the location can be estimated within 1 meter over 500 meters (around 0.1% localization error averagely) without the use of GPS information.

  16. Combining Speedup Techniques based on Landmarks and Containers with parallelised preprocessing in Random and Planar Graphs

    Directory of Open Access Journals (Sweden)

    R. Kalpana

    2011-02-01

    Full Text Available The Dijkstra’s algorithm is applied in many real world problems like mobile routing, road maps,railway networks, etc,. There are many techniques available to speedup the algorithm while guaranteeingthe optimality of the solution. Almost all of the speedup techniques have a substantial amount of parallelism that can be exploited to decrease its running time. By suitably modifying portions of theexisting system various degrees of parallelism can be achieved. The rapidly growing field of multiprocessing systems and multi-core processors provide many opportunities for such improvements. Inthese techniques there’s always a demand for the running time and the time required for pre-processing.Space requirements for the pre-processing also have a major influence on the running time of thealgorithm. The main focus of the work is to implement landmark technique and to identify the segment of the code in landmark pre-processing which can be parallelized to obtain better speedup. The results are applied to the combined speedup technique which is based on landmarks and containers. The experimental results were compared and analysed for determining better performance improvements in random graphs and planar graphs.

  17. Reproducibility of lateral cephalometric landmarks on conventional radiographs and spatial frequency-processed digital images

    International Nuclear Information System (INIS)

    Computed radiography (CR) has been used in cephalometric radiography and many studies have been carried out to improve image quality using various digital enhancement and filtering techniques. During CR image acquisition, the frequency rank and type affect to the image quality. The aim of this study was to compare the diagnostic quality of conventional cephalometric radiographs to those of computed radiography. The diagnostic quality of conventional cephalometric radiographs (M0) and their digital image counterparts were compared, and at the same time, six modalities (M1-M6) of spatial frequency-processed digital images were compared by evaluating the reproducibility of 23 cephalometric landmark locations. Reproducibility was defined as an observer's deviation (in mm) from the mean between all observers. In comparison with the conventional cephalometric radiograph (M0), M1 showed statistically significant differences in 8 locations, M2 in 9, M3 12, M4 in 7, M5 in 12, and M6 showed significant differences in 14 of 23 landmark locations (p<0.05). The number of reproducible landmarks that each modality possesses were 7 in M6, 6 in M5, 5 in M3, 4 in M4, 3 in M2, 2 in M1, and 1 location in M0. The image modality that observers selected as having the best image quality was M5.

  18. A low-cost test-bed for real-time landmark tracking

    Science.gov (United States)

    Csaszar, Ambrus; Hanan, Jay C.; Moreels, Pierre; Assad, Christopher

    2007-04-01

    A low-cost vehicle test-bed system was developed to iteratively test, refine and demonstrate navigation algorithms before attempting to transfer the algorithms to more advanced rover prototypes. The platform used here was a modified radio controlled (RC) car. A microcontroller board and onboard laptop computer allow for either autonomous or remote operation via a computer workstation. The sensors onboard the vehicle represent the types currently used on NASA-JPL rover prototypes. For dead-reckoning navigation, optical wheel encoders, a single axis gyroscope, and 2-axis accelerometer were used. An ultrasound ranger is available to calculate distance as a substitute for the stereo vision systems presently used on rovers. The prototype also carries a small laptop computer with a USB camera and wireless transmitter to send real time video to an off-board computer. A real-time user interface was implemented that combines an automatic image feature selector, tracking parameter controls, streaming video viewer, and user generated or autonomous driving commands. Using the test-bed, real-time landmark tracking was demonstrated by autonomously driving the vehicle through the JPL Mars yard. The algorithms tracked rocks as waypoints. This generated coordinates calculating relative motion and visually servoing to science targets. A limitation for the current system is serial computing-each additional landmark is tracked in order-but since each landmark is tracked independently, if transferred to appropriate parallel hardware, adding targets would not significantly diminish system speed.

  19. Identification of a Novel Risk Locus for Multiple Sclerosis at 13q31.3 by a Pooled Genome-Wide Scan of 500,000 Single Nucleotide Polymorphisms

    Science.gov (United States)

    Camiña-Tato, Montse; Morcillo, Carlos; Lopez, Cristina; Navarro, Arcadi; Rio, Jordi; Montalban, Xavier; Martin, Roland

    2008-01-01

    Multiple sclerosis is a chronic inflammatory demyelinating disease of the central nervous system with an important genetic component and strongest association driven by the HLA genes. We performed a pooling-based genome-wide association study of 500,000 SNPs in order to find new loci associated with the disease. After applying several criteria, 320 SNPs were selected from the microarrays and individually genotyped in a first and independent Spanish Caucasian replication cohort. The 8 most significant SNPs validated in this cohort were also genotyped in a second US Caucasian replication cohort for confirmation. The most significant association was obtained for SNP rs3129934, which neighbors the HLA-DRB/DQA loci and validates our pooling-based strategy. The second strongest association signal was found for SNP rs1327328, which resides in an unannotated region of chromosome 13 but is in linkage disequilibrium with nearby functional elements that may play important roles in disease susceptibility. This region of chromosome 13 has not been previously identified in MS linkage genome screens and represents a novel risk locus for the disease. PMID:18941528

  20. Anatomical landmarks for the localization of the greater palatine foramen--a study of 1200 head CTs, 150 dry skulls, systematic review of literature and meta-analysis.

    Science.gov (United States)

    Tomaszewska, Iwona M; Tomaszewski, Krzysztof A; Kmiotek, Elizabeth K; Pena, Iwona Z; Urbanik, Andrzej; Nowakowski, Micha?; Walocha, Jerzy A

    2014-10-01

    Accurate knowledge of greater palatine foramen (GPF) anatomy is necessary when performing a variety of anaesthesiological, dental or surgical procedures. The first aim of this study was to localize the GPF in relation to multiple anatomical landmarks. The second aim was to perform a systematic review of literature, and to conduct a meta-analysis on the subject of GPF position to aid clinicians in their practice. One-hundred and fifty dry, adult, human skulls and 1200 archived head computed tomography scans were assessed and measured in terms of GPF relation to other anatomical reference points. A systematic literature search was performed using the PubMed, Embase and Web of Science databases, and a meta-analysis on the subject of GPF relation to the maxillary molars was conducted. On average, in the Polish population, the GPF was positioned 15.9?±?1.5?mm from the midline maxillary suture (MMS), 3.0?±?1.2?mm from the alveolar ridge (AR) and 17.0?±?1.5?mm from the posterior nasal spine (PNS); 74.7% of GPF were positioned opposite the third maxillary molar (M3). Twenty-seven studies were included in the systematic review and 23 in the meta-analysis (n?=?6927 GPF). The pooled prevalence of the GPF being positioned opposite the M3 was 63.9% (95% confidence interval?=?56.6-70.9%). Concluding, the GPF is most often located opposite the M3 in the majority of the world's populations. The maxillary molars are the best landmarks for locating the GPF. In edentulous patients the most useful points for approximating the position of the GPF are the AR, MMS and PNS. This study introduces an easy and repeatable classification to reference the GPF to the maxillary molars. PMID:25131842

  1. Delivering high-resolution landmarks using inkjet micropatterning for spatial monitoring of leaf expansion

    Directory of Open Access Journals (Sweden)

    Cronk Quentin CB

    2011-01-01

    Full Text Available Abstract Background Inkjet micropatterning is a versatile deposition technique with broad applications in numerous fields. However, its application in plant science is largely unexplored. Leaf expansion is one of the most important parameters in the field of plant science and many methods have been developed to examine differential expansion rates of different parts of the leaf lamina. Among them, methods based on the tracking of natural landmarks through digital imaging require a complicated setup in which the leaf must remain fixed and under tension. Furthermore, the resolution is limited to that of the natural landmarks, which are often difficult to find, particularly in young leaves. To study the fine scale expansion dynamics of the leaf lamina using artificial landmarks it is necessary to place small, noninvasive marks on a leaf surface and then recover the location of those marks after a period of time. Results To monitor leaf expansion in two dimensions, at very fine scales, we used a custom designed inkjet micropatterning system to print a grid composed of c. 0.19 mm2 cells on small developing leaves of ivy (Hedera helix using 40 ?m dots at a spacing of c. 91 ?m. The leaves in different growing stages were imaged under magnification to extract the coordinates of the marks which were then used in subsequent computer-assisted leaf expansion analyses. As an example we obtained quantified global and local expansion information and created expansion maps over the entire leaf surface. The results reveal a striking pattern of fine-scale expansion differences over short periods of time. In these experiments, the base of the leaf is a "cold spot" for expansion, while the leaf sinuses are "hot spots" for expansion. We have also measured a strong shading effect on leaf expansion. We discuss the features required to build an inkjet printing apparatus optimized for use in plant science, which will further maximize the range of tissues that can be printed at these scales. Conclusions To apply inkjet micropatterning to plant studies, we have successfully delivered landmarks on ivy leaf surfaces and achieved high-resolution, two-dimensional monitoring of leaf expansion at different growing stages. The measurement is capable of reliably identifying the fine scale changes during plant growth. As well as delivering landmarks, this technology may be used to deliver microscale targeted biological components such as growth hormones, and possibly be used to pattern sensors directly on the leaves.

  2. Getting a CAT Scan

    Medline Plus

    Full Text Available ... People, Places & Things That Help Feelings Q&A Movies & More Quizzes Games Kids' Medical Dictionary En Español ... Page Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print ...

  3. Heart CT scan

    Science.gov (United States)

    ... Computed tomography scan - heart; Calcium scoring; Multi-detector CT scan - heart; Electron beam computed tomography - heart; Agaston ... table that slides into the center of the CT scanner. You will lie on your back with ...

  4. Getting a CAT Scan

    Medline Plus

    Full Text Available ... System How the Body Works Main Page Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print A A A Text Size CAT stands for "computerized ...

  5. Nuclear Scans (Cancer)

    Science.gov (United States)

    ... more References Previous Topic Mammography Next Topic Ultrasound Nuclear medicine scans Other names include nuclear imaging , radionuclide ... to more radiation. Use of monoclonal antibodies in nuclear scans: A special type of antibody made in ...

  6. The Human Genome Unveiled: Publication of Sequence and Initial Scientific Analyses

    Science.gov (United States)

    Payne, Laura X.

    This week's In The News highlights the landmark publication of the complete human genome sequence and its scientific interpretation. Spearheaded by two separate approaches and funding sources, the outcome of some ten years of hard work -- and moments of intense competition -- is the release of two complete sequences: one led by Craig Venter of Celera Genomics (a private venture with limited access to data, previously discussed in the April 7, 2000 Scout Report) and the other by a consortium of publicly funded laboratories (led by Francis Collins of the National Human Genome Research Institute (NHGRI)). The two sequences provide an excellent opportunity for comparison and convergence, opportunities that would not have been possible through a single approach. Also published this week are the first scientific analyses of the genome. These initial analyses uncover new details on the organization of the human genome and how it evolved -- including the surprising fact that humans have a smaller number of genes than previously thought, indications that some human genes may have come directly from bacteria, and variability in mutation rates among males and females. With these advances, researchers have begun to unlock the secrets of our genetic heritage and to better understand our relationship to other living creatures. Although more work lies ahead to refine and, in some places, re-sequence the human genome, this first draft, and its initial interpretation, represents a landmark achievement in science.

  7. Scanning gamma camera

    International Nuclear Information System (INIS)

    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

  8. Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape

    Directory of Open Access Journals (Sweden)

    Li Dongmei

    2009-05-01

    Full Text Available Abstract Background Universally accepted landmark stages are necessary to highlight key events in plant reproductive development and to facilitate comparisons among species. Domestication and selection of tomato resulted in many varieties that differ in fruit shape and size. This diversity is useful to unravel underlying molecular and developmental mechanisms that control organ morphology and patterning. The tomato fruit shape gene SUN controls fruit elongation. The most dramatic effect of SUN on fruit shape occurs after pollination and fertilization although a detailed investigation into the timing of the fruit shape change as well as gene expression profiles during critical developmental stages has not been conducted. Results We provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new floral and fruit landmarks to present a framework for tomato developmental studies. In addition, gene expression profiles of three key stages in floral and fruit development are presented, namely floral buds 10 days before anthesis (floral landmark 7, anthesis-stage flowers (floral landmark 10 and fruit landmark 1, and 5 days post anthesis fruit (fruit landmark 3. To demonstrate the utility of the landmarks, we characterize the tomato shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post-anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. The expression profiles of the NILs that differ at sun show that only 34 genes were differentially expressed and most of them at a less than 2-fold difference. Conclusion The landmarks for flower and fruit development in tomato were outlined and integrated with the effect of SUN on fruit shape. Although we did not identify many genes differentially expressed in the NILs that differ at the sun locus, higher or lower transcript levels for many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit were found between developmental time points.

  9. 123Genomics

    Science.gov (United States)

    The providers of this searchable metasite have, over the years, accumulated hundreds of genomics-related bookmarks which they now share freely. The eighteen major categories at 123 genomics each contain dozens of links to bioinformatics- and genomics-related science news, research labs, databases, scientific societies, protocol guides, etc. Examples of the category headings include Microarrays, Molecular Pathways, Sequence Databases, Journals and Publications, and Diseases and Disorders. This simply designed site provides enough good resources to keep most graduate students and researchers of bioinformatics happy and well informed.

  10. Your Genome

    Science.gov (United States)

    2002-01-01

    This Web siteby the Wellcome Trust Sanger Institute provides information about genome science for various levels of awareness. Although the advanced section is not yet complete, the beginner and intermediate touch on genes, DNA, RNA, and the Human Genome Project. If your curiosity is not satisfied by the Web site, there is a form for submitting questions directly to the Sanger Institute. Two nice features are the links (with descriptions and organized by level) and a timeline of genome science from the 1950's to the present.

  11. Identification of greater occipital nerve landmarks for the treatment of occipital neuralgia.

    Science.gov (United States)

    Loukas, M; El-Sedfy, A; Tubbs, R S; Louis, R G; Wartmann, C H T; Curry, B; Jordan, R

    2006-11-01

    Important structures involved in the pathogenesis of occipital headache include the aponeurotic attachments of the trapezius and semispinalis capitis muscles to the occipital bone. The greater occipital nerve (GON) can become entrapped as it passes through these aponeuroses, causing symptoms of occipital neuralgia. The aim of this study was to identify topographic landmarks for accurate identification of GON, which might facilitate its anaesthetic blockade. The course and distribution of GON and its relation to the aponeuroses of the trapezius and semispinalis capitis were examined in 100 formalin-fixed adult cadavers. In addition, the relative position of the nerve on a horizontal line between the external occipital protuberance and the mastoid process, as well as between the mastoid processes was measured. The greater occipital nerve was found bilaterally in all specimens. It was located at a mean distance of 3.8 cm (range 1.5-7.5 cm) lateral to a vertical line through the external occipital protuberance and the spinous processes of the cervical vertebrae 2-7. It was also located approximately 41% of the distance along the intermastoid line (medial to a mastoid process) and 22% of the distance between the external occipital protuberance and the mastoid process. The location of GON for anaesthesia or any other neurosurgical procedure has been established as one thumb's breadth lateral to the external occipital protuberance (2 cm laterally) and approximately at the base of the thumb nail (2 cm inferior). This is the first study proposing the use of landmarks in relation to anthropometric measurements. On the basis of these observations we propose a target zone for local anaesthetic injection that is based on easily identifiable landmarks and suggest that injection at this target point could be of benefit in the relief of occipital neuralgia. PMID:17171613

  12. Menopausa: marco biopsicossocial do envelhecimento feminino / Menopause: biopsychossocial landmark of female aging

    Scientific Electronic Library Online (English)

    Vanessa Nolasco, Ferreira; Renata Silva de Carvalho, Chinelato; Marcela Rodrigues, Castro; Maria Elisa Caputo, Ferreira.

    Full Text Available O presente estudo é derivado da pesquisa "Gênero, Corpo e Envelhecimento em Mulheres de Meia-Idade" e versa sobre a emersão da categoria menopausa como marco biopsicossocial do envelhecimento feminino, apontada através das entrevistas realizadas pelo estudo qualitativo exploratório em questão. Tal c [...] ategoria deriva da utilização da Análise de Conteúdo como metodologia para o tratamento dos dados obtidos através de um painel amostral de 47 participantes de uma mesma realidade social e cadastradas na Unidade Básica de Saúde utilizada como referência. Foi constatado que 41 das 47 entrevistadas citaram a menopausa como marcador determinante do envelhecimento, sendo que 37 o fizeram diretamente. Dessa forma, o artigo proporciona uma discussão entre o que é proposto na literatura e marcador apontado pelas participantes da pesquisa. Abstract in english The present study is derived from the research "Gender, Body and Aging in Women at Middle Age" and deals with the emergence of the category menopause as a biopsychossocial landmark of female aging, indicated through the interviews conducted by the qualitative exploratory study in question. This clas [...] s comes from the use of content analysis as a methodology for processing data obtained from a panel sample of 47 participants from the same social reality and registered in the Basic Health Unit used as reference. It was noted that 41 of the 47 interviewed cited the menopause as determinant landmark of aging process, and 37 did it directly. Thus, the article provides a discussion between what is proposed by the literature and the landmark pointed by the participants of the research.

  13. PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use.

    Science.gov (United States)

    Vähämaa, Heidi; Koskinen, Ville R; Hosia, Waltteri; Moulder, Robert; Nevalainen, Olli S; Lahesmaa, Riitta; Aittokallio, Tero; Salmi, Jussi

    2011-01-01

    We present a versatile user-friendly software tool, PolyAlign, for the alignment of multiple LC-MS signal maps with the option of manual landmark setting or automated alignment. One of the spectral images is selected as a reference map, and after manually setting the landmarks, the program warps the images using either polynomial or Hermite transformation. The software provides an option for automated landmark finding. The software includes a very fast zoom-in function synchronized between the images, which facilitate detecting correspondences between the adjacent images. Such an interactive visual process enables the analyst to decide when the alignment is satisfactory and to correct known irregularities. We demonstrate that the software provides significant improvements in the alignment of LC-MALDI data, with 10-15 landmark pairs, and it is also applicable to correcting electrospray LC-MS data. The results with practical data show substantial improvement in peak alignment compared to MZmine, which was among the best analysis packages in a recent assessment. The PolyAlign software is freely available and easily accessible as an integrated component of the popular MZmine software, and also as a simpler stand-alone Perl implementation to preview data and apply landmark directed polynomial transformation. PMID:22084688

  14. Automatic Insall-Salvati ratio measurement on lateral knee x-ray images using model-guided landmark localization

    International Nuclear Information System (INIS)

    The Insall-Salvati ratio (ISR) is important for detecting two common clinical signs of knee disease: patella alta and patella baja. Furthermore, large inter-operator differences in ISR measurement make an objective measurement system necessary for better clinical evaluation. In this paper, we define three specific bony landmarks for determining the ISR and then propose an x-ray image analysis system to localize these landmarks and measure the ISR. Due to inherent artifacts in x-ray images, such as unevenly distributed intensities, which make landmark localization difficult, we hence propose a registration-assisted active-shape model (RAASM) to localize these landmarks. We first construct a statistical model from a set of training images based on x-ray image intensity and patella shape. Since a knee x-ray image contains specific anatomical structures, we then design an algorithm, based on edge tracing, for patella feature extraction in order to automatically align the model to the patella image. We can estimate the landmark locations as well as the ISR after registration-assisted model fitting. Our proposed method successfully overcomes drawbacks caused by x-ray image artifacts. Experimental results show great agreement between the ISRs measured by the proposed method and by orthopedic clinicians.

  15. Automatic Insall-Salvati ratio measurement on lateral knee x-ray images using model-guided landmark localization

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hsin-Chen; Wu, Chia-Hsing; Sun, Yung-Nien [Department of Computer Science and Information Engineering, National Cheng Kung University, 1 University Road, Tainan 701, Taiwan (China); Lin, Chii-Jeng [Department of Orthopedics, College of Medicine, National Cheng Kung University, 138 Sheng Li Road, Tainan 704, Taiwan (China); Wang, Chien-Kuo, E-mail: ynsun@mail.ncku.edu.t, E-mail: wale1212@gmail.co, E-mail: btmage@gmail.co, E-mail: mark@mail.ncku.edu.t, E-mail: n044206@mail.hosp.ncku.edu.t [Department of Radiology, National Cheng Kung University Hospital, 138 Sheng Li Road, Tainan 704, Taiwan (China)

    2010-11-21

    The Insall-Salvati ratio (ISR) is important for detecting two common clinical signs of knee disease: patella alta and patella baja. Furthermore, large inter-operator differences in ISR measurement make an objective measurement system necessary for better clinical evaluation. In this paper, we define three specific bony landmarks for determining the ISR and then propose an x-ray image analysis system to localize these landmarks and measure the ISR. Due to inherent artifacts in x-ray images, such as unevenly distributed intensities, which make landmark localization difficult, we hence propose a registration-assisted active-shape model (RAASM) to localize these landmarks. We first construct a statistical model from a set of training images based on x-ray image intensity and patella shape. Since a knee x-ray image contains specific anatomical structures, we then design an algorithm, based on edge tracing, for patella feature extraction in order to automatically align the model to the patella image. We can estimate the landmark locations as well as the ISR after registration-assisted model fitting. Our proposed method successfully overcomes drawbacks caused by x-ray image artifacts. Experimental results show great agreement between the ISRs measured by the proposed method and by orthopedic clinicians.

  16. Automatic Insall-Salvati ratio measurement on lateral knee x-ray images using model-guided landmark localization

    Science.gov (United States)

    Chen, Hsin-Chen; Lin, Chii-Jeng; Wu, Chia-Hsing; Wang, Chien-Kuo; Sun, Yung-Nien

    2010-11-01

    The Insall-Salvati ratio (ISR) is important for detecting two common clinical signs of knee disease: patella alta and patella baja. Furthermore, large inter-operator differences in ISR measurement make an objective measurement system necessary for better clinical evaluation. In this paper, we define three specific bony landmarks for determining the ISR and then propose an x-ray image analysis system to localize these landmarks and measure the ISR. Due to inherent artifacts in x-ray images, such as unevenly distributed intensities, which make landmark localization difficult, we hence propose a registration-assisted active-shape model (RAASM) to localize these landmarks. We first construct a statistical model from a set of training images based on x-ray image intensity and patella shape. Since a knee x-ray image contains specific anatomical structures, we then design an algorithm, based on edge tracing, for patella feature extraction in order to automatically align the model to the patella image. We can estimate the landmark locations as well as the ISR after registration-assisted model fitting. Our proposed method successfully overcomes drawbacks caused by x-ray image artifacts. Experimental results show great agreement between the ISRs measured by the proposed method and by orthopedic clinicians.

  17. Historic landmarks in radiation chemistry since early observations by Marie Sklodowska-Curie and Pierre Curie

    International Nuclear Information System (INIS)

    The origin of the radiation chemistry history is contemporary with the X-rays and uranic rays discoveries. The complexity of the phenomena induced by the radiation effects, which involve electrons, ions and free radicals and a specific spatial distribution of the energy deposit along the tracks, was progressively understood, particularly when pulse radiolysis and time-resolved detection permitted to observe the short-lived transient species and to explain the chemical or biochemical mechanism. This short review summarizes the most important landmarks of the concepts and their applications. (author)

  18. Genomics Glossary

    Science.gov (United States)

    Chitty, Mary Glen.

    Because genomics is an interdisciplinary science that unites biology, chemistry, physics, and mathematics, its language is diverse and includes terms not always found in dictionaries. This site from Cambridge Healthtech Institute of Massachusetts was designed to help scientists keep on top of this complex language. Loads of terms in categories such as basic genetics, functional and structural genomics, informatics, and genomic-related technology are defined here. Users can access the glossary terms either through a short index of major subject headings or by a longer alphabetically-arranged subject list. The Genomics Glossary deserves bonus points for including links to related resources in the text of its definitions. For example, within the definition of "polymerase chain reaction" are links to sites at Yale Medical School and the National Library of Medicine. In addition, links to pages on nomenclature, a bibliography of Web and print resources, and a FAQ page are available at this fantastic Website.

  19. Genome Size.

    Czech Academy of Sciences Publication Activity Database

    Greilhuber, J.; Doležel, Jaroslav; Leitch, I.J.; Loureiro, J.; Suda, Jan

    2010-01-01

    Ro?. 2010, ?. 946138 (2010), s. 1-4. ISSN 2090-0120 Institutional research plan: CEZ:AV0Z50380511; CEZ:AV0Z60050516 Keywords : cytometry * ploidy * genome size Subject RIV: EB - Genetics ; Molecular Biology

  20. Neandrtálský genom.

    Czech Academy of Sciences Publication Activity Database

    Martínková, Natália

    2010-01-01

    Ro?. 2010, ?. 9 (2010), s. 88-89. ISSN 1213-8215 Institutional research plan: CEZ:AV0Z60930519 Keywords : evolutionary biology * Homo neanderthal ensis * whole-genome sequencing Subject RIV: EB - Genetics ; Molecular Biology

  1. Case history and genome-wide scans for copy number variants in a family with patient having 15q11.1-q11.2 duplication and 22q11.2 deletion, and schizophrenia.

    Science.gov (United States)

    Takahashi, Sakae; Suzuki, Takahiro; Nakamura-Tomizuka, Sakura; Osaki, Koichi; Sotome, Yuta; Sagawa, Tomoaki; Uchiyama, Makoto

    2015-06-01

    Many studies have indicated that chromosomes 15q11 and 22q11 may be associated with the genetic etiologies of schizophrenia. We have followed an adult schizophrenia case with 15q11.1-q11.2 duplication and 22q11.2 deletion. Here we report his clinical history, and copy number variants (CNVs) identified by microarray and real-time PCR in the patient and his parents. This is the first report describing a detailed phenotype of an adult schizophrenic case with both 15q11 and 22q11 CNVs as revealed by novel and trustworthy technologies. Subjects were a 33-year-old male patient with 15q11 and 22q11 CNVs, and his normal parents. He fulfilled the DSM-IV criteria for schizophrenia at age 18 years. He was also diagnosed with 22q11.2 deletion syndrome by fluorescence in situ hybridization (FISH) at age 18 years. To search for CNVs in more detail, whole-genome array-CGH analyses including ?420,000 probes were carried out in the patient and his parents. For validations of the CNVs detected by array-CGH, real-time PCR analyses of these CNVs were performed. The patient had two disease-specific CNVs, 15q11.1-q11.2 duplication (?2.7?Mb) and 22q11.21 deletion (?2.9?Mb). These two regions are important for the development of schizophrenia, and this patient had shown symptoms of schizophrenia. Thus, the two areas may contain causal genes for schizophrenia. © 2015 Wiley Periodicals, Inc. PMID:25776014

  2. Brachypodium Genomics

    Directory of Open Access Journals (Sweden)

    Hikmet Budak

    2008-02-01

    Full Text Available Brachypodium distachyon (L. Beauv. is a temperate wild grass species; its morphological and genomic characteristics make it a model system when compared to many other grass species. It has a small genome, short growth cycle, self-fertility, many diploid accessions, and simple growth requirements. In addition, it is phylogenetically close to economically important crops, like wheat and barley, and several potential biofuel grasses. It exhibits agricultural traits similar to those of these target crops. For cereal genomes, it is a better model than Arabidopsis thaliana and Oryza sativa (rice, the former used as a model for all flowering plants and the latter hitherto used as model for genomes of all temperate grass species including major cereals like barley and wheat. Increasing interest in this species has resulted in the development of a series of genomics resources, including nuclear sequences and BAC/EST libraries, together with the collection and characterization of other genetic resources. It is expected that the use of this model will allow rapid advances in generation of genomics information for the improvement of all temperate crops, particularly the cereals.

  3. Limitations of parotid scans

    International Nuclear Information System (INIS)

    In 1967, Gates and Work proposed technetium scanning as a diagnostic tool for salivary neoplasms. Since then, many publications have dealt with the results of scanning. The impression has been that it has certain diagnostic implications, especially in regard to the lesions which are radiopositive on the scan. A review of 29 salivary scans from the University of Iowa Hospitals was carried out, and the conclusion reached was that nuclear scanning using technetium gave little assurance of a specific histological entity in any individual case. Cases having both cold and hot nodules ran the gamut from benign and nonneoplastic to frankly malignant lesions. These cases are illustrated, and the conclusion is reached that salivary scanning at its present stage of development may only delay the proper diagnostic step of excisional (at least lateral lobectomy) biopsy for all nondiffuse parotid mass lesions

  4. Pulmonary ventilation/perfusion scan

    Science.gov (United States)

    V/Q scan; Ventilation/perfusion scan; Lung ventilation/perfusion scan ... A pulmonary ventilation/perfusion scan is actually two tests. They may be done separately or together. During the perfusion ...

  5. The scanning proton microprobe

    International Nuclear Information System (INIS)

    Some basic principles of ion-atom interactions are reviewed in order to discuss the characteristics and unique features of a scanning proton microprobe and to assess the potential of such an instrument. After a brief description of the instrument, examples are given of some applications, including spot analysis, depth profiling and scanning analysis with the Melbourne total data handling technique. This technique is applicable to all scanning probes and is of particular value with sensitive specimens

  6. Scanning of bone metastases

    International Nuclear Information System (INIS)

    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

  7. Fusion of WiFi, smartphone sensors and landmarks using the Kalman filter for indoor localization.

    Science.gov (United States)

    Chen, Zhenghua; Zou, Han; Jiang, Hao; Zhu, Qingchang; Soh, Yeng Chai; Xie, Lihua

    2015-01-01

    Location-based services (LBS) have attracted a great deal of attention recently. Outdoor localization can be solved by the GPS technique, but how to accurately and efficiently localize pedestrians in indoor environments is still a challenging problem. Recent techniques based on WiFi or pedestrian dead reckoning (PDR) have several limiting problems, such as the variation of WiFi signals and the drift of PDR. An auxiliary tool for indoor localization is landmarks, which can be easily identified based on specific sensor patterns in the environment, and this will be exploited in our proposed approach. In this work, we propose a sensor fusion framework for combining WiFi, PDR and landmarks. Since the whole system is running on a smartphone, which is resource limited, we formulate the sensor fusion problem in a linear perspective, then a Kalman filter is applied instead of a particle filter, which is widely used in the literature. Furthermore, novel techniques to enhance the accuracy of individual approaches are adopted. In the experiments, an Android app is developed for real-time indoor localization and navigation. A comparison has been made between our proposed approach and individual approaches. The results show significant improvement using our proposed framework. Our proposed system can provide an average localization accuracy of 1 m. PMID:25569750

  8. Gene Expression Data to Mouse Atlas Registration Using a Nonlinear Elasticity Smoother and Landmark Points Constraints.

    Science.gov (United States)

    Lin, Tungyou; Guyader, Carole Le; Dinov, Ivo; Thompson, Paul; Toga, Arthur; Vese, Luminita

    2012-03-01

    This paper proposes a numerical algorithm for image registration using energy minimization and nonlinear elasticity regularization. Application to the registration of gene expression data to a neuroanatomical mouse atlas in two dimensions is shown. We apply a nonlinear elasticity regularization to allow larger and smoother deformations, and further enforce optimality constraints on the landmark points distance for better feature matching. To overcome the difficulty of minimizing the nonlinear elasticity functional due to the nonlinearity in the derivatives of the displacement vector field, we introduce a matrix variable to approximate the Jacobian matrix and solve for the simplified Euler-Lagrange equations. By comparison with image registration using linear regularization, experimental results show that the proposed nonlinear elasticity model also needs fewer numerical corrections such as regridding steps for binary image registration, it renders better ground truth, and produces larger mutual information; most importantly, the landmark points distance and L (2) dissimilarity measure between the gene expression data and corresponding mouse atlas are smaller compared with the registration model with biharmonic regularization. PMID:24273381

  9. Fusion of WiFi, Smartphone Sensors and Landmarks Using the Kalman Filter for Indoor Localization

    Science.gov (United States)

    Chen, Zhenghua; Zou, Han; Jiang, Hao; Zhu, Qingchang; Soh, Yeng Chai; Xie, Lihua

    2015-01-01

    Location-based services (LBS) have attracted a great deal of attention recently. Outdoor localization can be solved by the GPS technique, but how to accurately and efficiently localize pedestrians in indoor environments is still a challenging problem. Recent techniques based on WiFi or pedestrian dead reckoning (PDR) have several limiting problems, such as the variation of WiFi signals and the drift of PDR. An auxiliary tool for indoor localization is landmarks, which can be easily identified based on specific sensor patterns in the environment, and this will be exploited in our proposed approach. In this work, we propose a sensor fusion framework for combining WiFi, PDR and landmarks. Since the whole system is running on a smartphone, which is resource limited, we formulate the sensor fusion problem in a linear perspective, then a Kalman filter is applied instead of a particle filter, which is widely used in the literature. Furthermore, novel techniques to enhance the accuracy of individual approaches are adopted. In the experiments, an Android app is developed for real-time indoor localization and navigation. A comparison has been made between our proposed approach and individual approaches. The results show significant improvement using our proposed framework. Our proposed system can provide an average localization accuracy of 1 m. PMID:25569750

  10. Fusion of WiFi, Smartphone Sensors and Landmarks Using the Kalman Filter for Indoor Localization

    Directory of Open Access Journals (Sweden)

    Zhenghua Chen

    2015-01-01

    Full Text Available Location-based services (LBS have attracted a great deal of attention recently. Outdoor localization can be solved by the GPS technique, but how to accurately and efficiently localize pedestrians in indoor environments is still a challenging problem. Recent techniques based on WiFi or pedestrian dead reckoning (PDR have several limiting problems, such as the variation of WiFi signals and the drift of PDR. An auxiliary tool for indoor localization is landmarks, which can be easily identified based on specific sensor patterns in the environment, and this will be exploited in our proposed approach. In this work, we propose a sensor fusion framework for combining WiFi, PDR and landmarks. Since the whole system is running on a smartphone, which is resource limited, we formulate the sensor fusion problem in a linear perspective, then a Kalman filter is applied instead of a particle filter, which is widely used in the literature. Furthermore, novel techniques to enhance the accuracy of individual approaches are adopted. In the experiments, an Android app is developed for real-time indoor localization and navigation. A comparison has been made between our proposed approach and individual approaches. The results show significant improvement using our proposed framework. Our proposed system can provide an average localization accuracy of 1 m.

  11. The contribution of obstruent consonants and acoustic landmarks to speech recognition in noise.

    Science.gov (United States)

    Li, Ning; Loizou, Philipos C

    2008-12-01

    The obstruent consonants (e.g., stops) are more susceptible to noise than vowels, raising the question whether the degradation of speech intelligibility in noise can be attributed, at least partially, to the loss of information carried by obstruent consonants. Experiment 1 assesses the contribution of obstruent consonants to speech recognition in noise by presenting sentences containing clean obstruent consonants but noise-corrupted voiced sounds (e.g., vowels). Results indicated substantial (threefold) improvement in speech recognition, particularly at low signal-to-noise ratio levels (-5 dB). Experiment 2 assessed the importance of providing partial information, within a frequency region, of the obstruent-consonant spectra while leaving the remaining spectral region unaltered (i.e., noise corrupted). Access to the low-frequency (0-1000 Hz) region of the clean obstruent-consonant spectra was found to be sufficient to realize significant improvements in performance and that was attributed to improvement in transmission of voicing information. The outcomes from the two experiments suggest that much of the improvement in performance must be due to the enhanced access to acoustic landmarks, evident in spectral discontinuities signaling the onsets of obstruent consonants. These landmarks, often blurred in noisy conditions, are critically important for understanding speech in noise for better determination of the syllable structure and word boundaries. PMID:19206819

  12. Extracción de puntos característicos del rostro para medidas antropométricas Face landmarks extraction for anthropometric measures

    Directory of Open Access Journals (Sweden)

    Alejandro González

    2010-07-01

    Full Text Available En este documento se propone una técnica para la extracción de 22 puntos característicos del rostro, orientada a aplicaciones de antropometría. La técnica se fundamenta en la transformada wavelets-Gabor y el uso del algoritmo EBGM (del término en inglés: Elastic Bunch Graph Matching. Este último algoritmo fue modificado para que los puntos extraídos correspondan a puntos característicos del rostro, los cuales se utilizan comúnmente en medidas antropométricas faciales. Las modificaciones consisten en un conjunto de restricciones geométricas para ajustar inicialmente la ubicación de los centros de búsqueda, y posteriormente para la definición de la región de esta búsqueda. Los resultados mostraron que los puntos centrales del rostro presentan errores de ubicación inferiores al milímetro, lo cual es consistente con las medidas en antropometría facial directa.In this research, a technique for the extraction of a 22 face landmarks set oriented to anthropometry applications has been proposed. The technique is based on wavelets Gabor transformation and the Elastic Bunch Graph Matching (EBGM algorithm. The EBGM algorithm was modified so that the extracted points correspond to face landmarks which are commonly used in face anthropometric measures. Modifications were: some geometric restrictions to initially fit the centers location of the region search, and later for the definition of the region. Results show that the face central points present location errors smaller than a millimeter, which is consistent with the measures in direct face anthropometry.

  13. Extracción de puntos característicos del rostro para medidas antropométricas / Face landmarks extraction for anthropometric measures

    Scientific Electronic Library Online (English)

    Alejandro, González; Flavio, Prieto.

    2010-07-01

    Full Text Available En este documento se propone una técnica para la extracción de 22 puntos característicos del rostro, orientada a aplicaciones de antropometría. La técnica se fundamenta en la transformada wavelets-Gabor y el uso del algoritmo EBGM (del término en inglés: Elastic Bunch Graph Matching). Este último al [...] goritmo fue modificado para que los puntos extraídos correspondan a puntos característicos del rostro, los cuales se utilizan comúnmente en medidas antropométricas faciales. Las modificaciones consisten en un conjunto de restricciones geométricas para ajustar inicialmente la ubicación de los centros de búsqueda, y posteriormente para la definición de la región de esta búsqueda. Los resultados mostraron que los puntos centrales del rostro presentan errores de ubicación inferiores al milímetro, lo cual es consistente con las medidas en antropometría facial directa. Abstract in english In this research, a technique for the extraction of a 22 face landmarks set oriented to anthropometry applications has been proposed. The technique is based on wavelets Gabor transformation and the Elastic Bunch Graph Matching (EBGM) algorithm. The EBGM algorithm was modified so that the extracted p [...] oints correspond to face landmarks which are commonly used in face anthropometric measures. Modifications were: some geometric restrictions to initially fit the centers location of the region search, and later for the definition of the region. Results show that the face central points present location errors smaller than a millimeter, which is consistent with the measures in direct face anthropometry.

  14. Geometric sensitivity of patient-specific finite element models of the spine to variability in user-selected anatomical landmarks.

    Science.gov (United States)

    Little, J P; Adam, C J

    2015-01-01

    Software to create individualised finite element (FE) models of the osseoligamentous spine using pre-operative computed tomography (CT) data-sets for spinal surgery patients has recently been developed. This study presents a geometric sensitivity analysis of this software to assess the effect of intra-observer variability in user-selected anatomical landmarks. User-selected landmarks on the osseous anatomy were defined from CT data-sets for three scoliosis patients and these landmarks were used to reconstruct patient-specific anatomy of the spine and ribcage using parametric descriptions. The intra-observer errors in landmark co-ordinates for these anatomical landmarks were calculated. FE models of the spine and ribcage were created using the reconstructed anatomy for each patient and these models were analysed for a loadcase simulating clinical flexibility assessment. The intra-observer error in the anatomical measurements was low in comparison to the initial dimensions, with the exception of the angular measurements for disc wedge and zygapophyseal joint (z-joint) orientation and disc height. This variability suggested that CT resolution may influence such angular measurements, particularly for small anatomical features, such as the z-joints, and may also affect disc height. The results of the FE analysis showed low variation in the model predictions for spinal curvature with the mean intra-observer variability substantially less than the accepted error in clinical measurement. These findings demonstrate that intra-observer variability in landmark point selection has minimal effect on the subsequent FE predictions for a clinical loadcase. PMID:24261987

  15. 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.

  16. Radionuclide bone scan utility

    International Nuclear Information System (INIS)

    Radionuclide imaging can supply formation about organs and systems function. The radionuclide bone scan have a sensibility greater than radiology, to demonstrate any functional bone change before that radiology, being an easy, sure, quick method. We review discuss applications more common in benign osseous disease, neoplasic, traumatic or metabolic by bone scan. (The author)

  17. Environmental Scanning Report.

    Science.gov (United States)

    Truckee Meadows Community Coll., Sparks, NV.

    This report describes Truckee Meadows Community College's (Nevada) environmental scanning process and results. The college decided that environmental scanning and forecasting techniques should be used to plan for both short-term and long-term external factors that impact programs, enrollment, and budgets. Strategic goals include: (1) keeping pace…

  18. Getting a CAT Scan

    Medline Plus

    Full Text Available ... How the Body Works Main Page Getting a CAT Scan (Video) KidsHealth > Kids > Movies & More > Movies > Getting a CAT Scan (Video) Print A A A Text Size CAT stands for "computerized axial tomography." Translated, that means ...

  19. Transverse section scanning mechanism

    International Nuclear Information System (INIS)

    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)

  20. Arts & Genomics

    Science.gov (United States)

    Based at the University of Leiden in the Netherlands, The Arts & Genomics Centre is interested in expanding the "public debate on (future) goals, means, possibilities and use of results of genomics, from the specific point of view of bio-genetic art." The homepage provides ample information about their most recent initiatives, which have included a symposium on food, art and science and a video on their VivoArts program, which attempts to bring together biology and various contemporary arts. Moving on, the "Research" section of the site includes project documents and proposals that deal with their representational space program and the "Imagining Genomics" initiative. The site is rounded out by a collection of links to other germane sites and online resources.

  1. Discovery of Genomic DNA Polymorphisms using oligonucleotide arrays

    Science.gov (United States)

    We are applying oligonucleotide microarray technology as a means of rapidly discovering DNA-based markers for genetic mapping in finger millet and rice. A test genome scan was conducted using the full genome sequences of rice varieties 93-11 (indica) and Nipponbare (japonica) compared with the Affy...

  2. Interfraction Displacement of Primary Tumor and Involved Lymph Nodes Relative to Anatomic Landmarks in Image Guided Radiation Therapy of Locally Advanced Lung Cancer

    International Nuclear Information System (INIS)

    Purpose: To analyze primary tumor (PT) and lymph node (LN) position changes relative to each other and relative to anatomic landmarks during conventionally fractionated radiation therapy for patients with locally advanced lung cancer. Methods and Materials: In 12 patients with locally advanced non-small cell lung cancer PT, LN, carina, and 1 thoracic vertebra were manually contoured on weekly 4-dimensional fan-beam CT scans. Systematic and random interfraction displacements of all contoured structures were identified in the 3 cardinal directions, and resulting setup margins were calculated. Time trends and the effect of volume changes on displacements were analyzed. Results: Three-dimensional displacement vectors and systematic/random interfraction displacements were smaller for carina than for vertebra both for PT and LN. For PT, mean (SD) 3-dimensional displacement vectors with carina-based alignment were 7 (4) mm versus 9 (5) mm with bony anatomy (P.05). Displacements between PT and bone (P=.04) and between PT and LN (P=.01) were significantly correlated with PT volume regression. Displacements between LN and carina were correlated with LN volume change (P=.03). Conclusions: Carina-based setup results in a more reproducible PT and LN alignment than bony anatomy setup. Considering the independence of PT and LN displacement and the impact of volume regression on displacements over time, repeated CT imaging even with PT-based alignment is recommended in locally advanced disease

  3. Scanning with Iodine-125

    International Nuclear Information System (INIS)

    The use of I125 as I125-iodide for scanning of the thyroid and of thyroid carcinoma métastasés and as I125-labelled Rose Bengal for scanning of the liver has been investigated in our laboratories. In some patients, the thyroid scans and the scans of thyroid carcinoma metastases were repeated with I131. The liver scans were repeated with colloidal Au198. Cold nodules in the thyroid which could not be detected with I131 were clearly seen with I125. Anterior métastasés in the lungs could be differentiated from posterior métastasés with I125, while with I131 this was not possible. Using the same doses of radioactivity the background with I131 was much higher and could not be eliminated, as this would have reduced the counting rate over the lesions to levels which could not be detected. Some of the photoscans and mechanical scans of livers carried out with colloidal Au198 could not be interpreted. However, ''cold'' lesions were clearly seen on the scans of the same livers with I125-labelled Rose Bengal. (author)

  4. Resonant scanning mechanism

    Science.gov (United States)

    Wallace, John; Newman, Mike; Gutierrez, Homero; Hoffman, Charlie; Quakenbush, Tim; Waldeck, Dan; Leone, Christopher; Ostaszewski, Miro

    2014-10-01

    Ball Aerospace & Technologies Corp. developed a Resonant Scanning Mechanism (RSM) capable of combining a 250- Hz resonant scan about one axis with a two-hertz triangular scan about the orthogonal axis. The RSM enables a rapid, high-density scan over a significant field of regard (FOR) while minimizing size, weight, and power requirements. The azimuth scan axis is bearing mounted allowing for 30° of mechanical travel, while the resonant elevation axis is flexure and spring mounted with five degrees of mechanical travel. Pointing-knowledge error during quiescent static pointing at room temperature across the full range is better than 100 ?rad RMS per axis. The compact design of the RSM, roughly the size of a soda can, makes it an ideal mechanism for use on low-altitude aircraft and unmanned aerial vehicles. Unique aspects of the opto-mechanical design include i) resonant springs which allow for a high-frequency scan axis with low power consumption; and ii) an independent lower-frequency scan axis allowing for a wide FOR. The pointing control system operates each axis independently and employs i) a position loop for the azimuth axis; and ii) a unique combination of parallel frequency and amplitude control loops for the elevation axis. All control and pointing algorithms are hosted on a 200-MHz microcontroller with 516 KB of RAM on a compact 3"×4" digital controller, also of Ball design.

  5. Dorsolateral striatal lesions impair navigation based on landmark-goal vectors but facilitate spatial learning based on a "cognitive map".

    Science.gov (United States)

    Kosaki, Yutaka; Poulter, Steven L; Austen, Joe M; McGregor, Anthony

    2015-03-01

    In three experiments, the nature of the interaction between multiple memory systems in rats solving a variation of a spatial task in the water maze was investigated. Throughout training rats were able to find a submerged platform at a fixed distance and direction from an intramaze landmark by learning a landmark-goal vector. Extramaze cues were also available for standard place learning, or "cognitive mapping," but these cues were valid only within each session, as the position of the platform moved around the pool between sessions together with the intramaze landmark. Animals could therefore learn the position of the platform by taking the consistent vector from the landmark across sessions or by rapidly encoding the new platform position on each session with reference to the extramaze cues. Excitotoxic lesions of the dorsolateral striatum impaired vector-based learning but facilitated cognitive map-based rapid place learning when the extramaze cues were relatively poor (Experiment 1) but not when they were more salient (Experiments 2 and 3). The way the lesion effects interacted with cue availability is consistent with the idea that the memory systems involved in the current navigation task are functionally cooperative yet associatively competitive in nature. PMID:25691518

  6. Scanning Probe Microscopy

    Science.gov (United States)

    Published by the National Nanotechnology Infrastructure Network, this hour-long activity has students "simulate the function of a scanning probe microscope" by creating their own scanning probe microscope (SPM) boxes. The Teacher's Guide contains everything the instructor needs to carry out the lesson: goals and objectives, advanced preparation notes, safety considerations, materials, questions, and even variations for different classrooms. The Student Worksheet walks students through the activity by having them begin by making a prediction, giving the procedures, providing space to record observations, and asking open questions for students to respond to. This is a ready-to-use activity for classrooms looking to explore nanotechnology and scanning probe microscopes.

  7. Physiological Genomics

    Science.gov (United States)

    1969-12-31

    Five journals with free (or recently extended) online trial periods were recently announced; online content includes full text, figures, and tables. The American Physiological Society has announced free, online access to Physiological Genomics through December 31, 2001; full text and abstracts are available from 1999. The journal is published in conjunction with Stanford University's HighWire Press.

  8. Maximized Posteriori Attributes Selection from Facial Salient Landmarks for Face Recognition

    CERN Document Server

    Gupta, Phalguni; Sing, Jamuna Kanta; Tistarelli, Massimo

    2010-01-01

    This paper presents a robust and dynamic face recognition technique based on the extraction and matching of devised probabilistic graphs drawn on SIFT features related to independent face areas. The face matching strategy is based on matching individual salient facial graph characterized by SIFT features as connected to facial landmarks such as the eyes and the mouth. In order to reduce the face matching errors, the Dempster-Shafer decision theory is applied to fuse the individual matching scores obtained from each pair of salient facial features. The proposed algorithm is evaluated with the ORL and the IITK face databases. The experimental results demonstrate the effectiveness and potential of the proposed face recognition technique also in case of partially occluded faces.

  9. Alzheimer's centennial legacy: origins, landmarks and the current status of knowledge concerning cognitive aspects.

    Science.gov (United States)

    Hodges, John R

    2006-11-01

    This review commemorates 100 years of research into Alzheimer's disease and, by happy coincidence, the publication of 100 papers in Brain on the topic. The first part of the review traces the evolution of concepts and landmarks in the modern history of Alzheimer's disease. It highlights the continuing role of careful clinico-pathological studies which have set the stage for each major leap forwards, such as the emergence of the cholinergic hypothesis, and the realistation that subjects pass through an amnestic prodrome which is thought to reflect dysfunction of the hippocampal formation before the onset of full blown dementia. The contribution of structural and functional imaging is briefly described. The important contribution of publications in Brain is illustrated throughout the first section. The second part attempts to review the current status of our knowledge concerning behavioural, neuropsychological and neuropsychiatric aspects of the disease, emphasizing areas of continuing controversy. PMID:17071920

  10. Landmarks in particle physics at Brookhaven National Laboratory: Brookhaven Lecture Series, Number 238

    International Nuclear Information System (INIS)

    Robert Adair's lecture on Landmarks in Particle Physics at Brookhaven National Laboratory (BNL) is a commemoration of the 40th Anniversary of Brookhaven National Laboratory. Adair describes ten researches in elementary particle physics at Brookhaven that had a revolutionary impact on the understanding of elementary particles. Two of the discoveries were made in 1952 and 1956 at the Cosmotron, BNL's first proton accelerator. Four were made in 1962 and 1964 at the Alternating Gradient Synchrotron, the Cosmotron's replacement. Two other discoveries in 1954 and 1956 were theoretical, and strong focusing (1952) is the only technical discovery. One discovery (1958) happened in an old barrack. Four of the discoveries were awarded the Nobel prize in Physics. Adair believes that all of the discoveries are worthy of the Nobel prize. 14 figs

  11. Volume rendering and bicolour scale in double isotope studies: Application to immunoscintigraphy and bone landmarking

    International Nuclear Information System (INIS)

    Combining the volume rendering and bicolour visualization techniques is proposed as an aird in interpreting single photon emission tomography (SPET) immunoscintigraphy (IS) recorded simultaneously with SPECT bone landmarking (BL). The combination helps in localizing abnormal monoclonal uptake and in differentiating it from a physiological radioactivity distribution. The so-called rendered images (RIs) are obtained in both IS and BL studies according to a depth-weighted maximum activity projection algorithm. Fused BL and IS RIs are constructed by a simple, pixel by pixel addition. They are displayed using a bicolour grey-red scale, which makes it possible to visualize both studies by a transparency effect. This method was applied to patients suspected of suffering colorectal or ovarian cancer recurrences, in whom monoclonal antibodies against carcinoembryonic antigen, B72-3 or OC125 labelled with indium-111 were used. (orig.)

  12. Global polity in adult education and UNESCO: landmarking, brokering, and framing policy

    DEFF Research Database (Denmark)

    Milana, Marcella

    2015-01-01

    Taking into account the complexity and multidimensionality of local-global interconnections, the author argues for the adoption of a global polity perspective in adult education, which is applied to study mobilization processes that occur through UNESCO. The findings point to three processes, neither within nor outside, but across geo-political borders and professional interests: ‘landmarking’, by which a shared sense of a common past in adult education is created; ‘brokering’, which helps shape a common future direction in adult education; and ‘framing’, which is used to convert ideational landscapes into material government-led actions. Both the theoretical perspectives and the analytical insights presented here could be used in analogous studies in other areas of education or with a focus on different political actors.

  13. Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results

    OpenAIRE

    Yoo, Yun Joo; Pinnaduwage, Dushanthi; Waggott, Daryl; Bull, Shelley B.; Sun, Lei

    2009-01-01

    The power of genome-wide association studies can be improved by incorporating information from previous study findings, for example, results of genome-wide linkage analyses. Weighted false-discovery rate (FDR) control can incorporate genome-wide linkage scan results into the analysis of genome-wide association data by assigning single-nucleotide polymorphism (SNP) specific weights. Stratified FDR control can also be applied by stratifying the SNPs into high and low linkage strata. We applied ...

  14. Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results

    OpenAIRE

    Yoo Yun; Pinnaduwage Dushanthi; Waggott Daryl; Bull Shelley B; Sun Lei

    2009-01-01

    Abstract The power of genome-wide association studies can be improved by incorporating information from previous study findings, for example, results of genome-wide linkage analyses. Weighted false-discovery rate (FDR) control can incorporate genome-wide linkage scan results into the analysis of genome-wide association data by assigning single-nucleotide polymorphism (SNP) specific weights. Stratified FDR control can also be applied by stratifying the SNPs into high and low linkage strata. We...

  15. Fast, shape-directed, landmark-based deep gray matter segmentation for quantification of iron deposition

    Science.gov (United States)

    Ekin, Ahmet; Jasinschi, Radu; van der Grond, Jeroen; van Buchem, Mark A.; van Muiswinkel, Arianne

    2006-03-01

    This paper introduces image processing methods to automatically detect the 3D volume-of-interest (VOI) and 2D region-of-interest (ROI) for deep gray matter organs (thalamus, globus pallidus, putamen, and caudate nucleus) of patients with suspected iron deposition from MR dual echo images. Prior to the VOI and ROI detection, cerebrospinal fluid (CSF) region is segmented by a clustering algorithm. For the segmentation, we automatically determine the cluster centers with the mean shift algorithm that can quickly identify the modes of a distribution. After the identification of the modes, we employ the K-Harmonic means clustering algorithm to segment the volumetric MR data into CSF and non-CSF. Having the CSF mask and observing that the frontal lobe of the lateral ventricle has more consistent shape accross age and pathological abnormalities, we propose a shape-directed landmark detection algorithm to detect the VOI in a speedy manner. The proposed landmark detection algorithm utilizes a novel shape model of the front lobe of the lateral ventricle for the slices where thalamus, globus pallidus, putamen, and caudate nucleus are expected to appear. After this step, for each slice in the VOI, we use horizontal and vertical projections of the CSF map to detect the approximate locations of the relevant organs to define the ROI. We demonstrate the robustness of the proposed VOI and ROI localization algorithms to pathologies, including severe amounts of iron accumulation as well as white matter lesions, and anatomical variations. The proposed algorithms achieved very high detection accuracy, 100% in the VOI detection , over a large set of a challenging MR dataset.

  16. Germ band retraction as a landmark in glucose metabolism during Aedes aegypti embryogenesis

    Directory of Open Access Journals (Sweden)

    Logullo Carlos

    2010-02-01

    Full Text Available Abstract Background The mosquito A. aegypti is vector of dengue and other viruses. New methods of vector control are needed and can be achieved by a better understanding of the life cycle of this insect. Embryogenesis is a part of A. aegypty life cycle that is poorly understood. In insects in general and in mosquitoes in particular energetic metabolism is well studied during oogenesis, when the oocyte exhibits fast growth, accumulating carbohydrates, lipids and proteins that will meet the regulatory and metabolic needs of the developing embryo. On the other hand, events related with energetic metabolism during A. aegypti embryogenesis are unknown. Results Glucose metabolism was investigated throughout Aedes aegypti (Diptera embryonic development. Both cellular blastoderm formation (CBf, 5 h after egg laying - HAE and germ band retraction (GBr, 24 HAE may be considered landmarks regarding glucose 6-phosphate (G6P destination. We observed high levels of glucose 6-phosphate dehydrogenase (G6PDH activity at the very beginning of embryogenesis, which nevertheless decreased up to 5 HAE. This activity is correlated with the need for nucleotide precursors generated by the pentose phosphate pathway (PPP, of which G6PDH is the key enzyme. We suggest the synchronism of egg metabolism with carbohydrate distribution based on the decreasing levels of phosphoenolpyruvate carboxykinase (PEPCK activity and on the elevation observed in protein content up to 24 HAE. Concomitantly, increasing levels of hexokinase (HK and pyruvate kinase (PK activity were observed, and PEPCK reached a peak around 48 HAE. Glycogen synthase kinase (GSK3 activity was also monitored and shown to be inversely correlated with glycogen distribution during embryogenesis. Conclusions The results herein support the hypothesis that glucose metabolic fate changes according to developmental embryonic stages. Germ band retraction is a moment that was characterized as a landmark in glucose metabolism during Aedes aegypti embryogenesis. Furthermore, the results also suggest a role for GSK3 in glycogen balance/distribution during morphological modifications.

  17. 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 by a trade-off between the efficiency and the scanning angle, or by using a better amplitude distribution.

  18. CT scan (image)

    Science.gov (United States)

    CT stands for computerized tomography. In this procedure, a thin X-ray beam is rotated around the ... D image of a section through the body. CT scans are very detailed and provide excellent information ...

  19. Knee CT scan

    Science.gov (United States)

    A computed tomography (CT) scan of the knee is test that uses x-rays to make detailed images of the knee. ... table that slides into the center of the CT scanner. When you are inside the scanner, the ...

  20. Photothermal imaging scanning microscopy

    Science.gov (United States)

    Chinn, Diane (Pleasanton, CA); Stolz, Christopher J. (Lathrop, CA); Wu, Zhouling (Pleasanton, CA); Huber, Robert (Discovery Bay, CA); Weinzapfel, Carolyn (Tracy, CA)

    2006-07-11

    Photothermal Imaging Scanning Microscopy produces a rapid, thermal-based, non-destructive characterization apparatus. Also, a photothermal characterization method of surface and subsurface features includes micron and nanoscale spatial resolution of meter-sized optical materials.

  1. Terahertz Scanning Array Radiometers

    International Science & Technology Center (ISTC)

    Ultrasensitive Terahertz Range Radiometers of Sub-Diffraction Resolution with Receiving Arrays Based on the Superconducting Hot-Electron Nanobolometers-Sensors and the Procedure for Scanning and Reconstruction of Received Images

  2. Chest CT Scan

    Science.gov (United States)

    ... pictures to create a very detailed, three-dimensional (3D) model of organs. Sometimes, a substance called contrast dye is injected into a vein in your arm for the CT scan. This substance highlights areas in your chest, which ...

  3. Scanning ultrafast electron microscopy

    OpenAIRE

    Yang, Ding-shyue; Mohammed, Omar F.; Zewail, Ahmed H.

    2010-01-01

    Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for whi...

  4. Scanning Tunneling Microscopy

    Science.gov (United States)

    The Concord Consortium

    2011-12-11

    Use a virtual scanning tunneling microscope (STM) to observe electron behavior in an atomic-scale world. Walk through the principles of this technology step-by-step. First learn how the STM works. Then try it yourself! Use a virtual STM to manipulate individual atoms by scanning for, picking up, and moving electrons. Finally, explore the advantages and disadvantages of the two modes of an STM: the constant-height mode and the constant-current mode.

  5. Intricate Port Scanning

    OpenAIRE

    Pratik Kanani; Hiral Raveshiya

    2013-01-01

    In today’s scenario due to advancement in computing power, technology, advance tools and coding techniques password cracking and finding vulnerability has become simpler. One of the most common techniques used by intruders is port scanning, by which attacker identifies running applications and makes entry in the system.In this paper the idea of random port selection is suggested to make the port scanning more difficult for intruders

  6. Josephson scanning tunneling microscopy

    Science.gov (United States)

    Šmakov, Jurij; Martin, Ivar; Balatsky, Alexander V.

    2001-12-01

    We propose a set of scanning tunneling microscopy experiments in which the surface of a superconductor is scanned by a superconducting tip. Potential capabilities of such experimental setup are discussed. Most important anticipated results of such an experiment include the position-resolved measurement of the superconducting order parameter and the possibility to determine the nature of the secondary component of the order parameter at the surface. The theoretical description based on the tunneling Hamiltonian formalism is presented.

  7. V/SCAN

    OpenAIRE

    Golab, T. J.; Ledley, R S; Buas, M.; Lubs, H A

    1988-01-01

    V/SCAN™ is a computerized video scanning instrument incorporating new concepts in the analysis of microscopic images, having applications to the detailed analysis and construction of chromosome karyotypes. Its primary use is for research applications in the areas of automating hybrid cell karyotyping where 150 or more chromosomes may appear, of automating prometaphase banding pattern analysis where complex banding patterns occur, and of automating fluorescence stains of chromosomal probes w...

  8. Rodent malaria parasites : genome organization & comparative genomics

    OpenAIRE

    Kooij, Taco W. A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparum and partial genome sequences of three RMPs (Plasmodium yoelii - Chapter 3; Plasmodium berghei and Plasmodium chabaudi - Chapter 4) enabled us to expand the analysis to a genome-wide survey. By al...

  9. Bone scanning in osteoporosis

    International Nuclear Information System (INIS)

    This paper reports on bone scanning in osteoporosis a diagnosis of osteoporosis most often follows fracture, and clearly this should be confirmed by x-ray. The bone scan therefore does not have an important role to play in the initial diagnosis of osteoporosis. While the exact mechanism by which the 99mTc-labeled diphosphonates localize in the skeleton is not fully understood, it is believed that they adsorb onto bone surfaces most probably via the calcium of hydroxyapatite crystals. Because the major factors that affect adsorption are osteoblastic activity and to a lesser extent skeletal vascularity, it is apparent that a bone scan image presents a functional display of skeletal metabolic activity. However, osteoporosis is a disorder in which gradual change in bone mass may occur over many years and, in keeping with this minor imbalance in skeletal metabolism, the bone scan appearances are usually normal. However, the scan images may appear of poor quality because of relatively low bone uptake of tracer with, on occasion, a washed-out pattern of activity in the axial and appendicular bone. It has been suggested that such a pattern occurs in severe or end-stage osteoporosis caused by markedly reduced osteoblastic activity. If kyphosis is observed on the bone scan or if there appears to be loss of spinal height with proximity of ribs to each other or increased closeness of rib cage to pelvis, then appearances suggest vertebral collapse and would be in keepin vertebral collapse and would be in keeping with a diagnosis of osteoporosis. Such evidence is, however, indirect and in practice a bone scan is an extremely unreliable means of diagnosing osteoporosis

  10. Silencing Genomes

    Science.gov (United States)

    2007-06-12

    While we may have complete genome sequences for humans and some animals, scientists are now entering the "post genome" era. The challenges of this era include determining the physiological functions of the thousands of new genes "for which little is known beyond their sequences." The use of RNAi, along with bioinformatics, can provide scientists with the tools to determine these functions in living organisms. This interactive and informative site, created by Cold Spring Harbor Laboratory, allows visitors to learn about the ways in which RNAi functions. Visitors can make their way through the seven interactive features here, which include "Inducing RNAi by Feeding" and "Creating an RNAi Feeding Strain". Additionally, the site has a "Resources" area which contains more materials on RNAi (such as interviews with scientists and such), along with videos of different strains in action.

  11. New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome.

    Science.gov (United States)

    Garazha, Andrew; Ivanova, Alena; Suntsova, Maria; Malakhova, Galina; Roumiantsev, Sergey; Zhavoronkov, Alex; Buzdin, Anton

    2015-05-01

    Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ?8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ?110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci. PMID:25853282

  12. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  13. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten E

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  14. Theory of Radioisotope Scanning

    International Nuclear Information System (INIS)

    All scanning techniques, whether utilizing focusing collimators, positron detectors or the newer camera techniques, have certain basic problems. The success of these techniques depends in large measure upon the correct choice of various parameters of the collimating system, of which the most important is the resolution. In this paper the relationship of optimum resolution to radioisotope content and distribution are discussed. Radioisotope scanning may be considered as a process of information extraction and presentation. The primary information lies in the original radioisotope distribution. The collimator and detecting system provide the information transfer mechanism and the final scan presents the resultant information. As with all such techniques, only a small fraction of the information is retained in the final scan. It can be shown that for focusing collimator and scintillation camera systems, the number of counts per resolution area varies as the fourth power of the resolution distance. For certain radioisotope distributions it is possible to derive analytically an optimum value of resolution distance. However, for most systems the optimum resolution must be determined by trial and error. The problems here are similar to those of pattern recognition in other fields. A computer programme has been prepared to aid in determining the optimum resolution for various types of patterns. This computer is unique in having intermediate disc storage and CRT read-out. The ediate disc storage and CRT read-out. The results have general applicability to the design of many scanning systems. (author)

  15. Reliability of Determination of Bony Landmarks of the Distal Femur on MR Images and MRI-Based 3D Models

    Directory of Open Access Journals (Sweden)

    F. Esfandiarpour

    2009-12-01

    Full Text Available Background/Objective: Consistent determination of the anatomical landmarks on image or image-based three dimensional (3D models is a basic requirement for reliable analysis of the human joint kinematics using imaging techniques. We examined the intra- and inter-observer reliability of determination of the medial and lateral epicondyle landmarks on 2D MR images and 3D MRI-based models of the knee. "n"n Materials and Methods: Sixteen coronal plane MRI recordings were taken from 18 healthy knees using a knee coil with T2-weighted fast spin-echo sequence and 512×512 pixel size. They were then processed by the Mimics software to provide the coronal and axial plane views and to create a 3D image-based model of the femur. Each image was reviewed twice, at least one-day apart. The interclass correlation coefficient, standard error of measurement, and coefficient of variation were calculated to assess the intra- and inter-observer reliability of the landmark determination by six experienced radiologists. A mixed model analysis of variance (ANOVA with two days of observation as the within-subject factor, and observers (six radiologists and methods (2D vs. 3D as between-subject factors were used to test the effect of observer, two days of observation and method of evaluation on landmark determination. Results: The results indicated that the interclass correlation coefficients for the intra-observer and inter-observer determination of landmarks on images and image-based 3D models were above 0.97. The standard error of measurement ranged between 0.41 and 0.78 mm for x; 1.35 and 3.43 mm for y; and 1.03 and 4.71 mm for z coordinates. Furthermore, the results showed no significant difference for within and between-subject comparisons of each coordinate of the lateral epicondyle as well as x and z coordinates of the medial epicondyle. For the y coordinate of the medial epicondyle, the p value of within-subject comparison was borderlinely significant (p=0.049. Conclusion: It was concluded that the intra- and inter-observer reliability of the bony landmark determination on both image and image-based 3D models were excellent.    

  16. Lung scans and malignancy

    International Nuclear Information System (INIS)

    An experience of pulmonary isotope scanning carried out with mercury 197 labelled mercury chloride and acetate, cobalt 57-labelled bleomycin, and Cu67 and Cu64 labelled copper citrate was presented. The scans were carried out with various isotopes supplied by the French Atomic Energy Authority, and gave comparable results, which may be summarised as follows: increased uptake in more than 90% of cases of carcinoma, absent uptake in all cases of benign tumour, frequent increased uptake in acute or advanced inflammatory lesions, absence of uptake, very commonly, in tuberculoma and chronic lesions with scar formation. Radio-isotope scan using Cu67 labelled copper citrate permitted discrimination of malignant tumours (increased fixation which showed up best at the 24th hour) from inflammatory lesions (increased fixation which was reduced on the 24th hour). The positive or negative character of the fixation in a given lesions remains the same, whatever the isotope used in our experience

  17. Shipborne hydrographic laser scanning

    Science.gov (United States)

    Pfennigbauer, Martin; Rieger, Peter; Schaich, Martin

    2011-11-01

    Applications like hydro-archeology, hydrobiology, or hydraulic engineering sometimes require accurate surveying of submerged areas with point densities usually only achieved with mobile or terrestrial laser scanning. For navigable waterbodies, hydrographic laser scanning from a floating platform represents a viable solution. RIEGL's new hydrographic laser scanner VQ-820-G with its exceptionally high measurement rate of up to 110,000 net measurements per second and its small laser footprint is optimally suited for such applications. We present results from a measurement campaign surveying prehistoric lake dwellings at Lake Constance in Germany. While the aim of typical hydrographic laser scanning applications is to roughly acquire the ground's shape and structure, in this case it was tried to determine the exact position, shape, and attitude of the remainders of the piles. The special requirements with respect to mission planning and data processing are discussed and the performance of the laser scanner is assessed.

  18. Liver Scanning with Radiomolybdate

    International Nuclear Information System (INIS)

    Carrier- free Mo99 injected intravenously as molybdate concentrates rapidly and efficiently in the polygonal cells of the liver. The hepatic uptake of Mo99 is accompanied by a gradual build-up of the daughter Tc99m whose 0.140 MeV gamma radiation is particularly suitable for scanning purposes. Good visualization of the liver is obtained when scans are done 24 h after injection of 40 to 50 ?c of Mo99. At this time, the maximum count-rate of Tc99m is obtained over the liver, and the Tcm injected together with Mo99 has been almost lost, either by excretion or decay, thus securing low background count. Métastasés, abscesses and other space-occupying lesions are visible as defects. A hepatoma produced a ''hot'' nodule on the scan by selecting Mo99 to a greater extent than did the surrounding liver tissue. Decreased hepatic uptake of Mo99 is observed in diffuse hepatocellular diseases. Mo99 has several advantages over colloidal radiogold and I131-labelled Rose Bengal: (1) It accumulates in the polygonal cells and its uptake portrays effectively disease states of the parenchyma; (2) The concentration of the tracer does not change during the interval of the scan since Mo99 has a biological half-life of about 20 d. The scan can be repeated in case of technical failure without loss of quality; (3) The contrast ratio is superior by utilizing the ast ratio is superior by utilizing the low-energy gamma radiation of Tc99m. A comparative evaluation of the scanning resolution obtained with Mo99-Tc99m, I131 and Au198 using a liver phantom is presented; and (4) the low energy of the principal radiation permits greatly reduced scintillation crystal size and greatly enhances detector and collimator efficiency. The total radiation dose to the liver is of the order of two rad. (author)

  19. Automated placement of stereotactic injections using a laser scan of the skull

    CERN Document Server

    Henderson, Margaret; Tolpygo, Alexander; Savoia, Stephen; Grange, Pascal; Mitra, Partha

    2014-01-01

    Stereotactic targeting is a commonly used technique for performing injections in the brains of mice and other animals. The most common method for targeting stereoscopic injections uses the skull indentations bregma and lambda as reference points and is limited in its precision by factors such as skull curvature and individual variation, as well as an incomplete correspondence between skull landmarks and brain locations. In this software tool, a 3D laser scan of the mouse skull is taken in vitro and registered onto a reference skull using a point cloud matching algorithm, and the parameters of the transformation are used to position a glass pipette to place tracer injections. The software was capable of registering sample skulls with less than 100 micron error, and was able to target an injection in a mouse with error of roughly 500 microns. These results indicate that using skull scan registration has the potential to be widely applicable in automating stereotactic targeting of tracer injections.

  20. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    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.)

  1. V/SCAN

    Science.gov (United States)

    Golab, T.J.; Ledley, R.S.; Buas, M.; Lubs, H.A.

    1988-01-01

    V/SCAN™ is a computerized video scanning instrument incorporating new concepts in the analysis of microscopic images, having applications to the detailed analysis and construction of chromosome karyotypes. Its primary use is for research applications in the areas of automating hybrid cell karyotyping where 150 or more chromosomes may appear, of automating prometaphase banding pattern analysis where complex banding patterns occur, and of automating fluorescence stains of chromosomal probes which appear on interphase cells. The instrument also includes the capability of very high-speed locating of chromosome spreads and other objects, and of large-scale image archiving and retrieval.

  2. Scanning electrochemical microscopy

    CERN Document Server

    Bard, Allen J

    2012-01-01

    Because of its simplicity of use and quantitative results, Scanning Electrochemical Microscopy (SECM) has become an indispensable tool for the study of surface reactivity. The fast expansion of the SECM field during the last several years has been fueled by the introduction of new probes, commercially available instrumentation, and new practical applications. Scanning Electrochemical Microscopy, Second Edition offers essential background and in-depth overviews of specific applications in self-contained chapters. Recent methodological advances have greatly increased the capacity of SECM to char

  3. Genome wide scan maps mutations in deadly lung cancers

    Science.gov (United States)

    Scientists have completed a comprehensive map of genetic mutations linked to an aggressive and lethal type of lung cancer. Among the errors found in small cell lung cancers, the team of scientists, including those at the Johns Hopkins Kimmel Cancer Center, found an alteration in a gene called SOX2 associated with early embryonic development. The team also included scientists from the University of Texas Southwestern Medical Center, the University of Colorado Cancer Center, and Genentech.

  4. Lessons learned from the dog genome.

    Science.gov (United States)

    Wayne, Robert K; Ostrander, Elaine A

    2007-11-01

    Extensive genetic resources and a high-quality genome sequence position the dog as an important model species for understanding genome evolution, population genetics and genes underlying complex phenotypic traits. Newly developed genomic resources have expanded our understanding of canine evolutionary history and dog origins. Domestication involved genetic contributions from multiple populations of gray wolves probably through backcrossing. More recently, the advent of controlled breeding practices has segregated genetic variability into distinct dog breeds that possess specific phenotypic traits. Consequently, genome-wide association and selective sweep scans now allow the discovery of genes underlying breed-specific characteristics. The dog is finally emerging as a novel resource for studying the genetic basis of complex traits, including behavior. PMID:17963975

  5. Registration of prone and supine CT colonography scans using correlation optimized warping and canonical correlation analysis

    International Nuclear Information System (INIS)

    Purpose: In computed tomographic colonography (CTC), a patient will be scanned twice--Once supine and once prone--to improve the sensitivity for polyp detection. To assist radiologists in CTC reading, in this paper we propose an automated method for colon registration from supine and prone CTC scans. Methods: We propose a new colon centerline registration method for prone and supine CTC scans using correlation optimized warping (COW) and canonical correlation analysis (CCA) based on the anatomical structure of the colon. Four anatomical salient points on the colon are first automatically distinguished. Then correlation optimized warping is applied to the segments defined by the anatomical landmarks to improve the global registration based on local correlation of segments. The COW method was modified by embedding canonical correlation analysis to allow multiple features along the colon centerline to be used in our implementation. Results: We tested the COW algorithm on a CTC data set of 39 patients with 39 polyps (19 training and 20 test cases) to verify the effectiveness of the proposed COW registration method. Experimental results on the test set show that the COW method significantly reduces the average estimation error in a polyp location between supine and prone scans by 67.6%, from 46.27±52.97 to 14.98 mm±11.41 mm, compared to the normalized distance along the colon centerline algorithm (p<0.01). Conclusions: The proposed COW algorithm is more accurate for the COW algorithm is more accurate for the colon centerline registration compared to the normalized distance along the colon centerline method and the dynamic time warping method. Comparison results showed that the feature combination of z-coordinate and curvature achieved lowest registration error compared to the other feature combinations used by COW. The proposed method is tolerant to centerline errors because anatomical landmarks help prevent the propagation of errors across the entire colon centerline.

  6. Homing in the wolf spider Lycosa tarantula (Araneae, Lycosidae): the role of active locomotion and visual landmarks

    Science.gov (United States)

    Reyes-Alcubilla, Carmen; Ruiz, Miguel A.; Ortega-Escobar, Joaquín

    2009-04-01

    Previous studies on the homing of the wolf spider Lycosa tarantula have shown that it is carried out by path integration. Animals using this mechanism must measure the distance walked and the angles turned. This study aims to understand if wolf spider L. tarantula is able to estimate the walked distance in an outward path. As this information is more likely obtained by proprioceptive mechanisms, active or passive displacements have been performed. An active locomotion was found essential to estimate distances. During passive locomotion, spiders searched for their burrows near the release point while when displaced actively the inbound journey was longer than the outbound one. The possible use of visual landmarks near the burrow was also tested as a cue to complete the inbound journey. Our results did not show that L. tarantula used these visual landmarks to find the burrow. L. tarantula seems to use only proprioceptive information obtained during the outbound path to estimate the distance traveled.

  7. 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 transcriptional evidence. Analysis of repetitive sequences suggests that they are underrepresented in the reference assembly, reflecting an enrichment of gene-rich regions in the current assembly. Characterization of Lotus natural variation by resequencing of L. japonicus accessions and diploid Lotus species is currently ongoing, facilitated by the MG20 reference sequence

  8. Bone scan in rheumatology

    International Nuclear Information System (INIS)

    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

  9. Getting a CAT Scan

    Medline Plus

    Full Text Available ... CAT stands for "computerized axial tomography." Translated, that means a scanner takes computer pictures of what's going on inside your body. The scan itself is painless. All you'll need to do is hold still for a few minutes at a time so the pictures come out clear Sign up ...

  10. Tomographic scanning apparatus

    International Nuclear Information System (INIS)

    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.)

  11. Scanning Electron Microscope

    Science.gov (United States)

    Science Learning Network

    This site from the Museum of Science features an introduction to scanning electron microscopy and is suitable for high school or introductory college audiences. It includes resources for teachers, an image gallery, a self paced tour, links, and a QuickTime animation.

  12. Abscess scan - radioactive

    Science.gov (United States)

    ... injected back into a vein body through another needle stick. You will need to return to the office 6-24 hours later. At that time, you will have a nuclear medicine scan to ... in areas of your body where they would not be normally.

  13. DSQ Scanning Information: Westat

    Science.gov (United States)

    Westat, Inc. provides scanning and intelligent data capture for the Dietary Screener Questionnaire (DSQ). Services include providing printed questionnaires for data collection and processing completed questionnaires. Westat can provide a modified version of the DSQ for customized data collections. A verified data file along with images of the processed DSQ questionnaires are provided after processing.

  14. Virtual Scanning Electron Microscopy

    Science.gov (United States)

    Michael W. Davidson

    This site from Florida State University features an interactive Java tutorial that explores various aspects of virtual scanning electron microscopy. Users can see how specimens appear when magnified in the virtual SEM. The site also features an image gallery and extensive information about different types of microscopy.

  15. Stabilized radiographic scanning agent

    International Nuclear Information System (INIS)

    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.)

  16. Scan This Book!

    Science.gov (United States)

    Albanese, Andrew Richard

    2007-01-01

    In this article, the author presents an interview with Brewster Kahle, leader of the Open Content Alliance (OCA). OCA book scan program is an alternative to Google's library project that aims to make books accessible online. In this interview, Kahle discusses his views on the challenges of getting books on the Web, on Google's library…

  17. Medial calcar of proximal humeral fracture as landmark in restoration of humeral length in case of hemiarthroplasty.

    Czech Academy of Sciences Publication Activity Database

    Hromádka, R.; Kub?na, Aleš Antonín; Šmíd, Martin; Popelka, S.

    2014-01-01

    Ro?. 35, ?. 5 (2014), s. 473-479. ISSN 0930-1038 Institutional support: RVO:67985556 Keywords : Fracture of proximal humerus * Calcar of humeral fracture * Reconstruction of proximal humerus * Reconstruction of humeral length * Shoulder arthroplasty * Shoulder hemiarthroplasty Subject RIV: FJ - Surgery incl. Transplants Impact factor: 1.333, year: 2013 http://library.utia.cas.cz/separaty/2013/E/smid-medial calcar of proximal humeral fracture as landmark in restoration of humeral length in case of hemiarthroplasty.pdf

  18. Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

    OpenAIRE

    Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

    2009-01-01

    The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and t...

  19. Knowledge-based recognition of man-made landmarks in a simulated control cycle using a virtual-globe system

    OpenAIRE

    Michaelsen, Eckart

    2012-01-01

    Automatic knowledge-based recognition of landmarks in aerial images for UAV navigation is an alternative to GNSS navigation. It provides absolute position estimates thus complementing INS navigation. Relying on knowledge instead of template images or training samples is advantageous because the first may be out-of-date and the latter not representative. The robustness and precision of the method can be assessed using internet-based virtual globe systems such as Google Earth as camera simulato...

  20. Landmark-referenced Voxel-based Analysis of Diffusion Tensor Images of the Brainstem White Matter Tracts. Application in Patients with Middle Cerebral Artery Stroke

    OpenAIRE

    Zhang, Weihong; Li, Xin; Zhang, Jiangyang; Luft, Andreas; Hanley, Daniel F.; van Zijl, Peter; Miller, Michael I; YOUNES, LAURENT; Mori, Susumu

    2008-01-01

    Although DTI can provide detailed information about white matter anatomy, it is not yet straightforward enough to quantify the anatomical information it visualizes. In this study, we developed and tested a new tool to perform brain normalization and voxel-based analysis of DTI data. For the normalization part, manually placed landmarks ensured that the visualized white matter tracts were well-registered among the populations. A standard landmark set in ICBM-152 space and an interface to remap...

  1. Optimal landmarks selection and fiducial marker placement for minimal target registration error in image-guided neurosurgery

    Science.gov (United States)

    Shamir, Reuben R.; Joskowicz, Leo; Shoshan, Yigal

    2009-02-01

    We describe a new framework and method for the optimal selection of anatomical landmarks and optimal placement of fiducial markers in image-guided neurosurgery. The method allows the surgeon to optimally plan the markers locations on routine diagnostic images before preoperative imaging and to intraoperatively select the fiducial markers and the anatomical landmarks that minimize the Target Registration Error (TRE). The optimal fiducial marker configuration selection is performed by the surgeon on the diagnostic image following the target selection based on a visual Estimated TRE (E-TRE) map. The E-TRE map is automatically updated when the surgeon interactively adds and deletes candidate markers and targets. The method takes the guesswork out of the registration process, provides a reliable localization uncertainty error for navigation, and can reduce the localization error without additional imaging and hardware. Our clinical experiments on five patients who underwent brain surgery with a navigation system show that optimizing one marker location and the anatomical landmarks configuration reduces the average TRE from 4.7mm to 3.2mm, with a maximum improvement of 4mm. The reduction of the target registration error has the potential to support safer and more accurate minimally invasive neurosurgical procedures.

  2. The Vesta gravity field, spin pole and rotation period, landmark positions, and ephemeris from the Dawn tracking and optical data

    Science.gov (United States)

    Konopliv, A. S.; Asmar, S. W.; Park, R. S.; Bills, B. G.; Centinello, F.; Chamberlin, A. B.; Ermakov, A.; Gaskell, R. W.; Rambaux, N.; Raymond, C. A.; Russell, C. T.; Smith, D. E.; Tricarico, P.; Zuber, M. T.

    2014-09-01

    The Vesta gravity field and related physical parameters have been precisely measured using 10-months of radiometric Doppler and range data and optical landmark tracking from the Dawn spacecraft. The gravity field, orientation parameters, landmark locations, and Vesta’s orbit are jointly estimated. The resulting spherical harmonic gravity field has a half-wavelength resolution of 42 km (degree 20). The gravitational mass uncertainty is nearly 1 part in 106. The inertial spin pole location is determined to better than 0.0001° and the uncertainty in the rotation period has been reduced by nearly a factor of 100. The combined precession and nutation of the pole of Vesta has been detected with angular rates about 70% of expected values, but not well enough to constrain the moment of inertia. The optical landmark position estimates reduce the uncertainty in the center-of-mass and center-of-figure offset to 10 m. The Vesta ephemeris uncertainty during the Dawn stay was reduced from 20 km to better than 10 m in the Earth-Vesta direction.

  3. An anatomical landmark for the supplementary eye fields in human revealed with functional magnetic resonance imaging.

    Science.gov (United States)

    Grosbras, M H; Lobel, E; Van de Moortele, P F; LeBihan, D; Berthoz, A

    1999-01-01

    Together with the frontal and parietal eye fields, the supplementary eye field (SEF) is involved in the performance and control of voluntary and reflexive saccades and of ocular pursuit. This region was first described in non-human primates and is rather well localized on the dorsal surface of the medial frontal cortex. In humans the site of the SEF is still ill-defined. Functional imaging techniques have allowed investigation of the location and function of the SEF. However, there is great variability with regard to the published standardized coordinates of this area. We used here the spatial precision of functional magnetic resonance imaging (fMRI) in order to better localize the SEF in individuals. We identified as the SEF a region on the medial wall that was significantly activated when subjects executed self-paced horizontal saccades in darkness as compared to rest. This region appeared to be predominantly activated in the left hemisphere. We found that, despite a discrepancy of >2 cm found in the standardized Talairach coordinates, the location of this SEF-region could be precisely and reliably described by referring to a sulcal landmark found in each individual: the upper part of the paracentral sulcus. PMID:10554993

  4. Surgery without consent or miscommunication? A new look at a landmark legal case.

    Science.gov (United States)

    Chervenak, Judith; McCullough, Laurence B; Chervenak, Frank A

    2015-05-01

    Schloendorff v Society of New York Hospital is regarded widely as a landmark in the history of informed consent because it is thought to have established individual self-determination as the legal basis of consent and respect for patient autonomy as the ethical basis of consent. For a century, it has been understood as a laparotomy done without consent when a pelvic mass was discovered unexpectedly in an anesthetized patient after an examination. We believe it was a case of surgeons failing to communicate properly with each other and their patient. To support this reinterpretation, we present evidence from the original medical and surgical records, letters of key participants in the case, and the trial court record. We also consider the case from the perspective of the modern culture of safety in gynecologic surgery. Contrary to what is commonly assumed, Ms Schloendorff lost her legal case, and her surgery might not have been performed at all had her clinicians known, understood, communicated, documented, and reaffirmed what the patient actually wanted. This new perspective on Schloendorff is important for gynecologic surgeons because it vividly documents the perils of implicit consent, delegating the obtaining of consent, and miscommunication among clinicians. The Schloendorff case underscores the constant need for continuous quality improvement to reduce medical errors and the risk of litigation by improving communication among surgeons. PMID:24995772

  5. Analysis of anatomical landmarks of the mandibular interforaminal region using CBCT in a Brazilian population

    Scientific Electronic Library Online (English)

    Paloma Rodrigues, Genú; Ricardo José de Holanda, Vasconcellos; Bruna Paloma de, Oliveira; Bruna Caroline Gonçalves de, Vasconcelos; Nádia Cristina da Cruz, Delgado.

    2014-12-01

    Full Text Available Aim: To evaluate the position, presence, appearance and extent of various anatomical landmarks in the mandibular interforaminal region of Brazilian patients using cone-beam computed tomography (CBCT). Methods: A total of 142 CBCT examinations were analyzed to determine the most common location of th [...] e mental foramen (MF), the presence and extent of the anterior loop (AL) of the inferior alveolar nerve, and the appearance and length of the incisive canal (IC). The presence of sexual dimorphism and differences with relation to the left and right sides were also evaluated. Results: Most of the MF (45.5%) was located below the second premolar. The AL and the IC were observed in 18.9 and 96.5% of the images respectively. The average length of AL and IC was 3.14±1.25 mm and 13.68±5.94 mm respectively. No significant differences (p>0.05) between genders or left and right sides were observed for all evaluated parameters. Conclusions: The most common location of the MF, the high rate of visualization of the IC and the occasional presence of AL in the studied Brazilian population demonstrate the importance of using three-dimensional images of the mandibular anterior region, allowing proper surgical planning and preventing injury to the neurovascular bundle.

  6. An analysis of anatomic landmark mobility and setup deviations in radiotherapy for lung cancer

    International Nuclear Information System (INIS)

    Purpose: To identify thoracic structures that exhibit little internal motion during irradiation and to determine setup variations in patients with lung cancer. Methods and Materials: Intrafractional images were generated with an electronic portal-imaging device from the AP fields of 10 patients, during several fractions. To determine the intrafractional mobility of thoracic structures, visible structures were contoured in every image and matched with a reference image by means of a cross-correlation algorithm. Setup variations were determined by comparing portal images with the digitized simulator films using the stable structures as landmarks. Results: Mobility was limited in the lateral direction for the trachea, thoracic wall, paraspinal line, and aortic notch, and in the craniocaudal direction for the clavicle, aortic notch, and thoracic wall. Analysis of patient setup revealed random deviations of 2.0 mm (1 SD) in the lateral direction and 2.8 mm in the craniocaudal direction, while the systematic deviations were 2.5 and 2.0 mm (1 SD) respectively. Conclusions: We have identified thoracic structures that exhibit little internal motion in the frontal plane, and recommend that these structures be used for verifying patient setup during radiotherapy. The daily variation in the setup of lung cancer patients at our center appears to be acceptable

  7. Genome-wide prediction, display and refinement of binding sites with information theory-based models

    Directory of Open Access Journals (Sweden)

    Leeder J Steven

    2003-09-01

    Full Text Available Abstract Background We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. Results Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths. Conclusions Delila-Genome was used to scan the human genome sequence with information weight matrices of transcription factor binding sites, including PXR/RXR?, AHR and NF-?B p50/p65, and matrices for RNA binding sites including splice donor, acceptor, and SC35 recognition sites. Comparisons of genome scans with the original and refined PXR/RXR? information weight matrices indicate that the refined model more accurately predicts the strengths of known binding sites and is more sensitive for detection of novel binding sites.

  8. Avaliação da artéria etmoidal anterior pela tomografia computadorizada no plano coronal / Anterior ethmoidal artery evaluation on coronal CT scans

    Scientific Electronic Library Online (English)

    Soraia Ale, Souza; Marcia Maria Ale de, Souza; Luís Carlos, Gregório; Sergio, Ajzen.

    2009-02-01

    Full Text Available O conhecimento da localização da artéria etmoidal anterior (AEA) constitui etapa importante na cirurgia do recesso do seio frontal e do etmóide anterior. A tomografia computadorizada (TC), em especial no plano coronal pode fornecer reparos anatômicos que identificam o trajeto da AEA. OBJETIVO: Ident [...] ificar os reparos anatômicos que caracterizam o trajeto da AEA na parede medial da órbita e na parede lateral da fossa olfatória. Verificar a correlação entre a presença de pneumatização supra-orbitária e a visualização do etmoidal anterior (canal da AEA). CASUÍSTICA E MÉTODOS: Estudo retrospectivo de 198 tomografias computadorizadas dos seios paranasais no plano coronal do período de agosto a dezembro de 2006. RESULTADOS: Pneumatização supra-orbitária foi identificada em 35% (70 exames). O canal da AEA foi caracterizado em 41% (81 exames). O sulco etmoidal anterior foi visualizado em 98% (194 dos exames) e o forame etmoidal anterior foi identificado em todos os exames (100%). CONCLUSÃO: O forame etmoidal anterior e o sulco etmoidal anterior foram referências anatômicas presentes em quase 100% dos exames avaliados. Houve correlação entre a presença de pneumatização supra-orbitária e a caracterização do canal da AEA. Abstract in english The anterior ethmoidal artery (AEA) is an important point for frontal and ethmoid sinuses surgery. CT scans can identify landmarks to help the surgeon find the AEA. AIM: To identify the landmarks of the AEA on the orbital medial wall and on the lateral wall of the olfactory fossa. and to correlate t [...] he presence of supraorbital ethmoidal cells with spotting the anterior ethmoidal artery canal. MATERIALS AND METHODS: Retrospective review of 198 direct coronal paranasal sinuses computed tomography (CT) scans from August to December, 2006. RESULTS: Supraorbital pneumatization was seen in 35% (70 scans). The AEA canal was seen in 41% (81 scans). The anterior ethmoidal sulcus was seen in 98% (194 scans) and the anterior ethmoidal foramen was seen in all the scans (100%). CONCLUSION: The anterior ethmoidal foramen and the anterior ethmoidal sulcus were anatomical landmarks present in almost 100% of the scans studied. There was a correlation between the presence of supraorbital pneumatization and AEA canal visualization.

  9. Avaliação da artéria etmoidal anterior pela tomografia computadorizada no plano coronal Anterior ethmoidal artery evaluation on coronal CT scans

    Directory of Open Access Journals (Sweden)

    Soraia Ale Souza

    2009-02-01

    Full Text Available O conhecimento da localização da artéria etmoidal anterior (AEA constitui etapa importante na cirurgia do recesso do seio frontal e do etmóide anterior. A tomografia computadorizada (TC, em especial no plano coronal pode fornecer reparos anatômicos que identificam o trajeto da AEA. OBJETIVO: Identificar os reparos anatômicos que caracterizam o trajeto da AEA na parede medial da órbita e na parede lateral da fossa olfatória. Verificar a correlação entre a presença de pneumatização supra-orbitária e a visualização do etmoidal anterior (canal da AEA. CASUÍSTICA E MÉTODOS: Estudo retrospectivo de 198 tomografias computadorizadas dos seios paranasais no plano coronal do período de agosto a dezembro de 2006. RESULTADOS: Pneumatização supra-orbitária foi identificada em 35% (70 exames. O canal da AEA foi caracterizado em 41% (81 exames. O sulco etmoidal anterior foi visualizado em 98% (194 dos exames e o forame etmoidal anterior foi identificado em todos os exames (100%. CONCLUSÃO: O forame etmoidal anterior e o sulco etmoidal anterior foram referências anatômicas presentes em quase 100% dos exames avaliados. Houve correlação entre a presença de pneumatização supra-orbitária e a caracterização do canal da AEA.The anterior ethmoidal artery (AEA is an important point for frontal and ethmoid sinuses surgery. CT scans can identify landmarks to help the surgeon find the AEA. AIM: To identify the landmarks of the AEA on the orbital medial wall and on the lateral wall of the olfactory fossa. and to correlate the presence of supraorbital ethmoidal cells with spotting the anterior ethmoidal artery canal. MATERIALS AND METHODS: Retrospective review of 198 direct coronal paranasal sinuses computed tomography (CT scans from August to December, 2006. RESULTS: Supraorbital pneumatization was seen in 35% (70 scans. The AEA canal was seen in 41% (81 scans. The anterior ethmoidal sulcus was seen in 98% (194 scans and the anterior ethmoidal foramen was seen in all the scans (100%. CONCLUSION: The anterior ethmoidal foramen and the anterior ethmoidal sulcus were anatomical landmarks present in almost 100% of the scans studied. There was a correlation between the presence of supraorbital pneumatization and AEA canal visualization.

  10. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I; Nobrega, M A

    2005-02-07

    Synonymous gene regulation, defined as driving shared temporal and/or spatial expression of groups of genes, is likely predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identify synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in the search of SREs and the results are displayed as to provide an extensive annotation of genes containing detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. We illustrate how this new tool can be used to establish a linkage between human diseases and noncoding genomic content. SynoR is publicly available at http://synor.dcode.org.

  11. An investigation on the facial midline distance to some anatomic landmarks of the jaws among people with natural dentition

    Directory of Open Access Journals (Sweden)

    Mosharraf R

    2004-02-01

    Full Text Available The determination of the dental midline is necessary in most dental procedures."nOne of the methods to fulfill this goal is to determine the facial midline based on the midpoints of the"nforehead, nose, upper lip and chin. However, for various reasons, this method has not always been"nproved successful. In such cases, different techniques, based on the investigations in the edentulous"npatients, have been suggested."nPurpose: The aim of this study was to investigate the conformity of some landmarks such as labial"nfrenum, incisive papilla and mid palatal suture with dental and facial midlines among people with natural"ndentition in order to obtain accurate anatomic landmarks for denture replacement."nMaterials and Methods: In this descriptive study, 96 dental students, having all their permanent teeth"nand without any orthognathic problem, were chosen. For each subject, Alginate impressions and dental"ncasts were prepared. Then, centric occlusion was recorded with a biting wax and the facial mid line was"ndetermined on the anterior part of it. The distances from the facial midline to the upper teeth midline,"nincisive papilla, labial frenum and mid palatal suture were determined with a special tool and were"nmeasured by a VERNIEH two times. In order to analyze the results, Chi- Square and t-student tests were"nused."nResults: The average of facial midline distance to the upper teeth midline, the labial frenum, the incisive"npapilla and the mid palatal suture were 0.83±0.60, 0.67±G.54, 0.83±00.63 and 0.81±0.62 mm,"nrespectively. There was no significant difference between males and females. Labial frenum showed the"nminimum distance to the facial midline, while the incisive papilla had the maximum. There was no"nsignificant difference between these anatomic landmarks, in conformity or unconformity with the facial"nmidline"nConclusion: Considering the low percentage of the subjects with complete conformity and the lack of"nsignificant differences between these three landmarks, it is suggested that there is no superiority among"nthese landmarks for the determination of facial midline. The similar distances from the facial midline to"nthe incisive papilla and upper teeth midline indicate that using incisive papilla to determine the upper"nteeth midline in edentulous patients lead to normal face.

  12. Scanning in Thyroid Cancer

    International Nuclear Information System (INIS)

    Scanning in thyroid cancer is of value in - 1. The preoperative diagnosis of a thyroid nodule; 2. The localization of thyroid cancer metastases; 3. The treatment of thyroidectomize d patients with metastases from thyroid cancer. The appearance of thyroid nodules on the scintigram is described. Some prelimi- nary results of the use of radiophosphoru s and external counting with a Geiger- Mueller tube of ''cold'' nodules are reported. Localization of thyroid cancer metastases with particular emphasis on the use of thyrotropic hormone is described. With this method three-fourths of all patients with metastatic thyroid cancer were found to have functioning metastases. The technique of ablation of normal thyroid remnants following total thyroidectomy and the treatment of metastases is discussed in detail. Scanning of metastases is the best method to follow the patient's progress. (author)

  13. Unexpected cross-species contamination in genome sequencing projects

    Directory of Open Access Journals (Sweden)

    Samier Merchant

    2014-11-01

    Full Text Available The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.

  14. Scanning probe metrology

    Science.gov (United States)

    Grigg, David A.; Griffith, Joseph E.; Kochanski, G. P.; Vasile, Michael J.; Russell, Phillip E.

    1992-06-01

    The design of a scanning probe microscope suitable for metrology applications must include solutions to several problems. Actuator errors can be large because of their nonlinear behavior, but this can be solved by independently monitoring the actuator's motion. The probe must be shaped properly for a given measurement, and it must be characterized to allow interpretation of the measurement. We have studied the effects of interaction forces and probe shape with emphasis on surface roughness measurements.

  15. IMEF gamma scanning system

    International Nuclear Information System (INIS)

    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

  16. Scanning Electron Microscope - SEM

    Science.gov (United States)

    This website is from Boston Museum of Science and is an introduction to Scanning Electron Micrscope (SEM). It contains an image gallery of insects, plants and other items as seen with an SEM. A slide show and a movie explains how the microsope works. Teacher resources offer guidance on building your own microscope and setting up a lab, including wet mounts and staining cells. Information on how the Museum uses the scope, and additional electronic resources, completes the site.

  17. VariScan Software

    OpenAIRE

    Vilella Bertran, Albert; Blanco-García, Angel; Hutter, Stephan; Rozas Liras, Julio A.

    2010-01-01

    Linux / Mac OS X : The package includes executables for linux (variscan) and Mac OS X (variscan). For other Unix-based platforms you will have to compile it from the source files included in the VariScan package. Windows: The package includes (src directory), the source code, the project (variscan.dev) and makefile (variscan.win) files to be used, for instance, for the Dev-C++ (a free Integrated Development Environment for the C/C++ programming language)

  18. Scanning noise microscopy

    Science.gov (United States)

    Schaffert, J.; Cottin, M. C.; Sonntag, A.; Karacuban, H.; Utzat, D.; Bobisch, C. A.; Möller, R.

    2013-04-01

    The paper describes a simple scheme enabling the real-time characterization of fluctuations, e.g., of the conductance in scanning tunneling microscopy. The technique can be used in parallel to other data acquisition, evaluating the rate, the amplitude, and the duty cycle of telegraphic noise in the tunneling current. This kind of scanning probe microscopy allows to evaluate the noise parameters as a function of the average tunneling current, the electron energy, and the lateral position. Images of the noise with Ångstrom spatial resolution are acquired simultaneously to the topographic information providing a direct correlation between the structural information and the noise. The method can be applied to a large variety of systems to monitor dynamics on the nanoscale, e.g., the localization of tunneling current induced switching within a single molecule. Noise spectroscopy may reveal the involved molecular orbitals, even if they cannot be resolved in standard scanning tunneling spectroscopy. As an example we present experimental data of the organic molecule copper phthalocyanine on a Cu(111) surface [J. Schaffert, M. C. Cottin, A. Sonntag, H. Karacuban, C. A. Bobisch, N. Lorente, J.-P. Gauyacq, and R. Möller, Nature Mater. 12, 223-227 (2013), 10.1038/nmat3527].

  19. Translational genomics

    Directory of Open Access Journals (Sweden)

    Martin Kussmann

    2014-09-01

    Full Text Available The term “Translational Genomics” reflects both title and mission of this new journal. “Translational” has traditionally been understood as “applied research” or “development”, different from or even opposed to “basic research”. Recent scientific and societal developments have triggered a re-assessment of the connotation that “translational” and “basic” are either/or activities: translational research nowadays aims at feeding the best science into applications and solutions for human society. We therefore argue here basic science to be challenged and leveraged for its relevance to human health and societal benefits. This more recent approach and attitude are catalyzed by four trends or developments: evidence-based solutions; large-scale, high dimensional data; consumer/patient empowerment; and systems-level understanding.

  20. Descreening of scanned images

    Science.gov (United States)

    Kurilin, Ilya V.; Safonov, Ilia V.; Lee, HoKeun; Kim, Sang Ho

    2010-01-01

    Screen or halftone pattern appears on the majority of images printed on electrophotographic and ink-jet printers as well as offset machines. When such halftoned image is scanned, a noisy effect called a Moiré pattern often appears on the image. There are plenty of methods proposed for descreening of images. Common way is adaptive smoothing of scanned images. However the descreening techniques face the following dilemma: deep screen reduction and restoration of contone images leads to blurring of sharp edges of text and other graphics primitives, on the other hand insufficient smoothing keeps screen in halftoned areas. We propose novel descreening algorithm that is primarily intended for preservation of sharpness and contrast of text edges and for restoration contone images from halftone ones accurately. Proposed technique for descreening of scanned images comprises five steps. The first step is decrease of edge transition slope length via local tone mapping with ordering; it is carried out before adaptive smoothing, and it allows better preservation of edges. Adaptive low-pass filter applies simplified idea of Non-Local Means filter for area classification; similarity is calculated between central block of window and different adjacent block that is selected randomly. If similarity is high then current pixel relates to flat region, otherwise pixel relates to edge region. For prevention of edges blurring, flat regions are smoothed stronger than edge regions. By random selection of blocks we avoid the computational overhead related to excessive directional edge detection. Final three stages include additional decrease of edge transition slope length using local tone mapping, increase of local contrast via modified unsharp mask filter, that uses bilateral filter with special edge-stop function for modest smoothing of edges, and global contrast stretching. These stages are intended to compensate decreasing of sharpness and contrast due to low-pass filtering, it allows to enhance visual quality of scanned image. For parameters adjusting for different scanning resolutions and comparison with existing techniques test target and criteria were proposed. Also the quality of proposed approach is evaluated by surveying observer's opinions. According to obtained outcomes the proposed algorithm demonstrates good descreening capabilities.

  1. ABrowse - a customizable next-generation genome browser framework

    Directory of Open Access Journals (Sweden)

    Kong Lei

    2012-01-01

    Full Text Available Abstract Background With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Results Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. Conclusions ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

  2. Whole Genome Sequencing

    Science.gov (United States)

    ... used whole genome sequencing and diagnosed a rare genetic disease. This discovery is what saved his life. For the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out of a person’s unique DNA . Your genome ...

  3. Spinal cord localization in the treatment of lung cancer: use of radiographic landmarks

    International Nuclear Information System (INIS)

    Purpose: In the treatment of thoracic malignancies with radiotherapy, the critical dose-limiting structure is the spinal cord. Oblique fields typically are designed to exclude the spinal cord, and by convention, the field edge that shields the spinal cord is placed at the anterior border of the vertebral pedicles. Thus, the purpose of our study was to estimate the distance between the field edge and spinal cord in oblique fields that were designed by using the vertebral pedicle as a radiographic landmark. Methods and Materials: The spinal cord of a cadaver was wrapped in wire, and oblique fields were simulated at 15 deg. intervals. The distance from the spinal cord to a field edge placed at the anterior border of the pedicle was measured. In the second investigation, a three-dimensional treatment planning system was used to simulate hypothetical fields using actual patient data from computed tomography (n = 10), and measurements identical to those in the anatomical model were made (n = 1,100). Results: The results of the anatomical and computed tomographic models were in close agreement (mean difference, 0.6 mm). The computed tomographic model predicted a mean field edge to spinal cord distance of 8.7 mm (95% confidence interval, 5.6-11.8 mm) for (30 deg. (150 deg.)) oblique fields and 8.0 mm (95% confidence interval, 4.7-11.7 mm) for (45 deg. (135 deg.)) oblique fields. This distance was greatest at levels T-1, T-2, and T-11 (8 to 20% greater). Conclusions: The mean (8 to 20% greater). Conclusions: The mean distance from a field edge placed at the anterior border of a vertebral pedicle to the spinal cord for commonly used oblique angles constitutes a sufficient margin to account for expected differences in daily positional variations and mechanical uncertainties

  4. Comparison of Spine, Carina, and Tumor as Registration Landmarks for Volumetric Image-Guided Lung Radiotherapy

    International Nuclear Information System (INIS)

    Purpose: To assess the feasibility, reproducibility, and accuracy of volumetric lung image guidance using different thoracic landmarks for image registration. Methods and Materials: In 30 lung patients, four independent observers conducted automated and manual image registrations on Day 1 cone-beam computed tomography data sets using the spine, carina, and tumor (720 image registrations). The image registration was timed, and the couch displacements were recorded. The intraclass correlation was used to assess reproducibility, and the Bland-Altman analysis was used to compare the automatic and manual matching methods. Tumor coverage (accuracy) was assessed through grading the tumor position after image matching against the internal target volume and planning target volume. Results: The image-guided process took an average of 1 min for all techniques, with the exception of manual tumor matching, which took 4 min. Reproducibility was greatest for automatic carina matching (intraclass correlation, 0.90-0.93) and lowest for manual tumor matching (intraclass correlation, 0.07-0.43) in the left-right, superoinferior, and anteroposterior directions, respectively. The Bland-Altman analysis showed no significant difference between the automatic and manual registration methods. The tumor was within the internal target volume 62% and 60% of the time and was outside the internal target volume, but within the planning target volume, 38% and 40% of the time after automatic spine and 40% of the time after automatic spine and automatic carina matching, respectively. Conclusion: For advanced lung cancer, the spine or carina can be used equally for cone-beam computed tomography image registration without compromising target coverage. The carina was more reproducible than the spine, but additional analysis is required to confirm its validation as a tumor surrogate. Soft-tissue registration is unsuitable at present, given the limitations in contrast resolution and the high interobserver variability.

  5. Deep sulcal landmarks: Algorithmic and conceptual improvements in the definition and extraction of sulcal pits.

    Science.gov (United States)

    Auzias, G; Brun, L; Deruelle, C; Coulon, O

    2015-05-01

    Recent interest has been growing concerning points of maximum depth within folds, the sulcal pits, that can be used as reliable cortical landmarks. These remarkable points on the cortical surface are defined algorithmically as the outcome of an automatic extraction procedure. The influence of several crucial parameters of the reference technique (Im et al., 2010) has not been evaluated extensively, and no optimization procedure has been proposed so far. Designing an appropriate optimization framework for these parameters is mandatory to guarantee the reproducibility of results across studies and to ensure the feasibility of sulcal pit extraction and analysis on large cohorts. In this work, we propose a framework specifically dedicated to the optimization of the parameters of the method. This optimization framework relies on new measures for better quantifying the reproducibility of the number of sulcal pits per region across individuals, in line with the assumptions of one-to-one correspondence of sulcal roots across individuals which is an explicit aspect of the sulcal roots model (Régis et al., 2005). Our procedure benefits from a combination of improvements, including the use of a convenient sulcal depth estimation and is methodologically sound. Our experiments on two different groups of individuals, with a total of 137 subjects, show an increased reliability across subjects in deeper sulcal pits, as compared to the previous approach, and cover the entire cortical surface, including shallower and more variable folds that were not considered before. The effectiveness of our method ensures the feasibility of a systematic study of sulcal pits on large cohorts. On top of these methodological advances, we quantify the relationship between the reproducibility of the number of sulcal pits per region across individuals and their respective depth and demonstrate the relatively high reproducibility of several pits corresponding to shallower folds. Finally, we report new results regarding the local pit asymmetry, providing evidence that the algorithmic and conceptual approach defended here may contribute to better understanding of the key role of sulcal pits in neuroanatomy. PMID:25676916

  6. Bone Densitometry (Bone Density Scan)

    Science.gov (United States)

    ... limitations of DXA Bone Densitometry? What is a Bone Density Scan (DXA)? Bone density scanning, also called ... of page What are the limitations of DXA Bone Densitometry? A DXA test cannot predict who will ...

  7. Between Two Fern Genomes

    OpenAIRE

    Sessa, Emily B; Jo Banks; Michael S. Barker; Der, Joshua P.; Duffy, Aaron M.; Graham, Sean W; Mitsuyasu Hasebe; Jane Langdale; Fay-Wei Li; D Marchant; Pryer, Kathleen M.; Rothfels, Carl J; Roux, Stanley J.; Salmi, Mari L; Sigel, Erin M

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense divers...

  8. Eukaryotic genome size databases

    OpenAIRE

    Gregory, T. Ryan; Nicol, James A.; Tamm, Heidi; Kullman, Bellis; Kullman, Kaur; Leitch, Ilia J.; Murray, Brian G.; Kapraun, Donald F.; Greilhuber, Johann; Bennett, Michael D.

    2006-01-01

    Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundame...

  9. From Genomes of Species

    Science.gov (United States)

    R. Brian Watts (C�©gep de la Gasp�©sie et des ��les, Gasp�©; )

    2005-12-01

    The teacher resource will help students gain an understanding of genomic research on model organisms, understand the implications of such genomic research to our knowledge of the human genome, be able to explain the potential such research has for understanding, treating, and possibly curing human genetic conditions, be able to summarize the current state of comparative genomic research, and examine the potential of proteomic research as a companion to comparative genomics.

  10. Scanning radiographic apparatus

    International Nuclear Information System (INIS)

    Visual display of dental, medical or other radiographic images is realized with an x-ray tube in which an electron beam is scanned through an x-y raster pattern on a broad anode plate, the scanning being synchronized with the x-y sweep signals of a cathode ray tube display and the intensity signal for the display being derived from a small x-ray detector which receives x-rays that have passed through the subject to be imaged. Positioning and support of the detector are provided for by disposing the detector in a probe which may be attached to the x-ray tube at any of a plurality of different locations and by providing a plurality of such probes of different configuration in order to change focal length, to accommodate to different detector placements relative to the subject, to enhance patient comfort and to enable production of both periapical images and wider angle pantomographic images. High image definition with reduced radiation dosage is provided for by a lead glass collimator situated between the x-ray tube and subject and having a large number of spaced-apart minute radiation transmissive passages convergent on the position of the detector. Releasable mounting means enable changes of collimator in conjunction with changes of the probe to change focal length. A control circuit modifies the x-y sweep signals applied to the x-ray tube and modulates electron beam energy and current in order to correct for image distortions and other undesirable effects which can o and other undesirable effects which can otherwise be present in a scanning x-ray system

  11. Scanning Productivity in Interlibrary Loan

    Science.gov (United States)

    Pedersen, Wayne A.; Runestad, Anders

    2009-01-01

    The authors report findings of a research study conducted at the Iowa State University Library. Data was gathered on the scanning of library materials by students working in the Interlibrary Loan (ILL) unit. The goals of the study were fourfold: (1) Develop measures of scanning productivity in ILL, (2) Determine if it is more productive to scan

  12. Scanning apparatus and method

    International Nuclear Information System (INIS)

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

  13. Radiographic scanning agent

    International Nuclear Information System (INIS)

    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

  14. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  15. Tracking footprints of artificial selection in the dog genome

    OpenAIRE

    Akey, Joshua M.; Ruhe, Alison L.; Akey, Dayna T.; Wong, Aaron K.; Connelly, Caitlin F.; Madeoy, Jennifer; Nicholas, Thomas J.; Neff, Mark W.

    2010-01-01

    The size, shape, and behavior of the modern domesticated dog has been sculpted by artificial selection for at least 14,000 years. The genetic substrates of selective breeding, however, remain largely unknown. Here, we describe a genome-wide scan for selection in 275 dogs from 10 phenotypically diverse breeds that were genotyped for over 21,000 autosomal SNPs. We identified 155 genomic regions that possess strong signatures of recent selection and contain candidate genes for phenotypes that va...

  16. Ultrafast scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Botkin, D.A. [California Univ., Berkeley, CA (United States). Dept. of Physics]|[Lawrence Berkeley Lab., CA (United States)

    1995-09-01

    I have developed an ultrafast scanning tunneling microscope (USTM) based on uniting stroboscopic methods of ultrafast optics and scanned probe microscopy to obtain nanometer spatial resolution and sub-picosecond temporal resolution. USTM increases the achievable time resolution of a STM by more than 6 orders of magnitude; this should enable exploration of mesoscopic and nanometer size systems on time scales corresponding to the period or decay of fundamental excitations. USTM consists of a photoconductive switch with subpicosecond response time in series with the tip of a STM. An optical pulse from a modelocked laser activates the switch to create a gate for the tunneling current, while a second laser pulse on the sample initiates a dynamic process which affects the tunneling current. By sending a large sequence of identical pulse pairs and measuring the average tunnel current as a function of the relative time delay between the pulses in each pair, one can map the time evolution of the surface process. USTM was used to measure the broadband response of the STM`s atomic size tunnel barrier in frequencies from tens to hundreds of GHz. The USTM signal amplitude decays linearly with the tunnel junction conductance, so the spatial resolution of the time-resolved signal is comparable to that of a conventional STM. Geometrical capacitance of the junction does not appear to play an important role in the measurement, but a capacitive effect intimately related to tunneling contributes to the measured signals and may limit the ultimate resolution of the USTM.

  17. Parathyroid scanning by computed tomography

    International Nuclear Information System (INIS)

    Conventional parathyroid computed-tomographic scanning detected 51% (29/57) of tumors averaging 1.5 x 1.0 x 0.8 cm in size at surgery. Forty-six percent (7/43) of the scans were uninterpretable due to shoulder-streak artifacts. Using a specially designed patient positioning device and a new imaging protocol involving dynamic scanning and the intravenous administration of a bolus of contrast material, 14 patients were scanned; 78% (18/23) of tumors averaging 1.4 x 1.0 x 0.8 cm in size were detected. All 14 scans were interpretable, and image quality was markedly improved

  18. An elliptic spatial scan statistic.

    Science.gov (United States)

    Kulldorff, Martin; Huang, Lan; Pickle, Linda; Duczmal, Luiz

    2006-11-30

    The spatial scan statistic is commonly used for geographical disease cluster detection, cluster evaluation and disease surveillance. The most commonly used shape of the scanning window is circular. In this paper we explore an elliptic version of the spatial scan statistic, using a scanning window of variable location, shape (eccentricity), angle and size, and with and without an eccentricity penalty. The method is applied to breast cancer mortality data from Northeastern United States and female oral cancer mortality in the United States. Power comparisons are made with the circular scan statistic. PMID:16435334

  19. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  20. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  1. SCAN: a Fortran syntax analyzer

    International Nuclear Information System (INIS)

    SCAN is a computer program which analyzes the syntax of a Fortran program. It reads statements of a Fortran program, checks the grammatical validity of them, and produces tables of the analyzed results and intermediate codes for further use. SCAN recognizes the Fortran syntax of the Japan Industrial Standards-7000, plus some Fortran-H statements. In this report, the structure of SCAN, the methods used by the SCAN to analyze statements, tables and intermediate Buckus form texts produced by the SCAN, are presented. The SCAN itself is also written in Fortran language and consists of about 5000 statements. By slight modifications the SCAN may be useful for any application which needs analysis operations of Fortran syntax. (author)

  2. Scan mirrors relay for high resolution laser scanning systems

    Science.gov (United States)

    Kessler, David

    2014-09-01

    Two dimensional beam deflection is often required in medical laser scanning systems such as OCT or confocal microscopy. Commonly two linear galvo mirrors are used for performance in terms of their large apertures and scan angles. The galvo mirrors are placed at the vicinity of entrance pupil of the scan lens with a "displacement distance" separating them. This distance limits the scan fields and/or reduces the effective aperture of the scan lens. Another option is to use a beam or pupil relay, and image one galvo mirror onto the other. However, beam (or pupil) relays are notoriously complicated, expensive and can add significant aberrations. This paper discusses a simple, all reflective, diffraction limited, color corrected, beam relay, capable of large scan angles and large deflecting mirrors. The design is based on a unique combination of an Offner configuration with a Schmidt aspheric corrector. The design is highly corrected up to large scan mirrors and large scan angles down to milliwaves of aberrations. It allows significantly larger scan field and or scan lenses with higher numerical aperture as compared with scanners using galvos separated by the displacement distance. While this relay is of exceptionally high performance, it has one element located where the beam is focused which may present a problem for high power lasers. Thus modifications of the above design are introduced where the beam is focused in mid air thus making it usable for high power systems such including laser marking and fabrication systems.

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

    Science.gov (United States)

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

    2015-03-01

    Near-field scanning microwave microscopy offers great potential to facilitate characterization, development and modeling of materials. By acquiring microwave images at multiple frequencies and amplitudes (along with the other modalities) one can study material and device physics at different lateral and depth scales. Images are typically noisy and contaminated by artifacts that can vary from scan line to scan line and planar-like trends due to sample tilt errors. Here, we level images based on an estimate of a smooth 2-d trend determined with a robust implementation of a local regression method. In this robust approach, features and outliers which are not due to the trend are automatically downweighted. We denoise images with the Adaptive Weights Smoothing method. This method smooths out additive noise while preserving edge-like features in images. We demonstrate the feasibility of our methods on topography images and microwave |S11| images. For one challenging test case, we demonstrate that our method outperforms alternative methods from the scanning probe microscopy data analysis software package Gwyddion. Our methods should be useful for massive image data sets where manual selection of landmarks or image subsets by a user is impractical. PMID:25463325

  4. High-throughput scanning with single-molecule sensitivity

    Science.gov (United States)

    Sonnleitner, Max; Freudenthaler, Gunter; Hesse, Jan; Schuetz, Gerhard J.

    2005-03-01

    We report on the application of a novel fluorescence-microscope based scanning device with single molecule sensitivity to microarray readout. The device is based on a CCD camera operated in time delay and integration (TDI) mode synchronized with the movement of a sample scanning stage, enabling continuous data acquisition. The implementation of a focus hold system keeps the sample in focus during scanning. Results from ultra-sensitive high-resolution microarray readout provide clear evidence for the superiority of the novel detection method over conventional microarray readout systems in particular regarding to sensitivity and dynamic range. Minute sample amount and lacking amplification methods will demand for this ultra-sensitive readout technology in future genomic and proteomic research.

  5. Plant genomics: an overview

    Scientific Electronic Library Online (English)

    HUGO, CAMPOS-DE QUIROZ.

    Full Text Available Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic a [...] rchitecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms

  6. A Scanning Cavity Microscope

    CERN Document Server

    Mader, Matthias; Hänsch, Theodor W; Hunger, David

    2014-01-01

    Imaging of the optical properties of individual nanosystems beyond fluorescence can provide a wealth of information. However, the minute signals for absorption and dispersion are challenging to observe, and only specialized techniques requiring sophisticated noise rejection are available. Here we use signal enhancement in a scanning optical microcavity to demonstrate ultra-sensitive imaging. Harnessing multiple interactions of probe light with a sample within an optical resonator, we achieve a 1700-fold signal enhancement compared to diffraction-limited microscopy. We demonstrate quantitative imaging of the extinction cross section of gold nanoparticles with a sensitivity below 1 nm2, we show a method to improve spatial resolution potentially below the diffraction limit by using higher order cavity modes, and we present measurements of the birefringence and extinction contrast of gold nanorods. The demonstrated simultaneous enhancement of absorptive and dispersive signals promises intriguing potential for opt...

  7. CT scans in encephalitis

    International Nuclear Information System (INIS)

    Generally, CT scans reveal a decrease in the volume of the ventricular system, sylvian fissures and cortical sulci in the acute stage of encephalitis, and softening of the cerebral lobes with dilatation of the lateral ventricles and subarachnoidian dilated spaces in the chronic stage. We encountered three cases of encephalitis: mumps (case 1), herpes simplex (case 2), and syphilis (case 3). In case 1, brain edema was seen in the acute stage and brain atrophy in the chronic stage. In case 2, necrosis of the temporal pole, which is pathognomonic in herpes simplex encephalitis, was recognized. And in case 3, multiple lesions whose CT appearance was enhanced by contrast materials were found scattered over the whole brain. These lesions were diagnosed as inflammatory granuloma by histological examination. (author)

  8. CT scan of orbits

    International Nuclear Information System (INIS)

    We measured the normal sizes of various anatomical structures in orbits using a CT (computed tomography) scan. The materials were nine healthy adults (18 eyes), and the CT scanner was a GE-9800 apparatus. Scanning parallel to Reid's base line was repeated 20 to 30 times using a slice of 1.5 mm and with a high resolution. The diameters of the optic nerve, the extraocular muscles, the cornea, and the sclera were measured both in an axial view and in reconstruction, the latter being measured directly on a diagnostic console. The results were as follows: 1) The diameter of the normal optic nerve was from 2.84 to 5.08 mm. The normal differentiation of diameter between the right and left eye was between 0.09 and 0.73 mm, and the optic nerve was significantly larger in the portion 5 mm posterior to the posterior pole of the eye than in the other parts. 2) The thicknesses of the extraocular muscle were as follows: lateral rectus muscle: 1.46 to 2.50 mm (axial view); medial rectus muscle: 2.08 to 3.18 mm (axial view); superior rectus muscle: 1.96 to 3.32 mm (reconstruction); inferior rectus muscle: 2.21 to 3.07 mm (reconstruction). 3) The thickness of the cornea was 1.23±0.25 mm (axial view), and the sclera was 1.49±0.17 mm (axial view). These data strongly suggested that the measuring of such anatomical structures as the optic nerve, the extraocular muscle, the cornea, and the sclera is very useful for the purpose of diagnosing various diseases, such as optic nerve atrophy,s diseases, such as optic nerve atrophy, retinal detachment, and dysthyroid ophthalmopathy. (author)

  9. Ultra-barcoding in cacao (Theobroma spp.; malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

    Science.gov (United States)

    High-throughput next-generation sequencing was used to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an indivi...

  10. Genomic Careers: Interactive Videos

    Medline Plus

    Full Text Available ... Institute in Bethesda, Maryland. 06:55 - Bioethicist Using Genomics - Dr. Carlton Haywood Jr. Bioethicist at the Johns ... Health in Bethesda, Maryland. 06:08 - Bioethicist Using Genomics - Dr. Ruth Faden Director of the Berman Institute ...

  11. Genomic Careers: Interactive Videos

    Science.gov (United States)

    ... Institute in Bethesda, Maryland. 06:55 - Bioethicist Using Genomics - Dr. Carlton Haywood Jr. Bioethicist at the Johns ... Health in Bethesda, Maryland. 06:08 - Bioethicist Using Genomics - Dr. Ruth Faden Director of the Berman Institute ...

  12. Public Health Genomics (PHG)

    Science.gov (United States)

    Public Health Genomics (PHG) is defined as "a multidisciplinary field concerned with the effective and responsible translation of genome based knowledge and technologies to improve population health" (Bellagio Statement, 2006).

  13. Human Genome Center

    Science.gov (United States)

    Human Genome Center At Lawrence Berkeley Lab (LBL), Berkeley, California: offering information about projects in Biology, Informatics and Instrumentation, photos of LBL robotic instruments, software, and online access to one LBL genomic database.

  14. Radioisotope scanning in osseous sarcoidosis

    International Nuclear Information System (INIS)

    Technetium-99m (/sup 99m/Tc)-labeled pyrophosphate or diphosphonate compounds and gallium-67 citrate (67Ga) are two radionuclide scanning agents that are in widespread use in clinical practice. Technetium-99m pyrophosphate is used extensively for bone scanning to detect metastatic bone disease, benign bone tumors, osteomyelitis, benign hypertrophic osteoarthropathy, and Paget's disease. Only two reports describe abnormal /sup 99m/Tc/ pyrophosphate bone scans in four patients with osseous sarcoidosis. Gallium-67 scans are used primarily to localize neoplastic or inflammatory lesions anywhere in the body. In recent years 67Ga scans have also been used to detect the presence of both pulmonary and extrapulmonary sarcoidosis, but there are no reports describing abnormal uptake of gallium in patients with osseous sarcoidosis. This report describes experience with radioisotope scanning in two patients with osseous sarcoidosis

  15. Megaliths as land-marks. Chronicle of the territorial role of the megalithic monuments through written sources

    Directory of Open Access Journals (Sweden)

    Martinón-Torres, Marcos

    2001-06-01

    Full Text Available Megalithic monuments have played dijferent roles throughout History. One of them has a spatial function, i.e. as landmarks. The aim of this paper has been to collect and analyse every written reference concerning Galician megaliths operating as landmarks between the 6th and 19th centuries AD. On this basis, the evolution of this social-territorial function of the monuments through time is reconstructed, and an interpretative hypothesis for this phenomenon is proposed. Finally, the importance of reviewing written sources as a methodology for archaeological survey and for studies of the topographic settings of monuments is emphasised.

    A lo largo de la Historia, los monumentos megalíticos han desempeñado, entre otras, una función espacial, como marcos de territorio. Para este artículo se recogen y analizan las referencias escritas a megalitos gallegos funcionando como marcadores o identificadores espaciales, entre los siglos VI y XIX d.C. A partir de este registro de fuentes se reconstruye la evolución de este papel social-territorial de los monumentos en las distintas épocas. Se plantea un modelo interpretativo para este fenómeno, y se valora la revisión de fuentes escritas como metodología para la prospección arqueológica y para los estudios de emplazamiento de megalitos.

  16. Adiponectin is associated with cardiovascular disease in male renal transplant recipients: baseline results from the LANDMARK 2 study

    Directory of Open Access Journals (Sweden)

    Mudge David

    2009-10-01

    Full Text Available Abstract Background Adiponectin is a major adipocyte-derived protein with insulin-sensitizing, anti-inflammatory and anti-atherogenic properties. Adiponectin levels correlate inversely with renal function and higher levels are predictive of lower cardiovascular disease (CVD in patients with normal renal function and chronic kidney disease. No data exists on the association between adiponectin and CVD in renal transplant recipients (RTR. Methods Standard biochemistry, clinical data and adiponectin were collected from 137 RTR recruited to the LANDMARK 2 study at baseline. The LANDMARK 2 study is an ongoing randomized controlled study that compares the outcome of aggressive risk factor modification for cardiovascular disease versus standard post-transplant care in renal transplant recipients with impaired glucose tolerance or diabetes mellitus. Results Mean patient age was 53.4 ± 12 years and the median post-transplantation period was 5 (0.5-31.9 years. Mean serum adiponectin level was 12.3 ± 7.1 ?g/mL. On univariate analysis, adiponectin was positively associated with female gender (P = 0.01 and serum high-density lipoprotein (HDL concentration (P Conclusion In conclusion, adiponectin is positively correlated with inflammation, dyslipidemia and abnormal glucose tolerance in RTR. Furthermore, hypoadiponectinemia correlated with increased baseline CVD in male RTR.

  17. Radiological study of the knee joint line position measured from the fibular head and proximal tibial landmarks.

    Science.gov (United States)

    Havet, Eric; Gabrion, Antoine; Leiber-Wackenheim, Frederic; Vernois, Joël; Olory, Bruno; Mertl, Patrice

    2007-06-01

    Restoring the joint line level is one of the surgical challenges during revision of total knee arthroplasty. The position of the tibial surface is commonly estimated by its distance to the apex of fibular head, but no study evaluating this distance accurately has been published yet. The purpose of this work was to study the distance between the knee joint line and the apex of the fibular head and the proximal tibia, particularly the tibial tuberosity. Variability with clinical data and relations with other local measurements have been evaluated on knee radiographs (an antero-posterior view, a medio-lateral view and an anteroposterior full length view) of 100 subjects (125 knees). Results showed no correlation between the joint line-fibular head apex distance and any clinical data of the patients, or any other performed measurements. Relations between tibial measurements and the sexe or the height of the subjects were noted. Besides, the review of the 25 bilateral cases did not show statistically significant side difference but the descriptive analysis showed too large discrepancies for the joint line-fibular head apex distance to be used as a landmark. We conclude that the fibular head apex cannot be used as a morphologic landmark to determine the knee joint line position. Its interest in clinical and surgical practice must be discussed. PMID:17440678

  18. Dual isotope scanning with gallium-67 citrate and technetium-99m radiopharmaceuticals

    International Nuclear Information System (INIS)

    The interpretation of Ga-67 scans is limited by the complex anatomic and physiologic distribution of Ga-67 and by the low resolution possible with this isotope. The use of a second isotope Tc-99m, tagged to an appropriate pharmaceutical allows the identification of anatomic landmarks. Computer acquisition of both the Ga-67 and Tc-99m images allows for subtraction of the Tc-99m images from the Ga-67 images and leads to precise localization of abnormal Ga-67 accumulations. Only a small percentage of the counts in the Tc-99m window are due to Ga-67 scatter and do not degrade the Tc-99m images. Cases illustrating the value of the dual-isotope technique are presented

  19. Genomic Instability and Cancer

    OpenAIRE

    Yao, Yixin; Dai, Wei

    2014-01-01

    Genomic instability is a characteristic of most cancer cells. It is an increased tendency of genome alteration during cell division. Cancer frequently results from damage to multiple genes controlling cell division and tumor suppressors. It is known that genomic integrity is closely monitored by several surveillance mechanisms, DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. A defect in the regulation of any of these mechanisms often results in genomic instability, which p...

  20. Mössbauer Magnetic Scan experiments

    Energy Technology Data Exchange (ETDEWEB)

    Pasquevich, G.A., E-mail: gpasquev@fisica.unlp.edu.ar [Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, P.O. Box 67, 1900 La Plata (Argentina); Instituto de Física La Plata, CONICET, P.O. Box 67, 1900 La Plata (Argentina); Facultad de Ingeniería, Universidad Nacional de La Plata, P.O. Box 91, 1900 La Plata (Argentina); Mendoza Zélis, P. [Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, P.O. Box 67, 1900 La Plata (Argentina); Instituto de Física La Plata, CONICET, P.O. Box 67, 1900 La Plata (Argentina); Facultad de Ingeniería, Universidad Nacional de La Plata, P.O. Box 91, 1900 La Plata (Argentina); Lencina, A. [Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, P.O. Box 67, 1900 La Plata (Argentina); Centro de Investigaciones Ópticas (CONICET La Plata – CIC), P.O. Box 3, 1897 Gonnet (Argentina); Veiga, A. [Instituto de Física La Plata, CONICET, P.O. Box 67, 1900 La Plata (Argentina); Facultad de Ingeniería, Universidad Nacional de La Plata, P.O. Box 91, 1900 La Plata (Argentina); Fernández van Raap, M.B.; Sánchez, F.H. [Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, P.O. Box 67, 1900 La Plata (Argentina); Instituto de Física La Plata, CONICET, P.O. Box 67, 1900 La Plata (Argentina)

    2014-06-01

    We report an application of the Mössbauer Effect designed to retrieve specific information on the magnetic response of iron-containing materials. It consists in the measurement of the nuclear absorption of gamma-rays as a function of an external magnetic field for a specific nuclear transition between magnetically-split nuclear levels. The experiments, here termed Mössbauer Magnetic Scan experiments, were carried out recording the absorption of {sup 57}Fe 14.4 keV gamma-ray in ?-Fe at constant Doppler energies coincident with some of the spectral lines of the magnetically split Mössbauer spectrum. Due to the dependence of the transition probabilities on the relative orientation between the nuclear magnetic moment and the gamma-ray direction, the present application results in a useful method to study the magnetic-field evolution of the distribution of atomic-magnetic-moment orientations. The proposed technique inherit from the Mössbauer Spectroscopy the chemical-element selectiveness as well as the ability to differentiate responses from iron atoms located at inequivalent site or at different phases. In this work, we show that the data analysis for these experiments depends on the sample thickness that the gamma-ray has to cross. For thin samples (i.e.samples with Mössbauer effective thicknesses lower than one) the magnetic-field dependence of the second-order-moment of the orientation distribution in the direction of the gamma ray is obtained. On the other hand, for thicker samples, although the data analysis is more complex, the dependences of the three second-order-moments of the orientation distribution are obtained. The experiments were performed on two ?-Fe foils of different Mössbauer effective thicknesses. They were chosen to represent the cases of thin and thick Mössbauer absorbers. The magnetic evolution of the orientations distribution is compared with results obtained from magnetometric measurements showing a good agreement as well indicating the complementarity of both techniques. A complete description of the experimental set up and the formalism for Mössbauer Magnetic Scan data analysis are presented.

  1. Mössbauer Magnetic Scan experiments

    International Nuclear Information System (INIS)

    We report an application of the Mössbauer Effect designed to retrieve specific information on the magnetic response of iron-containing materials. It consists in the measurement of the nuclear absorption of gamma-rays as a function of an external magnetic field for a specific nuclear transition between magnetically-split nuclear levels. The experiments, here termed Mössbauer Magnetic Scan experiments, were carried out recording the absorption of 57Fe 14.4 keV gamma-ray in ?-Fe at constant Doppler energies coincident with some of the spectral lines of the magnetically split Mössbauer spectrum. Due to the dependence of the transition probabilities on the relative orientation between the nuclear magnetic moment and the gamma-ray direction, the present application results in a useful method to study the magnetic-field evolution of the distribution of atomic-magnetic-moment orientations. The proposed technique inherit from the Mössbauer Spectroscopy the chemical-element selectiveness as well as the ability to differentiate responses from iron atoms located at inequivalent site or at different phases. In this work, we show that the data analysis for these experiments depends on the sample thickness that the gamma-ray has to cross. For thin samples (i.e.samples with Mössbauer effective thicknesses lower than one) the magnetic-field dependence of the second-order-moment of the orientation distribution in the direction of the gamma ray is obtained. On the other hand, for thicker samples, although the data analysis is more complex, the dependences of the three second-order-moments of the orientation distribution are obtained. The experiments were performed on two ?-Fe foils of different Mössbauer effective thicknesses. They were chosen to represent the cases of thin and thick Mössbauer absorbers. The magnetic evolution of the orientations distribution is compared with results obtained from magnetometric measurements showing a good agreement as well indicating the complementarity of both techniques. A complete description of the experimental set up and the formalism for Mössbauer Magnetic Scan data analysis are presented

  2. An unusual case of gallium scan mimicking a bone scan.

    Science.gov (United States)

    Puranik, Ameya; Luthra, Karuna; Lele, R D

    2012-01-01

    Gallium-67 localization is based on the fact that it binds to plasma proteins like transferrin and lactoferrin, which have iron-binding sites. Abnormal biodistribution of gallium-67 citrate can occur in iron-overload states. We report one such case of gallium scan mimicking a bone scan due to skeletal uptake of gallium. PMID:22616033

  3. An Unusual Case of Gallium Scan Mimicking a Bone Scan

    OpenAIRE

    Puranik, Ameya; Luthra, Karuna; Lele, R. D.

    2012-01-01

    Gallium-67 localization is based on the fact that it binds to plasma proteins like transferrin and lactoferrin, which have iron-binding sites. Abnormal biodistribution of gallium-67 citrate can occur in iron-overload states. We report one such case of gallium scan mimicking a bone scan due to skeletal uptake of gallium.

  4. Gastrointestinal scanning agent

    International Nuclear Information System (INIS)

    An easily prepared radiolabeled gastrointestinal scanning agent is described. Technetium-99m has ideal characteristics for imaging the upper and lower GI tract and determining stomach emptying and intestinal transit time when used with an insoluble particulate material. For example, crystalline and amorphous calcium phosphate particles can be effectively labeled in a one-step process using sup(99m)TcO4 and SnCl2. These labeled particles have insignificant mass and when administered orally pass through the GI tract unchanged, without affecting the handling and density of the intestinal contents. Visualization of the esophageal entry into the stomach, the greater and lesser curvatures of the stomach, ejection into the duodenum, and rates of passage through the upper and lower GI tract are obtained. The slurry of sup(99m)TC particulate can be given rectally by enema. Good images of the cecum and the ascending, transverse, and descending colon are obtained. Mucosal folds and the splenic and hepatic flexures are visualized. The resilience of the large intestine is also readily visualized by pneumocolonographic techniques. (author)

  5. Radionuclide brain scanning

    International Nuclear Information System (INIS)

    At one stage of medical imaging development, radionuclide brain scanning was the only technique available for imaging of the brain. Advent of CT and MRI pushed it to the background. It regained some of the grounds lost to ''allied advances'' with the introduction of brain perfusion radiopharmaceuticals. Positron emission tomography is a promising functional imaging modality that at present will remain as a research tool in special centres in developed countries. However, clinically useful developments will gradually percolate from PET to SPECT. The non-nuclear imaging methods are totally instrument dependent; they are somewhat like escalators, which can go that far and no further. Nuclear imaging has an unlimited scope for advance because of the new developments in radiopharmaceuticals. As the introduction of a radiopharmaceutical is less costly than buying new instruments, the recent advances in nuclear imaging are gradually perfusing through the developing countries also. Therefore, it is essential to follow very closely PET developments because what is research today might become routine tomorrow

  6. Differential scanning calorimetry.

    Science.gov (United States)

    Spink, Charles H

    2008-01-01

    Differential scanning calorimetry (DSC) has emerged as a powerful experimental technique for determining thermodynamic properties of biomacromolecules. The ability to monitor unfolding or phase transitions in proteins, polynucleotides, and lipid assemblies has not only provided data on thermodynamic stability for these important molecules, but also made it possible to examine the details of unfolding processes and to analyze the characteristics of intermediate states involved in the melting of biopolymers. The recent improvements in DSC instrumentation and software have generated new opportunities for the study of the effects of structure and changes in environment on the behavior of proteins, nucleic acids, and lipids. This review presents some of the details of application of DSC to the examination of the unfolding of biomolecules. After a brief introduction to DSC instrumentation used for the study of thermal transitions, the methods for obtaining basic thermodynamic information from the DSC curve are presented. Then, using DNA unfolding as an example, methods for the analysis of the melting transition are presented that allow deconvolution of the DSC curves to determine more subtle characteristics of the intermediate states involved in unfolding. Two types of transitions are presented for analysis, the first example being the unfolding of two large synthetic polynucleotides, which display high cooperativity in the melting process. The second example shows the application of DSC for the study of the unfolding of a simple hairpin oligonucleotide. Details of the data analysis are presented in a simple spreadsheet format. PMID:17964930

  7. Thermocouple homogeneity scanning

    Science.gov (United States)

    Webster, E.; White, D. R.

    2015-02-01

    The inhomogeneities within a thermocouple influence the measured temperature and contribute the largest component to uncertainty. Currently there is no accepted best practice for measuring the inhomogeneities or for forecasting their effects on real-world measurements. The aim of this paper is to provide guidance on the design and performance assessment of thermocouple inhomogeneity scanners by characterizing the qualitative performance of the various designs reported in the literature, and developing a quantitative measure of scanner resolution. Numerical simulations incorporating Fourier transforms and convolutions are used to gauge the levels of attenuation and distortion present in single- and double-gradient scanners. Single-gradient scanners are found to be far superior to double-gradient scanners, which are unsuitable for quantitative measurements due to their blindness to inhomogeneities at many spatial frequencies and severe attenuation of signals at other frequencies. It is recommended that the standard deviation of the temperature gradient within the scanner is used as a measure of the scanner resolution and spatial bandwidth. Recommendations for the design of scanners are presented, and include advice on the basic design of scanners, the media employed, operating temperature, scan rates, construction of survey probes, data processing, gradient symmetry, and the spatial resolution required for research and calibration applications.

  8. A completed audit cycle of the lateral scan projection radiograph in CT pulmonary angiography (CTPA); the impact on scan length and radiation dose

    International Nuclear Information System (INIS)

    Aim: To investigate the effect of incorporating a lateral scan projection radiograph (topogram) in addition to the standard frontal topogram on excess scan length in computed tomography pulmonary angiography (CTPA) and to quantify the impact on effective dose. Materials and methods: Fifty consecutive patients referred for exclusion of pulmonary embolism who had undergone a CTPA examination with conventional frontal topogram to plan scan length (protocol A) were compared with 50 consecutive patients who had undergone a CTPA study with frontal and additional lateral topogram for planning (protocol B) in a retrospective audit. Optimal scan length was defined from lung apex to lung base. Mean excess scan length beyond these landmarks was determined. The mean organ doses to the thyroid, liver, and stomach, as well as mean effective dose, were estimated using standard conversion factors. Results: The mean excess scan length was significantly lower in protocol B compared to the protocol A cohort (19.5 ± 17.4 mm [mean ± standard deviation] versus 39.1 ± 20.4 mm, p < 0.0001). The mean excess scan length below the lung bases was significantly lower in the protocol B cohort compared to the protocol A group (7.5 ± 12.7 mm versus 23 ± 16.6 mm, p < 0.0001), as were the mean organ doses to the stomach (4.24 ± 0.81 mGy versus 5.22 ± 1.06 mGy, p < 0.0001) and liver (5.60 ± 0.64 mGy versus 6.38 ± 0.81 mGy, p < 0.0001). A non-significant reduction in over-scanning above the apices in protocol B was observed compared with protocol A (12 ± 8.8 mm versus 16.2 ± 13.6 mm, p = 0.07), which equated to lower mean thyroid organ dose in (3.28 ± 1.76 mGy versus 4.11 ± 3.11 mGy, p = 0.104). Conclusion: The present audit indicates that incorporation of a lateral topogram into the CTPA protocol, together with radiographer education, reduces excess scan length, which significantly reduces the dose to the liver and stomach, and potentially lowers the dose to the thyroid. This simple dose-saving technique can be applied to all CT investigations of the chest on all CT systems with immediate effect

  9. Scanning tunneling microscopy II further applications and related scanning techniques

    CERN Document Server

    Güntherodt, Hans-Joachim

    1992-01-01

    Scanning Tunneling Microscopy II, like its predecessor, presents detailed and comprehensive accounts of the basic principles and broad range of applications of STM and related scanning probe techniques. The applications discussed in this volume come predominantly from the fields of electrochemistry and biology. In contrast to those described in Vol. I, these sudies may be performed in air and in liquids. The extensions of the basic technique to map other interactions are described inchapters on scanning force microscopy, magnetic force microscopy, scanning near-field optical microscopy, together with a survey of other related techniques. Also described here is the use of a scanning proximal probe for surface modification. Togehter, the two volumes give a comprehensive account of experimental aspcets of STM. They provide essentialreading and reference material for all students and researchers involvedin this field.

  10. Scanning tunneling microscopy II further applications and related scanning techniques

    CERN Document Server

    Güntherodt, Hans-Joachim

    1995-01-01

    Scanning Tunneling Microscopy II, like its predecessor, presents detailed and comprehensive accounts of the basic principles and broad range of applications of STM and related scanning probe techniques. The applications discussed in this volume come predominantly from the fields of electrochemistry and biology. In contrast to those described in STM I, these studies may be performed in air and in liquids. The extensions of the basic technique to map other interactions are described in chapters on scanning force microscopy, magnetic force microscopy, and scanning near-field optical microscopy, together with a survey of other related techniques. Also described here is the use of a scanning proximal probe for surface modification. Together, the two volumes give a comprehensive account of experimental aspects of STM. They provide essential reading and reference material for all students and researchers involved in this field. In this second edition the text has been updated and new methods are discussed.

  11. An analysis of anatomic landmark mobility and setup errors in radiotherapy for lung cancer

    International Nuclear Information System (INIS)

    Purpose: To identify visible structures in the thorax which exhibit little internal motion during irradiation and, to determine random and systematic setup deviations in lung cancer patients with the use of these structures. Methods: Ten patients with lung cancer were set up in the supine position, and aligned using lasers. No immobilization devices were used. With an electronic portal imaging device (Siemens Beam ViewPLUS), 12 sequential images (exposure 0.54 sec.; processing time 1.5 sec.) were obtained during a single fraction of radiotherapy. These 'movie loops' were generated for the A-P fields during each of 3-5 fractions. In order to determine the mobility of internal structures during each fraction, visible structures such as the trachea, carina, the upper chest wall, aortic arch, clavicle and paraspinal line were contoured manually in each image and matched with the first image of the corresponding movie loop by means of a cross-correlation algorithm. Translations in the cranial and lateral directions and in-plane rotations were determined for each structure separately. As the reference image represents a random position, relative movements were determined by comparing the translations and rotation for every image to the calculated means per movie-loop. Standard deviations of the relative movements were determined for each structure and each patient. Patient setup was evaluated for 15 patients with lung cancer. Setup was not corrected at any time dcer. Setup was not corrected at any time during the treatment. The electronic portal images of each fraction were matched with the digitized simulator films by using a combination of the structures which had been determined to be relatively stable in the infra-fractional analysis. Results: In the infra-fractional analysis 120 to 380 matches were made per structure (a total of 1400). The standard deviation (SD) of translations in the lateral direction was small (?1 mm) for the trachea, thoracic wall, paraspinal line and aortic arch. This was also the case for the SD of the translations in the cranial direction of the clavicle, aortic arch and upper thoracic wall. The carina was found to be relatively mobile (up to 6 mm) in both directions. The SD for in-plane rotations was negligible (<0.5 deg.) for all structures. The interpatient variation was very small (SD < 0.5 mm). In a preliminary analysis of patient setup, the random errors for translations are 2.0 mm in the lateral direction and 2.4 mm in the cranial direction (1 SD). The standard deviations of systematic errors are about 3 mm in both directions. In plane rotations were found to be negligible. Conclusions: We have identified a number of structures which exhibit little internal motion in the frontal plane, and recommend that a combination of these structures be used as anatomic landmarks for setup verification during radiotherapy of thoracic tumors. Preliminary results indicate that setup errors of patients with lung cancer in our center appear to be acceptable, even though no specific immobilization devices were used

  12. A CPG ISLAND AT THE PROMOTER OF THE PDE8B GENE IS METHYLATED IN PLACENTA AND HYDATIDIFORM MOLES, BUT NOT IN CONTROL DNA

    Science.gov (United States)

    Objective: We used a genome-wide CpG methylation screen, restriction landmark genome scanning (RLGS) to identify CpG islands that have altered methylation in complete hydatidiform moles (CHM), compared to control genomic DNA. Because CHM are diploid, but of uniparental parental inheritance and uniq...

  13. Statistics of genome architecture

    Energy Technology Data Exchange (ETDEWEB)

    Chechetkin, V.R., E-mail: vladimir_chechet@mail.ru

    2013-12-17

    The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks.

  14. Statistics of genome architecture

    International Nuclear Information System (INIS)

    The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well fitted by the different statistical approximations, the interpretation of observed regularities may strongly depend on the chosen scheme. We discuss the possible evolution scenarios and describe the main characteristics obtained with different distributions. The expression for the assessment of levels in hierarchical chromatin folding is derived and the quantitative measure of genome architecture inhomogeneity is suggested. This theory provides the ground for the regular statistical study of genome architecture and genome tracks.

  15. Broad scan linkage analysis in a large Tourette family pedigree

    Energy Technology Data Exchange (ETDEWEB)

    Peiffer, A.; Leppert, M. [Univ. of Utah Health Sciences Center, Salt Lake City, UT (United States); Wetering, B.J.M. van der [Univ. Hospital Rotterdam (Netherlands)

    1994-09-01

    Attempts to find a gene causing Tourette syndrome (TS) using linkage analysis have been unsuccessful even though as much as 65% of the autosomal genetic map has been excluded by the pooled results from several laboratories collaborating worldwide. One reason for this failure may be the misclassification of affection status of marry-in spouses. Specifically, we have found that six unrelated spouses in our Utah TS pedigree suffer from TS, obsessive-compulsive disorder or chronic motor tics. In light of these findings we decided to conduct a complete genomic scan from this Utah kindred with polymorphic markers in three related sibships in which there was no assortative mating. A linkage study assuming autosomal dominant inheritance was done using tetranucleotide repeat markers developed at the University of Utah. We selected markers that were less than 300 bp in size and that gave a heterozygosity of over 70% upon analysis in 4 CEPH families. Results to date with 95 markers run at an interval of 30 cM (covering 61% of the genome) show no evidence of linkage. We intend to extend the coverage to 100% of the genome. Pending completion of this scan, failure to provide evidence of linkage in our TS pedigree might then be attributed to phenotypic misclassification or erroneous assumptions regarding the genetic model of transmission.

  16. Hyperchromatic laser scanning cytometry

    Science.gov (United States)

    Tárnok, Attila; Mittag, Anja

    2007-02-01

    In the emerging fields of high-content and high-throughput single cell analysis for Systems Biology and Cytomics multi- and polychromatic analysis of biological specimens has become increasingly important. Combining different technologies and staining methods polychromatic analysis (i.e. using 8 or more fluorescent colors at a time) can be pushed forward to measure anything stainable in a cell, an approach termed hyperchromatic cytometry. For cytometric cell analysis microscope based Slide Based Cytometry (SBC) technologies are ideal as, unlike flow cytometry, they are non-consumptive, i.e. the analyzed sample is fixed on the slide. Based on the feature of relocation identical cells can be subsequently reanalyzed. In this manner data on the single cell level after manipulation steps can be collected. In this overview various components for hyperchromatic cytometry are demonstrated for a SBC instrument, the Laser Scanning Cytometer (Compucyte Corp., Cambridge, MA): 1) polychromatic cytometry, 2) iterative restaining (using the same fluorochrome for restaining and subsequent reanalysis), 3) differential photobleaching (differentiating fluorochromes by their different photostability), 4) photoactivation (activating fluorescent nanoparticles or photocaged dyes), and 5) photodestruction (destruction of FRET dyes). With the intelligent combination of several of these techniques hyperchromatic cytometry allows to quantify and analyze virtually all components of relevance on the identical cell. The combination of high-throughput and high-content SBC analysis with high-resolution confocal imaging allows clear verification of phenotypically distinct subpopulations of cells with structural information. The information gained per specimen is only limited by the number of available antibodies and by sterical hindrance.

  17. Introduction to Scanning Probe Microscopy

    Science.gov (United States)

    Bullen, Heather

    This learning module teaches the principles behind scanning tunneling microscopy and atomic force microscopy. The module includes example applications and ample literature citations. Scanning tunneling (STM), atomic force (AFM), lateral (friction) force, magnetic force, chemical force and phase imaging are discussed.

  18. An interchangeable scanning Hall probe/scanning SQUID microscope

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chiu-Chun; Lin, Hui-Ting; Wu, Sing-Lin [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Chen, Tse-Jun; Wang, M. J. [Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 10617, Taiwan (China); Ling, D. C. [Department of Physics, Tamkang University, Tamsui Dist., New Taipei City 25137, Taiwan (China); Chi, C. C.; Chen, Jeng-Chung [Department of Physics, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan (China)

    2014-08-15

    We have constructed a scanning probe microscope for magnetic imaging, which can function as a scanning Hall probe microscope (SHPM) and as a scanning SQUID microscope (SSM). The scanning scheme, applicable to SHPM and SSM, consists of a mechanical positioning (sub) micron-XY stage and a flexible direct contact to the sample without a feedback control system for the Z-axis. With the interchangeable capability of operating two distinct scanning modes, our microscope can incorporate the advantageous functionalities of the SHPM and SSM with large scan range up to millimeter, high spatial resolution (?4 ?m), and high field sensitivity in a wide range of temperature (4.2 K-300 K) and magnetic field (10{sup ?7} T-1 T). To demonstrate the capabilities of the system, we present magnetic images scanned with SHPM and SSM, including a RbFeB magnet and a nickel grid pattern at room temperature, surface magnetic domain structures of a La{sub 2/3}Ca{sub 1/3}MnO{sub 3} thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K.

  19. An interchangeable scanning Hall probe/scanning SQUID microscope

    International Nuclear Information System (INIS)

    We have constructed a scanning probe microscope for magnetic imaging, which can function as a scanning Hall probe microscope (SHPM) and as a scanning SQUID microscope (SSM). The scanning scheme, applicable to SHPM and SSM, consists of a mechanical positioning (sub) micron-XY stage and a flexible direct contact to the sample without a feedback control system for the Z-axis. With the interchangeable capability of operating two distinct scanning modes, our microscope can incorporate the advantageous functionalities of the SHPM and SSM with large scan range up to millimeter, high spatial resolution (?4 ?m), and high field sensitivity in a wide range of temperature (4.2 K-300 K) and magnetic field (10?7 T-1 T). To demonstrate the capabilities of the system, we present magnetic images scanned with SHPM and SSM, including a RbFeB magnet and a nickel grid pattern at room temperature, surface magnetic domain structures of a La2/3Ca1/3MnO3 thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K

  20. Anatomical landmarks for positioning the head in preparation for the transsphenoidal approach: the spheno-sellar point.

    Science.gov (United States)

    Campero, Alvaro; Socolovsky, Mariano; Torino, Rafael; Martins, Carolina; Yasuda, Alexandre; Rhoton, Albert L

    2009-06-01

    The transnasal approach is the most utilized approach to the sellar region. This study was conducted to identify an anatomical landmark on the lateral surface of the head that corresponds to the midpoint of the sellar floor at the level of sphenoidal rostrum. This point, lined up with the nostril, simulates the surgical path and facilitates the transnasal access to the sella turcica. Four adult, formalin-fixed and silicon-injected cadaveric heads, and ten dried skulls were used for laboratory dissection. The heads and skulls were sectioned along the midline; and the spheno-sellar point, corresponding to the midpoint of the sellar floor at the level of sphenoid rostrum, was determined. The spheno-sellar point was plotted on the lateral surface of the skull, and its position measured relative to the external acoustic meatus. Linking the spheno-sellar point with the nostril created the spheno-nostril line. This line represents the surgical path to be taken for direct access to the sphenoid rostrum, and was used to align the cadaveric heads as in surgery. The endonasal transsphenoidal approach was then utilized in one hundred and two adult patients with sellar lesions, using the spheno-sellar point and the spheno-nostril line as the superficial landmarks to guide the approach. The results of this clinical experience are summarized. The spheno-sellar point was found to be located an average of 40.1 mm (SD+/-2.9 mm) anterior and 23.3 mm (SD+/-3.2 mm) superior to the external acoustic meatus. The spheno-nostril line represents the straight surgical path to the sphenoidal rostrum. This landmark was used in 102 correlative transnasal surgeries for sellar lesions of adult patients, and has allowed an easy and straightforward access to the sella. In only 3 cases with poor pneumatisation of the sphenoid sinus (presellar type), the actual location of the surgical instruments had to be confirmed by fluoroscopy. The application of the spheno-sellar point and the spheno-nostril line is a fast, reliable and very simple way to facilitate transsphenoidal surgery, and their use may avoid complications associated with misdirection of this approach. Its use may be limited in cases of poor pneumatisation of the sphenoid sinus, where fluoroscopic guidance could be necessary as a rule. PMID:19533460

  1. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  2. Cranial allometry, phylogeography, and systematics of large-bodied papionins (primates: Cercopithecinae) inferred from geometric morphometric analysis of landmark data.

    Science.gov (United States)

    Frost, Stephen R; Marcus, Leslie F; Bookstein, Fred L; Reddy, David P; Delson, Eric

    2003-12-01

    The cranial morphology of the African Old World monkeys Mandrillus, Papio, and Theropithecus (i.e., baboons) has been the subject of a number of studies investigating their systematic relationships, patterns of scaling, and growth. In this study, we use landmark-based geometric morphometrics and multivariate analysis to assess the effects of size, sex, taxonomy, and geographic location on cranial shape. Forty-five landmarks were digitized in three dimensions on 452 baboon crania and subjected to generalized Procrustes analysis (GPA), which standardizes geometric size but leaves scaling-based shape differences in the data. The resulting shape coordinates were submitted to regression analysis, principal components analysis (PCA), partial least-squares (PLS) analysis, and various clustering techniques. Scaling (shape differences correlated with size) was the largest single factor explaining cranial shape variation. For instance, most (but not all) of the shape differences between the sexes were explained by size dimorphism. However, central tendencies of shape clearly varied by taxon (both specific and subspecific) even after variations in size and sex were adjusted out. Within Papio, about 60% of the size- and sex-adjusted shape variations were explained by the geographic coordinates of the specimen's provenance, revealing a stepped cline in cranial morphology, with the greatest separation between northern and southern populations. Based on evidence from genetic studies, and the presence of at least two major hybrid/interbreeding zones, we interpret the phylogeographic pattern of cranial variation as indicating that these populations are best ranked as subspecies of a single species, rather than as two or more distinct biological species. This objective approach can be applied to other vertebrate species or species groups to help determine the taxonomic rank of problematic taxa. PMID:14613306

  3. Establishing Cephalometric Landmarks for the Translational Study of Le Fort-based Facial Transplantation in Swine: Enhanced applications using computer-assisted surgery and custom cutting guides

    Science.gov (United States)

    Santiago, Gabriel F.; Susarla, Srinivas M.; Al Rakan, Mohammed; Coon, Devin; Rada, Erin M.; Sarhane, Karim; Shores, Jamie T.; Bonawitz, Steven C.; Cooney, Damon; Sacks, Justin; Murphy, Ryan J.; Fishman, Elliot K.; Brandacher, Gerald; Lee, WP Andrew; Liacouras, Peter; Grant, Gerald; Armand, Mehran; Gordon, Chad R.

    2014-01-01

    Background Le Fort-based, maxillofacial allotransplantation is a reconstructive alternative gaining clinical acceptance. However, the vast majority of single-jaw transplant recipients demonstrate less-than-ideal skeletal and dental relationships with suboptimal aesthetic harmony. The purpose of this study was to investigate reproducible cephalometric landmarks in a large animal model, where refinement of computer-assisted planning, intra-operative navigational guidance, translational bone osteotomies, and comparative surgical techniques could be performed. Methods Cephalometric landmarks that could be translated into the human craniomaxillofacial skeleton, and would remain reliable following maxillofacial osteotomies with mid-facial alloflap inset, were sought on six miniature swine. Le Fort I-and Le Fort III-based alloflaps were harvested in swine with osteotomies, and all alloflaps were either auto-replanted or transplanted. Cephalometric analyses were performed on lateral cephalograms pre- and post-operatively. Critical cephalometric data sets were identified with the assistance of surgical planning and virtual prediction software, and evaluated for reliability and translational predictability. Results Several pertinent landmarks and human analogues were identified including pronasale (PRN), zygion (Zy), parietale (PA), gonion (GO), gnathion (GN), lower incisior base (LIB), and alveolare (ALV). PA-PRN-ALV and PA-PRN-LIB were found to be reliable correlates of SNA and SNB measurements in humans, respectively. Conclusions There is a set of reliable cephalometric landmarks and measurement angles pertinent for utilization within a translational large animal model. These craniomaxillofacial landmarks will allow us to develop novel navigational software technology, improve our cutting guide designs, and explore new avenues for investigation and collaboration. Level of Evidence N/A (Large Animal Study) PMID:24445879

  4. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

    Science.gov (United States)

    Bahbahani, Hussain; Clifford, Harry; Wragg, David; Mbole-Kariuki, Mary N; Van Tassell, Curtis; Sonstegard, Tad; Woolhouse, Mark; Hanotte, Olivier

    2015-01-01

    The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics. PMID:26130263

  5. Horse Genome Project

    Science.gov (United States)

    What's in a horse? As it turns out, what's in a horse is quite important, and the Horse Genome Project at the University of Kentucky is currently defining the genome of this animal. The Project is a cooperative international effort which involves some 100 scientists working in 20 countries. On the left-hand side of the page, visitors can make their way through five sections, including "The People", "The Horses", "Genomics 101", and "Applications of Genome Study". "The Horses" area is a good place to start, as it gives an overview of the animals being used in the project. In "Genomics 101", interested parties will find an overview of some basic terms used in the field, such as gene, allele, and mutation. The "Applications of Genome Study" area focuses in on how their work will be used to benefit the health and welfare of horses.

  6. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  7. Genomics of Sorghum

    Directory of Open Access Journals (Sweden)

    Andrew H. Paterson

    2008-04-01

    Full Text Available Sorghum (Sorghum bicolor (L. Moench is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relating sorghum genes to their functions. Further characterization of the genomes other than Saccharinae cereals may shed light on mechanisms, levels, and patterns of evolution of genome size and structure, laying the foundation for further study of sugarcane and other economically important members of the group.

  8. Environmental Scanning and the Information Manager.

    Science.gov (United States)

    Newsome, James; McInerney, Claire

    1990-01-01

    Discusses nine components of an environmental scanning model: selecting the scanning team; selecting resources to scan; choosing criteria for scanning; scanning the resources; identifying signals of new issues; selecting key events/issues; monitoring and analyzing events/issues; disseminating information; and deciding on appropriate organizational…

  9. Genome of Mycoplasma arthritidis? †

    OpenAIRE

    Dybvig, Kevin; Zuhua, Cao; Lao, Ping; Jordan, David S.; French, C. Todd; Tu, Anh-hue T.; Loraine, Ann E.

    2008-01-01

    The genomes of several species of mycoplasma have been sequenced. Most of these species rely on the glycolytic pathway for energy production, with the one exception of Ureaplasma, a species that breaks down urea as its principle source of acquiring energy. Several species, including as Mycoplasma arthritidis, are nonglycolytic and can use arginine as their source of energy. Described here are the genome sequence and a transposon library of M. arthritidis. The genome of 820,453 bp is typical i...

  10. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B; Rossmann, Michael G

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  11. The Genome Atlas Resource

    OpenAIRE

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik; Hansson, Lena; Ussery, David

    2010-01-01

    Abstract. The Genome Atlas is a resource for addressing the challenges of synchronising prokaryotic genomic sequence data from multiple public repositories. This resource can integrate bioinformatic analyses in various data format and quality. Existing open source tools have been used together with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. Th...

  12. Chromium and Genomic Stability

    OpenAIRE

    Wise, Sandra S.; Wise, John Pierce

    2011-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as high...

  13. Cancer Genomics Overview

    Science.gov (United States)

    Cancer Genomics Overview Cancer is a group of diseases caused by changes in a person's genome that allow a tumor to form. These changes can be inherited from one's parents, caused by environmental factors, or occur during natural processes such as cell division. The field of cancer genomics studies these changes. Once the cancer-causing changes are identified, scientists may be able to develop drugs to target these changes, resulting in a better understanding of cancer as well as improved treatments.

  14. The Banana Genome Hub

    OpenAIRE

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up esse...

  15. Bacillus subtilis Genome Diversity? †

    OpenAIRE

    Earl, Ashlee M.; Losick, Richard; Kolter, Roberto

    2006-01-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridizatio...

  16. Genomics in Bacillus subtilis

    OpenAIRE

    Noback, Michiel Andries,

    1999-01-01

    Genomics cioncerns the aquisition of knowledge of structure and funcyion of gemomes. The scope of genomics researxh is wide: it includes the determination of the nucleotide sequence of all of an organisms' DNA, the analysis of the information that resides in it, the assessment of the functions of the uncovered information and how these functions interact, and the study how and why genomes have evolved the way they did. Zie: Summary

  17. Eddy current scanning at Fermilab

    International Nuclear Information System (INIS)

    In the framework of SRF cavity development, Fermilab is creating the infrastructure needed for the characterization of the material used in the cavity fabrication. An important step in the characterization of ''as received'' niobium sheets is the eddy current scanning. Eddy current scanning is a non-destructive technique first adopted and further developed by DESY with the purpose of checking the cavity material for sub-surface defects and inclusions. Fermilab has received and further upgraded a commercial eddy current scanner previously used for the SNS project. The upgrading process included developing new filtering software. This scanner is now used daily to scan the niobium sheets for the Fermilab third harmonic and transverse deflecting cavities. This paper gives a status report on the scanning results obtained so far, including a discussion of the typology of signals being detected. We also report on the efforts to calibrate this scanner, a work conducted in collaboration with DESY

  18. Establishing an Environmental Scanning Process.

    Science.gov (United States)

    Morrison, James L.

    1985-01-01

    A formal environmental scanning system designed to identify emerging issues, events, or trends threatening or bringing opportunity to an institution is discussed that uses a committee to systematically collect and analyze data from a variety of sources. (MSE)

  19. Scanning Probe Microscope Animation Gallery

    Science.gov (United States)

    This site, hosted by Nanoscience Instruments, has several animations from a scanning probe microscope (SPM). The topics include such items as atomic resolution, buckyballs and electrochemistry. These are good resources that could be used to explore nanoscience through visual means.

  20. Scanning Gate Spectroscopy on Nanoclusters

    OpenAIRE

    Gurevich, L; Canali, L.; Kouwenhoven, L. P.

    1999-01-01

    A gated probe for scanning tunnelling microscopy (STM) has been developed. The probe extends normal STM operations by means of an additional electrode fabricated next to the tunnelling tip. The extra electrode does not make contact with the sample and can be used as a gate. We report on the recipe used for fabricating the tunnelling tip and the gate electrode on a silicon nitride cantilever. We demonstrate the functioning of the scanning gate probes by performing single-elec...

  1. CT scanning of selectron insertions

    International Nuclear Information System (INIS)

    A brief article discusses the use of computerized tomographic scanning of Selectron insertions used in radiotherapy. Topics covered include program changes engendered by scanning, retrospective studies of the dose distribution for any patients showing symptoms which could be attributed to the radiotherapy and prospective studies which are using CT information to establish variations in relative positioning of applicators with respect to anatomical structures and variations in bladder dose. (author)

  2. Scanning electron microscopy of biomaterials

    OpenAIRE

    Mckinlay, K. J.; Scotchford, C. A.; Grant, D. M.; Oliver, J. M.; King, John R.; Brown, Paul D.

    2004-01-01

    A comparison of conventional high vacuum scanning electron microscopy (HVSEM), environmental SEM (ESEM) and confocal laser scanning microscopy (CLSM) in the assessment of cell-material interactions is made. The processing of cells cultured for conventional HVSEM leads to the loss of morphological features that are retained when using ESEM. The use of ESEM in conjunction with CLSM of the labeled cytoskeleton gives an indication of changes to the cell morphology as a consequence of incubation t...

  3. Scanning System for Laser Velocimeter

    Science.gov (United States)

    Gunter, William D.; De Young, Anemarie

    1987-01-01

    Interference fringes remain parallel and focus-spot diameter same. Scanning system proposed for laser velocimeter (laser Doppler anemometer) to maintain constant beam-crossing angle and beam-waist diameter maintaining beam waist locations at crossing points. As target fluid scanned, interference fringes formed by crossing beams remain parallel and the focus-spot diameter same. System allows accurate velocity profiles obtained in wind tunnels and other fluid flow systems.

  4. Principles of Scanning Probe Microscopy

    Science.gov (United States)

    Frenken, Joost

    This site offers a beautifully illustrated introduction to the principles of scanning probe microscopy. The text is interspersed with links to additional information, much of it from the Interface Physics Group at Leiden University. There are several animations included and links to visual galleries which illustrate both principles and utilization of scanning probe microscopy. An additional "links" page takes the user to sites of research groups involved in ongoing developmental work in surface science.

  5. The Geee! in Genome

    Science.gov (United States)

    It's too late to catch the Geee! in Genome exhibit at the Canadian Museum of Nature, but virtual visitors can still check out the exhibit's excellent Web companion. The Web site, which is also available in French, is loaded with cool, interactive features on the everyday side of genomics. The Geee! in Genome Web site also contains a set of downloadable lesson plans and activities for grades 5 through 12. Together with the online features, these lesson plans offer a fun and engaging way to learn about genomics in the classroom.

  6. Genomics of Clostridium tetani

    DEFF Research Database (Denmark)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta

    2015-01-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.

  7. Human Genome Resources

    Science.gov (United States)

    In an effort to track the progress of and provide access to the work of the Human Genome Project (see the October 14, 1998 Scout Report for Science & Engineering), the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM) has expanded their Web resource. An international research program "designed to construct detailed genetic and physical maps of the human genome." The Human Genome Resources page provides a wealth of relevant resources, from background information on the project, to specific sequences for each human chromosome (click on the desired chromosome), to Genome Maps of other organisms.

  8. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  9. Scan registration using planar features

    Science.gov (United States)

    Previtali, M.; Barazzetti, L.; Brumana, R.; Scaioni, M.

    2014-06-01

    Point cloud acquisition by using laser scanners provides an efficient way for 3D as-built modelling of indoor/outdoor urban environments. In the case of large structures, multiple scans may be required to cover the entire scene and registration is needed to merge them together. In general, the identification of corresponding geometric features among a series of scans can be used to compute the 3D rigid-body transformation useful for the registration of each scan into the reference system of the final point cloud. Different automatic or semi-automatic methods have been developed to this purpose. Several solutions based on artificial targets are available, which however may not be suitable in any situations. Methods based on surface matching (like ICP and LS3D) can be applied if the scans to align have a proper geometry and surface texture. In the case of urban and architectural scenes that present the prevalence of a few basic geometric shapes ("Legoland" scenes) the availability of many planar features is exploited here for registration. The presented technique does not require artificial targets to be added to the scanned scene. In addition, unlike other surface-based techniques (like ICP) the planar feature-based registration technique is not limited to work in a pairwise manner but it can handle the simultaneous alignment of multiple scans. Finally, some applications are presented and discussed to show how this technique can achieve accuracy comparable to a consolidated registration method.

  10. Genomics and Health Impact Update

    Science.gov (United States)

    ... other upcoming events Top of Page CDC-Authored Genomics Publications CDC authors are indicated in bold Intestinal ... update View current update Back Issues About the Genomics & Health Impact Update The Update includes genomics and ...

  11. The generic genome browser: a building block for a model organism system database.

    Science.gov (United States)

    Stein, Lincoln D; Mungall, Christopher; Shu, ShengQiang; Caudy, Michael; Mangone, Marco; Day, Allen; Nickerson, Elizabeth; Stajich, Jason E; Harris, Todd W; Arva, Adrian; Lewis, Suzanna

    2002-10-01

    The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org. PMID:12368253

  12. Simulation of four-dimensional CT images from deformable registration between inhale and exhale breath-hold CT scans

    International Nuclear Information System (INIS)

    Purpose: We propose to simulate an artificial four-dimensional (4-D) CT image of the thorax during breathing. It is performed by deformable registration of two CT scans acquired at inhale and exhale breath-hold. Materials and methods: Breath-hold images were acquired with the ABC (Active Breathing Coordinator) system. Dense deformable registrations were performed. The method was a minimization of the sum of squared differences (SSD) using an approximated second-order gradient. Gaussian and linear-elastic vector field regularizations were compared. A new preprocessing step, called a priori lung density modification (APLDM), was proposed to take into account lung density changes due to inspiration. It consisted of modulating the lung densities in one image according to the densities in the other, in order to make them comparable. Simulated 4-D images were then built by vector field interpolation and image resampling of the two initial CT images. A variation in the lung density was taken into account to generate intermediate artificial CT images. The Jacobian of the deformation was used to compute voxel values in Hounsfield units. The accuracy of the deformable registration was assessed by the spatial correspondence of anatomic landmarks located by experts. Results: APLDM produced statistically significantly better results than the reference method (registration without APLDM preprocessing). The mean (and standard deviation) of distances between automatically found landmistances between automatically found landmark positions and landmarks set by experts were 2.7(1.1) mm with APLDM, and 6.3(3.8) mm without. Interexpert variability was 2.3(1.2) mm. The differences between Gaussian and linear elastic regularizations were not statistically significant. In the second experiment using 4-D images, the mean difference between automatic and manual landmark positions for intermediate CT images was 2.6(2.0) mm. Conclusion: The generation of 4-D CT images by deformable registration of inhale and exhale CT images is feasible. This can lower the dose needed for 4-D CT acquisitions or can help to correct 4-D acquisition artifacts. The 4-D CT model can be used to propagate contours, to compute a 4-D dose map, or to simulate CT acquisitions with an irregular breathing signal. It could serve as a basis for 4-D radiation therapy planning. Further work is needed to make the simulation more realistic by taking into account hysteresis and more complex voxel trajectories

  13. Hepatobiliary scan in neonatal Jaundice

    International Nuclear Information System (INIS)

    Jaundice is more or less common in newborn babies. Through physiological jaundice is most common cause of neonatal jaundice, possibility of obstructive jaundice especially biliary atresia should be kept in mind. Early diagnosis of biliary atresia followed by surgical treatment can save baby's life. Otherwise death is inevitable due to liver failure. Hepatobiliary scan is the imaging study of choice in neonatal jaundice especially when there is persistent conjugated hyperbilirubinaemia. Total 27 newborn babies of suspected biliary atresia, aged 14 days to 4 months were referred to Institute of Nuclear Medicine for Hepatobiliary scan. All of them had high serum bilirubin ranged from 6.0 mg/dl with an average of 9.35 ng/dl serum bilirubin level. Ultrasonography of hepatobiliary system was performed in 14 cases showing normal sized liver in 4 cases and hepatomegaly in 10 cases. Hepatobiliary scan was done with 99mTc-Mebrofenin (Br IDA) after preparing the baby with phenobarbitone for 3-5 days. 20 (67%) cases were scan positive suggesting biliary atresia (BA) and 7(27%) cases were scan negative. In BA there will be increased hepatic uptake of the radionuclide without any significant excretion even in 24 hours delayed images. Presence of radiotracer in the bowel exclude the diagnosis of BA. Early diagnosis of biliary atresia is very important because in this condition surgery should be performed early (within 60 days of life). Studies suggest that hepatobiliary sife). Studies suggest that hepatobiliary scan after hepatic stimulation with phenobarbitone for a period of 3-5 days is highly accurate for differentiating biliary atresia from other causes of neonatal jaundice. It is very important to perform hepatobiliary scan in a case of neonatal jaundice to exclude biliary atresia for the sake of baby's life.(author)

  14. Identifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape

    Directory of Open Access Journals (Sweden)

    French Andrew P

    2012-03-01

    Full Text Available Abstract Background The ability to quantify the geometry of plant organs at the cellular scale can provide novel insights into their structural organization. Hitherto manual methods of measurement provide only very low throughput and subjective solutions, and often quantitative measurements are neglected in favour of a simple cell count. Results We present a tool to count and measure individual neighbouring cells along a defined file in confocal laser scanning microscope images. The tool allows the user to extract this generic information in a flexible and intuitive manner, and builds on the raw data to detect a significant change in cell length along the file. This facility can be used, for example, to provide an estimate of the position of transition into the elongation zone of an Arabidopsis root, traditionally a location sensitive to the subjectivity of the experimenter. Conclusions Cell-o-tape is shown to locate cell walls with a high degree of accuracy and estimate the location of the transition feature point in good agreement with human experts. The tool is an open source ImageJ/Fiji macro and is available online.

  15. Plant genomics and agriculture: From model organisms to crops, the role of data mining for gene discovery

    Scientific Electronic Library Online (English)

    Viswanathan, Mahalakshmi; Rodomiro, Ortiz.

    2001-12-15

    Full Text Available Sequencing and analysing of the Arabidopsis thaliana genome, the first plant kingdom genome to be unraveled, will always remain a scientific landmark. International initiatives to sequence rice, the most important cereal in Asia, are underway. However as functional information piles up in Arabidopsi [...] s and rice, researchers working in other crops will benefit from this new knowledge and apply it to their studied plants or crop species. The increasing role of public databases of model organisms and bio-informatics in data mining, presents a new opportunity as well as a challenge to researchers to develop more focused molecular tools for gene discovery and deployment. The work presented in here describes how such an approach has benefited sorghum, a rainfed semi-arid troprical cereal.

  16. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina. Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic prediction. To validate the genomic prediction accuracy leave one out cross-validation was performed. The accuracy was the correlation between corrected phenotype for fixed effect and averaged across plots and breeding values predicted from the genomic model. The accuracies were 0.49 (yield), 0.55 (height) and 0.64 (height). The results showed the high potential of using the genomic prediction in barley breeding programs.

  17. Plant Functional Genomics

    Science.gov (United States)

    Chris Somerville (Carnegie Institution of Washington; Department of Plant Biology)

    1999-07-16

    Nucleotide sequencing of the Arabidopsis genome is nearing completion, sequencing of the rice genome has begun, and large amounts of expressed sequence tag information are being obtained for many other plants. There are many opportunities to use this wealth of sequence information to accelerate progress toward a comprehensive understanding of the genetic mechanisms that control plant growth and development and responses to the environment.

  18. GENOME OF HORSEPOX VIRUS

    Science.gov (United States)

    Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212 kbp genome contained 7.5 kbp inverted terminal repeats (ITR) and lacked extensive terminal tandem repetition. HSPV contained 236 ORFs with sim...

  19. Human genome I

    International Nuclear Information System (INIS)

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  20. Species: Comparing Their Genome

    Science.gov (United States)

    Howard Hughes Medical Institute (Howard Hughes Medical Institute; )

    2001-06-01

    The reprinted resource illustrates how mapping the genome of different species reveals that: all living things share parallel genes, the genome of other species can be used for human disease research, many diseases are caused by defective genes or proteins, and so far, the mouse offers the best insight into human disease.

  1. Interesting bone scans - unusual findings

    International Nuclear Information System (INIS)

    A 59-year-old female with carcinoma of the colon and known liver metastatic disease was referred for bone scan to evaluate for bone metastases. Although no bone metastases were found, there was abnormal uptake noted in the liver corresponding to a metastatic calcified lesion. The only other findings were of degenerative disease in the cervical spine, right shoulder and small joints of the hands. A 69-year-old male with carcinoma of the prostate and right side low back pain was referred for bone scan. No focal abnormalities to suggest metastatic disease were identified; findings within the cervical spine, lumber spine and knees were presumed secondary to degenerative disease. Intermittent pain persisted and the patient was referred for a repeat bone scan six months later. Previous scan findings of degenerative disease and no metastatic disease were confirmed; however, closer inspection revealed an enlarged right kidney with significant retention of tracer in the pelvicalyceal system suggesting possible obstruction. A Retrograde pyelogram was performed, and no obvious obstruction demonstrated. As bone scan findings were very suggestive of obstruction, a DTPA scan with lasix was performed showing a dilated right collecting system with no functional obstruction. Given the degree of dilation, it is possible that the patient experiences intermittent PUJ obstruction causing his symptoms. A 33-year-old male with insulin dependent diabetes mellitus and viral arthritis was refeetes mellitus and viral arthritis was referred for a bone scan. A three phase revealed increased uptake in the region of the knee and leR proximal tibia. Delayed whole body images revealed multiple focal areas of osteoblastic activity in the leR tibia. Abnormal uptake was also seen in the upper third of the leR femur. The remainder of the skeletal survey was normal. X-ray correlation of the leR tibia and femoral findings was undertaken. Combinating unilateral changes on bone scan and X-ray although very suggestive of sclerotic polyostotic fibrous dysplasia. Three cases with interesting and unusual bone scan findings assisted in further management and treatment of patients

  2. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution.

    OpenAIRE

    Murata, S.; Takasaki, N.; Saitoh, M.; Okada, N.

    1993-01-01

    Several subfamilies of the salmonid Hpa I short interspersed element (SINE) family were isolated from salmonid genomes and were sequenced. For each genomic locus that represented the subfamily, amplification by PCR of the orthologous loci in the 12 fish allowed us to determine the order of branching of the Pacific salmonid species. The deduced phylogeny suggests three evolutionary lines, namely, a line of chum salmon, pink salmon, and kokanee; a line of coho salmon and chinook salmon; and a l...

  3. Gene sequencing by scanning molecular excitation microscopy. Progress report, June 1990--June 1993

    Energy Technology Data Exchange (ETDEWEB)

    Kopelman, R.

    1993-07-01

    We propose to complete the development of scanning molecular excitation microscopy to rapidly sequence DNA. This new type of scanned-tip microscopy is specifically designed to map individual DNA bases in a non-destructive fashion. Base recognition is based on the external heavy atom effect between a heavy atom label on a specific DNA base and a fluorescent sensor molecule at the end of a scanned optical tip. As the tip is scanned very close to the heavy atom its emissions will change intensity and wavelength. For sequencing, heavy-atom labeled single-stranded DNA molecules will be synthesized and oriented on a flat substrate such as mica. An optical tag an one end of each DNA molecule will be rapidly located at low resolution using conventional fluorescence or scanning near-field optical microscopy. Scanning with the same optical tip, the low-resolution path of the DNA will be mapped using long-range interactions such as attractive van der Waals forces or Forester energy transfer. Subsequently, the labeled bases will be mapped at better than 5{Angstrom} resolution with the same tip using the external heavy atom effect, and the coordinates stored and processed by computer. The proposed microscope could be automated to quickly sequence intact lambda clones, YACK, or genomic Not I fragments, making genomic sequencing much more rapid and economical.

  4. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  5. CDC: Public Health Genomics

    Science.gov (United States)

    Created in 1997, the Office of Public Health Genomics (OPHG) was established "to integrate genomics into public health research, policy, and programs, which could improve interventions designed to prevent and control the country's leading chronic, infectious, environmental, and occupational diseases." Visitors to the site should start by looking over their "Focus Areas", which include "Genomics and Health", "Family Health History", and "Genetic Testing". The "Genomics and Health" area is a great place to begin looking through the site, as it contains materials that explain the relationship between genetic history and family health. Here visitors will find activities that explain and illuminate environmental health, hereditary blood disorders, and pediatric genetics. Also, the site includes a "For Health Professionals" area which is perfect for current public health practitioners and those teaching about these subjects. Rounding out the site is their "Genomics and Health Impact" blog, which is definitely worth a look.

  6. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Full text: Improving plant cell wall (fiber) degradation remains one of the highest priority goals for all livestock enterprises, whether it is the intensively managed dairy herds in the United States, or the nomadic cattle herds in sub-Saharan Africa. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created in 2000 to promote the sequencing and comparative analysis of rumen microbial genomes. High throughput genome sequencing offers the potential to obtain a complete blueprint for the lifestyle of a specific microbe, and to assess its genetic potential in a functional and comparative fashion. So far, a combination of funds from U.S. Department of Agriculture's (USDA's) Initiative for Future Agriculture and Food Systems and the National Science Foundation (USDA-NSF) Microbe Sequencing Program has supported the sequencing of three rumen bacterial genomes to closure. Genome closure and annotation is complete for Fibrobacter succinogenes, and the Ruminococcus albus and Prevotella ruminicola genomes should be completed during 2004. In addition to these sequencing projects, Consortium members have used subtractive hybridization methods to characterize the genomic differences among the sequenced genomes and the genomes of additional strains and species of ruminal bacteria. A database has also been developed by bioinformaticians at The Institute for Genomic Research (www.tigr.org), which will contain the sequence information arising from this prosequence information arising from this project, as well as in silico tools for genome examination. Accordingly, our Consortium will have provided a comprehensive suite of resources and tools useful to microbiologists and animal scientists throughout the world, especially those interested in the conversion of cellulose-rich materials into useful commodities, such as meat, milk and draught animal power. The inherent value associated with whole genome sequencing is already apparent for the F. succinogenes project. The genome sequence has revealed that there are many more genes encoding endoglucanases and cellodextrinases than what had previously been isolated from clone libraries propagated in Escherichia coli. Additionally, we have yet to identify either exo-acting cellulases or processive endoglucanases in the F. succinogenes genome. The cellulase system of F. succinogenes S85 therefore differs from all other studied cellulolytic microorganisms. Subtractive hybridization studies between strain S85 and closely related bacteria (F. succinogenes strain A3C and F. intestinalis DR7) have revealed that the DR7 genome encodes several transporters and a xylanase, which are either absent, or possess limited sequence identity, to genes found in the S85 genome. Genome sequence data has also empowered studies underway with R. albus, by combining the sequence data with findings made from RNA and protein-based studies. For instance, several new processive endoglucanases have been identified by proteomic analysis of R. albus wild-type and mutant strains, and R. albus is now known to employ a variety of strategies for its adhesion to fiber. The subtractive hybridization studies also include the examination of a non-cellulolytic strain of R. albus (B199) with the sequenced genome, and have revealed that strain B199 is missing several endoglucanases. As such, the genome sequencing projects are revealing, for the first time, those gene products rate-limiting to the process of cellulose degradation. Even at these early stages, the ramifications of acquiring genome sequence data for rumen microorganisms are profound. The potential to elucidate which enzyme(s) or other ecological or physiological process(es) are rate-limiting to fiber degradation by these bacteria, and how this might change relative to dietary composition, are now greatly enhanced. With specific reference to cellulases, the Consortium projects have revealed that only a small percentage (? 25%) of these genes had been previously identified, and that novel cellulase systems are employed by at least some ruminal ba

  7. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  8. Flight versus simulator scan behavior

    Science.gov (United States)

    Spady, A. A., Jr.; Harris, R. L., Sr.; Comstock, R.

    1984-01-01

    It is pointed out that most of the modern flight simulators used for pilot training have included expensive motion bases, while the quantitative justification for motion is lacking. The present investigation is concerned with the effects of flight versus simulator conditions on scan behavior as a function of control mode and the presence or absence of traffic on the map display. Matching tests conducted in flight and in a fixed-base simulator permitted an evaluation of the differences in scanning behavior in the real world (flight) and in the 'less real' world (simulator). Scanning behavior in flight was found to be significantly different from the simulator. In flight, the dwell percentage increased on the Electronic Attitude Direction Indicator (EADI), and decreased on the Electronic Horizontal Situation Indicator (EHSI). The average dwell time on all instruments decreased in flight.

  9. Scanning Terahertz Heterodyne Imaging Systems

    Science.gov (United States)

    Siegel, Peter; Dengler, Robert

    2007-01-01

    Scanning terahertz heterodyne imaging systems are now at an early stage of development. In a basic scanning terahertz heterodyne imaging system, (see Figure 1) two far-infrared lasers generate beams denoted the local-oscillator (LO) and signal that differ in frequency by an amount, denoted the intermediate frequency (IF), chosen to suit the application. The LO beam is sent directly to a mixer as one of two inputs. The signal beam is focused to a spot on or in the specimen. After transmission through or reflection from the specimen, the beams are focused to a spot on a terahertz mixer, which extracts the IF outputs. The specimen is mounted on a translation stage, by means of which the focal spot is scanned across the specimen to build up an image.

  10. Nanobits: customizable scanning probe tips

    DEFF Research Database (Denmark)

    Kumar, Rajendra; Shaik, Hassan Uddin

    2009-01-01

    We present here a proof-of-principle study of scanning probe tips defined by planar nanolithography and integrated with AFM probes using nanomanipulation. The so-called 'nanobits' are 2-4 mu m long and 120-150 nm thin flakes of Si3N4 or SiO2, fabricated by electron beam lithography and standard silicon processing. Using a microgripper they were detached from an array and fixed to a standard pyramidal AFM probe or alternatively inserted into a tipless cantilever equipped with a narrow slit. The nanobit-enhanced probes were used for imaging of deep trenches, without visible deformation, wear or dislocation of the tips of the nanobit after several scans. This approach allows an unprecedented freedom in adapting the shape and size of scanning probe tips to the surface topology or to the specific application.

  11. Software framework for scanning cytometry

    Science.gov (United States)

    Hunter, Edward; Callaway, Scott, III; Price, Jeffrey H.

    2000-04-01

    This paper introduces a new object-oriented software framework suitable for scanning image cytometry application development. The goal of scanning image cytometry is the development of an instrument that locates and measures every cell on a microscope slide at high speed without requiring operator interaction. This capability extends traditional quantitative techniques, such as flow cytometry, through the availability of image data that can provide similar intensity measurement as well as detailed image morphometry and population geometry. Domain concepts are identified, abstracted and categorized into three thematic families: (1) physical cytometer hardware components, (2) image and image- derived measurement data, and (3) runtime dynamic and extendible image processing components. Additional abstractions are provided for the image table, an embedded database for disk archival and general access to metaimage areas-of-interest, and for the cytometer, which manages physical hardware abstractions and organizes their collaboration into high-level scanning operations. Detailed examples of framework mechanisms are given to illustrate use.

  12. Scanning Gate Spectroscopy on Nanoclusters

    CERN Document Server

    Gurevich, L A; Kouwenhoven, Leo P

    1999-01-01

    A gated probe for scanning tunnelling microscopy (STM) has been developed. The probe extends normal STM operations by means of an additional electrode fabricated next to the tunnelling tip. The extra electrode does not make contact with the sample and can be used as a gate. We report on the recipe used for fabricating the tunnelling tip and the gate electrode on a silicon nitride cantilever. We demonstrate the functioning of the scanning gate probes by performing single-electron tunnelling spectroscopy on 20-nm gold clusters for different gate voltages.

  13. Producing colour pictures from SCAN

    International Nuclear Information System (INIS)

    The computer code SCAN.TSK has been written for use on the Interdata 7/32 minicomputer which will convert the pictures produced by the SCAN program into colour pictures on a colour graphics VDU. These colour pictures are a more powerful aid to detecting errors in the MONK input data than the normal lineprinter pictures. This report is intended as a user manual for using the program on the Interdata 7/32, and describes the method used to produce the pictures and gives examples of JCL, input data and of the pictures that can be produced. (U.K.)

  14. High precision prism scanning system

    Science.gov (United States)

    García-Torales, G.; Flores, J. L.; Muñoz, Roberto X.

    2007-03-01

    Risley prisms are commonly used in continuous scanning manner. Each prism is capable of rotating separately about a common axis at different speeds. Scanning patterns are determined by the ratios of the wedge angles, the speed and direction of rotation of both prisms. The use of this system is conceptually simple. However, mechanical action in most applications becomes a challenge often solved by the design of complex control algorithms. We propose an electronic servomotor system that controls incremental and continuous rotations of the prisms wedges by means of an auto-tuning PID control using a Adaline Neural Network Algorithm, NNA.

  15. Nonosseous abnormalities on bone scans.

    Science.gov (United States)

    Loutfi, Issa; Collier, B David; Mohammed, Ahmed M

    2003-09-01

    Although bone scanning is a test primarily concerned with skeletal abnormalities, important nonosseous findings are occasionally present on the images. To gauge the significance of such nonosseous uptake and, in particular, to determine whether these findings contain useful diagnostic information, the technical and medical staff in nuclear medicine must recognize the various patterns of nonbony uptake and understand their causes. The objectives of this article are to demonstrate the appearances of nonosseous uptake on bone scans, to categorize the forms of soft-tissue uptake, to emphasize technical artifacts leading to soft-tissue uptake, and to highlight the clinical significance of pathologic soft-tissue uptake. PMID:12968045

  16. Linking world scan and image

    International Nuclear Information System (INIS)

    In march 1994 the Central Planning Bureau (CPB) in the Hague, the National Institute of Public Health and Environmental Protection (RIVM) in Bilthoven and the Institute of Environmental Studies (IES) in Amsterdam started the first phase of a joint research program aimed at creating integrated scenarios of the global economy, GHG emissions, and climate impacts. The goal of the first phase of this project was to design and test a linked version of the economic model WORLD SCAN of the former, and the climate model IMAGE 2 of the latter institute. This first phase has resulted in the planned test runs with an operational version of the linked models by May 1995. The experiences in the first year were encouraging, both in the scientific and the organizational sense. In a sense, a link was made between scientific disciplines: a coupling of disciplines concerning with global economic development and the global physical climate system is difficult and novel. The goal of the project was to integrate long-term economic developments and effects of climate change. Both the WORLD SCAN model and IMAGE 2 provide a consistent analysis of the global system, but from different perspectives. IMAGE 2 simulates climate change and its effects in a global context but treats the economic system as exogenous. WORLD SCAN covers the world economic system in a consistent manner but does not take into account the global environment. The links are constructed in the area of agriculture and energy.ted in the area of agriculture and energy. The basic idea is that WORLD SCAN determines demand and supply on economic principles, while IMAGE 2 provides information on changes of land area and average quality of productive land, and other damage costs based on its three sub-systems. The demand for energy is fed into IMAGE 2's Energy Industry subsystem (EIS), which in turn determines emissions of greenhouse gases. Furthermore, some additional output from WORLD SCAN on activity levels, prices and capital structure can be used to determine activity-based variables in IMAGE 2. Emissions determine concentration as they run through the Atmosphere Ocean subsystem (AOS) in IMAGE 2. Agricultural demand, which is also an output of WORLD SCAN, is fed into IMAGE 2 and determines land use in the Terrestrial Environment subsystem (TES), again affecting climate change. The feedbacks from IMAGE 2 to WORLD SCAN include the land use and average quality of land which determine the so-called fixed factor in the WORLD SCAN production function of agriculture, and climate change related damage costs which affect a region's consumption possibilities. 9 refs

  17. NCBI viral genomes resource.

    Science.gov (United States)

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets. PMID:25428358

  18. Common Carotid Artery Bifurcation Levels Related to Clinical Relevant Anatomical Landmarks Niveles de Bifurcación de la Arteria Carótida Común en Relación a Puntos de Referencia Anatómicos Relevantes en Clínica

    OpenAIRE

    Rogério Alves Ribeiro; João Alberto de Souza Ribeiro; Omar Andrade Rodrigues Filho; Abadio Gonçalves Caetano; Valéria Paula Sassoli Fazan

    2006-01-01

    In head and neck surgery, the common carotid arteries are important landmarks, defining dissection plane during radical neck surgeries. The objectives of the present study were to add information on the diameter of the carotid arteries and to correlate the common carotid artery (CCA) bifurcation level with important anatomical landmarks used regularly in clinical practice. Forty-six necks from male embalmed human cadavers were evaluated. The CCA as the external (ECA) and internal (ICA) caroti...

  19. GenomeView: a next-generation genome browser

    OpenAIRE

    Abeel, Thomas; Parys, Thomas; Saeys, Yvan; Galagan, James; Peer, Yves

    2011-01-01

    Due to ongoing advances in sequencing technologies, billions of nucleotide sequences are now produced on a daily basis. A major challenge is to visualize these data for further downstream analysis. To this end, we present GenomeView, a stand-alone genome browser specifically designed to visualize and manipulate a multitude of genomics data. GenomeView enables users to dynamically browse high volumes of aligned short-read data, with dynamic navigation and semantic zooming, from the whole genom...

  20. Genome size analyses of Pucciniales reveal the largest fungal genomes

    OpenAIRE

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G.; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T.; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (...

  1. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  2. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  3. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ? 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.

  4. Meeting Highlights: Genome Informatics

    Directory of Open Access Journals (Sweden)

    Jennifer Ashurst

    2006-04-01

    Full Text Available We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust ‘Genome Informatics’ Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz a month later.

  5. The Genomic Revolution

    Science.gov (United States)

    This Web site, created to complement the museum's The Genomic Revolution exhibition, examines the mapping of the genome and its implications. It includes overviews of our genetic identity, our genome, choosing our genes, changing our genes, reshaping our world through genetics, and the many uses of DNA evidence. There is information about the museum's Institute for Comparative Genetics, ongoing research projects, and conferences on genetics. A timeline has highlights from the field of genetics, beginning with the 1859 publication of Darwin's The Origin of Species.

  6. Scanning tunneling microscope nanoetching method

    Science.gov (United States)

    Li, Yun-Zhong (West Lafayette, IN); Reifenberger, Ronald G. (West Lafayette, IN); Andres, Ronald P. (West Lafayette, IN)

    1990-01-01

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

  7. Introduction to scanning tunneling microscopy

    CERN Document Server

    Chen, C Julian

    2008-01-01

    The scanning tunneling and the atomic force microscope, both capable of imaging individual atoms, were crowned with the Physics Nobel Prize in 1986, and are the cornerstones of nanotechnology today. This is a thoroughly updated version of this 'bible' in the field.

  8. Broadband antenna with frequency scanning

    Directory of Open Access Journals (Sweden)

    A. A. Shekaturin

    2014-06-01

    Full Text Available Relevance of this study. The main advantage of frequency scanning is simplicity of implementation. At this point, multifunctional usage of microwave modules is an urgent task, as well as their maximum simpler and cheaper. Antenna design and operation. The study is aimed at providing electric antenna with frequency scanning. It was based on the log-periodic antenna due to its wideband and negotiation capability over the entire operating frequency range. For this distribution line is bent in an arc of a circle in a plane blade while vibrators are arranged along the radius. Computer modeling of antennas with frequency scanning. Modeled with a non-mechanical motion antenna beam emitters representing system for receiving a radio frequency signal on mobile objects calculated for 1.8 GHz ... 4.2 GHz. The simulation was performed in a software environment for numerical modeling of electromagnetic «Feko 5.5». Analysis of the interaction of radiation is based on the method of moments. Findings. The result of this work is to propose a new design of the antenna with a frequency scanning method as agreed in a wide frequency range. In the studied technical solution provided by the rotation of NAM in the frequency range, and the matching of the antenna to the feed line is maintained. Application of this type of antennas on the proposed technical solution in communication systems will improve the communication reliability by maintaining coordination in the frequency range

  9. Developing an Environmental Scanning System.

    Science.gov (United States)

    Morrison, James L.

    A step-by-step approach is provided for developing an environmental scanning system for colleges and universities to assist them in planning for the future. The objectives of such a system are to detect social, scientific, economic, technical, and political interactions important to the organization; define potential threats and opportunities from…

  10. Environmental Scanning, Vancouver Community College.

    Science.gov (United States)

    Yao, Min

    This 1994 environmental scanning report from Vancouver Community College (VCC) reviews the expected effects of the separation of VCC into a new Vancouver Community College and Langara College (LC). The report examines the projected service area student-intake capacity; student characteristics; population growth trends; other postsecondary…

  11. Thermal radiation scanning tunnelling microscopy.

    Science.gov (United States)

    De Wilde, Yannick; Formanek, Florian; Carminati, Rémi; Gralak, Boris; Lemoine, Paul-Arthur; Joulain, Karl; Mulet, Jean-Philippe; Chen, Yong; Greffet, Jean-Jacques

    2006-12-01

    In standard near-field scanning optical microscopy (NSOM), a subwavelength probe acts as an optical 'stethoscope' to map the near field produced at the sample surface by external illumination. This technique has been applied using visible, infrared, terahertz and gigahertz radiation to illuminate the sample, providing a resolution well beyond the diffraction limit. NSOM is well suited to study surface waves such as surface plasmons or surface-phonon polaritons. Using an aperture NSOM with visible laser illumination, a near-field interference pattern around a corral structure has been observed, whose features were similar to the scanning tunnelling microscope image of the electronic waves in a quantum corral. Here we describe an infrared NSOM that operates without any external illumination: it is a near-field analogue of a night-vision camera, making use of the thermal infrared evanescent fields emitted by the surface, and behaves as an optical scanning tunnelling microscope. We therefore term this instrument a 'thermal radiation scanning tunnelling microscope' (TRSTM). We show the first TRSTM images of thermally excited surface plasmons, and demonstrate spatial coherence effects in near-field thermal emission. PMID:17151664

  12. Transverse section radionuclide scanning system

    International Nuclear Information System (INIS)

    The transverse section radionuclide scanning apparatus is used with an electronic system for the high sensitivity quantification of brain radioactivity in cross-section picture format to permit accurate assessment of regional brain function localized in three dimensions. The apparatus detects high energy radiation emanating from sources at fixed locations in a human head, and the electronic system produces and displays resulting data that correspond spatially with the location of the sources and quantitatively with the intensity of the radiation emanating from the sources in a transverse plane. The invention described possesses several advantages over the previous scanning system. It avoids the alternating direction detector movements previously required and obtains increased sensitivity, as well as decreased total patient scanning time, by rotating a picture frame of detectors that completely enclose the scan field around a single axis of rotation in a slip ring. The detector data are continuously transmitted by means of laser-emitting diodes with the advantage that the data can be continuously collected, processed and displayed with high sesitivity according to a suitable computer program. It also provides a reduction of data from multiple large detectors that are offset and interlaced for improved spatial resolution without detector translation, as well as improved detail, reduced noise, and continuous operator monitoring and control. (JTA)nd control. (JTA)

  13. Laser-scanned interactive whiteboard

    Science.gov (United States)

    Mallicoat, Samuel W.

    1995-05-01

    Laser scanning method has been applied to an interactive computer screen to provide a large- scale whiteboard interface to computer generated images. Optimizations in pen tracking and ink simulation were found necessary to give a natural pen feel attractive as an alterative to the keyboard and mouse.

  14. Principles: Confocal Laser Scanning Microscopy

    Science.gov (United States)

    Stefan Wilhelm (Zeiss)

    2011-01-01

    Following a description of the fundamental differences between a conventional and a confocal microscope, this monograph will set out the special features of the confocal Laser Scanning Microscope (LSM) and the capabilities resulting from them. The conditions in fluorescence applications will be given priority treatment throughout.

  15. Be a Scanning Probe Microscope

    Science.gov (United States)

    IEEE

    2013-02-25

    In this activity, learners investigate Scanning Probe Microscopes (SPM) and then work in teams using a pencil to explore and identify the shape of objects they cannot see, just as SPMs do at the nano level. Learners draw what their mind "sees" on paper, compare their results with other teams, and share observations with their group.

  16. Bone scan indications in oncology

    International Nuclear Information System (INIS)

    The scintigraphic method is described and a critical analysis of its value in the research of bone metastases is presented. The method validity, the positivity of bone scan for metastases at the first examination and the preferencial distribution metastases in skeleton are related.Bone pain and the results of bone scintigram are correlated. (M.A.C.)

  17. Reference frames for spatial cognition: different brain areas are involved in viewer-, object-, and landmark-centered judgments about object location.

    Science.gov (United States)

    Committeri, Giorgia; Galati, Gaspare; Paradis, Anne-Lise; Pizzamiglio, Luigi; Berthoz, Alain; LeBihan, Denis

    2004-11-01

    Functional magnetic resonance imaging was used to compare the neural correlates of three different types of spatial coding, which are implicated in crucial cognitive functions of our everyday life, such as visuomotor coordination and orientation in topographical space. By manipulating the requested spatial reference during a task of relative distance estimation, we directly compared viewer-centered, object-centered, and landmark-centered spatial coding of the same realistic 3-D information. Common activation was found in bilateral parietal, occipital, and right frontal premotor regions. The retrosplenial and ventromedial occipital-temporal cortex (and parts of the parietal and occipital cortex) were significantly more activated during the landmark-centered condition. The ventrolateral occipital-temporal cortex was particularly involved in object-centered coding. Results strongly demonstrate that viewer-centered (egocentric) coding is restricted to the dorsal stream and connected frontal regions, whereas a coding centered on external references requires both dorsal and ventral regions, depending on the reference being a movable object or a landmark. PMID:15601516

  18. Complete genome sequencing and variant analysis of a Pakistani individual.

    Science.gov (United States)

    Azim, Muhammad Kamran; Yang, Chuanchun; Yan, Zhixiang; Choudhary, Muhammad Iqbal; Khan, Asifullah; Sun, Xiao; Li, Ran; Asif, Huma; Sharif, Sana; Zhang, Yong

    2013-09-01

    We sequenced the genome of a Pakistani male at 25.5x coverage using massively parallel sequencing technology. More than 90% of the sequence reads were mapped to the human reference genome. In subsequent analysis, we identified 3,224,311 single-nucleotide polymorphisms (SNPs), of which 388,532 (12% of the total SNPs) had not been previously recorded in single nucleotide polymorphism database (dbSNP) or the 1000 Genomes Project database. The 5991 non-synonymous coding variants were screened for deleterious or disease-associated SNPs. Analysis of genes with deleterious SNPs identified 'retinoic acid signaling' and 'regulation of transcription' as the enriched Gene Ontology terms. Scanning of non-synonymous SNPs against the OMIM revealed several disease and phenotype-associated variants in Pakistani genome. Comparative analysis with Indian genome sequence revealed >1.8 million shared SNPs; 32% of which were annotated in ~14,000 genes. Gene Ontology (GO) terms analysis of these genes identified 'response to jasmonic acid stimulus', 'aminoglycoside antibiotic metabolic process' and 'glycoside metabolic process' with considerable enrichment. A total of 59,558 of small indels (1-5 bp) and 16,063 large structural variations were found; 54% of which was novel. Substantial number of novel structural variations discovered in Pakistani genome enforced previous inferences that (a) structural variations are major type of variation in the genome and (b) compared with SNPs, they putatively exhibit equivalent or superior functional roles. This genome sequence information will be an important reference for population-wide genomics studies of ethnically diverse South Asian subcontinent. PMID:23842039

  19. Vertical Scan-Conversion for Filling Purposes

    OpenAIRE

    Hersch, R. D.

    1988-01-01

    Conventional scan-conversion algorithms were developed independently of filling algorithms. They cause many problems, when used for filling purposes. However, today's raster printers and plotters require extended use of filling, especially for the generation of typographic characters and graphic line art. A new scan-conversion algorithm, called vertical scan-conversion has been specifically designed to meet the requirements of parity scan line fill algorithms. Vertical scan-conversion ensures...

  20. A millikelvin scanning tunneling microscope with two independent scanning systems

    CERN Document Server

    Roychowdhury, A; Anderson, J R; Lobb, C J; Wellstood, F C; Dreyer, M

    2013-01-01

    We describe the design, construction and operation of a scanning tunneling microscope (STM) with two tips that can independently acquire simultaneous scans of a sample. The STM is mounted on a dilution refrigerator and the setup includes vibration isolation, rf-filtered wiring, an ultra high vacuum (UHV) sample preparation chamber and sample transfer mechanism. We present images and spectroscopy taken with superconducting Nb tips with the refrigerator at 35 mK that indicate that the effective temperature of our tips/sample is approximately 184 mK, corresponding to an energy resolution of 16 $\\mu$eV. Atomic resolution topographic images of an Au(100) surface taken with the inner and outer tips were found to have root mean square roughness of 1.75 $\\pm$ 0.01 pm and 3.55 $\\pm$ 0.03 pm respectively.