WorldWideScience

Sample records for landmark genome scanning

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

    Tomoko Takamiya

    2009-01-01

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

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

    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

  3. Genome-Wide Scan Reveals Mutation Associated with Melanoma

    ... historical) Genome-Wide Scan Reveals Mutation Associated with Melanoma A team of international researchers supported by the ... when they divide and grow uncontrollably, develop into melanoma. Also, MITF activity is known to be amplified ...

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

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

    2002-01-01

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

  5. An optimal set of landmarks for metopic craniosynostosis diagnosis from shape analysis of pediatric CT scans of the head

    Mendoza, Carlos S.; Safdar, Nabile; Myers, Emmarie; Kittisarapong, Tanakorn; Rogers, Gary F.; Linguraru, Marius George

    2013-02-01

    Craniosynostosis (premature fusion of skull sutures) is a severe condition present in one of every 2000 newborns. Metopic craniosynostosis, accounting for 20-27% of cases, is diagnosed qualitatively in terms of skull shape abnormality, a subjective call of the surgeon. In this paper we introduce a new quantitative diagnostic feature for metopic craniosynostosis derived optimally from shape analysis of CT scans of the skull. We built a robust shape analysis pipeline that is capable of obtaining local shape differences in comparison to normal anatomy. Spatial normalization using 7-degree-of-freedom registration of the base of the skull is followed by a novel bone labeling strategy based on graph-cuts according to labeling priors. The statistical shape model built from 94 normal subjects allows matching a patient's anatomy to its most similar normal subject. Subsequently, the computation of local malformations from a normal subject allows characterization of the points of maximum malformation on each of the frontal bones adjacent to the metopic suture, and on the suture itself. Our results show that the malformations at these locations vary significantly (p<0.001) between abnormal/normal subjects and that an accurate diagnosis can be achieved using linear regression from these automatic measurements with an area under the curve for the receiver operating characteristic of 0.97.

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

    Mei Lingling

    2011-11-01

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

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

    Kun Tang

    2007-07-01

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

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

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

    2013-11-01

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

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

    Jingjing Gu

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

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

    Bradley Todd Webb

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

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

    2008-01-01

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

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

    2008-01-01

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

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

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

    2001-04-01

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

  14. Landmarks in Hybrid Planning

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

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

    2008-01-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is an enduring public health problem globally, particularly in sub-Saharan Africa. Several studies have suggested a role for host genetic susceptibility in increased risk for TB but results across studies have been equivocal. As part of a household contact study of Mtb infection and disease in Kampala, Uganda, we have taken a unique approach to the study of genetic susceptibility to TB, by studying three phenotypes. First, we analyzed culture confirmed TB disease compared to latent Mtb infection (LTBI) or lack of Mtb infection. Second, we analyzed resistance to Mtb infection in the face of continuous exposure, defined by a persistently negative tuberculin skin test (PTST-); this outcome was contrasted to LTBI. Third, we analyzed an intermediate phenotype, tumor necrosis factor-alpha (TNFalpha) expression in response to soluble Mtb ligands enriched with molecules secreted from Mtb (culture filtrate). We conducted a full microsatellite genome scan, using genotypes generated by the Center for Medical Genetics at Marshfield. Multipoint model-free linkage analysis was conducted using an extension of the Haseman-Elston regression model that includes half sibling pairs, and HIV status was included as a covariate in the model. The analysis included 803 individuals from 193 pedigrees, comprising 258 full sibling pairs and 175 half sibling pairs. Suggestive linkage (p<10(-3)) was observed on chromosomes 2q21-2q24 and 5p13-5q22 for PTST-, and on chromosome 7p22-7p21 for TB; these findings for PTST- are novel and the chromosome 7 region contains the IL6 gene. In addition, we replicated recent linkage findings on chromosome 20q13 for TB (p = 0.002). We also observed linkage at the nominal alpha = 0.05 threshold to a number of promising candidate genes, SLC11A1 (PTST- p = 0.02), IL-1 complex (TB p = 0.01), IL12BR2 (TNFalpha p = 0.006), IL12A (TB p = 0.02) and IFNGR2 (TNFalpha p = 0.002). These results confirm not

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

    Catherine M Stein

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

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

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

    2015-01-01

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

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

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

    2011-01-01

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

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

    Gautier, Mathieu

    2015-01-01

    In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (i...

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

    Gautam Aggarwal; Ramakrishna Ramaswamy

    2002-02-01

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

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

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

    2014-01-01

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

  2. Accounting for Linkage Disequilibrium in genome scans for selection without individual genotypes: the local score approach.

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

    2017-04-10

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

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

    Børglum Anders D

    2011-07-01

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

  4. Landmarks in Insulin Research

    Ward, Colin W.; Lawrence, Michael C.

    2011-01-01

    Ever since the discovery of insulin and its role in the regulation of glucose uptake and utilization, there has been great interest in insulin, its structure and the way in which it interacts with its receptor and effects signal transduction. As the 90th anniversary of the discovery of insulin approaches, it is timely to provide an overview of the landmark discoveries relating to the structure and function of this remarkable molecule and its receptor.

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

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

    2008-01-01

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

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

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

    2009-01-01

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

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

    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.

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

    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.

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

    ZHANG Wen-guang

    2013-01-01

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

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

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

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early ...... 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....

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

    Laurent, R; Toupance, B; Chaix, R

    2012-02-01

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

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

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

    2016-04-01

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

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

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

    2008-12-01

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

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

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

    2011-01-01

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

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

    Ikhide G. Imumorin

    2011-07-01

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

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

    Perola, Markus; Sammalisto, Sampo; Hiekkalinna, Tero

    2007-01-01

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

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

    Gautier, Mathieu

    2015-12-01

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

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

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

    2013-01-01

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

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

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

    2004-01-01

    of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.......An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399-404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99...

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

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

    2004-01-01

    of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.......An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes......-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99...

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

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

    2005-12-30

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

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

    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.

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

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

    2013-01-01

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

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

    2007-01-01

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

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

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

    2003-01-01

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

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

    Anouk Georges

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

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

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

    1997-03-01

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

  8. Collaborative regression-based anatomical landmark detection

    Gao, Yaozong; Shen, Dinggang

    2015-12-01

    Anatomical landmark detection plays an important role in medical image analysis, e.g. for registration, segmentation and quantitative analysis. Among the various existing methods for landmark detection, regression-based methods have recently attracted much attention due to their robustness and efficiency. In these methods, landmarks are localised through voting from all image voxels, which is completely different from the classification-based methods that use voxel-wise classification to detect landmarks. Despite their robustness, the accuracy of regression-based landmark detection methods is often limited due to (1) the inclusion of uninformative image voxels in the voting procedure, and (2) the lack of effective ways to incorporate inter-landmark spatial dependency into the detection step. In this paper, we propose a collaborative landmark detection framework to address these limitations. The concept of collaboration is reflected in two aspects. (1) Multi-resolution collaboration. A multi-resolution strategy is proposed to hierarchically localise landmarks by gradually excluding uninformative votes from faraway voxels. Moreover, for informative voxels near the landmark, a spherical sampling strategy is also designed at the training stage to improve their prediction accuracy. (2) Inter-landmark collaboration. A confidence-based landmark detection strategy is proposed to improve the detection accuracy of ‘difficult-to-detect’ landmarks by using spatial guidance from ‘easy-to-detect’ landmarks. To evaluate our method, we conducted experiments extensively on three datasets for detecting prostate landmarks and head & neck landmarks in computed tomography images, and also dental landmarks in cone beam computed tomography images. The results show the effectiveness of our collaborative landmark detection framework in improving landmark detection accuracy, compared to other state-of-the-art methods.

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

    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.

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

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

    2002-04-01

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

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

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

    2011-08-01

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

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

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

    2009-08-01

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

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

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

    2015-01-01

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

  14. Landmark learning by juvenile salamanders (Ambystoma maculatum).

    Heuring, Whitney L; Mathis, Alicia

    2014-10-01

    Learning to use a landmark as a beacon to locate resources is one of the simplest forms of spatial learning. We tested whether landmark learning occurs in a semifossorial salamander that migrates annually to breeding ponds as adults. Juvenile spotted salamanders (Ambystoma maculatum) were tested in square containers with a plastic feeding dish in each corner, and a piece of earthworm was placed in one randomly-chosen dish. For landmark-trained salamanders, a rock was placed beside the dish containing the prey. For control salamanders, the rock was placed beside a randomly selected feeding dish. Each salamander was trained once every 2 days for 30 days. Significantly more landmark-trained salamanders than control salamanders entered the landmark area first, and landmark-trained individuals had faster latencies to enter the landmark area and longer stay-times. These results suggest that spotted salamanders are able to locate resources by associating their positions with landmarks.

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

    Abigail Bigham

    2010-09-01

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

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

    Niu Xiao-Yan

    2010-06-01

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

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

    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.

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

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

    2012-12-01

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

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

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

    2008-07-01

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

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

    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.

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

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

    2015-01-01

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

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

    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.

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

    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

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

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

    2016-03-01

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

  5. Localization of skeletal and aortic landmarks in trauma CT data based on the discriminative generalized Hough transform

    Lorenz, Cristian; Hansis, Eberhard; Weese, Jürgen; Carolus, Heike

    2016-03-01

    Computed tomography is the modality of choice for poly-trauma patients to assess rapidly skeletal and vascular integrity of the whole body. Often several scans with and without contrast medium or with different spatial resolution are acquired. Efficient reading of the resulting extensive set of image data is vital, since it is often time critical to initiate the necessary therapeutic actions. A set of automatically found landmarks can facilitate navigation in the data and enables anatomy oriented viewing. Following this intention, we selected a comprehensive set of 17 skeletal and 5 aortic landmarks. Landmark localization models for the Discriminative Generalized Hough Transform (DGHT) were automatically created based on a set of about 20 training images with ground truth landmark positions. A hierarchical setup with 4 resolution levels was used. Localization results were evaluated on a separate test set, consisting of 50 to 128 images (depending on the landmark) with available ground truth landmark locations. The image data covers a large amount of variability caused by differences of field-of-view, resolution, contrast agent, patient gender and pathologies. The median localization error for the set of aortic landmarks was 14.4 mm and for the set of skeleton landmarks 5.5 mm. Median localization errors for individual landmarks ranged from 3.0 mm to 31.0 mm. The runtime performance for the whole landmark set is about 5s on a typical PC.

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

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

    2012-01-01

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

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

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

    2010-01-01

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

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

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

    2014-01-01

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

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

    Bo Pang

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

  10. Optical processing for landmark identification

    Casasent, D.; Luu, T. K.

    1981-09-01

    A study of optical pattern recognition techniques, available components and airborne optical systems for use in landmark identification was conducted. A data base of imagery exhibiting multisensor, seasonal, snow and fog cover, exposure, and other differences was assembled. These were successfully processed in a scaling optical correlator using weighted matched spatial filter synthesis. Distinctive data classes were defined and a description of the data (with considerable input information and content information) emerged from this study. It has considerable merit with regard to the preprocessing needed and the image difference categories advanced. A optical pattern recognition airborne applications was developed, assembled and demontrated. It employed a laser diode light source and holographic optical elements in a new lensless matched spatial filter architecture with greatly reduced size and weight, as well as component positioning toleranced.

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

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

    2016-01-01

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

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

    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.

  13. Combination of automatic non-rigid and landmark based registration: the best of both worlds

    Fischer, Bernd; Modersitzki, Jan

    2003-05-01

    Automatic, parameter-free, and non-rigid registration schemes are known to be valuable tools in various (medical) image processing applications. Typically, these approaches aim to match intensity patterns in each scan by minimizing an appropriate distance measure. The outcome of an automatic registration procedure in general matches the target image quite good on the average. However, it may be inaccurate for specific, important locations as for example anatomical landmarks. On the other hand, landmark based registration techniques are designed to accurately match user specified landmarks. A drawback of landmark based registration is that the intensities of the images are completely neglected. Consequently, the registration result away from the landmarks may be very poor. Here we propose a framework for novel registration techniques which are capable to combine automatic and landmark driven approaches in order to benefit from the advantages of both strategies. We also propose a general, mathematical treatment of this framework and a particular implementation. The procedure computes a displacement field which is guaranteed to produce a one-to-one match between given landmarks and at the smae time minimizes an intensity based measure for the remaining parts of the images. The properties of the new scheme are demonstrated for a variety of numerical example. It is worthwhile noticing, that we not only present a new approach. Instead, we propose a general framework for a variety of different approaches. The choice of the main building blocks, the distance measure and the smoothness constraint, is essentially free.

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

    Sugawara, Yasushi; Harii, Kiyonori (Tokyo Univ. (Japan). Faculty of Medicine); Hirabayashi, Shinichi

    1994-05-01

    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 on the skull. (N.K.).

  15. Enhancing SAT Based Planning with Landmark Knowledge

    Elffers, J.; Konijnenberg, D.; Walraven, E.M.P.; Spaan, M.T.J.

    2013-01-01

    Several approaches exist to solve Artificial Intelligence planning problems, but little attention has been given to the combination of using landmark knowledge and satisfiability (SAT). Landmark knowledge has been exploited successfully in the heuristics of classical planning. Recently it was also s

  16. Haptic Landmark Positioning and Automatic Landmark Transfer in 4D Lung CT Data

    Färber, Matthias; Gawenda, Björn; Bohn, Christian-Arved; Handels, Heinz

    Manual landmark positioning in volumetric image data is a complex task and often results in erroneous landmark positions. The landmark positioning tool presented uses image curvature features to precompute suitable candidates for landmark positions on surface data of anatomical structures. A force-feedback I/O device is then used to haptically guide the user during the definition of the correct landmarks in the 3D data volume. Furthermore, existing landmarks in a time-point of a sequence of 3D volumes (4D data set) can iteratively be transferred to other time-points using a surface based registration technique. First results show significant time savings and small interobserver variability (IROV) compared to the IROV of manually defined landmark positions using orthogonal slices of the image data.

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

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

    1996-01-01

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

  18. Visual EKF-SLAM from Heterogeneous Landmarks.

    Esparza-Jiménez, Jorge Othón; Devy, Michel; Gordillo, José L

    2016-04-07

    Many applications require the localization of a moving object, e.g., a robot, using sensory data acquired from embedded devices. Simultaneous localization and mapping from vision performs both the spatial and temporal fusion of these data on a map when a camera moves in an unknown environment. Such a SLAM process executes two interleaved functions: the front-end detects and tracks features from images, while the back-end interprets features as landmark observations and estimates both the landmarks and the robot positions with respect to a selected reference frame. This paper describes a complete visual SLAM solution, combining both point and line landmarks on a single map. The proposed method has an impact on both the back-end and the front-end. The contributions comprehend the use of heterogeneous landmark-based EKF-SLAM (the management of a map composed of both point and line landmarks); from this perspective, the comparison between landmark parametrizations and the evaluation of how the heterogeneity improves the accuracy on the camera localization, the development of a front-end active-search process for linear landmarks integrated into SLAM and the experimentation methodology.

  19. Visual EKF-SLAM from Heterogeneous Landmarks

    Jorge Othón Esparza-Jiménez

    2016-04-01

    Full Text Available Many applications require the localization of a moving object, e.g., a robot, using sensory data acquired from embedded devices. Simultaneous localization and mapping from vision performs both the spatial and temporal fusion of these data on a map when a camera moves in an unknown environment. Such a SLAM process executes two interleaved functions: the front-end detects and tracks features from images, while the back-end interprets features as landmark observations and estimates both the landmarks and the robot positions with respect to a selected reference frame. This paper describes a complete visual SLAM solution, combining both point and line landmarks on a single map. The proposed method has an impact on both the back-end and the front-end. The contributions comprehend the use of heterogeneous landmark-based EKF-SLAM (the management of a map composed of both point and line landmarks; from this perspective, the comparison between landmark parametrizations and the evaluation of how the heterogeneity improves the accuracy on the camera localization, the development of a front-end active-search process for linear landmarks integrated into SLAM and the experimentation methodology.

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

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

    2010-01-01

    Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD fa

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

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

    2009-01-01

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

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

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

    2014-01-01

    BACKGROUND:  Selection by host immunity and antimalarial drugs has driven extensive adaptive evolution in Plasmodium falciparum and continues to produce ever-changing landscapes of genetic variation. METHODS:  We performed whole-genome sequencing of 69 P. falciparum isolates from Malawi and used ...

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

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

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

    Hanxiang Gao

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

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

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

    2009-01-01

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

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

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

    2005-09-01

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

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

    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

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

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

    2007-01-01

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

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

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

    2009-05-01

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

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

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

    2012-03-19

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

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

    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.

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

    Alfred Amambua-Ngwa

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

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

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

    2005-01-01

    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...

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

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

    2010-10-15

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

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

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

    2016-08-01

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

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

    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.

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

    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

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

    Rasmus Nielsen

    2005-06-01

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

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

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

    2005-12-30

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

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

    Chiao-Ling Lo

    2016-08-01

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

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

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

    2016-08-01

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

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

    Xin-Sheng Hu

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

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

    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.

  4. Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture

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

    2014-01-01

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

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

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

    2015-10-01

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

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

    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.

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

    Avinash M. Veerappa

    2016-01-01

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

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

    Cecilia M Lindgren

    2009-06-01

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

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

    Lei Zhang

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

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

    Qin Li

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

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

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

    2003-01-01

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

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

    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.

  13. Reproducibility of the sella turcica landmark in three dimensions using a sella turcica-specific reference system

    Pittayapat, Pisha; Jacobs, Reinhilde [University Hospitals Leuven, University of Leuven, Leuven (Belgium); Odri, Guillaume A. [Service de Chirurgie Orthopedique et Traumatologique, Centre Hospitalier Regional d' Orleans, Orleans Cedex2 (France); De Faria Vasconcelos, Karla [Dept. of Oral Diagnosis, Division of Oral Radiology, Piracicaba Dental School, University of Campinas, Sao Paulo (Brazil); Willems, Guy [Dept. of Oral Health Sciences, Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, University of Leuven, Leuven (Belgium); Olszewski, Raphael [Dept. of Oral and Maxillofacial Surgery, Cliniques Universitaires Saint Luc, Universite Catholique de Louvain, Brussels (Belgium)

    2015-03-15

    This study was performed to assess the reproducibility of identifying the sella turcica landmark in a three-dimensional (3D) model by using a new sella-specific landmark reference system. Thirty-two cone-beam computed tomographic scans (3D Accuitomo 170, J. Morita, Kyoto, Japan) were retrospectively collected. The 3D data were exported into the Digital Imaging and Communications in Medicine standard and then imported into the Maxilim software (Medicim NV, Sint-Niklaas, Belgium) to create 3D surface models. Five observers identified four osseous landmarks in order to create the reference frame and then identified two sella landmarks. The x, y, and z coordinates of each landmark were exported. The observations were repeated after four weeks. Statistical analysis was performed using the multiple paired t-test with Bonferroni correction (intraobserver precision: p<0.005, interobserver precision: p<0.0011). The intraobserver mean precision of all landmarks was <1 mm. Significant differences were found when comparing the intraobserver precision of each observer (p<0.005). For the sella landmarks, the intraobserver mean precision ranged from 0.43±0.34 mm to 0.51±0.46 mm. The intraobserver reproducibility was generally good. The overall interobserver mean precision was <1 mm. Significant differences between each pair of observers for all anatomical landmarks were found (p<0.0011). The interobserver reproducibility of sella landmarks was good, with >50% precision in locating the landmark within 1 mm. A newly developed reference system offers high precision and reproducibility for sella turcica identification in a 3D model without being based on two-dimensional images derived from 3D data.

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

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

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

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

    2003-01-01

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

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

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

    2003-01-01

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

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

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

    2009-01-01

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

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

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

    2009-01-01

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

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

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

    2000-03-01

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

  20. Using Local Symmetry for Landmark Selection

    Kootstra, Gert; de Jong, Sjoerd; Schomaker, Lambert R. B.; Fritz, M; Schiele, B; Piater, JH

    2009-01-01

    Most visual Simultaneous Localization And Mapping (SLAM) methods use interest points as landmarks in their maps of the environment. Often the interest points are detected using contrast features, for instance those of the Scale Invariant Feature Transform (SIFT). The SIFT interest points, however, h

  1. Automated landmark-guided deformable image registration

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

    Yannick Allanore

    2011-07-01

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

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

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

    2003-11-01

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

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

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

    1996-03-15

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

  5. Strategies in Landmark Use by Children, Adults, and Marmoset Monkeys

    MacDonald, Suzanne E.; Spetch, Marcia L.; Kelly, Debbie M.; Cheng, Ken

    2004-01-01

    Common marmosets ("Callithrix jacchus jacchus"), human children, and human adults learned to find a goal that was located in the center of a square array of four identical landmarks. The location of the landmark array and corresponding goal varied across trials, so the task could not be solved without using the landmark array. In Experiment 1, a…

  6. Autonomous Robot Navigation based on Visual Landmarks

    Livatino, Salvatore

    2005-01-01

    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...... 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...... 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...

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

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

    1998-01-01

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

  8. Mapped Landmark Algorithm for Precision Landing

    Johnson, Andrew; Ansar, Adnan; Matthies, Larry

    2007-01-01

    A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.

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

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

    2010-07-01

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

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

    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.

  11. Longwall automation - an ACARP Landmark Project

    Kelly, M.; Hainsworth, D.; Lever, P.; Gurgenci, H. [CSIRO Exploration and Mining, Kenmore, Qld. (Australia)

    2002-07-01

    A Landmark Longwall Automation project was commenced in July 2001. The major outcome of automation using on-face observation has been divided into ten outcome areas that have been fully scoped for a three-year initial project life. A major facilitating technology has been the implementation of inertial navigation system (INS) technology that can map the shearer position in 3D. A focus of the project is to deliver a system that is at least as productive as the current most productive manually controlled longwall face. 4 refs., 6 figs.

  12. Landmark experiments in twentieth-century physics

    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

  13. Efficient and Accurate Indoor Localization Using Landmark Graphs

    Gu, F.; Kealy, A.; Khoshelham, K.; Shang, J.

    2016-06-01

    Indoor localization is important for a variety of applications such as location-based services, mobile social networks, and emergency response. Fusing spatial information is an effective way to achieve accurate indoor localization with little or with no need for extra hardware. However, existing indoor localization methods that make use of spatial information are either too computationally expensive or too sensitive to the completeness of landmark detection. In this paper, we solve this problem by using the proposed landmark graph. The landmark graph is a directed graph where nodes are landmarks (e.g., doors, staircases, and turns) and edges are accessible paths with heading information. We compared the proposed method with two common Dead Reckoning (DR)-based methods (namely, Compass + Accelerometer + Landmarks and Gyroscope + Accelerometer + Landmarks) by a series of experiments. Experimental results show that the proposed method can achieve 73% accuracy with a positioning error less than 2.5 meters, which outperforms the other two DR-based methods.

  14. High-precision Detection of Facial Landmarks to Estimate Head Motions Based on Vision Models

    Xiaohong W. Gao

    2007-01-01

    Full Text Available A new approach of determination of head movement is presented from the pictures recorded via digital cameras monitoring the scanning processing of PET. Two human vision models of CIECAMs and BMV are applied to segment the face region via skin colour and to detect local facial landmarks respectively. The developed algorithms are evaluated on the pictures (n=12 monitoring a subject’s head while simulating PET scanning captured by two calibrated cameras (located in the front and left side from a subject. It is shown that centers of chosen facial landmarks of eye corners and middle point of nose basement have been detected with very high precision (1 0.64 pixels. Three landmarks on pictures received by the front camera and two by the side camera have been identified. Preliminary results on 2D images with known moving parameters show that movement parameters of rotations and translations along X, Y, and Z directions can be obtained very accurately via the described methods.

  15. Landmark-based autonomous navigation for pinpoint planetary landing

    Xu, Chao; Wang, Dayi; Huang, Xiangyu

    2016-12-01

    A landmark-based autonomous navigation scheme is presented for pinpoint planetary landing. The dynamic model is built on the basis of measurements from Inertial Measurement Unit. Measurement models of landmarks with known coordinates and landmarks with unknown coordinates extracted from sequential descent images are developed and used to calculated the state corrections in Extend Kalman Filter, respectively. Then, the corrections are fused by a covariance intersection fusion algorithm to perform state updates. The tight coupling of the two types of landmark observations yields accurate and robust state estimates. Extensive simulations are performed, which confirm the validity of the proposed navigation scheme and analyze the effects of factors, such as the horizonal position errors and the densities of landmarks with known coordinates and the roughness of the landing surface, on the navigation accuracy.

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

    Moradi Mohammad Hossein

    2012-02-01

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

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

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

    2016-03-01

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

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

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

    2009-02-01

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

  19. A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer

    Yue Gen

    2006-10-01

    Full Text Available Abstract Background Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL and environmental factors. It is usually difficult to dissect the genetic and environmental effects. Asian seabass (Lates calcarifer is an important marine foodfish species with a compact genome (~700 Mb. The recent construction of a first generation linkage map of Asian seabass with 240 microsatellites provides a good opportunity to determine the number and position of QTL, and the magnitude of QTL effects with a genome scan. Results We conducted a genome scan for QTL affecting body weight, standard length and condition factors in an F1 family containing 380 full-sib individuals from a breeding stock by using 97 microsatellites evenly covering 24 chromosomes. Interval mapping and multiple QTL model mapping detected five significant and 27 suggestive QTL on ten linkage groups (LGs. Among the five significant QTL detected, three (qBW2-a, qTL2-a and qSL2-a controlling body weight, total and standard length respectively, were mapped on the same region near Lca287 on LG2, and explained 28.8, 58.9 and 59.7% of the phenotypic variance. The other two QTL affecting body weight, qBW2-b and qBW3, were located on LG2 and 3, and accounted for 6.4 and 8.8% of the phenotypic variance. Suggestive QTL associated with condition factors are located on six different LGs. Conclusion This study presents the first example of QTL detection for growth-related traits in an F1 family of a marine foodfish species. The results presented here will enable further fine-mapping of these QTL for marker-assisted selection of the Asian seabass, eventually identifying individual genes responsible for growth-related traits.

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

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

    2010-06-01

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

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

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

    2016-01-01

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

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

    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.

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

    Kristy R Crooks

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

  4. Landmark detection and coupled patch registration for cardiac motion tracking

    Wang, Haiyan; Shi, Wenzhe; Zhuang, Xiahai; Wu, Xianliang; Tung, Kai-Pin; Ourselin, Sebastien; Edwards, Philip; Rueckert, Daniel

    2013-03-01

    Increasing attention has been focused on the estimation of the deformation of the endocardium to aid the diagnosis of cardiac malfunction. Landmark tracking can provide sparse, anatomically relevant constraints to help establish correspondences between images being tracked or registered. However, landmarks on the endocardium are often characterized by ambiguous appearance in cardiac MR images which makes the extraction and tracking of these landmarks problematic. In this paper we propose an automatic framework to select and track a sparse set of distinctive landmarks in the presence of relatively large deformations in order to capture the endocardial motion in cardiac MR sequences. To achieve this a sparse set of the landmarks is identified using an entropy-based approach. In particular we use singular value decomposition (SVD) to reduce the search space and localize the landmarks with relatively large deformation across the cardiac cycle. The tracking of the sparse set of landmarks is performed simultaneously by optimizing a two-stage Markov Random Field (MRF) model. The tracking result is further used to initialize registration based dense motion tracking. We have applied this framework to extract a set of landmarks at the endocardial border of the left ventricle in MR image sequences from 51 subjects. Although the left ventricle undergoes a number of different deformations, we show how the radial, longitudinal motion and twisting of the endocardial surface can be captured by the proposed approach. Our experiments demonstrate that motion tracking using sparse landmarks can outperform conventional motion tracking by a substantial amount, with improvements in terms of tracking accuracy of 20:8% and 19:4% respectively.

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

    Ting Wang

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

  6. TIBIAL LANDMARKS IN ACL ANATOMIC REPAIR

    M. V. Demesсhenko

    2016-01-01

    Full Text Available Purpose: to identify anatomical landmarks on tibial articular surface to serve as reference in preparing tibial canal with respect to the center of ACL footprint during single bundle arthroscopic repair.Materials and methods. Twelve frozen knee joint specimens and 68 unpaired macerated human tibia were studied using anatomical, morphometric, statistical methods as well as graphic simulation.Results. Center of the tibial ACL footprint was located 13,1±1,7 mm anteriorly from posterior border of intercondylar eminence, at 1/3 of the distance along the line connecting apexes of internal and external tubercles and 6,1±0,5 mm anteriorly along the perpendicular raised to this point.Conclusion. Internal and external tubercles, as well as posterior border of intercondylar eminence can be considered as anatomical references to determine the center of the tibial ACL footprint and to prepare bone canals for anatomic ligament repair.

  7. Pterion: An anatomical variation and surgical landmark

    Prashant E Natekar

    2011-01-01

    Full Text Available Introduction : The frontal and the parietal bones superiorly and the greater wing of the sphenoid and the squamous temporal inferiorly of one side meet at an H-shaped sutural junction termed the pterion. This is an important anatomical and anthropological landmark as it overlies both the anterior branch of middle meningeal artery and the lateral fissure of the cerebral hemisphere. The knowledge of sutural joints between frontal, parietal, sphenoid and temporal bones at pterion is clinically, radiologically and surgically important during surgical interventions involving burr hole surgeries. Materials and Methods : Study performed on 150 dry temporal bones. The pterion, and its sutural articulations with frontal, parietal, sphenoid and temporal bones and also anatomical variations, if any, were studied. Results : Four types of pterion, i.e. sphenoparietal, frontotemporal, stellate and epipteric, were observed. Conclusions : The knowledge of the variations of pterion and its surgical anatomy, in Indian population are important for surgeons operating in the fieldThe present study will also contribute additional information of skull bone fractures in infancy and early childhood, which may be associated with large intersutural bones giving false appearance of fracture radiologically and also during surgical interventions involving burr hole surgeries, as their extensions may lead to continuation of fracture lines.

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

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

    2016-10-01

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

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

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

    2004-11-01

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

  10. Virtual skeletal complex model- and landmark-guided orthognathic surgery system.

    Lee, Sang-Jeong; Woo, Sang-Yoon; Huh, Kyung-Hoe; Lee, Sam-Sun; Heo, Min-Suk; Choi, Soon-Chul; Han, Jeong Joon; Yang, Hoon Joo; Hwang, Soon Jung; Yi, Won-Jin

    2016-05-01

    In this study, correction of the maxillofacial deformities was performed by repositioning bone segments to an appropriate location according to the preoperative planning in orthognathic surgery. The surgery was planned using the patient's virtual skeletal models fused with optically scanned three-dimensional dentition. The virtual maxillomandibular complex (MMC) model of the patient's final occlusal relationship was generated by fusion of the maxillary and mandibular models with scanned occlusion. The final position of the MMC was simulated preoperatively by planning and was used as a goal model for guidance. During surgery, the intraoperative registration was finished immediately using only software processing. For accurate repositioning, the intraoperative MMC model was visualized on the monitor with respect to the simulated MMC model, and the intraoperative positions of multiple landmarks were also visualized on the MMC surface model. The deviation errors between the intraoperative and the final positions of each landmark were visualized quantitatively. As a result, the surgeon could easily recognize the three-dimensional deviation of the intraoperative MMC state from the final goal model without manually applying a pointing tool, and could also quickly determine the amount and direction of further MMC movements needed to reach the goal position. The surgeon could also perform various osteotomies and remove bone interference conveniently, as the maxillary tracking tool could be separated from the MMC. The root mean square (RMS) difference between the preoperative planning and the intraoperative guidance was 1.16 ± 0.34 mm immediately after repositioning. After surgery, the RMS differences between the planning and the postoperative computed tomographic model were 1.31 ± 0.28 mm and 1.74 ± 0.73 mm for the maxillary and mandibular landmarks, respectively. Our method provides accurate and flexible guidance for bimaxillary orthognathic surgery based on

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

    Roberto Amato

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

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

    Yuri Tani Utsunomiya

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

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

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

    2007-08-01

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

  14. Indoor monocular mobile robot navigation based on color landmarks

    LUO Yuan; ZHANG Bai-sheng; ZHANG Yi; LI Ling

    2009-01-01

    A robot landmark navigation system based on monocular camera was researched theoretically and experimentally. First the landmark setting and its data structure in programming was given; then the coordinates of them getting by robot and global localization of the robot was described; finally experiments based on Pioneer III mobile robot show that this system can work well at different topographic situation without lose of signposts.

  15. Influence of Head Motion on the Accuracy of 3D Reconstruction with Cone-Beam CT: Landmark Identification Errors in Maxillofacial Surface Model

    Song, Jin-Myoung; Cho, Jin-Hyoung

    2016-01-01

    Purpose The purpose of this study was to investigate the influence of head motion on the accuracy of three-dimensional (3D) reconstruction with cone-beam computed tomography (CBCT) scan. Materials and Methods Fifteen dry skulls were incorporated into a motion controller which simulated four types of head motion during CBCT scan: 2 horizontal rotations (to the right/to the left) and 2 vertical rotations (upward/downward). Each movement was triggered to occur at the start of the scan for 1 second by remote control. Four maxillofacial surface models with head motion and one control surface model without motion were obtained for each skull. Nine landmarks were identified on the five maxillofacial surface models for each skull, and landmark identification errors were compared between the control model and each of the models with head motion. Results Rendered surface models with head motion were similar to the control model in appearance; however, the landmark identification errors showed larger values in models with head motion than in the control. In particular, the Porion in the horizontal rotation models presented statistically significant differences (P CBCT scan might cause landmark identification errors on the 3D surface model in relation to the direction of the scanner rotation. Clinicians should take this into consideration to prevent patient movement during CBCT scan, particularly horizontal movement. PMID:27065238

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

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

    2016-01-01

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

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

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

    2014-02-01

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

  18. A new guide to the human genome

    Marx, J.

    1995-12-22

    The construction of a detailed physical map of the human genome, with 15,000 sequence-based landmarks, opens the door to genome-wide sequencing. This article summarizes the researchers, the research, the approach, and the usefulness of a new physical map of the human genome.

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

    Nicole Soranzo

    2009-04-01

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

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

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

    2011-03-01

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

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

    Gray Joanna

    2010-11-01

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

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

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

    2014-12-01

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

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

    Shong Huang

    2013-04-01

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

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

    Yin-Ju Lien

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

  5. The reliability of tablet computers in depicting maxillofacial radiographic landmarks

    Tadinada, Aditya; Mahdian, Mina; Sheth, Sonam; Chandhoke, Taranpreet K.; Gopalakrishna, Aadarsh; Potluri, Anitha; Yadav, Sumit [University of Connecticut School of Dental Medicine, Farmington (United States)

    2015-09-15

    This study was performed to evaluate the reliability of the identification of anatomical landmarks in panoramic and lateral cephalometric radiographs on a standard medical grade picture archiving communication system (PACS) monitor and a tablet computer (iPad 5). A total of 1000 radiographs, including 500 panoramic and 500 lateral cephalometric radiographs, were retrieved from the de-identified dataset of the archive of the Section of Oral and Maxillofacial Radiology of the University Of Connecticut School Of Dental Medicine. Major radiographic anatomical landmarks were independently reviewed by two examiners on both displays. The examiners initially reviewed ten panoramic and ten lateral cephalometric radiographs using each imaging system, in order to verify interoperator agreement in landmark identification. The images were scored on a four-point scale reflecting the diagnostic image quality and exposure level of the images. Statistical analysis showed no significant difference between the two displays regarding the visibility and clarity of the landmarks in either the panoramic or cephalometric radiographs. Tablet computers can reliably show anatomical landmarks in panoramic and lateral cephalometric radiographs.

  6. WIKIPEDIA ENTRIES AS A SOURCE OF CAR NAVIGATION LANDMARKS

    N. Binski

    2016-06-01

    Full Text Available Car navigation system devices provide today with an easy and simple solution to the basic concept of reaching a destination. Although these systems usually achieve this goal, they still deliver a limited and poor sequence of instructions that do not consider the human nature of using landmarks during wayfinding. This research paper addresses the concept of enriching navigation route instructions by adding supplementary route information in the form of landmarks. We aim at using a contributed source of landmarks information, which is easy to access, available, show high update rate, and have a large scale of information. For this, Wikipedia was chosen, since it represents the world’s largest free encyclopaedia that includes information about many spatial entities. A survey and classification of available landmarks is implemented, coupled with ranking algorithms based on the entries’ categories and attributes. These are aimed at retrieving the most relevant landmark information required that are valuable for the enrichment of a specific navigation route. The paper will present this methodology, together with examples and results, showing the feasibility of using this concept and its potential of enriching navigation processes.

  7. Landmark learning by the Ozark zigzag salamander Plethodon angusticlavius

    Adam L. CRANE, Alicia MATHIS

    2011-08-01

    Full Text Available Although salamanders have been shown to respond to classical conditioning, spatial learning has been largely unstudied. We tested whether salamanders could learn to locate foraging areas by using landmarks. We trained 10 salamanders Plethodon angusticlavius to use landmarks (small rocks to locate patches within the arena containing food (blackworms Lumbriculus variegatus. At the corners of each square testing arena were four plastic dishes, one containing blackworms and the other three empty. A rock was placed in front of the dish containing blackworms, and the location of the food-dish was randomly chosen for each training trial. A control group was also trained to feed on blackworms in the presence of a rock, but the rock was positioned randomly among the four dish locations so that the rock was not a reliable landmark for the worms. Although the length of the training period for individual salamanders varied (22–38 trainings per individual, the mean number of trainings for salamanders in the control and experimental groups was equal (30 training trials. During testing, no blackworms were present to eliminate any visual or chemical cues emanating directly from the prey. Individuals trained with the rock landmarks spent significantly more time in the area of the landmark than did control salamanders [Current Zoology 57 (4: 485–490, 2011].

  8. Influence of Head Motion on the Accuracy of 3D Reconstruction with Cone-Beam CT: Landmark Identification Errors in Maxillofacial Surface Model.

    Kyung-Min Lee

    Full Text Available The purpose of this study was to investigate the influence of head motion on the accuracy of three-dimensional (3D reconstruction with cone-beam computed tomography (CBCT scan.Fifteen dry skulls were incorporated into a motion controller which simulated four types of head motion during CBCT scan: 2 horizontal rotations (to the right/to the left and 2 vertical rotations (upward/downward. Each movement was triggered to occur at the start of the scan for 1 second by remote control. Four maxillofacial surface models with head motion and one control surface model without motion were obtained for each skull. Nine landmarks were identified on the five maxillofacial surface models for each skull, and landmark identification errors were compared between the control model and each of the models with head motion.Rendered surface models with head motion were similar to the control model in appearance; however, the landmark identification errors showed larger values in models with head motion than in the control. In particular, the Porion in the horizontal rotation models presented statistically significant differences (P < .05. Statistically significant difference in the errors between the right and left side landmark was present in the left side rotation which was opposite direction to the scanner rotation (P < .05.Patient movement during CBCT scan might cause landmark identification errors on the 3D surface model in relation to the direction of the scanner rotation. Clinicians should take this into consideration to prevent patient movement during CBCT scan, particularly horizontal movement.

  9. Multirobot FastSLAM Algorithm Based on Landmark Consistency Correction

    Shi-Ming Chen

    2014-01-01

    Full Text Available Considering the influence of uncertain map information on multirobot SLAM problem, a multirobot FastSLAM algorithm based on landmark consistency correction is proposed. Firstly, electromagnetism-like mechanism is introduced to the resampling procedure in single-robot FastSLAM, where we assume that each sampling particle is looked at as a charged electron and attraction-repulsion mechanism in electromagnetism field is used to simulate interactive force between the particles to improve the distribution of particles. Secondly, when multiple robots observe the same landmarks, every robot is regarded as one node and Kalman-Consensus Filter is proposed to update landmark information, which further improves the accuracy of localization and mapping. Finally, the simulation results show that the algorithm is suitable and effective.

  10. Does spatial locative comprehension predict landmark-based navigation?

    Laura Piccardi

    Full Text Available In the present study we investigated the role of spatial locative comprehension in learning and retrieving pathways when landmarks were available and when they were absent in a sample of typically developing 6- to 11-year-old children. Our results show that the more proficient children are in understanding spatial locatives the more they are able to learn pathways, retrieve them after a delay and represent them on a map when landmarks are present in the environment. These findings suggest that spatial language is crucial when individuals rely on sequences of landmarks to drive their navigation towards a given goal but that it is not involved when navigational representations based on the geometrical shape of the environment or the coding of body movements are sufficient for memorizing and recalling short pathways.

  11. Does spatial locative comprehension predict landmark-based navigation?

    Piccardi, Laura; Palermo, Liana; Bocchi, Alessia; Guariglia, Cecilia; D'Amico, Simonetta

    2015-01-01

    In the present study we investigated the role of spatial locative comprehension in learning and retrieving pathways when landmarks were available and when they were absent in a sample of typically developing 6- to 11-year-old children. Our results show that the more proficient children are in understanding spatial locatives the more they are able to learn pathways, retrieve them after a delay and represent them on a map when landmarks are present in the environment. These findings suggest that spatial language is crucial when individuals rely on sequences of landmarks to drive their navigation towards a given goal but that it is not involved when navigational representations based on the geometrical shape of the environment or the coding of body movements are sufficient for memorizing and recalling short pathways.

  12. MICROSURGICAL LANDMARKS IN MINIMALLY INVASIVE TRANSFORAMINAL LUMBAR INTERBODY FUSION

    Javier Quillo-Olvera

    2015-12-01

    Full Text Available Microsurgical landmarks of the facet joint complex were defined to provide guidance and security within the tubular retractor during transforaminal surgery. A retrospective observational study was performed in segments L4-L5 by the left side approach. Microsurgical relevant photos, anatomical models and drawing were used to expose the suggested landmarks. The MI-TLIF technique has advantages compared with conventional open TLIF technique, however minimally invasive technique implies lack of security for the surgeon due to the lack of defined microanatomical landmarks compared to open spine surgery, and disorientation within the tubular retractor, the reason why to have precise microsurgical references and its recognition within the surgical field provide speed and safety when performing minimally invasive technique.

  13. Automated localization of vertebra landmarks in MRI images

    Pai, Akshay; Narasimhamurthy, Anand; Rao, V. S. Veeravasarapu; Vaidya, Vivek

    2011-03-01

    The identification of key landmark points in an MR spine image is an important step for tasks such as vertebra counting. In this paper, we propose a template matching based approach for automatic detection of two key landmark points, namely the second cervical vertebra (C2) and the sacrum from sagittal MR images. The approach is comprised of an approximate localization of vertebral column followed by matching with appropriate templates in order to detect/localize the landmarks. A straightforward extension of the work described here is an automated classification of spine section(s). It also serves as a useful building block for further automatic processing such as extraction of regions of interest for subsequent image processing and also in aiding the counting of vertebra.

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

    Haque, Mohammad Ahsanul; Nasrollahi, Kamal; Moeslund, Thomas B.

    2015-01-01

    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......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...

  15. Spatial Language and Children’s Spatial Landmark Use

    Amber A. Ankowski

    2012-01-01

    Full Text Available We examined how spatial language affected search behavior in a landmark spatial search task. In Experiment 1, two- to six-year-old children were trained to find a toy in the center of a square array of four identical landmarks. Children heard one of three spatial language cues once during the initial training trial (“here,” “in the middle,” “next to this one”. After search performance reached criterion, children received a probe test trial in which the landmark array was expanded. In Experiment 2, two- to four-year-old children participated in the search task and also completed a language comprehension task. Results revealed that children’s spatial language comprehension scores and spatial language cues heard during training trials were related to children’s performance in the search task.

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

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

    2007-10-01

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

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

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

    2008-01-01

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

  18. "Direct DICOM Slice Landmarking" A Novel Research Technique to Quantify Skeletal Changes in Orthognathic Surgery.

    Anas Almukhtar

    Full Text Available The limitations of the current methods of quantifying the surgical movements of facial bones inspired this study. The aim of this study was the assessment of the accuracy and reproducibility of directly landmarking of 3D DICOM images (Digital Imaging and Communications in Medicine to quantify the changes in the jaw bones following surgery. The study was carried out on plastic skull to simulate the surgical movements of the jaw bones. Cone beam CT scans were taken at 3mm, 6mm, and 9mm maxillary advancement; together with a 2mm, 4mm, 6mm and 8mm "down graft" which in total generated 12 different positions of the maxilla for the analysis. The movements of the maxilla were calculated using two methods, the standard approach where distances between surface landmarks on the jaw bones were measured and the novel approach where measurements were taken directly from the internal structures of the corresponding 3D DICOME slices. A one sample t-test showed that there was no statistically significant difference between the two methods of measurements for the y and z directions, however, the x direction showed a significant difference. The mean difference between the two absolute measurements were 0.34±0.20mm, 0.22±0.16mm, 0.18±0.13mm in the y, z and x directions respectively. In conclusion, the direct landmarking of 3D DICOM image slices is a reliable, reproducible and informative method for assessment of the 3D skeletal changes. The method has a clear clinical application which includes the analysis of the jaw movements "orthognathic surgery" for the correction of facial deformities.

  19. A field study investigating effects of landmarks on territory size and shape.

    Suriyampola, Piyumika S; Eason, Perri K

    2014-01-01

    Few studies have examined how landmarks affect territories' fundamental characteristics. In this field study, we investigated effects of landmarks on territory size, shape and location in a cichlid fish (Amatitlania siquia). We provided cans as breeding sites and used plastic plants as landmarks. During 10 min trials, we recorded locations where residents chased intruders and used those locations to outline and measure the territory. In two experiments, we observed pairs without landmarks and with either a point landmark (one plant) or linear landmark (four plants) placed near the nest can. We alternated which trial occurred first and performed the second trial 24 h after the first. Territories were approximately round without landmarks or with a point landmark but were significantly more elongated when we added a linear landmark. Without landmarks, nests were centrally located; however, with any landmark, pairs set territory boundaries closer to the landmark and thus the nest. Territory size was significantly reduced in the presence of any landmark. This reduction suggests that a smaller territory with well-defined boundaries has greater benefits than a larger territory with less well-defined borders.

  20. 36 CFR 62.8 - Natural landmark designation removal.

    2010-07-01

    ... the site did not meet the criteria for national significance at the time of designation; (ii) When the... whether the NPS considers the documentation sufficient to consider removal of the natural landmark... submits a recommendation for removal to the National Park System Advisory Board. The Advisory...

  1. Adaptive Landmark-Based Navigation System Using Learning Techniques

    Zeidan, Bassel; Dasgupta, Sakyasingha; Wörgötter, Florentin

    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...

  2. Landmark Finding Algorithms for Indoor Autonomous Mobile Robot Localization

    L. Tóth

    2015-12-01

    Full Text Available This contribution is oriented to ways of computer vision algorithms for mobile robot localization in internal and external agricultural environment. The main aim of this work was to design, create, verify and evaluate speed and functionality of computer vision localization algorithm. An input colour camera data and depth data were captured by MS® Kinect sensor that was mounted on 6-wheel-drive mobile robot chassis. The design of the localization algorithm was focused to the most significant blobs and points (landmarks on the colour picture. Actual coordinates of autonomous mobile robot were calculated out from measured distances (depth sensor and calculated angles (RGB camera with respect to landmark points. Time measurement script was used to compare the speed of landmark finding algorithm for localization in case of one and more landmarks on picture. The main source code was written in MS Visual studio C# programming language with Microsoft.Kinect.1.7.dll on Windows based PC. Algorithms described in this article were created for a future development of an autonomous agronomical m obile robot localization and control.

  3. Surface anatomy and surface landmarks for thoracic surgery: Part II.

    Smith, Shona E; Darling, Gail E

    2011-05-01

    Surface anatomy is an integral part of a thoracic surgeon's armamentarium to assist with the diagnosis, staging, and treatment of thoracic pathology. As reviewed in this article, the surface landmarks of the lungs, heart, great vessels, and mediastinum are critical for appropriate patient care and should be learned in conjunction with classic anatomy.

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

    Dang, Xuan-Hong; Ong, Kok-Leong; Lee, Vincent

    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 thresho...

  5. 36 CFR 65.4 - National Historic Landmark criteria.

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false National Historic Landmark criteria. 65.4 Section 65.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE... anthropologists familiar with the broad range of the nation's resources and historical themes. The...

  6. Recreation in the United States. National Historic Landmark Theme Study.

    Charleton, James H.

    This report examines a number of outstanding and illustrative examples of a broad range of properties representing recreational activities that suggest themselves for possible National Historic Landmark recognition. The properties described in the study have been selected to represent places and activities that have had a major impact on American…

  7. Using Desktop Virtual Environments To Investigate the Role of Landmarks.

    Jansen-Osmann, Petra

    2002-01-01

    Discusses research in spatial cognition that uses computer-simulated three dimensional environments and evaluates the use of virtual desktop environments by replicating an experiment which was formerly done in a laboratory or real world setting. Investigates the role of landmarks when acquiring route knowledge in a system of paths. (Author/LRW)

  8. Quantitative assessment of regional left ventricular motion using endocardial landmarks

    C.J. Slager (Cornelis); T.E.H. Hooghoudt (Ton); P.W.J.C. Serruys (Patrick); J.C.H. Schuurbiers (Johan); J.H.C. Reiber (Johan); G.T. Meester (Geert); P.D. Verdouw (Pieter); P.G. Hugenholtz (Paul)

    1986-01-01

    textabstractIn this study the hypothesis is tested that the motion pattern of small anatomic landmarks, recognizable at the left ventricular endocardial border in the contrast angiocardiogram, reflects the motion of the endocardial wall. To verify this, minute metal markers were inserted in the endo

  9. Learning-based landmarks detection for osteoporosis analysis

    Cheng, Erkang; Zhu, Ling; Yang, Jie; Azhari, Azhari; Sitam, Suhardjo; Liang, Xin; Megalooikonomou, Vasileios; Ling, Haibin

    2016-03-01

    Osteoporosis is the common cause for a broken bone among senior citizens. Early diagnosis of osteoporosis requires routine examination which may be costly for patients. A potential low cost diagnosis is to identify a senior citizen at high risk of osteoporosis by pre-screening during routine dental examination. Therefore, osteoporosis analysis using dental radiographs severs as a key step in routine dental examination. The aim of this study is to localize landmarks in dental radiographs which are helpful to assess the evidence of osteoporosis. We collect eight landmarks which are critical in osteoporosis analysis. Our goal is to localize these landmarks automatically for a given dental radiographic image. To address the challenges such as large variations of appearances in subjects, in this paper, we formulate the task into a multi-class classification problem. A hybrid feature pool is used to represent these landmarks. For the discriminative classification problem, we use a random forest to fuse the hybrid feature representation. In the experiments, we also evaluate the performances of individual feature component and the hybrid fused feature. Our proposed method achieves average detection error of 2:9mm.

  10. Career Landmarks in Science: Individual Differences and Interdisciplinary Contrasts.

    Simonton, Dean Keith

    1991-01-01

    Examined the location of the first, best, and last contributions of creative careers. Hypotheses specified the ways in which these landmarks should vary according to individual differences and interdisciplinary contrasts. Hypotheses were confirmed for scientists and inventors. Results lead to further theoretical constraints, new predictions, and…

  11. Place cells are more strongly tied to landmarks in deep than in superficial CA1

    Geiller, Tristan; Fattahi, Mohammad; Choi, June-Seek; Royer, Sébastien

    2017-01-01

    Environmental cues affect place cells responses, but whether this information is integrated versus segregated in distinct hippocampal cell populations is unclear. Here, we show that, in mice running on a treadmill enriched with visual-tactile landmarks, place cells are more strongly controlled by landmark-associated sensory inputs in deeper regions of CA1 pyramidal layer (CA1d). Many cells in CA1d display several firing fields correlated with landmarks, mapping positions slightly before or within the landmarks. Supporting direct involvement of sensory inputs, their firing fields show instantaneous responses to landmark manipulations, persist through change of context, and encode landmark identity and saliency. In contrast, cells located superficially in the pyramidal layer have single firing fields, are context specific and respond with slow dynamics to landmark manipulations. These findings suggest parallel and anatomically segregated circuits within CA1 pyramidal layer, with variable ties to landmarks, allowing flexible representation of spatial and non-spatial information. PMID:28218283

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

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

    2006-04-01

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

  13. A physical map of the mouse genome

    Gregory, SG; Sekhon, M; Schein, J; Zhao, SY; Osoegawa, K; Scott, CE; Evans, RS; Burridge, PW; Cox, TV; Fox, CA; Hutton, RD; Mullenger, IR; Phillips, KJ; Smith, J; Stalker, J; Threadgold, GJ; Birney, E; Wylie, K; Chinwalla, A; Wallis, J; Hillier, L; Carter, J; Gaige, T; Jaeger, S; Kremitzki, C; Layman, D; McGrane, R; Mead, K; Walker, R; Jones, S; Smith, M; Asano, J; Bosdet, I; Chan, S; Chittaranjan, S; Chiu, R; Fjell, C; Fuhrmann, D; Girn, N; Gray, C; Guin, R; Hsiao, L; Krzywinski, M; Kutsche, R; Lee, SS; Mathewson, C; McLeavy, C; Messervier, S; Ness, S; Pandoh, P; Prabhu, AL; Saeedi, P; Smailus, D; Spence, L; Stott, J; Taylor, S; Terpstra, W; Tsai, M; Vardy, J; Wye, N; Yang, G; Shatsman, S; Ayodeji, B; Geer, K; Tsegaye, G; Shvartsbeyn, A; Gebregeorgis, E; Krol, M; Russell, D; Overton, L; Malek, JA; Holmes, M; Heaney, M; Shetty, J; Feldblyum, T; Nierman, WC; Catanese, JJ; Hubbard, T; Waterston, RH; Rogers, J; de Jong, PJ; Fraser, CM; Marra, M; McPherson, JD; Bentley, DR

    2002-01-01

    A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs w

  14. Cephalometric landmark variability among orthodontists and dentomaxillofacial radiologists: a comparative study

    2015-01-01

    Purpose The aim this study was to compare the accuracy of orthodontists and dentomaxillofacial radiologists in identifying 17 commonly used cephalometric landmarks, and to determine the extent of variability associated with each of those landmarks. Materials and Methods Twenty digital lateral cephalometric radiographs were evaluated by two groups of dental specialists, and 17 cephalometric landmarks were identified. The x and y coordinates of each landmark were recorded. The mean value for ea...

  15. 78 FR 13377 - Landmarks Committee of the National Park System Advisory Board Meeting

    2013-02-27

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... INFORMATION: The purpose of the meeting of the Landmarks Committee of the National Park System Advisory Board... Historic Landmarks to the National Park System Advisory Board at a subsequent meeting at a place and...

  16. Cephalometric landmark variability among orthodontists and dentomaxillofacial radiologists: a comparative study

    Durao, Ana Paula Reis; Ferreira, Afonso P. [Dept.of Faculty of Dental Medicine, University of Porto, Porto (Portugal); Morosolli, Aline [Dept.of Surgery, Dentistry School, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul (Brazil); Pittayapat, Pisha [Dept.of Radiology, Faculty of Dentistry, Chulalongkorn University, Bangkok (Thailand); Bolstad, Napat [Dept.of Clinical Dentistry, Faculty of Health Science, UiT The Arctic University of Norway, Tromso (Norway); Jacobs, Reinhilde [Dept.of Oral Imaging Center, OMFS-IMPATH Research Group, Dept. of Imaging and Pathology, Faculty of Medicine, University of Leuven, Leuven (Belgium)

    2015-12-15

    The aim this study was to compare the accuracy of orthodontists and dentomaxillofacial radiologists in identifying 17 commonly used cephalometric landmarks, and to determine the extent of variability associated with each of those landmarks. Twenty digital lateral cephalometric radiographs were evaluated by two groups of dental specialists, and 17 cephalometric landmarks were identified. The x and y coordinates of each landmark were recorded. The mean value for each landmark was considered the best estimate and used as the standard. Variation in measurements of the distance between landmarks and measurements of the angles associated with certain landmarks was also assessed by a subset of two observers, and intraobserver and interobserver agreement were evaluated. Intraclass correlation coefficients were excellent for intraobserver agreement, but only good for interobserver agreement. The least reliable landmark for orthodontists was the gnathion (Gn) point (standard deviation [SD], 5.92 mm), while the orbitale (Or) was the least reliable landmark (SD, 4.41 mm) for dentomaxillofacial radiologists. Furthermore, the condylion (Co)-Gn plane was the least consistent (SD, 4.43 mm). We established that some landmarks were not as reproducible as others, both horizontally and vertically. The most consistently identified landmark in both groups was the lower incisor border, while the least reliable points were Co, Gn, Or, and the anterior nasal spine. Overall, a lower level of reproducibility in the identification of cephalometric landmarks was observed among orthodontists.

  17. Nuclear Scans

    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 ...

  18. The reliability of tablet computers in depicting maxillofacial radiographic landmarks

    2015-01-01

    Purpose This study was performed to evaluate the reliability of the identification of anatomical landmarks in panoramic and lateral cephalometric radiographs on a standard medical grade picture archiving communication system (PACS) monitor and a tablet computer (iPad 5). Materials and Methods A total of 1000 radiographs, including 500 panoramic and 500 lateral cephalometric radiographs, were retrieved from the de-identified dataset of the archive of the Section of Oral and Maxillofacial Radio...

  19. Surgical landmarks of the ureter in the cadaveric female pelvis.

    Barksdale, P A; Brody, S P; Garely, A D; Elkins, T E; Nolan, T E; Gasser, R F

    1997-01-01

    Our purpose was to delineate the course of the ureter in the female pelvis in relationship to several important surgical landmarks. Ten female cadavers with undissected pelves were used. The ureter was identified at the pelvic brim and traced inferiorly to the bladder. Sets of measurements (+/- 0.1 cm) that help define the location of the ureter were obtained at the three landmarks; the ischial spine, the obturator canal and the insertion of the arcus tendineus on the pubic bone. The mean distances from the ureter to the pelvic floor were ischial spine, 3.2 +/- 0.1 cm; obturator canal, 3.2 +/- 0.1 cm; and the insertion of the arcus tendineus on the pubic bone, 1.6 +/- 0.1 cm. The mean distances from the arcus tendineus to the pelvic floor were ischial spine, 1.9 +/- 0.1 cm; obturator canal, 2.8 +/- 0.1 cm; and the insertion of the arcus tendineus on the pubic bone, 3.2 +/- 0.1 cm. This study defines the relationship of the ureter to the pelvic floor through measurements taken at three landmarks. The data should be useful to pelvic surgeons and are important for the development of future surgical techniques.

  20. AUTOMATIC DETECTION AND CLASSIFICATION OF RETINAL VASCULAR LANDMARKS

    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. Locating landmarks on high-dimensional free energy surfaces.

    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.

  2. An Indoor Positioning Method for Smartphones Using Landmarks and PDR.

    Wang, Xi; Jiang, Mingxing; Guo, Zhongwen; Hu, Naijun; Sun, Zhongwei; Liu, Jing

    2016-12-15

    Recently location based services (LBS) have become increasingly popular in indoor environments. Among these indoor positioning techniques providing LBS, a fusion approach combining WiFi-based and pedestrian dead reckoning (PDR) techniques is drawing more and more attention of researchers. Although this fusion method performs well in some cases, it still has some limitations, such as heavy computation and inconvenience for real-time use. In this work, we study map information of a given indoor environment, analyze variations of WiFi received signal strength (RSS), define several kinds of indoor landmarks, and then utilize these landmarks to correct accumulated errors derived from PDR. This fusion scheme, called Landmark-aided PDR (LaP), is proved to be light-weight and suitable for real-time implementation by running an Android application designed for the experiment. We compared LaP with other PDR-based fusion approaches. Experimental results show that the proposed scheme can achieve a significant improvement with an average accuracy of 2.17 m.

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

    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

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

    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.

  5. Landmark Optimization Using Local Curvature for Point-Based Nonlinear Rodent Brain Image Registration

    Yutong Liu

    2012-01-01

    Full Text Available Purpose. To develop a technique to automate landmark selection for point-based interpolating transformations for nonlinear medical image registration. Materials and Methods. Interpolating transformations were calculated from homologous point landmarks on the source (image to be transformed and target (reference image. Point landmarks are placed at regular intervals on contours of anatomical features, and their positions are optimized along the contour surface by a function composed of curvature similarity and displacements of the homologous landmarks. The method was evaluated in two cases (=5 each. In one, MRI was registered to histological sections; in the second, geometric distortions in EPI MRI were corrected. Normalized mutual information and target registration error were calculated to compare the registration accuracy of the automatically and manually generated landmarks. Results. Statistical analyses demonstrated significant improvement (<0.05 in registration accuracy by landmark optimization in most data sets and trends towards improvement (<0.1 in others as compared to manual landmark selection.

  6. A physical map of the human genome

    McPherson, J.D.; Marra, M.; Hillier, L.; Waterston, R.H.; Chinwalla, A.; Wallis, J.; Sekhon, M.; Wylie, K.; Mardis, E.R.; Wilson, R.K.; Fulton, R.; Kucaba, T.A.; Wagner-McPherson, C.; Barbazuk, W.B.; Gregory, S.G.; Humphray, S.J.; French, L.; Evans, R.S.; Bethel, G.; Whittaker, A.; Holden, J.L.; McCann, O.T.; Dunham, A.; Soderlund, C.; Scott, C.E.; Bentley, D.R.; Schuler, G.; Chen, H.-C.; Jang, W.; Green, E.D.; Idol, J.R.; Maduro, V.V. Braden; Montgomery, K.T.; Lee, E.; Miller, A.; Emerling, S.; Kucherlapati; Gibbs, R.; Scherer, S.; Gorrell, J.H.; Sodergren, E.; Clerc-Blankenburg, K.; Tabor, P.; Naylor, S.; Garcia, D.; de Jong, P.J.; Catanese, J.J.; Nowak, N.; Osoegawa, K.; Qin, S.; Rowen, L.; Madan, A.; Dors, M.; Hood, L.; Trask, B.; Friedman, C.; Massa, H.; Cheung, V.G.; Kirsch, I.R.; Reid, T.; Yonescu, R.; Weissenbach, J.; Bruls, T.; Heilig, R.; Branscomb, E.; Olsen, A.; Doggett, N.; Cheng, J.F.; Hawkins, T.; Myers, R.M.; Shang, J.; Ramirez, L.; Schmutz, J.; Velasquez, O.; Dixon, K.; Stone, N.E.; Cox, D.R.; Haussler, D.; Kent, W.J.; Furey, T.; Rogic, S.; Kennedy, S.; Jones, S.; Rosenthal, A.; Wen, G.; Schilhabel, M.; Gloeckner, G.; Nyakatura, G.; Siebert, R.; Schlegelberger, B.; Korenberg, J.; Chen, X.N.; Fujiyama, A.; Hattori, M.; Toyoda, A.; Yada, T.; Park, H.S.; Sakaki, Y.; Shimizu, N.; Asakawa, S.; Kawasaki, K.; Sasaki, T.; Shintani, A.; Shimizu, A.; Shibuya, K.; Kudoh, J.; Minoshima, S.; Ramser, J.; Seranski, P.; Hoff, C.; Poustka, A.; Reinhardt, R.; Lehrach, H.

    2001-01-01

    The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

  7. Generalization decrement and not overshadowing by associative competition among pairs of landmarks in a navigation task.

    Chamizo, Victoria D; Rodríguez, Clara A; Espinet, Alfredo; Mackintosh, N J

    2012-07-01

    When they are trained in a Morris water maze to find a hidden platform, whose location is defined by a number of equally spaced visual landmarks round the circumference of the pool, rats are equally able to find the platform when tested with any two of the landmarks (Prados, & Trobalon, 1998; Rodrigo, Chamizo, McLaren, & Mackintosh, 1997). This suggests that none of the landmarks was completely overshadowed by any of the others. In Experiment 1 one pair of groups was trained with four equally salient visual landmarks spaced at equal intervals around the edge of the pool, while a second pair was trained with two landmarks only, either relatively close to or far from the hidden platform. After extensive training, both male and female rats showed a reciprocal overshadowing effect: on a test with two landmarks only (either close to or far from the platform), rats trained with four landmarks spent less time in the platform quadrant than those trained with only two. Experiment 2 showed that animals trained with two landmarks and then tested with four also performed worse on test than those trained and tested with two landmarks only. This suggests that generalization decrement, rather than associative competition, provides a sufficient explanation for the overshadowing observed in Experiment 1. Experiment 3 provided a within-experiment replication of the results of Experiments 1 and 2. Finally, Experiment 4 showed that rats trained with a configuration of two landmarks learn their identity.

  8. Automatic landmark generation for deformable image registration evaluation for 4D CT images of lung

    Vickress, J.; Battista, J.; Barnett, R.; Morgan, J.; Yartsev, S.

    2016-10-01

    Deformable image registration (DIR) has become a common tool in medical imaging across both diagnostic and treatment specialties, but the methods used offer varying levels of accuracy. Evaluation of DIR is commonly performed using manually selected landmarks, which is subjective, tedious and time consuming. We propose a semi-automated method that saves time and provides accuracy comparable to manual selection. Three landmarking methods including manual (with two independent observers), scale invariant feature transform (SIFT), and SIFT with manual editing (SIFT-M) were tested on 10 thoracic 4DCT image studies corresponding to the 0% and 50% phases of respiration. Results of each method were evaluated against a gold standard (GS) landmark set comparing both mean and proximal landmark displacements. The proximal method compares the local deformation magnitude between a test landmark pair and the closest GS pair. Statistical analysis was done using an intra class correlation (ICC) between test and GS displacement values. The creation time per landmark pair was 22, 34, 2.3, and 4.3 s for observers 1 and 2, SIFT, and SIFT-M methods respectively. Across 20 lungs from the 10 CT studies, the ICC values between the GS and observer 1 and 2, SIFT, and SIFT-M methods were 0.85, 0.85, 0.84, and 0.82 for mean lung deformation, and 0.97, 0.98, 0.91, and 0.96 for proximal landmark deformation, respectively. SIFT and SIFT-M methods have an accuracy that is comparable to manual methods when tested against a GS landmark set while saving 90% of the time. The number and distribution of landmarks significantly affected the analysis as manifested by the different results for mean deformation and proximal landmark deformation methods. Automatic landmark methods offer a promising alternative to manual landmarking, if the quantity, quality and distribution of landmarks can be optimized for the intended application.

  9. New Statistical Method to Analyze Three-Dimensional Landmark Configurations Obtained with Cone-Beam CT: Basic Features and Clinical Application for Rapid Maxillary Expansion

    Gamble, Jennifer; Lagravere, Manuel O.; Major, Paul W.; Heo, Giseon [University of Alberta, Edmonton (Canada)

    2012-03-15

    To describe a statistical method of three-dimensional landmark configuration data and apply it to an orthodontic data set comparing two types of rapid maxillary expansion (RME) treatments. Landmark configurations obtained from cone beam CT scans were used to represent patients in two types (please describe what were two types) of RME groups and a control group over four time points. A method using tools from persistent homology and dimensionality reduction is presented and used to identify variability between the subjects. The analysis was in agreement with previous results using conventional methods, which found significant differences between treatment groups and the control, but no distinction between the types of treatment. Additionally, it was found that second molar eruption varied considerably between the subjects, and this has not been evaluated in previous analyses. This method of analysis allows entire configurations to be considered as a whole, and does not require specific inter-landmark distances or angles to be selected. Sources of variability present themselves, without having to be individually sought after. This method is suggested as an additional tool for the analysis of landmark configuration data.

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

    Lavoie, Caroline; Higgins, Jane; Bissonnette, Jean-Pierre [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada); Le, Lisa W. [Department of Biostatistics, Princess Margaret Hospital, Toronto, Ontario, M5G 2M9 (Canada); Sun, Alexander; Brade, Anthony; Hope, Andrew; Cho, John [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada); Bezjak, Andrea, E-mail: andrea.bezjak@rmp.uhn.on.ca [Department of Radiation Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, M5G 2M9 (Canada)

    2012-12-01

    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 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.

  11. Notes on the Landmark Development of CBR in China

    Dahong Zhuo

    2009-01-01

    Community-based rehabilitation has a history of 22 years in China.In spite of the preliminary achievement and experiences obtained by the pioneering and trial projects,it was not until the beginning of the new century that CBR in China experienced a landmark development.This iS characterized by a number of favorable pohcy by the government for CBR;the mechanism facilitating primary health care with CBR,a new work-force system of CBR reorganized with better motivation and efficiency,99 demonstration projects of CBR bringing about benchmark promotion effect and the active involvement in CBR by social resources agents.

  12. Automatic Registration and Error Detection of Multiple Slices Using Landmarks

    Hans Frimmel

    2001-01-01

    Full Text Available Objectives. When analysing the 3D structure of tissue, serial sectioning and staining of the resulting slices is sometimes the preferred option. This leads to severe registration problems. In this paper, a method for automatic registration and error detection of slices using landmark needles has been developed. A cost function takes some parameters from the current state of the problem to be solved as input and gives a quality of the current solution as output. The cost function used in this paper, is based on a model of the slices and the landmark needles. The method has been used to register slices of prostates in order to create 3D computer models. Manual registration of the same prostates has been undertaken and compared with the results from the algorithm. Methods. Prostates from sixteen men who underwent radical prostatectomy were formalin fixed with landmark needles, sliced and the slices were computer reconstructed. The cost function takes rotation and translation for each prostate slice, as well as slope and offset for each landmark needle as input. The current quality of fit of the model, using the input parameters given, is returned. The function takes the built‐in instability of the model into account. The method uses a standard algorithm to optimize the prostate slice positions. To verify the result, s standard method in statistics was used. Results. The methods were evaluated for 16 prostates. When testing blindly, a physician could not determine whether the registration shown to him were created by the automated method described in this paper, or manually by an expert, except in one out of 16 cases. Visual inspection and analysis of the outlier confirmed that the input data had been deformed. The automatic detection of erroneous slices marked a few slices, including the outlier, as suspicious. Conclusions. The model based registration performs better than traditional simple slice‐wise registration. In the case of prostate

  13. Learning Combinatorial Map Information from Permutations of Landmarks

    2010-10-04

    Learning Combinatorial Map Information from Permutations of Landmarks Benjamı́n Tovar ∗, Luigi Freda†, and Steven M. LaValle‡ Abstract This paper...is B. Tovar . This work was founded by NSF grant 0904501 (IIS robotics), DARPA SToMP grant HR0011-05-1-0008, and MURI/ONR grant N00014-09-1-1052. ∗B... Tovar is with the Dept. of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 602081, USA. email: b- tovar

  14. Precision of cephalometric landmark identification: Cone-beam computed tomography vs conventional cephalometric views

    Ludlow, John B.; Gubler, Maritzabel; Cevidanes, Lucia; Mol, André

    2009-01-01

    Introduction In this study, we compared the precision of landmark identification using displays of multi-planar cone-beam computed tomographic (CBCT) volumes and conventional lateral cephalograms (Ceph). Methods Twenty presurgical orthodontic patients were radiographed with conventional Ceph and CBCT techniques. Five observers plotted 24 landmarks using computer displays of multi-planer reconstruction (MPR) CBCT and Ceph views during separate sessions. Absolute differences between each observer’s plot and the mean of all observers were averaged as 1 measure of variability (ODM). The absolute difference of each observer from any other observer was averaged as a second measure of variability (DEO). ANOVA and paired t tests were used to analyze variability differences. Results Radiographic modality and landmark were significant at P <0.0001 for DEO and ODM calculations. DEO calculations of observer variability were consistently greater than ODM. The overall correlation of 1920 paired ODM and DEO measurements was excellent at 0.972. All bilateral landmarks had increased precision when identified in the MPR views. Mediolateral variability was statistically greater than anteroposterior or caudal-cranial variability for 5 landmarks in the MPR views. Conclusions The MPR displays of CBCT volume images provide generally more precise identification of traditional cephalometric landmarks. More precise location of condylion, gonion, and orbitale overcomes the problem of superimposition of these bilateral landmarks seen in Ceph. Greater variability of certain landmarks in the mediolateral direction is probably related to inadequate definition of the landmarks in the third dimension. PMID:19732656

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

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

    2010-01-01

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

  16. Landmarks in nature to support wayfinding: the effects of seasons and experimental methods.

    Kettunen, Pyry; Irvankoski, Katja; Krause, Christina M; Sarjakoski, L Tiina

    2013-08-01

    Landmarks constitute an essential basis for a structural understanding of the spatial environment. Therefore, they are crucial factors in external spatial representations such as maps and verbal route descriptions, which are used to support wayfinding. However, selecting landmarks for these representations is a difficult task, for which an understanding of how people perceive and remember landmarks in the environment is needed. We investigated the ways in which people perceive and remember landmarks in nature using the thinking aloud and sketch map methods during both the summer and the winter seasons. We examined the differences between methods to identify those landmarks that should be selected for external spatial representations, such as maps or route descriptions, in varying conditions. We found differences in the use of landmarks both in terms of the methods and also between the different seasons. In particular, the participants used passage and tree-related landmarks at significantly different frequencies with the thinking aloud and sketch map methods. The results are likely to reflect the different roles of the landmark groups when using the two methods, but also the differences in counting landmarks when using both methods. Seasonal differences in the use of landmarks occurred only with the thinking aloud method. Sketch maps were drawn similarly in summertime and wintertime; the participants remembered and selected landmarks similarly independent of the differences in their perceptions of the environment due to the season. The achieved results may guide the planning of external spatial representations within the context of wayfinding as well as when planning further experimental studies.

  17. Genomic Database Searching.

    Hutchins, James R A

    2017-01-01

    The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

  18. The importance of context to the genetic architecture of diabetes-related traits is revealed in a genome-wide scan of a LG/J × SM/J murine model.

    Lawson, Heather A; Lee, Arthur; Fawcett, Gloria L; Wang, Bing; Pletscher, L Susan; Maxwell, Taylor J; Ehrich, Thomas H; Kenney-Hunt, Jane P; Wolf, Jason B; Semenkovich, Clay F; Cheverud, James M

    2011-04-01

    Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci that affect serum glucose and insulin levels and response to glucose stress in an F(16) Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG,SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We found that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context-dependent and that the same genomic sequence can affect traits differently depending on an individual's sex and/or dietary environment. Our results have important implications for studies of complex traits in humans.

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

    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.

  20. Chronic Pancreatitis: Landmark Papers, Management Decisions, and Future.

    DiMagno, Eugene P; DiMagno, Matthew J

    2016-01-01

    On May 16, 2015 at the invitation of the American Gastroenterological Association Institute Council E.P.D. presented a state-of-the-art lecture at Digestive Disease Week 2015. The aims were to discuss a selection of landmark papers in chronic pancreatitis (CP) that influence modern management and to conclude by suggesting some future directions. This is based on that presentation. We will specifically review the following: duct anatomy and pancreas divisum, description of chronic relapsing pancreatitis and its differentiation from recurrent acute pancreatitis and established CP (ECP), natural histories and gene discoveries of alcoholic, idiopathic and hereditary pancreatitis, development of pancreatic cancer in CP, exocrine pancreatic insufficiency and calculation of dose and delivery of enzymes, endoscopic ultrasonography, and autoimmune pancreatitis. With some exceptions, we exclude basic science and surgery.

  1. FACIAL LANDMARKING LOCALIZATION FOR EMOTION RECOGNITION USING BAYESIAN SHAPE MODELS

    Hernan F. Garcia

    2013-02-01

    Full Text Available This work presents a framework for emotion recognition, based in facial expression analysis using Bayesian Shape Models (BSM for facial landmarking localization. The Facial Action Coding System (FACS compliant facial feature tracking based on Bayesian Shape Model. The BSM estimate the parameters of the model with an implementation of the EM algorithm. We describe the characterization methodology from parametric model and evaluated the accuracy for feature detection and estimation of the parameters associated with facial expressions, analyzing its robustness in pose and local variations. Then, a methodology for emotion characterization is introduced to perform the recognition. The experimental results show that the proposed model can effectively detect the different facial expressions. Outperforming conventional approaches for emotion recognition obtaining high performance results in the estimation of emotion present in a determined subject. The model used and characterization methodology showed efficient to detect the emotion type in 95.6% of the cases.

  2. Bringing history to life: simulating landmark experiments in psychology.

    Boynton, David M; Smith, Laurence D

    2006-05-01

    The course in history of psychology can be challenging for students, many of whom enter it with little background in history and faced with unfamiliar names and concepts. The sheer volume of material can encourage passive memorization unless efforts are made to increase student involvement. As part of a trend toward experiential history, historians of science have begun to supplement their lectures with demonstrations of classic physics experiments as a way to bring the history of science to life. Here, the authors report on computer simulations of five landmark experiments from early experimental psychology in the areas of reaction time, span of attention, and apparent motion. The simulations are designed not only to permit hands-on replication of historically important results but also to reproduce the experimental procedures closely enough that students can gain a feel for the nature of early research and the psychological processes being studied.

  3. Segmentation of Pathological Structures by Landmark-Assisted Deformable Models.

    Ibragimov, Bulat; Korez, Robert; Likar, Bostjan; Pernus, Franjo; Xing, Lei; Vrtovec, Tomaz

    2017-02-13

    Computerized segmentation of pathological structures in medical images is challenging, as, in addition to unclear image boundaries, image artifacts and traces of surgical activities, the shape of pathological structures may be very different from the shape of normal structures. Even if a sufficient number of pathological training samples are collected, statistical shape modeling cannot always capture shape features of pathological samples as they may be suppressed by shape features of a considerably larger number of healthy samples. At the same time, landmarking can be efficient in analyzing pathological structures but often lacks robustness. In this paper, we combine the advantages of landmark detection and deformable models into a novel supervised multi-energy segmentation framework that can efficiently segment structures with pathological shape. The framework adopts the theory of Laplacian shape editing that was introduced in the field of computer graphics, so that the limitations of statistical shape modeling are avoided. The performance of the proposed framework was validated by segmenting fractured lumbar vertebrae from three-dimensional (3D) computed tomography (CT) images, atrophic corpora callosa from two-dimensional (2D) magnetic resonance (MR) crosssections and cancerous prostates from 3D MR images, resulting respectively in a Dice coefficient of 84.7 ± 5.0%, 85.3 ± 4.8% and 78.3 ± 5.1%, and boundary distance of 1.14 ± 0.49 mm, 1.42 ± 0.45mm and 2.27 ± 0.52 mm. The obtained results were shown to be superior in comparison to existing deformable modelbased segmentation algorithms.

  4. 78 FR 69437 - Landmarks Committee of the National Park System Advisory Board Meeting

    2013-11-19

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... Federal Regulations, that a meeting of the Landmarks Committee of the National Park System Advisory Board... National Park System Advisory Board at a subsequent meeting at a place and time to be determined....

  5. The Development of Landmark and Beacon Use in Young Children: Evidence from a Touchscreen Search Task

    Sutton, Jennifer E.

    2006-01-01

    Children ages 2, 3 and 4 years participated in a novel hide-and-seek search task presented on a touchscreen monitor. On beacon trials, the target hiding place could be located using a beacon cue, but on landmark trials, searching required the use of a nearby landmark cue. In Experiment 1, 2-year-olds performed less accurately than older children…

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

    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.

  7. STUDY ON COMPARISON BETWEEN LANDMARK GUIDED (BRINKMAN'S TECHNIQUE ) AND ULTRASOUND GUIDED INTERNAL JUGULAR VEIN CANNULATION

    Vinod; Sashi Walling

    2015-01-01

    Technique of cannulating the central veins , until recently has been based on landmark guided technique . Recently ultrasound machines with high frequency probes are being used to increase success rate and reducing complications. OBJECTIVE: In our study we compare landmark guided technique ( Brinkman's technique ) ( 1 ) with ultrasound guided technique. STUDY DESIGN: outcome was evaluated in terms of 1 ) Number of attempts 2 ) ...

  8. A method for lunar roving vehicle position determination from three landmark observations with a sun compass

    Blucker, T. J.; Stimmel, G. L.

    1971-01-01

    A simplified method is described for determining the position of the lunar roving vehicle on the lunar surface during Apollo 15. The method is based upon sun compass azimuth measurements of three lunar landmarks. The difference between the landmark azimuth and the sun azimuth is measured and the resulting data are voice relayed to the Mission Control Center for processing.

  9. 3D facial landmarks: Inter-operator variability of manual annotation

    Fagertun, Jens; Harder, Stine; Rosengren, Anders;

    2014-01-01

    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...

  10. Landmark and route knowledge in children’s spatial representation of a virtual environment

    Marion eNys

    2015-01-01

    Full Text Available This study investigates the development of landmark and route knowledge in complex wayfinding situations. Our study focuses on how children (aged 6, 8 and 10 years and young adults (n=79 indicate, recognize, and bind landmarks and directions in both verbal and visuo-spatial tasks after learning a virtual route. Performance in these tasks is also related to general verbal and visuo-spatial abilities as assessed by independent standardized tests (attention, working memory, perception of direction, production and comprehension of spatial terms, sentences and stories. The results first show that the quantity and quality of landmarks and directions produced and recognized by participants in both verbal and visuo-spatial tasks increased with age. In addition, an increase with age was observed in participants’ selection of decisional landmarks (i.e. landmarks associated with a change of direction, as well as in their capacity to bind landmarks and directions. Our results confirm the view that children first acquire landmark knowledge, then route knowledge, as shown by their late developing ability to bind knowledge of directions and landmarks. Overall, the quality of verbal and visuo-spatial information in participants’ spatial representations was found to vary mostly with their visuo-spatial abilities (attention and perception of directions and not with their verbal abilities. Interestingly, however, when asked to recognize landmarks encountered during the route, participants show an increasing bias with age toward choosing a related landmark of the same category, regardless of its visual characteristics, i.e. they incorrectly choose the picture of another fountain. The discussion highlights the need for further studies to determine more precisely the role of verbal and visuo-spatial knowledge and the nature of how children learn to represent and memorize routes.

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

    Matthew P Johnson

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

  12. MRI Scans

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from ...

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

    Gurkan Turker

    2009-01-01

    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 vein 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 < 0.01. Carotid puncture rate and hematoma were more frequent in the landmark group than in the ultrasound-guided group (p < 0.05. The number of attempts for successful placement was significantly higher in the landmark group than in the ultrasound-guided group, which was accompanied by a significantly increased access time observed in the landmark group (p < 0.05 and p < 0.01, respectively. Although there were a higher number of attempts, longer access time, and a more frequent complication rate in the landmark group, the success rate was found to be comparable between the two groups. CONCLUSION: The findings of this study indicate that internal jugular vein catheterization guided by real-time ultrasound results in a lower access time and a lower rate of immediate complications.

  14. Internal Jugular Vein Cannulation: An Ultrasound-Guided Technique Versus a Landmark-Guided Technique

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

    2009-01-01

    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 vein 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 < 0.01). Carotid puncture rate and hematoma were more frequent in the landmark group than in the ultrasound-guided group (p < 0.05). The number of attempts for successful placement was significantly higher in the landmark group than in the ultrasound-guided group, which was accompanied by a significantly increased access time observed in the landmark group (p < 0.05 and p < 0.01, respectively). Although there were a higher number of attempts, longer access time, and a more frequent complication rate in the landmark group, the success rate was found to be comparable between the two groups. CONCLUSION The findings of this study indicate that internal jugular vein catheterization guided by real-time ultrasound results in a lower access time and a lower rate of immediate complications. PMID:19841706

  15. [The landmarks of the measurement of cerebral blood flow].

    István, Nyáry

    2008-01-30

    History of the measurement of local cerebral blood flow may cover a period of one and a half centuries. Parallel forthcoming of both theoretical and technical development were the key elements of ensuing progress resulting in the present state, when by the aid of in vivo blood flow and metabolic maps, we can visualize locales of brain functioning and their interconnections. Two theoretical landmarks should be mentioned in this historic process. First, the work of Adolf Fick, as the starter of quantitative measurements in this field, and Seymour Kety's model of a single, homogenously perfused tissue element. The solution of this model, in the form of Kety's equation is still fundamental to present day blood flow mapping techniques. Among the numerous investigators over the past years, two Hungarian scientist can be named as major contributors. Kálmán Sántha made substantial studies with continuous registration of local cerebral blood flow by the aid of thermocouples, while Emil P6sztor invented the hydrogen clearance method for the measurement of local cerebral blood flow both in human and in animal studies.

  16. Hypoechoic media: a landmark for intravascular ultrasonic imaging

    Gussenhoven, Elma J.; Bom, Nicolaas; Li, Wenguang; van Urk, Hero; Pietermann, Herman; van Suylen, Robert J.; Salem, H. K.

    1991-05-01

    This paper describes the in vitro (40 MHz) and in vivo (30 MHz) results of studies performed on human vessels using a mechanically rotated single element ultrasonic imaging system. The in vitro images were matched with the corresponding histologic cross-sections. Morphology of vessels and possibility to determine the extent of atherosclerosis were assessed by two blinded observers. Echographic images with an echolucent zone were seen to correspond with muscular type of arteries. The echographic images showing no echographic distinction between the various layers were seen to correspond with either elastic type of arteries, veins, veins used for bypass, or bypass Goretex grafts. The extent of atherosclerosis could only be assessed in the muscular type of artery. The data showed close correlation with histology (r = 0.89). In vivo studies (30 patients) revealed a characteristic three-layered appearance of the distal iliac and femoral artery. Normal cross-sections were readily differentiated from non- obstructive and obstructive lesions. In all these patients the hypoechoic muscular media served as an important landmark.

  17. CBCT Assessment of Mental Foramen Position Relative to Anatomical Landmarks

    Sheikhi, Mahnaz

    2016-01-01

    Purpose. This study was carried out on an Iranian population aiming to investigate mental foramen position relative to inferior border of mandible and skeletal midline and its gender and age differences on CBCT projections. Materials and Methods. A number of 180 CBCT images of patients were analyzed in different planes (tangential, cross-sectional, and axial). The distances from the superior border of mental foramen to the inferior border of mandible and from the anterior border of mental foramen to the midline were calculated. Results. The mean distance from mental foramen to the inferior border of mandible in the right side was 13.26 mm (SD ± 2.34) and in the left side was 13.37 mm (SD ± 2.19). There was a statistically significant difference between genders in terms of the distance between mental foramen and inferior border of mandible (P value = 0.000). The mean distances from mental foramen to midline were 25.86 mm (SD ± 0.27) and 25.53 mm (SD ± 0.31) in the right and left sides, respectively. Conclusions. The vertical and horizontal positions of mental foramen can be determined from stable anatomical landmarks such as mandibular inferior border and skeletal midline in both dentulous and edentulous patients. The distance from the superior border of mental foramen to the inferior border of mandible exhibited sexual dimorphism. PMID:27999594

  18. Landmark matching based automatic retinal image registration with linear programming and self-similarities.

    Zheng, Yuanjie; Hunter, Allan A; Wu, Jue; Wang, Hongzhi; Gao, Jianbin; Maguire, Maureen G; Gee, James C

    2011-01-01

    In this paper, we address the problem of landmark matching based retinal image registration. Two major contributions render our registration algorithm distinguished from many previous methods. One is a novel landmark-matching formulation which enables not only a joint estimation of the correspondences and transformation model but also the optimization with linear programming. The other contribution lies in the introduction of a reinforced self-similarities descriptor in characterizing the local appearance of landmarks. Theoretical analysis and a series of preliminary experimental results show both the effectiveness of our optimization scheme and the high differentiating ability of our features.

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

    Dharambir K Sanghera

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

  20. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    Elsa García-Gámez

    Full Text Available Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7, platelet-derived growth factor alpha (PDGFRA and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

  1. A genome scan for quantitative trait loci affecting grain yield and its components of maize both in single-and two-locus levels

    YAN Jianbing; TANG Hua; HUANG Yiqin; ZHENG Yonglian; SUBHASH Chander; LI Jiansheng

    2006-01-01

    By adding thirty-one markers in the previous linkage map, a new genetic linkage map containing 205 markers was constructed, spanning a total of 2305.4 cM with an average interval of 11.2 cM. The genotypic errors in the whole genome were detected by the statistical method and removed manually. The precision of the linkage map was improved significantly. Main and epistatic QTL were detected by R/qtl, and main QTL were confirmed and refined by multiple interval mapping (MIM). Finally, MIM detected seven QTL for rows number, and five QTL for each grain yield, kernels per row and 100-kernel weight. The contribution to genetic variations of QTL varied from 35.3% for grain yield to 61.5% for rows number. Only kernels per row exhibited significant epistatic interactions between QTL. Twenty-four epistatic QTL were detected which distributed on almost all the ten chromosomes. About two-third epistatic QTL were observed between main QTL and another locus, which had no significant effects. These results indicate rather clearly that there are a number of QTL affecting trait expressions, not directly but indirectly through interactions with other loci. Thus, epistatic QTL effects may play a crucial role, if not more important than main QTL effects, in the genetic variation for the measured traits in present study.

  2. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    García-Gámez, Elsa; Reverter, Antonio; Whan, Vicki; McWilliam, Sean M; Arranz, Juan José; Kijas, James

    2011-01-01

    Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7), platelet-derived growth factor alpha (PDGFRA) and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

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

    Fu-Hui Xiao

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

  4. Scan Statistics

    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.

  5. Automatic Dent-landmark detection in 3-D CBCT dental volumes.

    Cheng, Erkang; Chen, Jinwu; Yang, Jie; Deng, Huiyang; Wu, Yi; Megalooikonomou, Vasileios; Gable, Bryce; Ling, Haibin

    2011-01-01

    Orthodontic craniometric landmarks provide critical information in oral and maxillofacial imaging diagnosis and treatment planning. The Dent-landmark, defined as the odontoid process of the epistropheus, is one of the key landmarks to construct the midsagittal reference plane. In this paper, we propose a learning-based approach to automatically detect the Dent-landmark in the 3D cone-beam computed tomography (CBCT) dental data. Specifically, a detector is learned using the random forest with sampled context features. Furthermore, we use spacial prior to build a constrained search space other than use the full three dimensional space. The proposed method has been evaluated on a dataset containing 73 CBCT dental volumes and yields promising results.

  6. 75 FR 16837 - Public Review of Draft United States Thoroughfare, Landmark, and Postal Address Data Standard

    2010-04-02

    ... public on the FGDC Web site. DATES: Comments on the draft United States Thoroughfare, Landmark, and... principles can be extended to all addresses. Dated: March 18, 2010. Ivan DeLoatch, FGDC Executive...

  7. Clinical application of anatomy landmarks for microscopic endonasal transsphenoidal surgery for pituitary adenomas.

    Wang, Shou-Sen; Li, Jun-Feng; Chen, Hong-Jie; Wang, Ru-Mi

    2013-01-01

    It is important to identify relevant anatomical landmarks on the route of endonasal transsphenoidal surgery (TSS) for pituitary adenomas to improve the gross total resection and the remission of disease. We therefore retrospectively studied the clinical outcomes of 148 patients who underwent single nostril endonasal TSS for pituitary adenomas. The anatomic basis of these procedures was evaluated. The important landmarks included the mucosal sphenoid ostia, the sphenoid keel, the osseous ostia and the nutrient arteries nearby, the sellar bulge, and the carotid protuberance, which outlined a clear route to the sella turcica with the best view and less tissue damage. Based on these landmarks, 148 cases of endonasal TSS were successfully performed to achieve 70.3% of gross total resection and remission, respectively. The complications were controlled to the least. Therefore, the application of these landmarks will help to prevent complications and improve the long-term outcomes.

  8. 75 FR 49520 - Landmarks Committee of the National Park System Advisory Board Meeting

    2010-08-13

    ... proposals for withdrawal of designation. The members of the Landmarks Committee are: Mr. Ronald James, Chair...) MEDICINE WHEEL/MEDICINE MOUNTAIN, Bighorn County, WY (updated documentation, boundary, and name...

  9. Obstacles Facing Promoting Tourism for Islamic Landmarks from the Perspective of Tour Operators in Egypt

    2015-01-01

    The UNESCO launched a campaign #unite4heritage in Egypt to defeat extremism and intolerance. The message of such campaigne is peace, dialogue and unity embedded in cultural heritage. As culture and tourism are linked together, such message could be delivered through improving culture heritage tourism in Egypt. Islamic landmarks  are considered as a part of human heritage. Therefore, the purpose of this study is to identify how much tour operators in Egypt include Islamic landmarks in their pr...

  10. Sequential egocentric navigation and reliance on landmarks in Williams syndrome and typical development.

    Broadbent, Hannah J; Farran, Emily K; Tolmie, Andrew

    2015-01-01

    Visuospatial difficulties in Williams syndrome (WS) are well documented. Recently, research has shown that spatial difficulties in WS extend to large-scale space, particularly in coding space using an allocentric frame of reference. Typically developing (TD) children and adults predominantly rely on the use of a sequential egocentric strategy to navigate a large-scale route (retracing a sequence of left-right body turns). The aim of this study was to examine whether individuals with WS are able to employ a sequential egocentric strategy to guide learning and the retracing of a route. Forty-eight TD children, aged 5, 7, and 9 years and 18 participants with WS were examined on their ability to learn and retrace routes in two (6-turn) virtual environment mazes (with and without landmarks). The ability to successfully retrace a route following the removal of landmarks (use of sequential egocentric coding) was also examined. Although in line with TD 5-year-olds when learning a route with landmarks, individuals with WS showed significantly greater detriment when these landmarks were removed, relative to all TD groups. Moreover, the WS group made significantly more errors than all TD groups when learning a route that never contained landmarks. On a perceptual view-matching task, results revealed a high level of performance across groups, indicative of an ability to use this visual information to potentially aid navigation. These findings suggest that individuals with WS rely on landmarks to a greater extent than TD children, both for learning a route and for retracing a recently learned route. TD children, but not individuals with WS, were able to fall back on the use of a sequential egocentric strategy to navigate when landmarks were not present. Only TD children therefore coded sequential route information simultaneously with landmark information. The results are discussed in relation to known atypical cortical development and perceptual-matching abilities in WS.

  11. Effects of image enhancement on reliability of landmark identification in digital cephalometry

    M Oshagh

    2013-01-01

    Full Text Available Introduction: Although digital cephalometric radiography is gaining popularity in orthodontic practice, the most important source of error in its tracing is uncertainty in landmark identification. Therefore, efforts to improve accuracy in landmark identification were directed primarily toward the improvement in image quality. One of the more useful techniques of this process involves digital image enhancement which can increase overall visual quality of image, but this does not necessarily mean a better identification of landmarks. The purpose of this study was to evaluate the effectiveness of digital image enhancements on reliability of landmark identification. Materials and Methods: Fifteen common landmarks including 10 skeletal and 5 soft tissues were selected on the cephalograms of 20 randomly selected patients, prepared in Natural Head Position (NHP. Two observers (orthodontists identified landmarks on the 20 original photostimulable phosphor (PSP digital cephalogram images and 20 enhanced digital images twice with an intervening time interval of at least 4 weeks. The x and y coordinates were further analyzed to evaluate the pattern of recording differences in horizontal and vertical directions. Reliability of landmarks identification was analyzed by paired t test. Results: There was a significant difference between original and enhanced digital images in terms of reliability of points Ar and N in vertical and horizontal dimensions, and enhanced images were significantly more reliable than original images. Identification of A point, Pogonion and Pronasal points, in vertical dimension of enhanced images was significantly more reliable than original ones. Reliability of Menton point identification in horizontal dimension was significantly more in enhanced images than original ones. Conclusion: Direct digital image enhancement by altering brightness and contrast can increase reliability of some landmark identification and this may lead to more

  12. Sequential egocentric navigation and reliance on landmarks in Williams syndrome and typical development

    Hannah eBroadbent

    2015-02-01

    Full Text Available Visuospatial difficulties in Williams syndrome (WS are well documented. Recently, research has shown that spatial difficulties in WS extend to large-scale space, particularly in coding space using an allocentric frame of reference. Typically developing (TD children and adults predominantly rely on the use of a sequential egocentric strategy to navigate a large-scale route (retracing a sequence of left-right body turns. The aim of this study was to examine whether individuals with WS are able to employ a sequential egocentric strategy to guide learning and the retracing of a route. Forty-eight TD children, aged 5, 7 and 9 years and 18 participants with WS were examined on their ability to learn and retrace routes in two (6-turn virtual environment mazes (with and without landmarks. The ability to successfully retrace a route following the removal of landmarks (use of sequential egocentric coding was also examined.Although in line with TD 5 year-olds when learning a route with landmarks, individuals with WS showed significantly greater detriment when these landmarks were removed, relative to all TD groups. Moreover, the WS group made significantly more errors than all TD groups when learning a route that never contained landmarks. On a perceptual view-matching task, results revealed a high level of performance across groups, indicative of an ability to use this visual information to potentially aid navigation. These findings suggest that individuals with WS rely on landmarks to a greater extent than TD children, both for learning a route and for retracing a recently learned route. TD children, but not individuals with WS, were able to fall back on the use of a sequential egocentric strategy to navigate when landmarks were not present. Only TD children therefore coded sequential route information simultaneously with landmark information. The results are discussed in relation to known atypical cortical development and perceptual-matching abilities

  13. Corrective surgery for canine patellar luxation in 75 cases (107 limbs): landmark for block recession

    Mitsuhiro Isaka; Masahiko Befu; Nami Matsubara; Mayuko Ishikawa; Yurie Arase; Toshiyuki Tsuyama; Akiko Doi; Shinichi Namba

    2014-01-01

    Canine medial patellar luxation (MPL) is a very common orthopedic disease in small animals. Because the pathophysiology of this disease involves various pathways, the surgical techniques and results vary according to the veterinarian. Further, the landmark for block recession is not completely clear. We retrospectively evaluated 75 dogs (107 limbs) with MPL in whom our landmark for block recession was used from July 2008 to May 2013. Information regarding the breed, age, sex, body weight, bod...

  14. Value of anatomical landmarks in single-nostril endonasal transnasal-sphenoidal surgery.

    Wei, Liang-Feng; Zhang, Jinchao; Chen, Hong-Jie; Wang, Rumi

    2013-04-01

    The sphenoid sinus occupies a central location in transsphenoidal surgery (TSS). It is important to identify relevant anatomical landmarks to enter the sphenoid sinus and sellar region properly. The aim of this study was to identify anatomical landmarks and their value in single-nostril endonasal TSS. A retrospective study was performed to review 148 cases of single-nostril endonasal TSS for pituitary lesions. The structure of the nasal cavities and sphenoid sinus, the position of apertures of the sphenoid sinus and relevant arteries and the morphological characteristics of the anterior wall of the sphenoid sinus and sellar floor were observed and recorded. The important anatomical landmarks included the mucosal aperture of the sphenoid sinus, a blunt longitudinal prominence on the posterior nasal septum, the osseocartilaginous junction of the nasal septum, the 'bow sign' of the anterior wall of the sphenoid sinus, the osseous aperture and its relationship with the nutrient arteries, the bulge of the sellar floor and the carotid protuberance. These landmarks outlined a clear route to the sella turcica with an optimal view and lesser tissue damage. Although morphological variation may exist, the position of these landmarks was generally consistent. Locating the sphenoid sinus aperture is the gold standard to direct the surgical route of TSS. The 'bow sign' and the sellar bulge are critical landmarks for accurate entry into the sphenoid sinus and sella fossa, respectively.

  15. Simultaneously mapping and superimposing landmark configurations with parsimony as optimality criterion.

    Catalano, S A; Goloboff, P A

    2012-05-01

    All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark configurations along the tree as changes in shape, the metric chosen to define the ancestral assignments should also form the basis to superimpose the configurations. Thus, we present here a method that merges both steps, map and align, into a single procedure that (for the given tree) produces a multiple alignment and ancestral assignments such that the sum of the Euclidean distances between the corresponding landmarks along tree nodes is minimized. This approach is an extension of the method proposed by Catalano et al. (2010. Phylogenetic morphometrics (I): the use of landmark data in a phylogenetic framework. Cladistics. 26:539-549) for mapping landmark data with parsimony as optimality criterion. In the context of phylogenetics, this method allows maximizing the degree to which similarity in landmark positions can be accounted for by common ancestry. In the context of morphometrics, this approach guarantees (heuristics aside) that all the transformations inferred on the tree represent changes in shape. The performance of the method was evaluated on different data sets, indicating that the method produces marked improvements in tree score (up to 5% compared with generalized superimpositions, up to 11% compared with ordinary superimpositions). These empirical results stress the importance of incorporating the phylogenetic information into the alignment step.

  16. Head CT scan

    Brain CT; Cranial CT; CT scan - skull; CT scan - head; CT scan - orbits; CT scan - sinuses; Computed tomography - cranial; CAT scan - brain ... hold your breath for short periods. A complete scan usually take only 30 seconds to a few ...

  17. Personal Landmarks from the Legacy of Arthur Phelps

    Lowke, John

    2013-09-01

    I have been influenced for my whole life by Art Phelps, more than by anyone else - other than my wife! I first heard of Art Phelps in 1960 when, in the middle of doing my PhD in Adelaide, South Australia, Frost and Phelps published their land-mark paper, not only on drift velocities, the subject of my PhD, but on Boltzmann analyses, which were to deliver detailed cross sections for all common gases. Later I dared to suggest to my university that one of my two external PhD examiners be Phelps, a move that led to me being accepted for a position at Westinghouse Research Laboratories in Pittsburgh for 6 years, with Phelps as my direct supervisor. Throughout this period, Phelps refused to be a co-author of any of my papers, leaving me with severe doubts as to what he thought of their quality! I list areas where insights from Phelps inspired the growth of new fruit. (1) That transverse and longitudinal electron diffusion coefficients differ, typically by a factor of two. (2) That averaging radiation absorption coefficients in electric arcs, using common weightings involving Black Body radiation, can and usually do lead to errors of orders of magnitude. (3) That CO2 laser discharges are largely controlled by electron attachment rather than by diffusion or recombination. (4) That boundary conditions for electrons at metal electrodes in arc welding, are not zero, but from an astrophysical analogy, are zero when extrapolated to one mean free path beyond the surface. (5) That the metastable vibrational states of nitrogen become an energy gain rather than a loss process for low energy electrons as occur in electrical breakdown in air, resulting in increases of the ionisation coefficient by orders of magnitude. Coupled with the detachment of electrons from negative ions by singlet delta states of metastable oxygen molecules, sustaining discharge electric fields are reduced a factor of five. Phelps worked on this problem with me until a few months before he died.

  18. Automatic aorta segmentation and valve landmark detection in C-arm CT for transcatheter aortic valve implantation.

    Zheng, Yefeng; John, Matthias; Liao, Rui; Nöttling, Alois; Boese, Jan; Kempfert, Jörg; Walther, Thomas; Brockmann, Gernot; Comaniciu, Dorin

    2012-12-01

    Transcatheter aortic valve implantation (TAVI) is a minimally invasive procedure to treat severe aortic valve stenosis. As an emerging imaging technique, C-arm computed tomography (CT) plays a more and more important role in TAVI on both pre-operative surgical planning (e.g., providing 3-D valve measurements) and intra-operative guidance (e.g., determining a proper C-arm angulation). Automatic aorta segmentation and aortic valve landmark detection in a C-arm CT volume facilitate the seamless integration of C-arm CT into the TAVI workflow and improve the patient care. In this paper, we present a part-based aorta segmentation approach, which can handle structural variation of the aorta in case that the aortic arch and descending aorta are missing in the volume. The whole aorta model is split into four parts: aortic root, ascending aorta, aortic arch, and descending aorta. Discriminative learning is applied to train a detector for each part separately to exploit the rich domain knowledge embedded in an expert-annotated dataset. Eight important aortic valve landmarks (three hinges, three commissures, and two coronary ostia) are also detected automatically with an efficient hierarchical approach. Our approach is robust under all kinds of variations observed in a real clinical setting, including changes in the field-of-view, contrast agent injection, scan timing, and aortic valve regurgitation. Taking about 1.1 s to process a volume, it is also computationally efficient. Under the guidance of the automatically extracted patient-specific aorta model, the physicians can properly determine the C-arm angulation and deploy the prosthetic valve. Promising outcomes have been achieved in real clinical applications.

  19. Online updating of context-aware landmark detectors for prostate localization in daily treatment CT images

    Dai, Xiubin [College of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210015, China and IDEA Lab, Department of Radiology and BRIC, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27510 (United States); Gao, Yaozong [IDEA Lab, Department of Radiology and BRIC, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27510 (United States); Shen, Dinggang, E-mail: dgshen@med.unc.edu [IDEA Lab, Department of Radiology and BRIC, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, North Carolina 27510 and Department of Brain and Cognitive Engineering, Korea University, Seoul (Korea, Republic of)

    2015-05-15

    Purpose: In image guided radiation therapy, it is crucial to fast and accurately localize the prostate in the daily treatment images. To this end, the authors propose an online update scheme for landmark-guided prostate segmentation, which can fully exploit valuable patient-specific information contained in the previous treatment images and can achieve improved performance in landmark detection and prostate segmentation. Methods: To localize the prostate in the daily treatment images, the authors first automatically detect six anatomical landmarks on the prostate boundary by adopting a context-aware landmark detection method. Specifically, in this method, a two-layer regression forest is trained as a detector for each target landmark. Once all the newly detected landmarks from new treatment images are reviewed or adjusted (if necessary) by clinicians, they are further included into the training pool as new patient-specific information to update all the two-layer regression forests for the next treatment day. As more and more treatment images of the current patient are acquired, the two-layer regression forests can be continually updated by incorporating the patient-specific information into the training procedure. After all target landmarks are detected, a multiatlas random sample consensus (multiatlas RANSAC) method is used to segment the entire prostate by fusing multiple previously segmented prostates of the current patient after they are aligned to the current treatment image. Subsequently, the segmented prostate of the current treatment image is again reviewed (or even adjusted if needed) by clinicians before including it as a new shape example into the prostate shape dataset for helping localize the entire prostate in the next treatment image. Results: The experimental results on 330 images of 24 patients show the effectiveness of the authors’ proposed online update scheme in improving the accuracies of both landmark detection and prostate segmentation

  20. The Use of Quick Response (QR Codes in Landmark-Based Pedestrian Navigation

    Anahid Basiri

    2014-01-01

    Full Text Available Vehicle navigation systems usually simply function by calculating the shortest fastest route over a road network. In contrast, pedestrian navigation can have more diverse concerns. Pedestrians are not constrained to road/path networks; their route may involve going into buildings (where accurate satellite locational signals are not available and they have different priorities, for example, preferring routes that are quieter or more sheltered from the weather. In addition, there are differences in how people are best directed: pedestrians noticing landmarks such as buildings, doors, and steps rather than junctions and sign posts. Landmarks exist both indoors and outdoors. A system has been developed that uses quick response (QR codes affixed to registered landmarks allowing users to localise themselves with respect to their route and with navigational instructions given in terms of these landmarks. In addition, the system includes images of each landmark helping users to navigate visually in addition to through textual instructions and route maps. The system runs on a mobile device; the users use the device’s camera to register each landmark’s QR code and so update their position (particularly indoors and progress through the route itinerary.

  1. A reinforcement learning approach to model interactions between landmarks and geometric cues during spatial learning.

    Sheynikhovich, Denis; Arleo, Angelo

    2010-12-13

    In contrast to predictions derived from the associative learning theory, a number of behavioral studies suggested the absence of competition between geometric cues and landmarks in some experimental paradigms. In parallel to these studies, neurobiological experiments suggested the existence of separate independent memory systems which may not always interact according to classic associative principles. In this paper we attempt to combine these two lines of research by proposing a model of spatial learning that is based on the theory of multiple memory systems. In our model, a place-based locale strategy uses activities of modeled hippocampal place cells to drive navigation to a hidden goal, while a stimulus-response taxon strategy, presumably mediated by the dorso-lateral striatum, learns landmark-approaching behavior. A strategy selection network, proposed to reside in the prefrontal cortex, implements a simple reinforcement learning rule to switch behavioral strategies. The model is used to reproduce the results of a behavioral experiment in which an interaction between a landmark and geometric cues was studied. We show that this model, built on the basis of neurobiological data, can explain the lack of competition between the landmark and geometry, potentiation of geometry learning by the landmark, and blocking. Namely, we propose that the geometry potentiation is a consequence of cooperation between memory systems during learning, while blocking is due to competition between the memory systems during action selection.

  2. Thyroid Scan and Uptake

    ... Physician Resources Professions Site Index A-Z Thyroid Scan and Uptake Thyroid scan and uptake uses small ... Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is a type ...

  3. The Architectural Features and Prevalence of Contemporary Landmarks in Kaunas City

    Almantas Bružas

    2011-03-01

    Full Text Available The article focuses on contemporary architectural accents and their architectural features in Kaunas city. The paper also analyses the prevalence of contemporary architectural accents in the city. Some tendencies towards creating Kaunas landmarks, relationship between them and the built environment and aesthetic measures are discussed on the basis of analyzing the most important and characteristic sacral, commercial, industrial and residential architecture patterns. It can be concluded that contemporary materials as well as a lightweight construction and the courage of architects helped with producing the image of modern architectural landmark, though the spread of Kaunas contemporary landmarks has a chaotic character and the cityscape has not been enriched by the powerful dominants of space structure.Article in Lithuanian

  4. The language of landmarks: the role of background knowledge in indoor wayfinding.

    Frankenstein, Julia; Brüssow, Sven; Ruzzoli, Felix; Hölscher, Christoph

    2012-08-01

    To effectively wayfind through unfamiliar buildings, humans infer their relative position to target locations not only by interpreting geometric layouts, especially length of line of sight, but also by using background knowledge to evaluate landmarks with respect to their probable spatial relation to a target. Questionnaire results revealed that participants have consistent background knowledge about the relative position of target locations. Landmarks were rated significantly differently with respect to their spatial relation to targets. In addition, results from a forced-choice task comparing snapshots of a virtual environment revealed that background knowledge influenced wayfinding decisions. We suggest that landmarks are interpreted semantically with respect to their function and spatial relation to the target location and thereby influence wayfinding decisions. This indicates that background knowledge plays a role in wayfinding.

  5. An Efficient Ceiling-view SLAM Using Relational Constraints Between Landmarks

    Hyukdoo Choi

    2014-01-01

    Full Text Available In this paper, we present a new indoor ‘simultaneous localization and mapping’ (SLAM technique based on an upward-looking ceiling camera. Adapted from our previous work [17], the proposed method employs sparsely-distributed line and point landmarks in an indoor environment to aid with data association and reduce extended Kalman filter computation as compared with earlier techniques. Further, the proposed method exploits geometric relationships between the two types of landmarks to provide added information about the environment. This geometric information is measured with an upward-looking ceiling camera and is used as a constraint in Kalman filtering. The performance of the proposed ceiling-view (CV SLAM is demonstrated through simulations and experiments. The proposed method performs localization and mapping more accurately than those methods that use the two types of landmarks without taking into account their relative geometries.

  6. Laplacian Eigenmaps manifold learning for landmark localization in brain MR images.

    Guerrero, Ricardo; Wolz, Robin; Rueckert, Daniel

    2011-01-01

    The identification of anatomical landmarks in medical images is an important task in registration and morphometry. Manual labeling is time consuming and prone to observer errors. We propose a manifold learning procedure, based on Laplacian Eigenmaps, that learns an embedding from patches drawn from multiple brain MR images. The position of the patches in the manifold can be used to predict the location of the landmarks via regression. New images are embedded in the manifold and the resulting coordinates are used to predict the landmark position in the new image. The output of multiple regressors is fused in a weighted fashion to boost the accuracy and robustness. We demonstrate this framework in 3D brain MR images from the ADNI database. We show an accuracy of -0.5mm, an increase of at least two fold when compared to traditional approaches such as registration or sliding windows.

  7. Boosting multi-features with prior knowledge for mini unmanned helicopter landmark detection

    2008-01-01

    Without sufficient real training data, the data driven classification algorithms based on boosting method cannot solely be utilized to applications such as the mini unmanned helicopter landmark image detection. In this paper, we propose an approach which uses a boosting algorithm with the prior knowledge for the mini unmanned helicopter landmark image detection. The stage forward stagewise additive model of boosting is analyzed, and the approach how to combine it with the prior knowledge model is presented. The approach is then applied to landmark image detection, where the multi-features are boosted to solve a series of problems, such as rotation, noises affected, etc. Results of real flight experiments demonstrate that for small training examples the boosted learning system using prior knowledge is dramatically better than the one driven by data only.

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

    Eleonora A M Festen

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

  9. Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus.

    Carolina Medina-Gomez

    2012-07-01

    Full Text Available To identify genetic loci influencing bone accrual, we performed a genome-wide association scan for total-body bone mineral density (TB-BMD variation in 2,660 children of different ethnicities. We discovered variants in 7q31.31 associated with BMD measurements, with the lowest P = 4.1 × 10(-11 observed for rs917727 with minor allele frequency of 0.37. We sought replication for all SNPs located ± 500 kb from rs917727 in 11,052 additional individuals from five independent studies including children and adults, together with de novo genotyping of rs3801387 (in perfect linkage disequilibrium (LD with rs917727 in 1,014 mothers of children from the discovery cohort. The top signal mapping in the surroundings of WNT16 was replicated across studies with a meta-analysis P = 2.6 × 10(-31 and an effect size explaining between 0.6%-1.8% of TB-BMD variance. Conditional analyses on this signal revealed a secondary signal for total body BMD (P = 1.42 × 10(-10 for rs4609139 and mapping to C7orf58. We also examined the genomic region for association with skull BMD to test if the associations were independent of skeletal loading. We identified two signals influencing skull BMD variation, including rs917727 (P = 1.9 × 10(-16 and rs7801723 (P = 8.9 × 10(-28, also mapping to C7orf58 (r(2 = 0.50 with rs4609139. Wnt16 knockout (KO mice with reduced total body BMD and gene expression profiles in human bone biopsies support a role of C7orf58 and WNT16 on the BMD phenotypes observed at the human population level. In summary, we detected two independent signals influencing total body and skull BMD variation in children and adults, thus demonstrating the presence of allelic heterogeneity at the WNT16 locus. One of the skull BMD signals mapping to C7orf58 is mostly driven by children, suggesting temporal determination on peak bone mass acquisition. Our life-course approach postulates that these genetic effects influencing peak bone mass accrual may impact the risk of

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

    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.

  11. Localization and navigation using a novel artificial landmark for indoor mobile robots

    Wen Feng; Yuan Kui; Zheng Rui

    2009-01-01

    This paper presents a practical topological navigation system for indoor mobile robots, making use of a novel artificial landmark which is called MR code. This new kind of paper-made landmarks can be easily attached on the ceilings or on the walls. Localization algorithms for the two cases are given respectively. A docking control algorithm is also described, which a robot employs to approach its current goal. A simple topological navigation algorithm is proposed. Experiment results show the effectiveness of the method in real environment.

  12. Application of a Fast Connected Components Labeling Algorithm in Processing Landmark Images

    2007-01-01

    Extracting geometric data of landmarks from fluoroscopic images plays an important role in camera calibration process of a fluoroscopic-image-based surgical navigation system. Connected components labeling is the essential technique for the extraction. A new fast connected components labeling algorithm was presented. The definition of upward concave set was introduced to explain the algorithm. Feasibility and efficiency of the algorithm were verified with experiments. This algorithm performs well in labeling non-upward concave set connected components and applies to landmarks labeling well. Moreover, the proposed algorithm possesses a desirable characteristic that will facilitate the subsequent processing of fluoroscopic images.

  13. UAV Control on the Basis of 3D Landmark Bearing-Only Observations.

    Karpenko, Simon; Konovalenko, Ivan; Miller, Alexander; Miller, Boris; Nikolaev, Dmitry

    2015-11-27

    The article presents an approach to the control of a UAV on the basis of 3D landmark observations. The novelty of the work is the usage of the 3D RANSAC algorithm developed on the basis of the landmarks' position prediction with the aid of a modified Kalman-type filter. Modification of the filter based on the pseudo-measurements approach permits obtaining unbiased UAV position estimation with quadratic error characteristics. Modeling of UAV flight on the basis of the suggested algorithm shows good performance, even under significant external perturbations.

  14. Helix Scan: A Scan Design for Diagnosis

    WANG Fei; HU Yu; LI Xiaowei

    2007-01-01

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

  15. Computed tomography landmark-based semi-automated mesh morphing and mapping techniques: generation of patient specific models of the human pelvis without segmentation.

    Salo, Zoryana; Beek, Maarten; Wright, David; Whyne, Cari Marisa

    2015-04-13

    Current methods for the development of pelvic finite element (FE) models generally are based upon specimen specific computed tomography (CT) data. This approach has traditionally required segmentation of CT data sets, which is time consuming and necessitates high levels of user intervention due to the complex pelvic anatomy. The purpose of this research was to develop and assess CT landmark-based semi-automated mesh morphing and mapping techniques to aid the generation and mechanical analysis of specimen-specific FE models of the pelvis without the need for segmentation. A specimen-specific pelvic FE model (source) was created using traditional segmentation methods and morphed onto a CT scan of a different (target) pelvis using a landmark-based method. The morphed model was then refined through mesh mapping by moving the nodes to the bone boundary. A second target model was created using traditional segmentation techniques. CT intensity based material properties were assigned to the morphed/mapped model and to the traditionally segmented target models. Models were analyzed to evaluate their geometric concurrency and strain patterns. Strains generated in a double-leg stance configuration were compared to experimental strain gauge data generated from the same target cadaver pelvis. CT landmark-based morphing and mapping techniques were efficiently applied to create a geometrically multifaceted specimen-specific pelvic FE model, which was similar to the traditionally segmented target model and better replicated the experimental strain results (R(2)=0.873). This study has shown that mesh morphing and mapping represents an efficient validated approach for pelvic FE model generation without the need for segmentation.

  16. Route-external and route-internal landmarks in route descriptions : Effects of route length and map design

    Westerbeek, Hans; Maes, Alfons

    2013-01-01

    Landmarks are basic ingredients in route descriptions. They often mark choice points: locations where travellers choose from different options how to continue the route. This study focuses on one of the loose ends in the taxonomy of landmarks. In a memory-based production experiment in which respond

  17. Lumbar spine CT scan

    CAT scan - lumbar spine; Computed axial tomography scan - lumbar spine; Computed tomography scan - lumbar spine; CT - lower back ... your breath for short periods of time. The scan should take only 10 to 15 minutes.

  18. 76 FR 60079 - Landmarks Committee of the National Park System Advisory Board Meeting

    2011-09-28

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... Advisory Board will be held beginning at 1 p.m. on November 8, 2011, at the following location. The meeting... System Advisory Board at a subsequent meeting at a place and time to be determined. The Committee...

  19. 76 FR 55701 - Landmarks Committee of the National Park System Advisory Board Meeting

    2011-09-08

    ... National Park Service Landmarks Committee of the National Park System Advisory Board Meeting AGENCY... Advisory Board will be held beginning at 1 p.m. on November 8, 2011, at the following location. The meeting... System Advisory Board at a subsequent meeting at a place and time to be determined. The Committee...

  20. 36 CFR 62.4 - Natural landmark designation and recognition process.

    2010-07-01

    ... sufficient representation of the significant natural features. (g) National Park System Advisory Board. (1... qualifies for national natural landmark designation. (2) Notice of Advisory Board meetings to review... also attend the board meeting and upon request may address the board concerning an area's...

  1. The use of visual landmarks in a wayfinding system for elderly with beginning dementia

    Veldkamp, D.; Hagethorn, F.; Kröse, B.; de Greef, P.

    2008-01-01

    This paper presents an experiment carried out to study the design options of a GPS-based navigation aid for elderly with beginning dementia. Results suggest that landmark based instructions may yield higher performance of the system then left/right instructions.

  2. Influence of anatomic landmarks in the virtual environment on simulated angled laparoscope navigation

    Buzink, S.N.; Christie, L.S.; Goossens, R.H.M.; De Ridder, H.; Jakimowicz, J.J.

    2010-01-01

    Background - The aim of this study is to investigate the influence of the presence of anatomic landmarks on the performance of angled laparoscope navigation on the SimSurgery SEP simulator. Methods - Twenty-eight experienced laparoscopic surgeons (familiar with 30º angled laparoscope, >100 basic lap

  3. A Parisian Walk along the Landmarks of the Discovery of Radioactivity

    Gablot, Ginette

    To see the landmarks associated with the discovery of radioactivity by Henri Becquerel a century ago and the transfer of this new field of research from the most prestigious scientific institutions of the day to new scientific sites is worth a walk that will take most of a morning or afternoon to complete.

  4. Illusionary Inclusion--What Went Wrong with New Labour's Landmark Educational Policy?

    Hodkinson, Alan

    2012-01-01

    This article examines the emergence and evolution of New Labour's landmark educational policy; namely that of inclusion. The author, Alan Hodkinson, associate professor at the Centre for Cultural and Disability Studies at Liverpool Hope University, illuminates his conceptual difficulties in attempting to define what inclusion was and what…

  5. Undecidability and temporal logic: some landmarks from Turing to the present

    Goranko, Valentin

    2012-01-01

    This is a selective survey and discussion of some of the landmark undecidability results in temporal logic, beginning with Turing's undecidability of the Halting problem which, in retrospect, can be regarded as the historically first undecidability result for a suitable temporal logic over config...

  6. Obstacles Facing Promoting Tourism for Islamic Landmarks from the Perspective of Tour Operators in Egypt

    Suzan Bakri Hassan

    2015-05-01

    Full Text Available The UNESCO launched a campaign #unite4heritage in Egypt to defeat extremism and intolerance. The message of such campaigne is peace, dialogue and unity embedded in cultural heritage. As culture and tourism are linked together, such message could be delivered through improving culture heritage tourism in Egypt. Islamic landmarks  are considered as a part of human heritage. Therefore, the purpose of this study is to identify how much tour operators in Egypt include Islamic landmarks in their programs to determine the obstacles facing promoting cultural tourism in Islamic landmarks' areas. Additionally, the study would identify positive results in the case of developing heritage tourism in Egypt. To achieve a high result, a survey approach was employed to collect data from 100 tour operators, using a completed questionnaire technique as well as a Likert Scale and statistical models in order to test and interpret the research outcomes. The research findings indicated that although tour operators in Egypt are convinced of the significance of the Islamic landmarks, there is no contradiction between creating global understanding and at the same time achieving benefit to the local community. However, there is a range of obstacles facing promoting such type of tourism in Egypt. Keywords: Culture heritage tourism, community, Egypt, Islamic civilization.

  7. Landmark-based morphometrics of the normal adult brain using MRI.

    Free, S L; O'Higgins, P; Maudgil, D D; Dryden, I L; Lemieux, L; Fish, D R; Shorvon, S D

    2001-05-01

    We describe the application of statistical shape analysis to homologous landmarks on the cortical surface of the adult human brain. Statistical shape analysis has a sound theoretical basis. Landmarks are identified on the surface of a 3-D reconstruction of the segmented cortical surface from magnetic resonance image (MRI) data. Using publicly available software (morphologika) the location and size dependence of the landmarks are removed and the differences in landmark distribution across subjects are analysed using principal component analysis. These differences, representing shape differences between subjects, can be visually assessed using wireframe models and transformation grids. The MRI data of 58 adult brains (27 female and 15 left handed) were examined. Shape differences in the whole brain are described which concern the relative orientation of frontal lobe sulci. Analysis of all 116 hemispheres revealed a statistically significant difference (P < 0.001) between left and right hemispheres. This finding was significant for right- but not left-handed subjects alone. No other significant age, gender, handedness, or brain-size correlations with shape differences were found.

  8. Automatic recognition of surface landmarks of anatomical structures of back and posture

    Michoński, Jakub; Glinkowski, Wojciech; Witkowski, Marcin; Sitnik, Robert

    2012-05-01

    Faulty postures, scoliosis and sagittal plane deformities should be detected as early as possible to apply preventive and treatment measures against major clinical consequences. To support documentation of the severity of deformity and diminish x-ray exposures, several solutions utilizing analysis of back surface topography data were introduced. A novel approach to automatic recognition and localization of anatomical landmarks of the human back is presented that may provide more repeatable results and speed up the whole procedure. The algorithm was designed as a two-step process involving a statistical model built upon expert knowledge and analysis of three-dimensional back surface shape data. Voronoi diagram is used to connect mean geometric relations, which provide a first approximation of the positions, with surface curvature distribution, which further guides the recognition process and gives final locations of landmarks. Positions obtained using the developed algorithms are validated with respect to accuracy of manual landmark indication by experts. Preliminary validation proved that the landmarks were localized correctly, with accuracy depending mostly on the characteristics of a given structure. It was concluded that recognition should mainly take into account the shape of the back surface, putting as little emphasis on the statistical approximation as possible.

  9. Single Landmark Learning in Rats: Sex Differences in a Navigation Task

    Forcano, L.; Santamaria, J.; Mackintosh, N. J.; Chamizo, V. D.

    2009-01-01

    In Experiments 1 and 2, rats were trained in a Morris pool to find a hidden platform located some distance away from a single landmark. Males learned to swim to the platform faster than females, but on test trials without the platform, males, unlike females, spent less time in the platform quadrant of the pool in the second half of each test trial…

  10. Observer Reliability of Three-Dimensional Cephalometric Landmark Identification on Cone-Beam CT

    de Oliveira, Ana Emilia F.; Cevidanes, Lucia Helena S.; Phillips, Ceib; Motta, Alexandre; Burke, Brandon; Tyndall, Donald

    2009-01-01

    Objective To evaluate reliability in 3D landmark identification using Cone-Beam CT. Study Design Twelve pre-surgery CBCTs were randomly selected from 159 orthognathic surgery patients. Three observers independently repeated three times the identification of 30 landmarks in the sagittal, coronal, and axial slices. A mixed effects ANOVA model estimated the Intraclass Correlations (ICC) and assessed systematic bias. Results The ICC was >0.9 for 86% of intra-observer assessments and 66% of inter-observer assessments. Only 1% of intra-observer and 3% of inter-observer coefficients were <0.45. The systematic difference among observers was greater in X and Z than in Y dimensions, but the maximum mean difference was quite small. Conclusion Overall, the intra- and inter-observer reliability was excellent. 3D landmark identification using CBCT can offer consistent and reproducible data, if a protocol for operator training and calibration is followed. This is particularly important for landmarks not easily specified in all three planes of space. PMID:18718796

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

    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.

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

    Elisabeth Jeannette Ploran

    2014-01-01

    Full Text Available 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.

  13. Within-compound associations explain potentiation and failure to overshadow learning based on geometry by discrete landmarks.

    Austen, Joe M; Kosaki, Yutaka; McGregor, Anthony

    2013-07-01

    In three experiments, rats were trained to locate a submerged platform in one of the base corners of a triangular arena above each of which was suspended one of two distinctive landmarks. In Experiment 1, it was established that these landmarks differed in their salience by the differential control they gained over behavior after training in compound with geometric cues. In Experiment 2, it was shown that locating the platform beneath the less salient landmark potentiated learning based on geometry compared with control rats for which landmarks provided ambiguous information about the location of the platform. The presence of the more salient landmark above the platform for another group of animals appeared to have no effect on learning based on geometry. Experiment 3 established that these landmark and geometry cues entered into within-compound associations during compound training. We argue that these within-compound associations can account for the potentiation seen in Experiment 2, as well as previous failures to demonstrate overshadowing of geometric cues. We also suggest that these within-compound associations need not be of different magnitudes, despite the different effects of each of the landmarks on learning based on geometry seen in Experiment 2. Instead, within-compound associations appear to mitigate the overshadowing effects that traditional theories of associative learning would predict.

  14. Millipixel scale landmark location in images: The optics, the imaging system, and the Cramer-Rao bound on performance

    Gutierrez, Jose Alejandro

    2005-11-01

    Landmark location uncertainty in digital images, which is extensively used in high precision photogrammetry and machine vision applications, consist of the error measurement when locating the position of a specific image feature. Landmark location uncertainty has been previously described in the literature for particular landmark designs within the scope of specific applications and using simplified models. For the first time, a general framework to determine landmark location uncertainty in presented in this work. The framework includes the determination of the performance floor by means of the Cramer-Rao Lower Bound (CRLB). The methodology presented, considers the complete physical model of image formation, including 6 degree of freedom, landmark to camera geometry, diffraction, defocus, lens distortion, gray-scale, pixel geometry, and pixel sensitive area. With the framework developed, an analysis tool was created to model true engineering cases to allow the investigator to predict performance for any configuration of landmark, camera, imager and estimator used. This tool includes the determination of the CRLB performance floor for the configuration used. Additionally, this work also pioneers novel landmark location estimation algorithms with confidence intervals at tens of milli-pixel level, which not only perform more than 10 times better than existing estimation algorithms but also has been experimentally verified. The Cramer-Rao Lower Bound methodology introduced in the present work establishes a theoretical statistical minimum limit on the landmark location uncertainty. Knowledge of this bound provides the means to evaluate the actual performance of both existing and future landmark location estimators. The approach presented in this work includes a mix of analysis, where feasible, and numerical work where required, including numerically deriving the partial derivatives needed to compute statistical distributions and the Cramer-Rao Lower Bound.

  15. Software Designation to Assess the Proximity of Different Facial Anatomic Landmarks to Midlines of the Mouth and Face

    Moshkelgosha V

    2014-12-01

    Full Text Available Statement of Problem: Recognition and determination of facial and dental midline is important in dentistry. Currently, there are no verifiable guidelines that direct the choice of specific anatomic landmarks to determine the midline of the face or mouth. Objectives: The purpose of this study was to determine which of facial anatomic landmarks is closest to the midline of the face as well as that of the mouth. Materials and Methods: Frontal full-face digital images of 92 subjects (men and women age range: 20-30 years in smile were taken under standardized conditions; commonly used anatomic landmarks, nasion, tip of the nose, and tip of the philtrum were digitized on the images of subjects and aesthetic analyzer software used for midline analysis using Esthetic Frame. Deviations from the midlines of the face and mouth were measured for the 3 clinical landmarks; the existing dental midline was considered as the fourth landmark. The entire process of midline analysis was done by a single observer and repeated twice. Reliability analysis and 1-sample t- tests were conducted. Results: The Intra-class correlation coefficients (ICCs for reliability analysis of RFV and RCV measures made two times revealed that the reliabilities were all acceptable. The results indicated that each of the 4 landmarks deviated uniquely and significantly (P<.001 from the midlines of the face as well as mouth in both males and females. Conclusions: There was a significant difference between the mean ratios of the chosen anatomic landmarks and the midlines of the face and mouth. The hierarchy of anatomic landmarks closest to the midline of the face is: (1 midline of the commissures, (2 nasion , (3 tip of philtrum,(4 dental midline, and (5 tip ofthe nose. The closest anatomic landmarks to the mouth midline are: (1 tip of philtrum, (2 dental midline, (3 tip of nose, and (4 nasion.

  16. Ultrasound Versus the Landmark Technique: A Prospective Randomized Comparative Study of Internal Jugular Vein Cannulation in an Intensive Care Unit

    B R Shrestha

    2011-06-01

    Full Text Available OBJECTIVE: The aim of this study is to find out if an ultrasound technique has advantages over the conventional landmark technique. METHODS: This is a prospective randomized comparative study on 120 patients requiring central venous cannulation of the right internal jugular vein. The study comprised of two groups: ultrasound and landmark groups, each consisting of 60 patients. The outcome measures were compared between the groups. RESULTS: Cannulation of the internal jugular vein was successful in 58 patients in the ultrasound group and in 53 in the landmark group. The number of attempts was 1.5 (1 - 3 and 2 (1 - 3 in the ultrasound and landmark group respectively (p = 0.001. The time taken for the successful cannulation was 4.9 +/- 1.7 minutes in the ultrasound approach and 8.0 +/- 2.8 minutes in the landmark approach (p = 0.00. The internal jugular vein diameter in the supine position was 11.2 +/- 1.5 mm which increased to 15.04 +/- 1.5 mm with a 15 degrees head-down position in the USG group (p = 0.001. The first attempt success rate was 39/60 (63% in the ultrasound group and 19/60 (32% with the landmark technique. The seven (12% failure cases in the landmark group were rescued by the ultrasound technique. Inadvertent carotid artery puncture occurred in 2/60 (3% and 6/60 (10% of patients in the ultrasound and land mark group respectively. CONCLUSIONS: Ultrasound improves success rate, minimizes cannulation time and complications during internal jugular vein cannulation. It can be employed as a rescue technique in cases of a failed landmark technique. Keywords:cannulation, central, landmark, technique, ultrasound.

  17. Lung gallium scan

    Gallium 67 lung scan; Lung scan; Gallium scan - lung; Scan - lung ... Gallium is injected into a vein. The scan will be taken 6 to 24 hours after the gallium is injected. (Test time depends on whether your condition is acute or chronic .) ...

  18. Comparison of Cone Beam Computed Tomography and Multi Slice Computed Tomography Image Quality of Human Dried Mandible using 10 Anatomical Landmarks

    Saati, Samira; Kaveh, Fatemeh

    2017-01-01

    Introduction Cone Beam Computed Tomography (CBCT) has gained a broad acceptance in dentomaxillofacial imaging. Computed Tomography (CT) is another imaging modality for diagnosis and preoperative assessments of the head and neck region. Aim Considering the increased radiation exposure and high cost of CT, this study sought to subjectively assess the image quality of CBCT and Multi Slice CT (MSCT). Materials and Methods A dry human mandible was scanned by five CBCT systems (New Tom 3G, Scanora, CRANEX 3D, Promax and Galileos) and one MSCT system. Three independent oral and maxillofacial radiologists reviewed the CBCT and MSCT scans for the quality of 10 landmarks namely mental foramen, trabecular bone, Periodontal Ligament (PDL), dentin, incisive canal, mandibular canal, dental pulp, enamel, lamina dura and cortical bone using a five-point scale. Results Significant differences were found between MSCT and CBCT and among the five CBCT systems (p<0.05) in visualization of different anatomical structures. A fine structure such as the incisive canal was significantly less visible and more variable among the systems in comparison with other anatomical landmarks such as the mental foramen, mandibular canal, cortical bone, dental pulp, enamel and dentin (p<0.05). The Cranex 3D and Promax systems were superior to MSCT and all other CBCT systems in visualizing anatomical structures. Conclusion The CBCT image quality was superior to that of MSCT even though some variability existed among different CBCT systems in visualizing fine structures. Considering the low radiation dose and high resolution, CBCT may be beneficial for dentomaxillofacial imaging. PMID:28384972

  19. Monocular vision for intelligent wheelchair indoor navigation based on natural landmark matching

    Xu, Xiaodong; Luo, Yuan; Kong, Weixi

    2010-08-01

    This paper presents a real-time navigation system in a behavior-based manner. We show that autonomous navigation is possible in different rooms with the use of a single camera and natural landmarks. Firstly the intelligent wheelchair is manually guided on a path passing through different rooms and a video sequence is recorded with a front-facing camera. A 3D structure map is then gotten from this learning sequence by calculating the natural landmarks. Finally, the intelligent wheelchair uses this map to compute its localization and it follows the learning path or a slightly different path to achieve the real-time navigation. Experimental results indicate that this method is effective even when the viewpoint and scale is changed.

  20. Building human genome maps with radiation hybrids

    Slonim, D.; Kruglyak, L.; Stein, L.; Lander, E. [MIT Center for Genome Research, Cambridge, MA (United States)

    1997-12-01

    Genome maps are crucial tools in human genetic research, providing known landmarks for locating disease genes and frameworks for large-scale sequencing. Radiation hybrid mapping is one technique for building genome maps. In this paper, we describe the methods used to build radiation hybrid maps of the entire human genome. We present the hidden Markov model that we employ to estimate the likelihood of a map despite uncertainty about the data, and we discuss the problem of searching for maximum-likelihood maps. We describe the graph algorithms used to find sparse but reliable initial maps and our methods of extending them. Finally, we show results validating our software on simulated data, and we describe our genome-wide human radiation hybrid maps and the evidence supporting them. 29 refs., 7 figs.

  1. Heart PET scan

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

  2. The genial tubercle: A prospective novel landmark for the diagnosis of mandibular asymmetry

    Lee, Seung-Youp; Choi, Dong-Soon; Jang, Insan; Song, Geun-Su

    2017-01-01

    Introduction Identifying menton (Me) on posteroanterior cephalograms and three-dimensional (3D) cone-beam computed tomography (CBCT) images is difficult, because the midpoint of the symphyseal area is not identifiable after the mandibular symphysis fuses at an early age. The aim of this study was to evaluate the reliability of the identification of the genial tubercle (GT) in patients with mandibular asymmetry and to compare it with that of the traditional landmark, Me. Methods The samples comprised 20 CBCT images of adults with mandibular asymmetry. Two examiners performed the identifications and measurements. Me and GT were marked, and the anteroposterior, vertical, and transverse distances to the three reference planes were measured on 3D-reconstructed CBCT images. The intra- and inter-examiner reliability of landmark identification of Me and GT were assessed using the intraclass correlation coefficient (ICC) and Bland-Altman plots. Results The Me and GT landmarks showed excellent reliability (ICC ≥ 0.993) three-dimensionally. In the transverse evaluation, the ICC values of the GT (range, 0.997–0.999) tended to be slightly higher than those of Me (range, 0.993–0.996). In the Bland-Altman plots for the two separate assessments, Me showed a maximum error of 1.76 mm in the transverse direction, whereas the GT showed a maximum error of 0.96 mm in the 95% limit. Conclusions Our results suggest that both Me and GT are clinically reliable and equally useful landmarks for the evaluation of mandibular asymmetry on CBCT images. PMID:28127539

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

    Schmook, Maria T.; Weber, Michael; Kasprian, Gregor; Nemec, Stefan; Prayer, Daniela [Medical University of Vienna, Department of Radiology/Division of Neuro- and Musculoskeletal Radiology, Vienna (Austria); Brugger, Peter C. [Medical University of Vienna, Integrative Morphology Group, Center for Anatomy and Cell Biology, Vienna (Austria); Krampl-Bettelheim, Elisabeth [Department of Obstetrics and Gynecology / Division of Obstetrics and Feto-maternal Medicine, Vienna (Austria)

    2010-06-15

    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 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.)

  4. Management of neovascular Age-related macular degeneration: A review on landmark randomized controlled trials

    Aniruddha Agarwal; Kanika Aggarwal; Vishali Gupta

    2016-01-01

    In the last decade, a number of prospective clinical trials with carefully designed study protocols have been conducted for the treatment of neovascular age-related macular degeneration (AMD). These landmark clinical trials such as ANCHOR and MARINA and, more recently, the Comparison of AMD Treatment Trials and VIEW studies have revolutionized the management of neovascular AMD. While AMD continues to remain a leading cause of severe visual loss worldwide, advances in pharmacotherapeutics have...

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

    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.

  6. Single Robot Localisation Approach for Indoor Robotic Systems through Integration of Odometry and Artificial Landmarks

    Ņikitenko, A; Liekna, A; Ekmanis, M.; Kuļikovskis, G; Andersone, I

    2013-01-01

    we present an integrated approach for robot localization that allows to integrate for the artificial landmark localization data with odometric sensors and signal transfer function data to provide means for different practical application scenarios. The sensor data fusion deals with asynchronous sensor data using inverse Laplace transform. We demonstrate a simulation software system that ensures smooth integration of the odometry-based and signal transfer – based localization into one approach.

  7. Design of an enhanced visual odometry by building and matching compressive panoramic landmarks online

    Wei LU; Zhi-yu XIANG; Ji-lin LIU

    2015-01-01

    Efficient and precise localization is a prerequisite for the intelligent navigation of mobile robots. Traditional visual localization systems, such as visual odometry (VO) and simultaneous localization and mapping (SLAM), suffer from two short-comings: a drift problem caused by accumulated localization error, and erroneous motion estimation due to illumination varia-tion and moving objects. In this paper, we propose an enhanced VO by introducing a panoramic camera into the traditional stereo-only VO system. Benefiting from the 360° field of view, the panoramic camera is responsible for three tasks: (1) detect-ing road junctions and building a landmark library online; (2) correcting the robot’s position when the landmarks are revisited with any orientation; (3) working as a panoramic compass when the stereo VO cannot provide reliable positioning results. To use the large-sized panoramic images efficiently, the concept of compressed sensing is introduced into the solution and an adap-tive compressive feature is presented. Combined with our previous two-stage local binocular bundle adjustment (TLBBA) stereo VO, the new system can obtain reliable positioning results in quasi-real time. Experimental results of challenging long-range tests show that our enhanced VO is much more accurate and robust than the traditional VO, thanks to the compressive panoramic landmarks built online.

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

    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.

  9. Scan BIST with biased scan test signals

    XIANG Dong; CHEN MingJing; SUN JiaGuang

    2008-01-01

    The conventional test-per-scan built-in self-test (BIST) scheme needs a number of shift cycles followed by one capture cycle.Fault effects received by the scan flip-flops are shifted out while shifting in the next test vector like scan testing.Unlike deterministic testing,it is unnecessary to apply a complete test vector to the scan chains.A new scan-based BIST scheme is proposed by properly controlling the test signals of the scan chains,Different biased random values are assigned to the test signals of scan flip-flops in separate scan chains.Capture cycles can be inserted at any clock cycle if necessary.A new testability estimation procedure according to the proposed testing scheme is presented.A greedy procedure is proposed to select a weight for each scan chain.Experimental results show that the proposed method can improve test effectiveness of scan-based BIST greatly,and most circuits can obtain complete fault coverage or very close to complete fault coverage.

  10. Assessment and feasibility of the four landmarks of the aortic root in a cohort of very preterm infants

    Sam Phillips

    2015-01-01

    Conclusion : We present reliability and reference values for all four anatomic landmarks of the aortic root in very preterm infants and demonstrated the importance of standardizing and reporting cardiac output measurements in preterm infants.

  11. Neural Network-Based Landmark Recognition and Navigation with IAMRs. Understanding the Principles of Thought and Behavior.

    Doty, Keith L.

    1999-01-01

    Research on neural networks and hippocampal function demonstrating how mammals construct mental maps and develop navigation strategies is being used to create Intelligent Autonomous Mobile Robots (IAMRs). Such robots are able to recognize landmarks and navigate without "vision." (SK)

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

    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 μm dots at a spacing of c. 91 μm. 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

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

    Marcel eMertes

    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.

  14. Transabdominal ultrasound for detection of pregnancy, fetal and placental landmarks, and fetal age before Day 45 of gestation in the sheep.

    Jones, Amanda K; Gately, Rachael E; McFadden, Katelyn K; Zinn, Steven A; Govoni, Kristen E; Reed, Sarah A

    2016-03-15

    Detection of pregnancy during early gestation is advantageous for flock breeding management. Transabdominal ultrasound is a practical and efficient approach for monitoring pregnancy and fetal growth in small ruminants. However, there is limited information using the transabdominal technique before Day 45 of gestation in sheep. Therefore, our objective was to determine how accurately transabdominal ultrasound could be used to detect pregnancy, to identify pregnancy landmarks, and to quantify fetal length before Day 45 in ewes. Multiparous Western White-faced ewes (n = 99) were estrus synchronized and exposed to one of four Dorset rams. The day a ewe was marked by a ram was considered Day 0 of gestation. Ewes not remarked by Day 20 were separated for ultrasonography. To detect pregnancy and landmarks, ewes were scanned three times per week between Day 26.0 ± 0.3 (mean ± standard error) and Day 40.0 ± 0.2. A single technician performed all scans in the right nonhaired abdominal pit using a real-time portable Eazi-Scan machine and a 5-MHz linear rectal transducer. All data were analyzed using the MIXED procedure in SAS (with repeated measures where appropriate). Because of rebreeding activity, 113 ultrasound periods were initiated. The specificity and positive predictive value were 100% during the entire study. The accuracy, sensitivity, and negative predictive value of ultrasound scanning were greater than 90% beginning at Day 33 ± 1. On average, pregnancy (n = 85) was detected at Day 28.7 ± 0.4 and nonpregnancy (n = 28) at Day 25.5 ± 0.6. Three early fetal losses were identified at Day 39.7 ± 0.7. In pregnant ewes (n = 82), the overall accuracy of fetal counting was 78%. The first observance of an enlarged uterus (P = 0.05) and pregnancy (P = 0.03) was detected earlier when multiple fetuses were developing compared with singletons. Placentome evagination was first observed earlier in triplets compared with twins and singletons (P = 0.02). Fetal length

  15. Construction and analysis of a head CT-scan database for craniofacial reconstruction.

    Tilotta, Françoise; Richard, Frédéric; Glaunès, Joan; Berar, Maxime; Gey, Servane; Verdeille, Stéphane; Rozenholc, Yves; Gaudy, J F

    2009-10-30

    This paper is devoted to the construction of a complete database which is intended to improve the implementation and the evaluation of automated facial reconstruction. This growing database is currently composed of 85 head CT-scans of healthy European subjects aged 20-65 years old. It also includes the triangulated surfaces of the face and the skull of each subject. These surfaces are extracted from CT-scans using an original combination of image-processing techniques which are presented in the paper. Besides, a set of 39 referenced anatomical skull landmarks were located manually on each scan. Using the geometrical information provided by triangulated surfaces, we compute facial soft-tissue depths at each known landmark positions. We report the average thickness values at each landmark and compare our measures to those of the traditional charts of [J. Rhine, C.E. Moore, Facial Tissue Thickness of American Caucasoïds, Maxwell Museum of Anthropology, Albuquerque, New Mexico, 1982] and of several recent in vivo studies [M.H. Manhein, G.A. Listi, R.E. Barsley, et al., In vivo facial tissue depth measurements for children and adults, Journal of Forensic Sciences 45 (1) (2000) 48-60; S. De Greef, P. Claes, D. Vandermeulen, et al., Large-scale in vivo Caucasian facial soft tissue thickness database for craniofacial reconstruction, Forensic Science International 159S (2006) S126-S146; R. Helmer, Schödelidentifizierung durch elektronische bildmischung, Kriminalistik Verlag GmbH, Heidelberg, 1984].

  16. [Dyspraxia: landmarks].

    Mazeau, M

    2010-03-01

    Despite its frequency, little is known about dyspraxia. Dyspraxia, which represents disorders in development and learning movements, within the context of a deficiency in the management of spatial information (in children whose verbal intelligence is spared), is often a severe handicap at school and in social life. Dyspraxia must be distinguished from "common" difficulties of unmotivated children at school, with which it is often confused. Hence, the diagnosis must correspond to rigorous methodology. And one should avoid proposing endless training for the deficient action (writing, getting dressed...); indeed such strategies only lead to short-term 'pseudo' progress, without any long term efficacy on the educational success of these intelligent children. To the contrary, the child should be rapidly oriented in two therapeutic directions: (1) a battle between the "double-task" effect stemming from the graphical and spatial difficulties; (2) the use of palliatives (including computing). In conditions of early diagnosis (at 4-8/9 years of age) and well-coordinated management with the school, the prognosis would be excellent in terms of schooling, choice of a profession and social insertion. If not, or if (as is the case in almost a third of cases) dyspraxia is not isolated (associated with dyslexia, hyperactivity, attentional deficit and psychotic traits), the child should be oriented towards a specialised classroom and care.

  17. Conventional cerebrospinal fluid scanning

    Schicha, H.

    1985-06-01

    Conventional cerebrospinal fluid scanning (CSF scanning) today is mainly carried out in addition to computerized tomography to obtain information about liquor flow kinetics. Especially in patients with communicating obstructive hydrocephalus, CSF scanning is clinically useful for the decision for shunt surgery. In patients with intracranial cysts, CSF scanning can provide information about liquor circulation. Further indications for CSF scanning include the assessment of shunt patency especially in children, as well as the detection and localization of cerebrospinal fluid leaks.

  18. 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.

    Tomaszewska, Iwona M; Tomaszewski, Krzysztof A; Kmiotek, Elizabeth K; Pena, Iwona Z; Urbanik, Andrzej; Nowakowski, Michał; 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.

  19. Ultrasonographic Validation of Anatomical Landmarks for Localization of the Tendon of the Long Head of Biceps Brachii

    Hou, Saiyun; Harrell, John

    2017-01-01

    Objectives. To establish anatomical landmarks for biceps tendon groove localization based on intrinsic anatomical relations and to validate the localization with ultrasonographic measurement. Design. Perspective, observational, single-blinded pilot study. Participants. 25 healthy male and female volunteers ages 24–50 years. Methods. We used two anatomical landmarks, the medial epicondyle vertical line related landmark and the coracoid process landmark. The distance from the groove skin mark to the medial epicondyle vertical line and the coracoid process was measured horizontally and was measured at 0° and 45° of shoulder external rotation, respectively. Results. Medial epicondyle vertical lines were 9.3 mm/21.5 mm medial to the groove at 0°/45° of shoulder external rotation, respectively. Correlation coefficients were 0.04/0.10, 0.32/0.42, and 0.26/0.37 for weight, height, and BMI in 0°/45° of shoulder external rotation, respectively. The distance between the coracoid process and the groove was 44.0 mm/62.2 mm in 0°/45° of shoulder external rotation, respectively. Correlation coefficients were 0.36/0.41, 0.36/0.54, and 0.18/0.12 for weight, height, and BMI in 0°/45° of shoulder external rotation, respectively. Conclusions. The medial epicondyle vertical line and the coracoid process landmark are both useful anatomical landmarks to localize the biceps groove. The anatomical landmark based localization is essentially not correlated with subject's weight, height, or BMI.

  20. Loss of anatomical landmarks with eutectic mixture of local anesthetic cream for neonatal male circumcision.

    Plank, Rebeca M; Kubiak, David W; Abdullahi, Rasak Bamidele; Ndubuka, Nnamdi; Nkgau, Maggie M; Dapaah-Siakwan, Fredrick; Powis, Kathleen M; Lockman, Shahin

    2013-02-01

    We report two cases of newborns who developed marked local edema after application of a eutectic mixture of local anesthetic (EMLA) topical anesthetic cream for neonatal male circumcision (NMC). Although local edema and erythema are known potential side effects of EMLA cream, a common anesthetic used for NMC, the loss of landmarks precluding safe NMC has not previously been reported, and is described here. Although we cannot recommend an alternate local anesthetic for neonates with this reaction to EMLA, based on a review of the published data we think that serious systemic adverse events related to EMLA are extremely rare.

  1. UAV Control on the Basis of 3D Landmark Bearing-Only Observations

    Simon Karpenko

    2015-11-01

    Full Text Available The article presents an approach to the control of a UAV on the basis of 3D landmark observations. The novelty of the work is the usage of the 3D RANSAC algorithm developed on the basis of the landmarks’ position prediction with the aid of a modified Kalman-type filter. Modification of the filter based on the pseudo-measurements approach permits obtaining unbiased UAV position estimation with quadratic error characteristics. Modeling of UAV flight on the basis of the suggested algorithm shows good performance, even under significant external perturbations.

  2. 100 years of Epilepsia: landmark papers and their influence in neuropsychology and neuropsychiatry.

    Hermann, Bruce

    2010-07-01

    As part of the 2009 International League Against Epilepsy (ILAE) Centenary Celebration, a special symposium was dedicated to Epilepsia (100 Years of Epilepsia: Landmark Papers and Their Influence). The Associate Editors were asked to identify a particularly salient and meaningful paper in their areas of expertise. From the content areas of neuropsychology and neuropsychiatry two very interesting papers were identified using quite different ascertainment techniques. One paper addressed the problem of psychosis in temporal lobe epilepsy, whereas the other represents the first paper to appear in Epilepsia presenting quantitative assessment of cognitive status in epilepsy. These two papers are reviewed in detail and placed in historical context.

  3. Registration of cortical surfaces using sulcal landmarks for group analysis of MEG data.

    Joshi, Anand A; Shattuck, David W; Thompson, Paul M; Leahy, Richard M

    2007-06-01

    We present a method to register individual cortical surfaces to a surface-based brain atlas or canonical template using labeled sulcal curves as landmark constraints. To map one cortex smoothly onto another, we minimize a thin-plate spline energy defined on the surface by solving the associated partial differential equations (PDEs). By using covariant derivatives in solving these PDEs, we compute the bending energy with respect to the intrinsic geometry of the 3D surface rather than evaluating it in the flattened metric of the 2D parameter space. This covariant approach greatly reduces the confounding effects of the surface parameterization on the resulting registration.

  4. Energy edge post-occupancy evaluation project: The Landmark Office Building, Yalima, Washington

    1990-06-01

    The Landmark Office Building Survey for the Energy Edge Post- Occupancy Project was administered to thirty of the building occupants. Eighteen respondents answered the questions which rated building features in the areas of (1) thermal factors; (2) air quality; (3) lighting; (4) acoustics; and, (5) overall workspace satisfaction. In addition to rating these ambient environmental features, these respondents also rated their satisfaction of various functional and aesthetic features and specific kinds of workplaces. Data was also collected on health characteristics and occupational demographics of the respondents. No analysis is made of the survey findings which are reported in graphic and tabular format. 20 figs., 8 tabs.

  5. The genomic landscape of cutaneous melanoma.

    Zhang, Tongwu; Dutton-Regester, Ken; Brown, Kevin M; Hayward, Nicholas K

    2016-05-01

    Somatic mutation analysis of melanoma has been performed at the single gene level extensively over the past several decades. This has provided considerable insight into the critical pathways controlling melanoma initiation and progression. During the last 5 yr, next-generation sequencing (NGS) has enabled even more comprehensive mutational screening at the level of multigene panels, exomes and genomes. These studies have uncovered many new and unexpected players in melanoma development. The recent landmark study from The Cancer Genome Atlas (TCGA) consortium describing the genomic architecture of 333 cutaneous melanomas provides the largest and broadest analysis to date on the somatic aberrations underlying melanoma genesis. It thus seems timely to review the mutational landscape of melanoma and highlight the key genes and cellular pathways that appear to drive this cancer.

  6. RBC nuclear scan

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

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

    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

  8. Thyroid Scan and Uptake

    Full Text Available ... of the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is ... encourage linking to this site. × Recommend RadiologyInfo to a friend Send to (friend's e-mail address): From ( ...

  9. Continuous Indoor Positioning Fusing WiFi, Smartphone Sensors and Landmarks

    Zhi-An Deng

    2016-09-01

    Full Text Available To exploit the complementary strengths of WiFi positioning, pedestrian dead reckoning (PDR, and landmarks, we propose a novel fusion approach based on an extended Kalman filter (EKF. For WiFi positioning, unlike previous fusion approaches setting measurement noise parameters empirically, we deploy a kernel density estimation-based model to adaptively measure the related measurement noise statistics. Furthermore, a trusted area of WiFi positioning defined by fusion results of previous step and WiFi signal outlier detection are exploited to reduce computational cost and improve WiFi positioning accuracy. For PDR, we integrate a gyroscope, an accelerometer, and a magnetometer to determine the user heading based on another EKF model. To reduce accumulation error of PDR and enable continuous indoor positioning, not only the positioning results but also the heading estimations are recalibrated by indoor landmarks. Experimental results in a realistic indoor environment show that the proposed fusion approach achieves substantial positioning accuracy improvement than individual positioning approaches including PDR and WiFi positioning.

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

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

    2015-01-05

    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. Continuous Indoor Positioning Fusing WiFi, Smartphone Sensors and Landmarks.

    Deng, Zhi-An; Wang, Guofeng; Qin, Danyang; Na, Zhenyu; Cui, Yang; Chen, Juan

    2016-09-05

    To exploit the complementary strengths of WiFi positioning, pedestrian dead reckoning (PDR), and landmarks, we propose a novel fusion approach based on an extended Kalman filter (EKF). For WiFi positioning, unlike previous fusion approaches setting measurement noise parameters empirically, we deploy a kernel density estimation-based model to adaptively measure the related measurement noise statistics. Furthermore, a trusted area of WiFi positioning defined by fusion results of previous step and WiFi signal outlier detection are exploited to reduce computational cost and improve WiFi positioning accuracy. For PDR, we integrate a gyroscope, an accelerometer, and a magnetometer to determine the user heading based on another EKF model. To reduce accumulation error of PDR and enable continuous indoor positioning, not only the positioning results but also the heading estimations are recalibrated by indoor landmarks. Experimental results in a realistic indoor environment show that the proposed fusion approach achieves substantial positioning accuracy improvement than individual positioning approaches including PDR and WiFi positioning.

  12. Landmark based shape analysis for cerebellar ataxia classification and cerebellar atrophy pattern visualization

    Yang, Zhen; Abulnaga, S. Mazdak; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M.; Onyike, Chiadi; Ying, Sarah H.; Prince, Jerry L.

    2016-03-01

    Cerebellar dysfunction can lead to a wide range of movement disorders. Studying the cerebellar atrophy pattern associated with different cerebellar disease types can potentially help in diagnosis, prognosis, and treatment planning. In this paper, we present a landmark based shape analysis pipeline to classify healthy control and different ataxia types and to visualize the characteristic cerebellar atrophy patterns associated with different types. A highly informative feature representation of the cerebellar structure is constructed by extracting dense homologous landmarks on the boundary surfaces of cerebellar sub-structures. A diagnosis group classifier based on this representation is built using partial least square dimension reduction and regularized linear discriminant analysis. The characteristic atrophy pattern for an ataxia type is visualized by sampling along the discriminant direction between healthy controls and the ataxia type. Experimental results show that the proposed method can successfully classify healthy controls and different ataxia types. The visualized cerebellar atrophy patterns were consistent with the regional volume decreases observed in previous studies, but the proposed method provides intuitive and detailed understanding about changes of overall size and shape of the cerebellum, as well as that of individual lobules.

  13. Searching chromosomal landmarks in Indian lentils through EMA-based Giemsa staining method.

    Jha, Timir Baran; Halder, Mihir

    2016-09-01

    Lentil is one of the oldest protein-rich food crop with only one cultivated and six wild species. India is one important cultivator, producer and consumer of lentils and possesses a large number of germplasms. All species of lentil show 2n = 14 chromosomes. The primary objective of the present paper is to search chromosomal landmarks through enzymatic maceration and air drying (EMA)-based Giemsa staining method in five Indian lentil species not reported elsewhere at a time. Additionally, gametic chromosome analysis, tendril formation and seed morphology have been studied to ascertain interspecific relationships in lentils. Chromosome analysis in Lens culinaris, Lens orientalis and Lens odemensis revealed that they contain intercalary sat chromosome and similar karyotypic formula, while Lens nigricans and Lens lamottei showed presence of terminal sat chromosomes not reported earlier. This distinct morphological feature in L. nigricans and L. lamottei may be considered as chromosomal landmark. Meiotic analysis showed n = 7 bivalents in L. culinaris, L. nigricans and L. lamottei. No tendril formation was observed in L. culinaris, L. orientalis and L. odemensis while L. nigricans and L. lamottei developed very prominent tendrils. Based on chromosomal analysis, tendril formation and seed morphology, the five lentil species can be separated into two distinct groups. The outcome of this research may enrich conventional and biotechnological breeding programmes in lentil and may facilitate an easy and alternative method for identification of interspecific hybrids.

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

    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.

  15. Visual navigation of the UAVs on the basis of 3D natural landmarks

    Karpenko, Simon; Konovalenko, Ivan; Miller, Alexander; Miller, Boris; Nikolaev, Dmitry

    2015-12-01

    This work considers the tracking of the UAV (unmanned aviation vehicle) on the basis of onboard observations of natural landmarks including azimuth and elevation angles. It is assumed that UAV's cameras are able to capture the angular position of reference points and to measure the angles of the sight line. Such measurements involve the real position of UAV in implicit form, and therefore some of nonlinear filters such as Extended Kalman filter (EKF) or others must be used in order to implement these measurements for UAV control. Recently it was shown that modified pseudomeasurement method may be used to control UAV on the basis of the observation of reference points assigned along the UAV path in advance. However, the use of such set of points needs the cumbersome recognition procedure with the huge volume of on-board memory. The natural landmarks serving as such reference points which may be determined on-line can significantly reduce the on-board memory and the computational difficulties. The principal difference of this work is the usage of the 3D reference points coordinates which permits to determine the position of the UAV more precisely and thereby to guide along the path with higher accuracy which is extremely important for successful performance of the autonomous missions. The article suggests the new RANSAC for ISOMETRY algorithm and the use of recently developed estimation and control algorithms for tracking of given reference path under external perturbation and noised angular measurements.

  16. Management of Neovascular Age-related Macular Degeneration: A Review on Landmark Randomized Controlled Trials.

    Agarwal, Aniruddha; Aggarwal, Kanika; Gupta, Vishali

    2016-01-01

    In the last decade, a number of prospective clinical trials with carefully designed study protocols have been conducted for the treatment of neovascular age-related macular degeneration (AMD). These landmark clinical trials such as ANCHOR and MARINA and, more recently, the Comparison of AMD Treatment Trials and VIEW studies have revolutionized the management of neovascular AMD. While AMD continues to remain a leading cause of severe visual loss worldwide, advances in pharmacotherapeutics have led to substantial improvements in the outcome of these patients. The introduction of anti-vascular endothelial growth factor agents has resulted in improvement of visual outcomes and has had a positive impact on the quality of life among elderly population. While the contemporary management of neovascular AMD has been successful in tremendously reducing the visual morbidity, the financial burden of therapy has increased exponentially. To overcome these challenges, newer pharmacologic agents are evaluated for their efficacy and safety in AMD. Ground-breaking advances in bench to bedside research have led to discovery of new pathways that appear to be viable targets for preventing visual loss in AMD. In this review, study designs and results of landmark clinical trials in AMD from the past decade have been summarized.

  17. Management of neovascular Age-related macular degeneration: A review on landmark randomized controlled trials

    Aniruddha Agarwal

    2016-01-01

    Full Text Available In the last decade, a number of prospective clinical trials with carefully designed study protocols have been conducted for the treatment of neovascular age.related macular degeneration (AMD. These landmark clinical trials such as ANCHOR and MARINA and, more recently, the Comparison of AMD Treatment Trials and VIEW studies have revolutionized the management of neovascular AMD. While AMD continues to remain a leading cause of severe visual loss worldwide, advances in pharmacotherapeutics have led to substantial improvements in the outcome of these patients. The introduction of anti.vascular endothelial growth factor agents has resulted in improvement of visual outcomes and has had a positive impact on the quality of life among elderly population. While the contemporary management of neovascular AMD has been successful in tremendously reducing the visual morbidity, the financial burden of therapy has increased exponentially. To overcome these challenges, newer pharmacologic agents are evaluated for their efficacy and safety in AMD. Ground.breaking advances in bench to bedside research have led to discovery of new pathways that appear to be viable targets for preventing visual loss in AMD. In this review, study designs and results of landmark clinical trials in AMD from the past decade have been summarized.

  18. Continuous Indoor Positioning Fusing WiFi, Smartphone Sensors and Landmarks

    Deng, Zhi-An; Wang, Guofeng; Qin, Danyang; Na, Zhenyu; Cui, Yang; Chen, Juan

    2016-01-01

    To exploit the complementary strengths of WiFi positioning, pedestrian dead reckoning (PDR), and landmarks, we propose a novel fusion approach based on an extended Kalman filter (EKF). For WiFi positioning, unlike previous fusion approaches setting measurement noise parameters empirically, we deploy a kernel density estimation-based model to adaptively measure the related measurement noise statistics. Furthermore, a trusted area of WiFi positioning defined by fusion results of previous step and WiFi signal outlier detection are exploited to reduce computational cost and improve WiFi positioning accuracy. For PDR, we integrate a gyroscope, an accelerometer, and a magnetometer to determine the user heading based on another EKF model. To reduce accumulation error of PDR and enable continuous indoor positioning, not only the positioning results but also the heading estimations are recalibrated by indoor landmarks. Experimental results in a realistic indoor environment show that the proposed fusion approach achieves substantial positioning accuracy improvement than individual positioning approaches including PDR and WiFi positioning. PMID:27608019

  19. Pulmonary ventilation/perfusion scan

    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 scan, a health care provider injects ...

  20. Effect of deformable registration on the dose calculated in radiation therapy planning CT scans of lung cancer patients

    Cunliffe, Alexandra R.; Armato, Samuel G.; White, Bradley; Justusson, Julia [Department of Radiology, The University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 (United States); Contee, Clay; Malik, Renuka; Al-Hallaq, Hania A., E-mail: hal-hallaq@radonc.uchicago.edu [Department of Radiation and Cellular Oncology, The University of Chicago, 5841 South Maryland Avenue, Chicago, Illinois 60637 (United States)

    2015-01-15

    Purpose: To characterize the effects of deformable image registration of serial computed tomography (CT) scans on the radiation dose calculated from a treatment planning scan. Methods: Eighteen patients who received curative doses (≥60 Gy, 2 Gy/fraction) of photon radiation therapy for lung cancer treatment were retrospectively identified. For each patient, a diagnostic-quality pretherapy (4–75 days) CT scan and a treatment planning scan with an associated dose map were collected. To establish correspondence between scan pairs, a researcher manually identified anatomically corresponding landmark point pairs between the two scans. Pretherapy scans then were coregistered with planning scans (and associated dose maps) using the demons deformable registration algorithm and two variants of the Fraunhofer MEVIS algorithm (“Fast” and “EMPIRE10”). Landmark points in each pretherapy scan were automatically mapped to the planning scan using the displacement vector field output from each of the three algorithms. The Euclidean distance between manually and automatically mapped landmark points (d{sub E}) and the absolute difference in planned dose (|ΔD|) were calculated. Using regression modeling, |ΔD| was modeled as a function of d{sub E}, dose (D), dose standard deviation (SD{sub dose}) in an eight-pixel neighborhood, and the registration algorithm used. Results: Over 1400 landmark point pairs were identified, with 58–93 (median: 84) points identified per patient. Average |ΔD| across patients was 3.5 Gy (range: 0.9–10.6 Gy). Registration accuracy was highest using the Fraunhofer MEVIS EMPIRE10 algorithm, with an average d{sub E} across patients of 5.2 mm (compared with >7 mm for the other two algorithms). Consequently, average |ΔD| was also lowest using the Fraunhofer MEVIS EMPIRE10 algorithm. |ΔD| increased significantly as a function of d{sub E} (0.42 Gy/mm), D (0.05 Gy/Gy), SD{sub dose} (1.4 Gy/Gy), and the algorithm used (≤1 Gy). Conclusions: An

  1. Landmark Orientation and Map Design for Pedestrians: Prototype of a Selcuk University Campus Area Pedestrian Navigation System

    Zahit Selvi, Huseyin; Oztug Bildirici, I.; Ulugtekin, Necla

    2016-10-01

    Orientation software produced today is generally designed for the navigation of cars. However, the navigation needs of pedestrians are different from those of drivers. The aim of this study is the design of a cartographic interface that supports the navigation of pedestrians in unfamiliar areas using landmarks and evaluation of this geo-mobile application by usability testing. In this study, an approach to landmark orientation based on the Voronoi diagram is proposed. Furthermore, the developed mobile application that uses this approach is explained in detail. The results of user tests are also given.

  2. Corrective surgery for canine patellar luxation in 75 cases (107 limbs: landmark for block recession

    Mitsuhiro Isaka

    2014-05-01

    Full Text Available Canine medial patellar luxation (MPL is a very common orthopedic disease in small animals. Because the pathophysiology of this disease involves various pathways, the surgical techniques and results vary according to the veterinarian. Further, the landmark for block recession is not completely clear. We retrospectively evaluated 75 dogs (107 limbs with MPL in whom our landmark for block recession was used from July 2008 to May 2013. Information regarding the breed, age, sex, body weight, body condition score (BCS, lateral vs bilateral, pre-operative grading, surgical techniques, removal of implants, concomitance with anterior cruciate ligament (ACL rupture, re-luxation, re-operation, and rehabilitation was obtained from the medical records. The breeds were as follows: Chihuahua (n=23, Pomeranian (n=12, Yorkshire Terrier (n=9, and so on. The study group consisted of 33 males (castrated n=13 and 42 females (spayed n=21. The median age was 53.3±35.9 months (32-146 months; 13 cases were less than 12 months of age (17.3%. The pre-surgical BCSs were as follows: 1 (n=0, 2 (n=20, 3 (n=24, 4 (n=24 and 5 (n=7. The body weight was 4.51±3.48 kg (1.34-23.0 kg; 71 cases (94.7% were less than 10 kg. The MPL grades (each limb were G1 (n=1, G2 (n=18, G3 (n=78, and G4 (n=10; 32 cases were bilateral and 43 cases were unilateral (right n=27; left n=16. The specific surgical procedure (distal femoral osteotomy was 3 stifles in Chihuahuas. Concurrent with ACL rupture was 16/107 stifles (15.0% corrected with the over-the-top method or the extracapsular method in Papillons (5/6, Chihuahuas (5/23, and so on. The occurrences of re-luxation and re-operation were 3 out of 107 stifles (2.8% and 0%, respectively. In this retrospective study, we present a potentially good surgical landmark for block recession of MPL in dogs.

  3. Laser Scanning in Forests

    Håkan Olsson; Juha Hyyppä; Markus Holopainen

    2012-01-01

    The introduction of Airborne Laser Scanning (ALS) to forests has been revolutionary during the last decade. This development was facilitated by combining earlier ranging lidar discoveries [1–5], with experience obtained from full-waveform ranging radar [6,7] to new airborne laser scanning systems which had components such as a GNSS receiver (Global Navigation Satellite System), IMU (Inertial Measurement Unit) and a scanning mechanism. Since the first commercial ALS in 1994, new ALS-based fore...

  4. Radionucleotide scanning in osteomyelitis

    Sachs, W.; Kanat, I.O.

    1986-07-01

    Radionucleotide bone scanning can be an excellent adjunct to the standard radiograph and clinical findings in the diagnosis of osteomyelitis. Bone scans have the ability to detect osteomyelitis far in advance of the standard radiograph. The sequential use of technetium and gallium has been useful in differentiating cellulitis and osteomyelitis. Serial scanning with technetium and gallium may be used to monitor the response of osteomyelitis to antibiotic therapy.

  5. Domestication genomics: evidence from animals.

    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.

  6. Image-based tracking system for vibration measurement of a rotating object using a laser scanning vibrometer

    Kim, Dongkyu; Khalil, Hossam; Jo, Youngjoon; Park, Kyihwan

    2016-06-01

    An image-based tracking system using laser scanning vibrometer is developed for vibration measurement of a rotating object. The proposed system unlike a conventional one can be used where the position or velocity sensor such as an encoder cannot be attached to an object. An image processing algorithm is introduced to detect a landmark and laser beam based on their colors. Then, through using feedback control system, the laser beam can track a rotating object.

  7. Intensity and sulci landmark combined brain atlas construction for Chinese pediatric population.

    Luo, Yishan; Shi, Lin; Weng, Jian; He, Hongjian; Chu, Winnie C W; Chen, Feiyan; Wang, Defeng

    2014-08-01

    Constructing an atlas from a population of brain images is of vital importance to medical image analysis. Especially in neuroscience study, creating a brain atlas is useful for intra- and inter-population comparison. Research on brain atlas construction has attracted great attention in recent years, but the research on pediatric population is still limited, mainly due to the limited availability and the relatively low quality of pediatric magnetic resonance brain images. This article is targeted at creating a high quality representative brain atlas for Chinese pediatric population. To achieve this goal, we have designed a set of preprocessing procedures to improve the image quality and developed an intensity and sulci landmark combined groupwise registration method to align the population of images for atlas construction. As demonstrated in experiments, the newly constructed atlas can better represent the size and shape of brains of Chinese pediatric population, and show better performance in Chinese pediatric brain image analysis compared with other standard atlases.

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

    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. Semi-Automatic Anatomical Tree Matching for Landmark-Based Elastic Registration of Liver Volumes

    Klaus Drechsler

    2010-01-01

    Full Text Available One promising approach to register liver volume acquisitions is based on the branching points of the vessel trees as anatomical landmarks inherently available in the liver. Automated tree matching algorithms were proposed to automatically find pair-wise correspondences between two vessel trees. However, to the best of our knowledge, none of the existing automatic methods are completely error free. After a review of current literature and methodologies on the topic, we propose an efficient interaction method that can be employed to support tree matching algorithms with important pre-selected correspondences or after an automatic matching to manually correct wrongly matched nodes. We used this method in combination with a promising automatic tree matching algorithm also presented in this work. The proposed method was evaluated by 4 participants and a CT dataset that we used to derive multiple artificial datasets.

  10. Evaluation of facial nerve and its landmarks in adult temporal bones

    Saeid Soheilipour

    2010-06-01

    Full Text Available Introduction: The aim of this study was to identify variations of different segments of facial nerve in temporal bone. Materials and Methods: In this descriptive study that conducted on drilled bones in the temporal bone center of the Al-Zahra Hospital of Isfahan University of Medical Sciences, the landmarks of facial nerve in temporal bone were identified as separate variables and their distances from outer cortex of temporal bone and Henles spine and distances between different segments of nerve were recorded. Results: In the 50 temporal bones dissected, the distance between the tip of incus short process to the cortex was 14.2±1.96 mm, the distance between the facial recess from the facial nerve to the cortex was 14.5±2.58 mm, the distance between the stylomastoid foramen to the cortex was 20.6±2.49 mm, the distance between the lateral semicircular canal to the cortex was 15.9±2.31 mm and the distance between the sigmoid sinus dome to the cortex was 14.08±2.83 mm. The mean length of tympanic and mastoid segments (2nd and 3rd segments of facial nerve were 11.35±0.68 mm and 13.28±1.11mm, respectively. Conclusion: The mean lengths of segment of facial nerve and distant of landmarks from outer cortex of temporal bone are partially similar compared to those described in the western literature and text books, but different compared to eastern researches.

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

    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

  12. A computational model of the integration of landmarks and motion in the insect central complex

    Sabo, Chelsea; Vasilaki, Eleni; Barron, Andrew B.; Marshall, James A. R.

    2017-01-01

    The insect central complex (CX) is an enigmatic structure whose computational function has evaded inquiry, but has been implicated in a wide range of behaviours. Recent experimental evidence from the fruit fly (Drosophila melanogaster) and the cockroach (Blaberus discoidalis) has demonstrated the existence of neural activity corresponding to the animal’s orientation within a virtual arena (a neural ‘compass’), and this provides an insight into one component of the CX structure. There are two key features of the compass activity: an offset between the angle represented by the compass and the true angular position of visual features in the arena, and the remapping of the 270° visual arena onto an entire circle of neurons in the compass. Here we present a computational model which can reproduce this experimental evidence in detail, and predicts the computational mechanisms that underlie the data. We predict that both the offset and remapping of the fly’s orientation onto the neural compass can be explained by plasticity in the synaptic weights between segments of the visual field and the neurons representing orientation. Furthermore, we predict that this learning is reliant on the existence of neural pathways that detect rotational motion across the whole visual field and uses this rotation signal to drive the rotation of activity in a neural ring attractor. Our model also reproduces the ‘transitioning’ between visual landmarks seen when rotationally symmetric landmarks are presented. This model can provide the basis for further investigation into the role of the central complex, which promises to be a key structure for understanding insect behaviour, as well as suggesting approaches towards creating fully autonomous robotic agents. PMID:28241061

  13. Bone scanning in otolaryngology.

    Noyek, A M

    1979-09-01

    Modern radionuclide bone scanning has introduced a new concept in physiologic and anatomic diagnostic imaging to general medicine. As otolaryngologists must diagnose and treat disease in relation to the bony and/or cartilaginous supporting structures of the neurocranium and upper airway, this modality should be included in the otolaryngologist's diagnostic armamentarium. It is the purpose of this manuscript to study the specific applications of bone scanning to our specialty at this time, based on clinical experience over the past three years. This thesis describes the development of bone scanning in general (history of nuclear medicine and nuclear physics; history of bone scanning in particular). General concepts in nuclear medicine are then presented; these include a discussion of nuclear semantics, principles of radioactive emmissions, the properties 99mTc as a radionuclide, and the tracer principle. On the basis of these general concepts, specific concepts in bone scanning are then brought forth. The physiology of bone and the action of the bone scan agents is presented. Further discussion considers the availability and production of the bone scan agent, patient factors, the gamma camera, the triphasic bone scan and the ultimate diagnostic principle of the bone scan. Clinical applications of bone scanning in otolaryngology are then presented in three sections. Proven areas of application include the evaluation of malignant tumors of the head and neck, the diagnosis of temporomandibular joint disorders, the diagnosis of facial fractures, the evaluation of osteomyelitis, nuclear medicine imaging of the larynx, and the assessment of systemic disease. Areas of adjunctive or supplementary value are also noted, such as diagnostic imaging of meningioma. Finally, areas of marginal value in the application of bone scanning are described.

  14. Chromosome landmarks and autosome-sex chromosome translocations in Rumex hastatulus, a plant with XX/XY1Y2 sex chromosome system.

    Grabowska-Joachimiak, Aleksandra; Kula, Adam; Książczyk, Tomasz; Chojnicka, Joanna; Sliwinska, Elwira; Joachimiak, Andrzej J

    2015-06-01

    Rumex hastatulus is the North American endemic dioecious plant with heteromorphic sex chromosomes. It is differentiated into two chromosomal races: Texas (T) race characterised by a simple XX/XY sex chromosome system and North Carolina (NC) race with a polymorphic XX/XY1Y2 sex chromosome system. The gross karyotype morphology in NC race resembles the derived type, but chromosomal changes that occurred during its evolution are poorly understood. Our C-banding/DAPI and fluorescence in situ hybridization (FISH) experiments demonstrated that Y chromosomes of both races are enriched in DAPI-positive sequences and that the emergence of polymorphic sex chromosome system was accompanied by the break of ancestral Y chromosome and switch in the localization of 5S rDNA, from autosomes to sex chromosomes (X and Y2). Two contrasting domains were detected within North Carolina Y chromosomes: the older, highly heterochromatinised, inherited from the original Y chromosome and the younger, euchromatic, representing translocated autosomal material. The flow-cytometric DNA estimation showed ∼3.5 % genome downsizing in the North Carolina race. Our results are in contradiction to earlier reports on the lack of heterochromatin within Y chromosomes of this species and enable unambiguous identification of autosomes involved in the autosome-heterosome translocation, providing useful chromosome landmarks for further studies on the karyotype and sex chromosome differentiation in this species.

  15. Evaluation and Comparison of Anatomical Landmark Detection Methods for Cephalometric X-Ray Images: A Grand Challenge.

    Wang, Ching-Wei; Huang, Cheng-Ta; Hsieh, Meng-Che; Li, Chung-Hsing; Chang, Sheng-Wei; Li, Wei-Cheng; Vandaele, Rémy; Marée, Raphaël; Jodogne, Sébastien; Geurts, Pierre; Chen, Cheng; Zheng, Guoyan; Chu, Chengwen; Mirzaalian, Hengameh; Hamarneh, Ghassan; Vrtovec, Tomaz; Ibragimov, Bulat

    2015-09-01

    Cephalometric analysis is an essential clinical and research tool in orthodontics for the orthodontic analysis and treatment planning. This paper presents the evaluation of the methods submitted to the Automatic Cephalometric X-Ray Landmark Detection Challenge, held at the IEEE International Symposium on Biomedical Imaging 2014 with an on-site competition. The challenge was set to explore and compare automatic landmark detection methods in application to cephalometric X-ray images. Methods were evaluated on a common database including cephalograms of 300 patients aged six to 60 years, collected from the Dental Department, Tri-Service General Hospital, Taiwan, and manually marked anatomical landmarks as the ground truth data, generated by two experienced medical doctors. Quantitative evaluation was performed to compare the results of a representative selection of current methods submitted to the challenge. Experimental results show that three methods are able to achieve detection rates greater than 80% using the 4 mm precision range, but only one method achieves a detection rate greater than 70% using the 2 mm precision range, which is the acceptable precision range in clinical practice. The study provides insights into the performance of different landmark detection approaches under real-world conditions and highlights achievements and limitations of current image analysis techniques.

  16. Automated Extraction of Cranial Landmarks from Computed Tomography Data using a Combined Method of Knowledge and Pattern Based Approaches

    Roshan N. RAJAPAKSE

    2016-03-01

    Full Text Available Accurate identification of anatomical structures from medical imaging data is a significant and critical function in the medical domain. Past studies in this context have mainly utilized two main approaches, the knowledge and learning methodologies based methods. Further, most of previous reported studies have focused on identification of landmarks from lateral X-ray Computed Tomography (CT data, particularly in the field of orthodontics. However, this study focused on extracting cranial landmarks from large sets of cross sectional CT slices using a combined method of the two aforementioned approaches. The proposed method of this study is centered mainly on template data sets, which were created using the actual contour patterns extracted from CT cases for each of the landmarks in consideration. Firstly, these templates were used to devise rules which are a characteristic of the knowledge based method. Secondly, the same template sets were employed to perform template matching related to the learning methodologies approach. The proposed method was tested on two landmarks, the Dorsum sellae and the Pterygoid plate, using CT cases of 5 subjects. The results indicate that, out of the 10 tests, the output images were within the expected range (desired accuracy in 7 instances and acceptable range (near accuracy for 2 instances, thus verifying the effectiveness of the combined template sets centric approach proposed in this study.

  17. Learning Your Way around Town: How Virtual Taxicab Drivers Learn to Use Both Layout and Landmark Information

    Newman, Ehren L.; Caplan, Jeremy B.; Kirschen, Matthew P.; Korolev, Igor O.; Sekuler, Robert; Kahana, Michael J.

    2007-01-01

    By having subjects drive a virtual taxicab through a computer-rendered town, we examined how landmark and layout information interact during spatial navigation. Subject-drivers searched for passengers, and then attempted to take the most efficient route to the requested destinations (one of several target stores). Experiment 1 demonstrated that…

  18. Scanning laser Doppler vibrometry

    Brøns, Marie; Thomsen, Jon Juel

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

  19. Frequency scanning microstrip antennas

    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...

  20. Optical Scanning Applications.

    Wagner, Hans

    The successful use of optical scanning at the University of the Pacific (UOP) indicates that such techniques can simplify a number of administrative data processing tasks. Optical scanning is regularly used at UOP to assist with data processing in the areas of admissions, registration and grade reporting and also has applications for other tasks…

  1. LIDAR COMBINED SCANNING UNIT

    V. V. Elizarov

    2016-11-01

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

  2. WE-D-9A-02: Automated Landmark-Guided CT to Cone-Beam CT Deformable Image Registration

    Kearney, V; Gu, X; Chen, S; Jiang, L; Liu, H; Chiu, T; Yordy, J; Nedzi, L; Mao, W [UT Southwestern Medical Center, Dallas, TX (United States)

    2014-06-15

    Purpose: The anatomical changes that occur between the simulation CT and daily cone-beam CT (CBCT) are investigated using an automated landmark-guided deformable image registration (LDIR) algorithm with simultaneous intensity correction. LDIR was designed to be accurate in the presence of tissue intensity mismatch and heavy noise contamination. Method: An auto-landmark generation algorithm was used in conjunction with a local small volume (LSV) gradient matching search engine to map corresponding landmarks between the CBCT and planning CT. The LSVs offsets were used to perform an initial deformation, generate landmarks, and correct local intensity mismatch. The landmarks act as stabilizing controlpoints in the Demons objective function. The accuracy of the LDIR algorithm was evaluated on one synthetic case with ground truth and data of ten head and neck cancer patients. The deformation vector field (DVF) accuracy was accessed using a synthetic case. The Root mean square error of the 3D canny edge (RMSECE), mutual information (MI), and feature similarity index metric (FSIM) were used to access the accuracy of LDIR on the patient data. The quality of the corresponding deformed contours was verified by an attending physician. Results: The resulting 90 percentile DVF error for the synthetic case was within 5.63mm for the original demons algorithm, 2.84mm for intensity correction alone, 2.45mm using controlpoints without intensity correction, and 1.48 mm for the LDIR algorithm. For the five patients the mean RMSECE of the original CT, Demons deformed CT, intensity corrected Demons CT, control-point stabilized deformed CT, and LDIR CT was 0.24, 0.26, 0.20, 0.20, and 0.16 respectively. Conclusion: LDIR is accurate in the presence of multimodal intensity mismatch and CBCT noise contamination. Since LDIR is GPU based it can be implemented with minimal additional strain on clinical resources. This project has been supported by a CPRIT individual investigator award RP11032.

  3. Sacro-Iliac Joint Sensory Block and Radiofrequency Ablation: Assessment of Bony Landmarks Relevant for Image-Guided Procedures

    Roberts, Shannon L.; Burnham, Robert S.; Loh, Eldon; Agur, Anne M.

    2016-01-01

    Image-guided sensory block and radiofrequency ablation of the nerves innervating the sacro-iliac joint require readily identifiable bony landmarks for accurate needle/electrode placement. Understanding the relative locations of the transverse sacral tubercles along the lateral sacral crest is important for ultrasound guidance, as they demarcate the position of the posterior sacral network (S1–S3 ± L5/S4) innervating the posterior sacro-iliac joint. No studies were found that investigated the spatial relationships of these bony landmarks. The purpose of this study was to visualize and quantify the interrelationships of the transverse sacral tubercles and posterior sacral foramina to inform image-guided block and radiofrequency ablation of the sacro-iliac joint. The posterior and lateral surfaces of 30 dry sacra (15 M/15 F) were digitized and modeled in 3D and the distances between bony landmarks quantified. The relationships of bony landmarks (S1–S4) were not uniform. The mean intertubercular and interforaminal distances decreased from S1 to S4, whereas the distance from the lateral margin of the posterior sacral foramina to the transverse sacral tubercles increased from S1 to S3. The mean intertubercular distance from S1 to S3 was significantly (p < 0.05) larger in males. The interrelationships of the sacral bony landmarks should be taken into consideration when estimating the site and length of an image-guided strip lesion targeting the posterior sacral network. PMID:27747222

  4. SU-E-J-220: Assessment of MRI Geometric Distortion in Head and Neck Cancer Patients Scanned in Immobilized Radiation Treatment Position

    Hansen, C; Mohamed, A; Weygand, J; Ding, Y; Fuller, C; Frank, S; Wang, J [MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose: Uncertainties about geometric distortion have somewhat hindered MRI simulation in radiation therapy. Most of the geometric distortion studies were performed with phantom measurements but another major aspect of MR distortion is patient related. We studied the geometric distortion in patient images by comparing their MRI scans with the corresponding CT, using CT as the non-distorted gold standard. Methods: Ten H&N cancer patients were imaged with MRI as part of a prospective IRB approved study. All patients had their treatment planning CT done on the same day or within one week of the MRI. MR Images were acquired with a T2 SE sequence (1×1×2.5mm voxel size) in the same immobilization position as in the CT scans. MRI to CT rigid registration was then done and geometric distortion comparison was done by measuring the corresponding anatomical landmarks on both the MRI and the CT images by two observers. Several skin to skin (9 landmarks), bone to bone (8 landmarks), and soft tissue (3 landmarks) were measured at specific levels in horizontal and vertical planes of both scans. Results: The mean distortion for all landmark measurements in all scans was 1.8±1.9mm. For each patient 11 measurements were done in the horizontal plane while 9 were done in the vertical plane. The measured geometric distortion were significantly lower in the horizontal axis compared to the vertical axis (1.3±0.16 mm vs 2.2±0.19 mm, respectively, P=0.003*). The magnitude of distortion was lower in the bone to bone landmarks compared to the combined soft tissue and skin to skin landmarks (1.2±0.19 mm vs 2.3±0.17 mm, P=0.0006*). The mean distortion measured by observer one was not significantly different compared toobserver 2 (2.3 vs 2.4 mm, P=0.4). Conclusion: MRI geometric distortions were quantified in H&N patients with mean error of less than 2 mm. JW received a corporate sponsored research grant from Elekta.

  5. Laser Scanning in Forests

    Håkan Olsson

    2012-09-01

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

  6. Resonant scanning mechanism

    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 μrad 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.

  7. CT scan of choristoma

    Moriki, A.; Morimoto, M.; Sada, Y.; Kurisaka, M.; Mori, K.

    1987-02-01

    Choristoma is a rare tumor that occurs in the pituitary gland. The case presented here is a 44-year-old male. A plain CT scan demonstrated a slight high-density mass near the posterior clinoid of the sella turcica, while a moderate and homogeneous enhancing effect and a clear borderline were shown by an enhanced CT scan. A cornal CT scan study showed that the tumor extended from the intrasellar to the suprasellar region. The diagnosis of choristoma was made by means of histology.

  8. Cancer genomics

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

    2007-01-01

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

  9. Evaluation of Distal Femoral Rotational Alignment with Spiral CT Scan before Total Knee Arthroplasty (A Study in Iranian Population

    Mahmoud Jabalameli

    2016-04-01

    Full Text Available Background: Evaluating the landmarks for rotation of the distal femur is a challenge for orthopedic surgeons. Although the posterior femoral condyle axis is a good landmark for surgeons, the surgical transepicondylar axis may be a better option with the help of preoperative CT scanning. The purpose of this study was to ascertain relationships among the axes’ guiding distal femur rotational alignment in preoperative CT scans of Iranian patients who were candidates for total knee arthroplasty and the effects of age, gender, and knee alignment on these relationships. Methods: One hundred and eight cases who were admitted to two university hospitals for total knee arthroplasty were included in this study. The rotation of the distal femur was evaluated using single axial CT images through the femoral epicondyle. Four lines were drawn digitally in this view: anatomical and surgical transepicondylar axes, posterior condylar axis and the Whiteside anteroposterior line. The alignment of the extremity was evaluated in the standing alignment view. Then the angles were measured along these lines and their relationship was evaluated. Results: The mean angle between the anatomical transepicondylar axis and posterior condylar axis and between the surgical transepicondylar axis and posterior condylar axis were 5.9 ± 1.6 degrees and 1.6±1.7 degrees respectively. The mean angle between the Whiteside’s anteroposterior line and the line perpendicular to the posterior condylar axis was 3.7±2.1 degrees. Significant differences existed between the two genders in these relationships. No significant correlation between the age of patients and angles of the distal femur was detected. The anatomical surgical transepicondylar axis was in 4.3 degrees external rotation in relation to the surgical transepicondylar axis. Conclusion: Preoperative CT scanning can help accurately determine rotational landmarks of the distal femur. If one of the reference axes cannot be

  10. Cervical spine CT scan

    ... defects of the cervical spine Bone problems Fracture Osteoarthritis Disc herniation Risks Risks of CT scans include: ... Ma, MD, Assistant Professor, Chief, Sports Medicine and Shoulder Service, UCSF Department of Orthopaedic Surgery, San Francisco, ...

  11. Scanning Auger Electron Microscope

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

  12. Scanning Auger Electron Microscope

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

  13. Shoulder MRI scan

    ... finding on an x-ray or bone scan Shoulder pain and fever Decreased motion of the shoulder joint ... of the shoulder joint Shoulder instability Shoulder weakness Shoulder pain and a history of cancer Shoulder pain that ...

  14. Slow Scan Telemedicine

    1984-01-01

    Originally developed under contract for NASA by Ball Bros. Research Corporation for acquiring visual information from lunar and planetary spacecraft, system uses standard closed circuit camera connected to a device called a scan converter, which slows the stream of images to match an audio circuit, such as a telephone line. Transmitted to its destination, the image is reconverted by another scan converter and displayed on a monitor. In addition to assist scans, technique allows transmission of x-rays, nuclear scans, ultrasonic imagery, thermograms, electrocardiograms or live views of patient. Also allows conferencing and consultation among medical centers, general practitioners, specialists and disease control centers. Commercialized by Colorado Video, Inc., major employment is in business and industry for teleconferencing, cable TV news, transmission of scientific/engineering data, security, information retrieval, insurance claim adjustment, instructional programs, and remote viewing of advertising layouts, real estate, construction sites or products.

  15. Thyroid Scan and Uptake

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

  16. Photothermal imaging scanning microscopy

    Chinn, Diane; Stolz, Christopher J.; Wu, Zhouling; Huber, Robert; Weinzapfel, Carolyn

    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.

  17. The conical scan radiometer

    Prosch, T.; Hennings, D.

    1982-07-01

    A satellite-borne conical scan radiometer (CSR) is proposed, offering multiangular and multispectral measurements of Earth radiation fields, including the total radiances, which are not available from conventional radiometers. Advantages of the CSR for meteorological studies are discussed. In comparison to conventional cross track scanning instruments, the CSR is unique with respect to the selected picture element size which is kept constant by means of a specially shaped detector matrix at all scan angles. The conical scan mode offers the chance to improve angular sampling. Angular sampling gaps of previous satellite-borne radiometers can be interpolated and complemented by CSR data. Radiances are measured through 10 radiometric channels which are selected to study cloudiness, water vapor, ozone, surface albedo, ground and mean stratospheric temperature, and aerosols.

  18. Thyroid Scan and Uptake

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

  19. Thyroid Scan and Uptake

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

  20. Thyroid Scan and Uptake

    Full Text Available ... of page What are some common uses of the procedure? The thyroid scan is used to determine ... you are undergoing. top of page What does the equipment look like? Special camera or imaging devices ...

  1. Anatomical landmarks and skin markers are not reliable for accurate labeling of thoracic vertebrae on MRI

    Shabshin, Nogah (Dept. of Diagnostic Imaging, Chaim Sheba Medical Center, Tel-HaShomer (Israel)), e-mail: shabshin@gmail.com; Schweitzer, Mark E. (Dept. of Diagnostic Imaging, Ottawa Hospital and Univ. of Ottawa, Ottawa (Canada)); Carrino, John A. (Dept. of Radiology, Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States))

    2010-11-15

    Background: Numbering of the thoracic spine on MRI can be tedious if C2 and L5-S1 are not included and may lead to errors in lesion level. Purpose: To determine whether anatomic landmarks or external markers are reliable as an aid for accurate numbering of thoracic vertebrae on MRI. Material and Methods: Sixty-seven thoracic spine MR studies of 67 patients (30 males, 37 females, age range 18-83 years) were studied, composed of 52 consecutive MR studies and an additional 15 MRI in which vitamin E markers were placed over the skin. In the 52 thoracic MR examinations potential numbering aids such as the level of the sternal apex, pulmonary artery, aortic arch, and osseous or disc abnormalities were numbered on both cervical localizer (standard of reference) and thoracic sagittal images. The additional 15 examinations in which vitamin E markers were placed over the skin were evaluated for consistency in the level of the markers on different sequences in the same exam. Results: The sternal apex level ranged from T2 to T5 [T3 in 28/51 patients (55%), T2 in 10/51 (20%)]. The aortic arch level ranged from T2 to T4 [T4 in 18/48 (38%) and T3 in 17 (35%)]. Pulmonary artery level ranged from T4 to T6-7 disc [T5 in 20/52 patients (38%) and T6 in 14/52 (27%)]. In 3 of 12 patients who had abnormalities in a vertebral body or disc as definite point reference, the non-localizer image mislabelled the level. In 11/15 (73%) patients with vitamin E markers that were placed over the upper thoracic spine, the results showed consistency in the level of the markers in relation to the reference points or consistent inter-marker gap between the sequences. Conclusion: There are only two reliable ways to accurately define the levels if no landmarking feature is available on the magnet. The first is by including C2 in the thoracic sequence of a diagnostic quality, and the second is by using an abnormality in the discs or vertebral bodies as a point of reference

  2. Scanning laser Doppler vibrometry

    2016-01-01

    With a Scanning Laser Doppler Vibrometer (SLDV) a vibrating surface is automatically scanned over predefined grid points, and data processed for displaying vibration properties like mode shapes, natural frequencies, damping ratios, and operational deflection shapes. Our SLDV – a PSV-500H from Polytec Inc. – was acquired and put to operation in October 2014, paid by a sub-donation of DKK 1,5 mill. of the total VILLUM CASMaT grant. Opening possibilities of measuring complicated vibration shapes...

  3. Advanced Network Scanning

    Ashiqur Rahman

    2016-07-01

    Full Text Available Network scanning is à procedure for identifying active hosts on a network, either for the purpose of attacking them or for network security assessment. Scanning procedures, such as ping sweeps and port scans, return information about which IP addresses map to live hosts that are active on the Internet and what services they offer. Another scanning method, inverse mapping, returns information about what IP addresses do not map to live hosts; this enables an attacker to make assumptions about viable addresses. Scanning is one of three components of intelligence gathering for an attacker. In the foot printing phase, the attacker creates a profile of the target organization, with information such as its domain name system (DNS and e-mail servers, and its IP address range. Most of this information is available online. In the scanning phase, the attacker finds information about the specific IP addresses that can be accessed over the Internet, their operating systems, the system architecture, and the services running on each computer. In the enumeration phase, the attacker gathers information such as network user and group names, routing tables, and Simple Network Management Protocol (SNMP data

  4. Can osseous landmarks in the distal medial humerus be used to identify the attachment sites of ligaments and tendons: paleopathologic-anatomic imaging study in cadavers

    Buck, Florian M. [Veterans Administration Medical Center, Department of Radiology, San Diego, CA (United States); Institut fuer Diagnostische Radiologie, Uniklinik Balgrist, Zurich (Switzerland); Zoner, Cristiane S.; Cardoso, Fabiano; Gheno, Ramon; Nico, Marcelo A.C.; Trudell, Debra J.; Resnick, Donald [Veterans Administration Medical Center, Department of Radiology, San Diego, CA (United States); Randall, Tori D. [San Diego Museum of Man, Physical Anthropology, San Diego, CA (United States)

    2010-09-15

    To describe osseous landmarks that allow identification of the attachments of the ligaments and tendons in the distal medial aspect of the humerus. Reliable osseous landmarks in the distal medial aspect of the humerus were identified in 34 well-preserved specimens from a paleopathologic collection. These osseous landmarks were then sought in magnetic resonance (MR) images of ten cadaveric elbow specimens so that the ease of their visualization and optimal imaging plane could be assessed. To assign these osseous landmarks to specific attachments of the tendons and ligaments in the distal medial humerus, we cut the specimens in slices and photographed and examined them. Subsequently, the prevalence of these osseous landmarks as well as the attachment sites of the tendons and ligaments in this location was determined. We determined ten reliable osseous landmarks in the distal medial aspect of the humerus, their prevalence and ease of identification, and their relationship to the attachments of the tendons and ligaments at the medial distal humerus. It is possible to use osseous landmarks at the distal medial humerus to facilitate identification of the different attachments of tendons and ligaments when MR images of the elbow are assessed. (orig.)

  5. Automatic localization of landmark sets in head CT images with regression forests for image registration initialization

    Zhang, Dongqing; Liu, Yuan; Noble, Jack H.; Dawant, Benoit M.

    2016-03-01

    Cochlear Implants (CIs) are electrode arrays that are surgically inserted into the cochlea. Individual contacts stimulate frequency-mapped nerve endings thus replacing the natural electro-mechanical transduction mechanism. CIs are programmed post-operatively by audiologists but this is currently done using behavioral tests without imaging information that permits relating electrode position to inner ear anatomy. We have recently developed a series of image processing steps that permit the segmentation of the inner ear anatomy and the localization of individual contacts. We have proposed a new programming strategy that uses this information and we have shown in a study with 68 participants that 78% of long term recipients preferred the programming parameters determined with this new strategy. A limiting factor to the large scale evaluation and deployment of our technique is the amount of user interaction still required in some of the steps used in our sequence of image processing algorithms. One such step is the rough registration of an atlas to target volumes prior to the use of automated intensity-based algorithms when the target volumes have very different fields of view and orientations. In this paper we propose a solution to this problem. It relies on a random forest-based approach to automatically localize a series of landmarks. Our results obtained from 83 images with 132 registration tasks show that automatic initialization of an intensity-based algorithm proves to be a reliable technique to replace the manual step.

  6. Prediction of the mid-tracheal level using surface anatomical landmarks in adults

    Jang, Young-Eun; Kim, Eun-Hee; Song, In-Kyung; Lee, Ji-Hyun; Ryu, Ho-Geoul; Kim, Hee-Soo; Kim, Jin-Tae

    2017-01-01

    Abstract Endotracheal tube (ETT) should be placed at the optimal level to avoid single lung ventilation or accidental extubation. This study was performed to estimate the mid-tracheal level by using surface anatomical landmarks in adult patients. Neck computed tomography images of 329 adult patients between the ages of 16 and 79 years were reviewed. In the midline sagittal plane, the levels corresponding to the vocal cords, cricoid cartilage, suprasternal notch, manubriosternal junction, and carina were identified. The surface distances from the cricoid cartilage to the suprasternal notch (extCC-SSN) and that from the suprasternal notch to the manubriosternal junction (extSSN-MSJ) were measured. The relationship between mid-tracheal level and the surface distances was analyzed using Bland–Altman plot. The difference between the extCC-SSN and the mid-tracheal level was −6.6 (12.5) mm, and the difference between the extSSN-MSJ and the mid-tracheal level was −19.2 (6.1) mm. The difference between the extCC-SSN and the mid-tracheal level was smaller in females compared with males [−1.7 (11.7) mm vs −12.8 (10.7) mm; P < 0.001]. The mid-tracheal level, which is helpful in planning the insertion depth of an ETT, can be predicted by the surface distance between the cricoid cartilage and suprasternal notch in adults, especially in females. PMID:28328810

  7. Robert Boyle's landmark book of 1660 with the first experiments on rarified air.

    West, John B

    2005-01-01

    In 1660, Robert Boyle (1627-1691) published his landmark book New Experiments Physico-Mechanicall, Touching the Spring of the Air, and its Effects... in which he described the first controlled experiments of the effects of reducing the pressure of the air. Critical to this work was the development of an air pump by Boyle with Robert Hooke (1635-1703). For the first time, it was possible to observe physical and physiological processes at both normal and reduced barometric pressures. The air pump was described in detail, although the exact design of the critical piston is unclear. Boyle reported 43 separate experiments, which can conveniently be divided into 7 groups. The first experiments were on the "spring of the air," that is the pressure developed by the air when its volume was changed. Several experiments described the behavior of the barometer invented by Torricelli just 16 years before when it was introduced into the low-pressure chamber. The behavior of burning candles was discussed, although this emphasized early misunderstandings of the nature of combustion. There were some physiological observations, although these were later extended by Boyle and Hooke. The effects of the low pressure on such diverse physical phenomena as magnetism, sound propagation, behavior of a pendulum, evolution of gases from liquids, and the behavior of smoke were described. This classic book is brimming with enthusiasm and fresh ideas even for today and deserves to be better known.

  8. A protocol for clinical evaluation of the carrying angle of the elbow by anatomic landmarks.

    Zampagni, Maria Luisa; Casino, Daniela; Martelli, Sandra; Visani, Andrea; Marcacci, Maurilio

    2008-01-01

    The aim of this work was to present an in vivo protocol to estimate the carrying angle of the elbow in full extension. Forty-four arms were measured by using an electrogoniometer to acquire 3-dimensional coordinates of the landmarks. An algorithm based on the Cardan decomposition method was used to compute the carrying angle and the flexion and pronation angles of the elbow. The mean carrying angle was 12.42 degrees +/- 4.06 degrees , in agreement with the literature and with values obtained by a standard goniometer (r = 0.46; P = .000). Our protocol provided excellent repeatability (interclass correlation coefficient [ICC] = 0.85), greater than a goniometer (ICC = 0.76), and a standard error of measurement of only 1.62 degrees . Flexion was a significant factor (P = .01) in carrying angle estimation. This study suggests that the carrying angle cannot be estimated independently by the flexion angle, even when measured in apparently full extension, and it could be useful in elbow disorders, such as fractures or epicondylar disease management and evaluation of elbow reconstruction.

  9. Comparison of Two Deformable Registration Algorithms in the Presence of Radiologic Change Between Serial Lung CT Scans.

    Cunliffe, Alexandra R; White, Bradley; Justusson, Julia; Straus, Christopher; Malik, Renuka; Al-Hallaq, Hania A; Armato, Samuel G

    2015-12-01

    We evaluated the image registration accuracy achieved using two deformable registration algorithms when radiation-induced normal tissue changes were present between serial computed tomography (CT) scans. Two thoracic CT scans were collected for each of 24 patients who underwent radiation therapy (RT) treatment for lung cancer, eight of whom experienced radiologically evident normal tissue damage between pre- and post-RT scan acquisition. For each patient, 100 landmark point pairs were manually placed in anatomically corresponding locations between each pre- and post-RT scan. Each post-RT scan was then registered to the pre-RT scan using (1) the Plastimatch demons algorithm and (2) the Fraunhofer MEVIS algorithm. The registration accuracy for each scan pair was evaluated by comparing the distance between landmark points that were manually placed in the post-RT scans and points that were automatically mapped from pre- to post-RT scans using the displacement vector fields output by the two registration algorithms. For both algorithms, the registration accuracy was significantly decreased when normal tissue damage was present in the post-RT scan. Using the Plastimatch algorithm, registration accuracy was 2.4 mm, on average, in the absence of radiation-induced damage and 4.6 mm, on average, in the presence of damage. When the Fraunhofer MEVIS algorithm was instead used, registration errors decreased to 1.3 mm, on average, in the absence of damage and 2.5 mm, on average, when damage was present. This work demonstrated that the presence of lung tissue changes introduced following RT treatment for lung cancer can significantly decrease the registration accuracy achieved using deformable registration.

  10. Cortical projection of the inferior choroidal point as a reliable landmark to place the corticectomy and reach the temporal horn through a middle temporal gyrus approach

    Thomas Frigeri

    2014-10-01

    Full Text Available Objective To establish preoperatively the localization of the cortical projection of the inferior choroidal point (ICP and use it as a reliable landmark when approaching the temporal horn through a middle temporal gyrus access. To review relevant anatomical features regarding selective amigdalohippocampectomy (AH for treatment of mesial temporal lobe epilepsy (MTLE. Method The cortical projection of the inferior choroidal point was used in more than 300 surgeries by one authors as a reliable landmark to reach the temporal horn. In the laboratory, forty cerebral hemispheres were examined. Conclusion The cortical projection of the ICP is a reliable landmark for reaching the temporal horn.

  11. Exploring the origin of the D genome of oat by fluorescence in situ hybridization.

    Luo, Xiaomei; Zhang, Haiqin; Kang, Houyang; Fan, Xing; Wang, Yi; Sha, Lina; Zhou, Yonghong

    2014-09-01

    Further understanding of the origin of cultivated oat would accelerate its genetic improvement. In particular, it would be useful to clarify which diploid progenitor contributed the D genome of this allohexaploid species. In this study, we demonstrate that the landmarks produced by fluorescence in situ hybridization (FISH) of species of Avena using probes derived from Avena sativa can be used to explore the origin of the D genome. Selected sets of probes were hybridized in several sequential experiments performed on exactly the same chromosome spreads, with multiple probes of cytological preparations. Probes pITS and A3-19 showed there might be a similar distribution of pITS between the Ac and D genomes. These results indicated that the Ac genome is closely related to the D genome, and that Avena canariensis (AcAc) could be the D-genome donor of cultivated oat.

  12. Validation of a three-dimensional facial scanning system based on structured light techniques.

    Ma, Lili; Xu, Tianmin; Lin, Jiuxiang

    2009-06-01

    The aim of this study was to validate a newly developed three-dimensional (3D) structured light scanning system in recording the facial morphology. The validation was performed in three aspects including accuracy, precision and reliability. The accuracy and precision were investigated using a plaster model with 19 marked landmarks. The accuracy was determined by comparing the coordinates from the 3D images and from the coordinates measure machine (CMM). The precision was quantified through the repeated landmarks location on 3D images. The reliability was investigated in 10 adult volunteers. Each was scanned five times in 3 weeks. The 3D images acquired at different times were compared with each other to measure the reliability. We found that the accuracy was 0.93 mm, the precision was 0.79 mm, the reliability was 0.2mm. These findings suggested that the structured light scanning system was accurate, precise and reliable to record the facial morphology for both clinic and research purposes.

  13. Comparing the Effectiveness of GPS-Enhanced Voice Guidance for Pedestrians with Metric- and Landmark-Based Instruction Sets

    Rehrl, Karl; Häusler, Elisabeth; Leitinger, Sven

    This paper reports on a field experiment comparing two different kinds of verbal turn instructions in the context of GPS-based pedestrian navigation. The experiment was conducted in the city of Salzburg with 20 participants. Both instruction sets were based on qualitative turn direction concepts. The first one was enhanced with metric distance information and the second one was enhanced with landmark-anchored directions gathered from participants of a previous field experiment. The results show that in context of GPS-enhanced pedestrian navigation both kinds of instruction sets lead to similar navigation performance. Results also demonstrate that effective voice-only guidance of pedestrians in unfamiliar environments at a minimal error rate and without stopping the walk is feasible. Although both kinds of instructions lead to similar navigation performance, participants clearly preferred landmark-enhanced instructions.

  14. A Support Model for Students with Learning Disabilities in Higher Education : A Study at Landmark College in the United States

    片岡, 美華; KATAOKA, Mika

    2008-01-01

    Landmark College specializes in students with learning disabilities and/or attention deficit hyperactivity disorders. The college provides support for students both in their academic learning and social life by specialist staff. This support includes help with reading and learning and guidance on how to complete assignments, choose themes, plan research and review literature. This support is structured and run by the Academic advisors and Coaching staff in the college. In addition, the Reside...

  15. The Many Flavors of Model-Based Meta-Analysis: Part I-Introduction and Landmark Data.

    Boucher, M; Bennetts, M

    2016-02-01

    Meta-analysis is an increasingly important aspect of drug development as companies look to benchmark their own compounds with the competition. There is scope to carry out a wide range of analyses addressing key research questions from preclinical through to postregistration. This set of tutorials will take the reader through key model-based meta-analysis (MBMA) methods with this first installment providing a general introduction before concentrating on classical and Bayesian methods for landmark data.

  16. Landmark-based robust navigation for tactical UGV control in GPS-denied communication-degraded environments

    Endo, Yoichiro; Balloch, Jonathan C.; Grushin, Alexander; Lee, Mun Wai; Handelman, David

    2016-05-01

    Control of current tactical unmanned ground vehicles (UGVs) is typically accomplished through two alternative modes of operation, namely, low-level manual control using joysticks and high-level planning-based autonomous control. Each mode has its own merits as well as inherent mission-critical disadvantages. Low-level joystick control is vulnerable to communication delay and degradation, and high-level navigation often depends on uninterrupted GPS signals and/or energy-emissive (non-stealth) range sensors such as LIDAR for localization and mapping. To address these problems, we have developed a mid-level control technique where the operator semi-autonomously drives the robot relative to visible landmarks that are commonly recognizable by both humans and machines such as closed contours and structured lines. Our novel solution relies solely on optical and non-optical passive sensors and can be operated under GPS-denied, communication-degraded environments. To control the robot using these landmarks, we developed an interactive graphical user interface (GUI) that allows the operator to select landmarks in the robot's view and direct the robot relative to one or more of the landmarks. The integrated UGV control system was evaluated based on its ability to robustly navigate through indoor environments. The system was successfully field tested with QinetiQ North America's TALON UGV and Tactical Robot Controller (TRC), a ruggedized operator control unit (OCU). We found that the proposed system is indeed robust against communication delay and degradation, and provides the operator with steady and reliable control of the UGV in realistic tactical scenarios.

  17. Femtosecond scanning tunneling microscope

    Taylor, A.J.; Donati, G.P.; Rodriguez, G.; Gosnell, T.R.; Trugman, S.A.; Some, D.I.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). By combining scanning tunneling microscopy with ultrafast optical techniques we have developed a novel tool to probe phenomena on atomic time and length scales. We have built and characterized an ultrafast scanning tunneling microscope in terms of temporal resolution, sensitivity and dynamic range. Using a novel photoconductive low-temperature-grown GaAs tip, we have achieved a temporal resolution of 1.5 picoseconds and a spatial resolution of 10 nanometers. This scanning tunneling microscope has both cryogenic and ultra-high vacuum capabilities, enabling the study of a wide range of important scientific problems.

  18. The impact of reorienting cone-beam computed tomographic images in varied head positions on the coordinates of anatomical landmarks

    Kim, Jae Hun; Hwang, Jae Joon; Lee, Jung-Hee

    2016-01-01

    Purpose The aim of this study was to compare the coordinates of anatomical landmarks on cone-beam computed tomographic (CBCT) images in varied head positions before and after reorientation using image analysis software. Materials and Methods CBCT images were taken in a normal position and four varied head positions using a dry skull marked with 3 points where gutta percha was fixed. In each of the five radiographic images, reference points were set, 20 anatomical landmarks were identified, and each set of coordinates was calculated. Coordinates in the images from the normally positioned head were compared with those in the images obtained from varied head positions using statistical methods. Post-reorientation coordinates calculated using a three-dimensional image analysis program were also compared to the reference coordinates. Results In the original images, statistically significant differences were found between coordinates in the normal-position and varied-position images. However, post-reorientation, no statistically significant differences were found between coordinates in the normal-position and varied-position images. Conclusion The changes in head position impacted the coordinates of the anatomical landmarks in three-dimensional images. However, reorientation using image analysis software allowed accurate superimposition onto the reference positions. PMID:27358821

  19. Resources or landmarks: which factors drive homing success in Tetragonula carbonaria foraging in natural and disturbed landscapes?

    Leonhardt, Sara D; Kaluza, Benjamin F; Wallace, Helen; Heard, Tim A

    2016-10-01

    To date, no study has investigated how landscape structural (visual) alterations affect navigation and thus homing success in stingless bees. We addressed this question in the Australian stingless bee Tetragonula carbonaria by performing marking, release and re-capture experiments in landscapes differing in habitat homogeneity (i.e., the proportion of elongated ground features typically considered prominent visual landmarks). We investigated how landscape affected the proportion of bees and nectar foragers returning to their hives as well as the earliest time bees and foragers returned. Undisturbed landscapes with few landmarks (that are conspicuous to the human eye) and large proportions of vegetation cover (natural forests) were classified visually/structurally homogeneous, and disturbed landscapes with many landmarks and fragmented or no extensive vegetation cover (gardens and plantations) visually/structurally heterogeneous. We found that proportions of successfully returning nectar foragers and earliest times first bees and foragers returned did not differ between landscapes. However, most bees returned in the visually/structurally most (forest) and least (garden) homogeneous landscape, suggesting that they use other than elongated ground features for navigation and that return speed is primarily driven by resource availability in a landscape.

  20. APFiLoc: An Infrastructure-Free Indoor Localization Method Fusing Smartphone Inertial Sensors, Landmarks and Map Information

    Jianga Shang

    2015-10-01

    Full Text Available The utility and adoption of indoor localization applications have been limited due to the complex nature of the physical environment combined with an increasing requirement for more robust localization performance. Existing solutions to this problem are either too expensive or too dependent on infrastructure such as Wi-Fi access points. To address this problem, we propose APFiLoc—a low cost, smartphone-based framework for indoor localization. The key idea behind this framework is to obtain landmarks within the environment and to use the augmented particle filter to fuse them with measurements from smartphone sensors and map information. A clustering method based on distance constraints is developed to detect organic landmarks in an unsupervised way, and the least square support vector machine is used to classify seed landmarks. A series of real-world experiments were conducted in complex environments including multiple floors and the results show APFiLoc can achieve 80% accuracy (phone in the hand and around 70% accuracy (phone in the pocket of the error less than 2 m error without the assistance of infrastructure like Wi-Fi access points.

  1. Automatic aorta segmentation and valve landmark detection in C-arm CT: application to aortic valve implantation.

    Zheng, Yefeng; John, Matthias; Liao, Rui; Boese, Jan; Kirschstein, Uwe; Georgescu, Bogdan; Zhou, S Kevin; Kempfert, Jörg; Walther, Thomas; Brockmann, Gernot; Comaniciu, Dorin

    2010-01-01

    C-arm CT is an emerging imaging technique in transcatheter aortic valve implantation (TAVI) surgery. Automatic aorta segmentation and valve landmark detection in a C-arm CT volume has important applications in TAVI by providing valuable 3D measurements for surgery planning. Overlaying 3D segmentation onto 2D real time fluoroscopic images also provides critical visual guidance during the surgery. In this paper, we present a part-based aorta segmentation approach, which can handle aorta structure variation in case that the aortic arch and descending aorta are missing in the volume. The whole aorta model is split into four parts: aortic root, ascending aorta, aortic arch, and descending aorta. Discriminative learning is applied to train a detector for each part separately to exploit the rich domain knowledge embedded in an expert-annotated dataset. Eight important aortic valve landmarks (three aortic hinge points, three commissure points, and two coronary ostia) are also detected automatically in our system. Under the guidance of the detected landmarks, the physicians can deploy the prosthetic valve properly. Our approach is robust under variations of contrast agent. Taking about 1.4 seconds to process one volume, it is also computationally efficient.

  2. The impact of reorienting cone-beam computed tomographic images in varied head positions on the coordinates of anatomical landmarks

    Kim, Jae Hun; Jeong, Ho Gul; Hwang, Jae Joon; Lee, Jung Hee; Han, Sang Sun [Dept. of Oral and Maxillofacial Radiology, Yonsei University, College of Dentistry, Seoul (Korea, Republic of)

    2016-06-15

    The aim of this study was to compare the coordinates of anatomical landmarks on cone-beam computed tomographic (CBCT) images in varied head positions before and after reorientation using image analysis software. CBCT images were taken in a normal position and four varied head positions using a dry skull marked with 3 points where gutta percha was fixed. In each of the five radiographic images, reference points were set, 20 anatomical landmarks were identified, and each set of coordinates was calculated. Coordinates in the images from the normally positioned head were compared with those in the images obtained from varied head positions using statistical methods. Post-reorientation coordinates calculated using a three-dimensional image analysis program were also compared to the reference coordinates. In the original images, statistically significant differences were found between coordinates in the normal-position and varied-position images. However, post-reorientation, no statistically significant differences were found between coordinates in the normal-position and varied-position images. The changes in head position impacted the coordinates of the anatomical landmarks in three-dimensional images. However, reorientation using image analysis software allowed accurate superimposition onto the reference positions.

  3. Adaptive Optical Scanning Holography

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

    2016-01-01

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

  4. Genome evolution in Reptilia, the sister group of mammals.

    Janes, Daniel E; Organ, Christopher L; Fujita, Matthew K; Shedlock, Andrew M; Edwards, Scott V

    2010-01-01

    The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.

  5. Applications. SCANS Plans Portfolio.

    Sample, Barbara

    This guide assists English-as-a-Second-Language educators in helping students fill out simple application forms. The guide discusses performance outcomes, communications teaching points, SCANS (Secretary's Committee on Achieving Necessary Skills) competencies, classroom configurations, materials, and procedures. Blank forms, suitable for…

  6. Sinus MRI scan

    ... A CT scan may be preferred in emergency cases, since it is faster and often available in the emergency room. Note: MRI is not as effective as CT in defining the anatomy of the sinuses, and therefore is not typically used for suspected acute sinusitis.

  7. Scanning bubble chamber pictures

    1974-01-01

    These were taken at the 2 m hydrogen bubble chamber. The photo shows an early Shiva system where the pre-measurements needed to qualify the event were done manually (cf photo 7408136X). The scanning tables were located in bld. 12. Gilberte Saulmier sits on foreground, Inge Arents at centre.

  8. SCANNING-DLTS

    Breitenstein, O.

    1989-01-01

    Scanning Deep Level Transient Spectroscopy (SDLTS) is a current SEM technique for the detection of the local distribution of deep level centres in semiconductors. The contribution deals with the physical foundations of the SDLTS technique and it discusses the demands on the instrumentation. The measurement practice is described and illustrated by several experimental examples. Finally, the possibilities and limitations of SDLTS are critically reviewed.

  9. [Landmarks of physiological development of the voice in childhood and adolescense (Part 1)].

    Fuchs, M

    2008-01-01

    The area of the functioning of the voice is a fundamental element of human communication apart from language, speaking, hearing and perceiving. Detailed knowledge of normal vocal development is a prerequisite for the diagnosis and therapy of vocal dysfunctions among children and adolescents by means of methods suitable for their age and their stages of development. In an overview, the landmarks of physiological development with normal value ranges relevant to practice are presented--from the newborn baby's first cry up to the age of young adults. The effects of various degrees of vocal activity on the part of children and adolescents on the parameters of vocal capacity and quality are taken into account, as well as the relationship between physical and vocal development. Furthermore, an overview of diagnostic methods suitable for this age group is given. Specialists for ENT and for Phoniatrics and Pediatric Audiology should be able to assess suitability for increased vocal activity and to care for vocal development during the vulnerable phase of the voice change. Manifold socio-cultural and pedagogical influences are already possible in early childhood and throughout the phase of the "voice in growth". They should be taken advantage of prophylactically--also with regard to the learning of physiological vocal behavior as a prerequisite for dealing with possible subsequent strain in vocally intensive professions. In the following second part of this publication, the fundamentals described here are applied to diagnostics and therapy of vocal dysfunctions in this age group by means of methods suitable for this stage of development.

  10. Looking for landmarks: the role of expert review and bibliometric analysis in evaluating scientific publication outputs.

    Liz Allen

    Full Text Available OBJECTIVE: To compare expert assessment with bibliometric indicators as tools to assess the quality and importance of scientific research papers. METHODS AND MATERIALS: Shortly after their publication in 2005, the quality and importance of a cohort of nearly 700 Wellcome Trust (WT associated research papers were assessed by expert reviewers; each paper was reviewed by two WT expert reviewers. After 3 years, we compared this initial assessment with other measures of paper impact. RESULTS: Shortly after publication, 62 (9% of the 687 research papers were determined to describe at least a 'major addition to knowledge' -6 were thought to be 'landmark' papers. At an aggregate level, after 3 years, there was a strong positive association between expert assessment and impact as measured by number of citations and F1000 rating. However, there were some important exceptions indicating that bibliometric measures may not be sufficient in isolation as measures of research quality and importance, and especially not for assessing single papers or small groups of research publications. CONCLUSION: When attempting to assess the quality and importance of research papers, we found that sole reliance on bibliometric indicators would have led us to miss papers containing important results as judged by expert review. In particular, some papers that were highly rated by experts were not highly cited during the first three years after publication. Tools that link expert peer reviews of research paper quality and importance to more quantitative indicators, such as citation analysis would be valuable additions to the field of research assessment and evaluation.

  11. [Therapy for systemic metabolic disorders based on the detection of basic corneal landmarks in childhood].

    Lisch, W; Pitz, S; Geerling, G

    2013-06-01

    Many systemic lysosomal storage disorders show basic corneal opacities already in childhood. The lysosome is a cell organelle, produced by Golgi's apparatus, that is surrounded by a membrane and contains hydrolytic enzymes that break down food molecules, especially proteins and other complex molecules. The ophthalmologist's precise diagnosis of corneal clouding at the slit-lamp may reveal the correct interpretation of the specific lysosomal storage disorder. It is very important to diagnose such diseases as soon as possible because today the development of systemic enzymatic therapies has broadened the therapeutic armamentarium for the current standard of care. The following corneal landmarks of systemic storage diseases and of the modern systemic therapy are presented: cornea verticillata in Fabry's disease, periodic infusion of alpha-galactosidase a; Kayser-Fleischer's ring in Wilson's disease, zinc, trienetin, low copper diet; multiple, punctiform crystals in cystinosis, cysteamine, Raptor RP 103(DR cysteamine) that reduces the cytotoxity in form of continous dissolving of cystine from lysosome, renal transplantation, haematopoietic stem cell transplantation; peripheral ring, but not true lipid arc, and moderate stromal haze in LCAT-deficiency, injection of recombinant enzyme or of encapsulated LCAT-secreting cells; diffuse stromal haze in mucopolysaccharidoses (MPS). Enzyme replacement therapy is currently indicated for MPS I, MPS II, and MPS VI, haematopoietic stem cell transplantation; painful, bilateral pseudo-dendritic opacities in tyrosinemia type II (eponym: Richner-Hanhart syndrome), low phenylalanine and tyrosine diet result in complete disappearance of corneal alterations with a consecutive painfree period. Strict diet during the whole life is necessary to prevent corneal recurrences and the occurrence of palmo-plantar keratoses. Such therapies can enable the patient to lead an otherwise normal life for decades.

  12. Institutional landmarks in Brazilian research on soil erosion: a historical overview

    Tiago Santos Telles

    2013-12-01

    Full Text Available The problem of soil erosion in Brazil has been a focus of agricultural scientific research since the 19th century. The aim of this study was to provide a historical overview of the institutional landmarks which gave rise to the first studies in soil erosion and established the foundations of agricultural research in Brazil. The 19th century and beginning of the 20th century saw the founding of a series of institutions in Brazil, such as Botanical Gardens, executive institutions, research institutes, experimental stations, educational institutions of agricultural sciences, as well as the creation and diversification of scientific journals. These entities, each in its own way, served to foster soil erosion research in Brazil. During the Imperial period (1808-1889, discussions focused on soil degradation and conserving the fertility of agricultural land. During the First Republic (1889-1930, with the founding of various educational institutions and consolidation of research on soil degradation conducted by the Agronomic Institute of Campinas in the State of São Paulo, studies focused on soil depletion, identification of the major factors causing soil erosion and the measures necessary to control it. During the New State period (1930-1945, many soil conservation practices were developed and disseminated to combat erosion and field trials were set up, mainly to measure soil and water losses induced by hydric erosion. During the Brazilian New Republic (1945-1964, experiments were conducted throughout Brazil, consolidating soil and water conservation as one of the main areas of Soil Science in Brazil. This was followed by scientific conferences on erosion and the institutionalization of post-graduate studies. During the Military Regime (1964-1985, many research and educational institutions were founded, experimental studies intensified, and coincidently, soil erosion reached alarming levels which led to the development of the no-tillage system.

  13. The orbit: A re-appraisal of the surgical landmarks of the medial and lateral walls.

    Yoon, Jisoo; Pather, Nalini

    2016-11-01

    The anterior ethmoidal foramen (AEF) and posterior ethmoidal foramina (AEF and PEF, respectively) on the medial wall and the cranio-orbital foramen (COF) on the lateral wall are used as landmarks in orbital surgeries. In surgery these foramina, the neurovascular structures they transmit and other orbital structures in close proximity need to be identified to minimise their risk of damage. Despite the clinical importance, the current understandings lack consistency in the precise location, microanatomy and morphology of the foramina. This study therefore aimed to document and analyze the microanatomy, location, and morphometric relations of the EF and COF to determine a standardized guideline to accessing the foramina. One hundred dry orbits were morphometrically analyzed, and a further six orbits were micro-dissected to determine the locations of the EF and COF. The orbital size dimensions were measured for each dry orbit and correlated with the morphometric distances. A complete morphometric and quantitative analysis showed the distances of the EF and COF to be variable, with greater variations observed in the incidence of the accessory EF and PEF distances in the medial wall, and in the presence of the COF and the accessory COF in the lateral orbital wall. Significant correlations were observed between the length of the medial orbital wall and some EF distances. This study is the first to suggest a standardized method of locating these foramina in the orbit irrespective of population and sex differences, in order to help improve clinical applications in crucial orbital surgeries. Clin. Anat. 29:998-1010, 2016. © 2016 Wiley Periodicals, Inc.

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

    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

  15. Iliohypogastric/ilioinguinal nerve block in inguinal hernia repair for postoperative pain management: comparison of the anatomical landmark and ultrasound guided techniques

    Abdurrahman Demirci; Esra Mercanoglu Efe; Gürkan Türker; Alp Gurbet; Fatma Nur Kaya; Ali Anil; İlker Çimen

    2014-01-01

    Objectives: The purpose of this study is to compare the efficacy of iliohypogastric/ilioinguinal nerve blocks performed with the ultrasound guided and the anatomical landmark techniques for postoperative pain management in cases of adult inguinal herniorrhaphy. Methods: 40 patients, ASA I-II status were randomized into two groups equally: in Group AN (anatomical landmark technique) and in Group ultrasound (ultrasound guided technique), iliohypogastric/ilioinguinal nerve block was performed w...

  16. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  17. Functional genomics of tomato: Opportunities and challenges in post-genome NGS era

    Rahul Kumar; Ashima Khurana

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger’s and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-à-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other ‘omics’ tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  18. Size-selected genomic libraries: the distribution and size-fractionation of restricted genomic DNA fragments by gel electrophoresis.

    Gondo, Y

    1995-02-01

    By using one-dimensional genome scanning, it is possible to directly identify the restricted genomic DNA fragment that reflects the site of genetic change. The subsequent strategies to obtain the molecular clones of the corresponding restriction fragment are usually as follows: (i) the restriction of a mass quantity of an appropriate genomic DNA, (ii) the size-fractionation of the restricted DNA on a preparative electrophoresis gel in order to enrich the corresponding restriction fragment, (iii) the construction of the size-selected libraries from the fractionated genomic DNA, and (iv) the screening of the library to obtain an objective clone which is identified on the analytical genome scanning gel. A knowledge of the size distribution pattern of restriction fragments of the genomic DNA makes it possible to calculate the heterogeneity or complexity of the restriction fragment in each size-fraction. This manuscript first describes the distribution of the restriction fragments with respect to their length. Some examples of the practical application of this theory to genome scanning is then discussed using presumptive genome scanning gels. The way to calculate such DNA complexities in the prepared size-fractionated samples is also demonstrated. Such information should greatly facilitate the design of experimental strategies for the cloning of a certain size of genomic DNA after digestion with restriction enzyme(s) as is the case with genome scanning.

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

    Jan, Nuzhat; Balik, Salim; Hugo, Geoffrey D. [Department of Radiation Oncology, Virginia Commonwealth University, Richmond, Virginia (United States); Mukhopadhyay, Nitai [Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia (United States); Weiss, Elisabeth, E-mail: eweiss@mcvh-vcu.edu [Department of Radiation Oncology, Virginia Commonwealth University, Richmond, Virginia (United States)

    2014-01-01

    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<.0001). For LN, smaller displacements were found with carina- (5 [3] mm, P<.0001) and vertebra-based (6 [3] mm, P=.002) alignment compared with using PT for setup (8 [5] mm). Primary tumor and LN displacements relative to bone and carina were independent (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.

  20. Scanning Quantum Decoherence Microscopy

    2008-01-01

    The use of qubits as sensitive magnetometers has been studied theoretically and recent demonstrated experimentally. In this paper we propose a generalisation of this concept, where a scanning two-state quantum system is used to probe the subtle effects of decoherence (as well as its surrounding electromagnetic environment). Mapping both the Hamiltonian and decoherence properties of a qubit simultaneously, provides a unique image of the magnetic (or electric) field properties at the nanoscale....

  1. Forensic Scanning Electron Microscope

    Keeley, R. H.

    1983-03-01

    The scanning electron microscope equipped with an x-ray spectrometer is a versatile instrument which has many uses in the investigation of crime and preparation of scientific evidence for the courts. Major applications include microscopy and analysis of very small fragments of paint, glass and other materials which may link an individual with a scene of crime, identification of firearms residues and examination of questioned documents. Although simultaneous observation and chemical analysis of the sample is the most important feature of the instrument, other modes of operation such as cathodoluminescence spectrometry, backscattered electron imaging and direct x-ray excitation are also exploited. Marks on two bullets or cartridge cases can be compared directly by sequential scanning with a single beam or electronic linkage of two instruments. Particles of primer residue deposited on the skin and clothing when a gun is fired can be collected on adhesive tape and identified by their morphology and elemental composition. It is also possible to differentiate between the primer residues of different types of ammunition. Bullets may be identified from the small fragments left behind as they pass through the body tissues. In the examination of questioned documents the scanning electron microscope is used to establish the order in which two intersecting ink lines were written and to detect traces of chemical markers added to the security inks on official documents.

  2. Scanning ultrafast electron microscopy.

    Yang, Ding-Shyue; Mohammed, Omar F; Zewail, Ahmed H

    2010-08-24

    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 which the pulse contains at most one or a few electrons, thus achieving imaging without the space-charge effect between electrons, and still in ten(s) of seconds. For imaging, the secondary electrons from surface structures are detected, as demonstrated here for material surfaces and biological specimens. By recording backscattered electrons, diffraction patterns from single crystals were also obtained. Scanning pulsed-electron microscopy with the acquired spatiotemporal resolutions, and its efficient heat-dissipation feature, is now poised to provide in situ 4D imaging and with environmental capability.

  3. Comparison of difference registration landmarks for image - guided radiotherapy for lung cancer%肺癌图像引导IMRT配准标志的比较研究

    张彦新; 惠周光; 李明辉; 章众; 符贵山; 戴建荣

    2015-01-01

    Objective To investigate the impact of anatomical landmarks on registration in image⁃guided radiotherapy (IGRT) for central and peripheral lung cancer. Methods Twenty⁃five patients with central or peripheral lung cancer for IGRT were enrolled in this study. Kilo⁃voltage cone⁃beam CT ( kV⁃CBCT) scanning was acquired before irradiotion. Tumor coverage on CBCT was assessed using gross tumor volume (GTV), clinical target volume (CTV), and planning target volume (PTV) contours according to tumor alignment, carina registration, and spine registration, respectively. The grading analysiswas based on visual tumor assessment as follows:grade 0, tumor within GTV;grade 1, tumor outside GTV but inside CTV;grade 2, tumor outside CTV but inside PTV;and grade 3, tumor outside PTV. Results Totally 177 sets of kV⁃CBCT of 25 patients was collected. According to the registration landmarks of the tumor, carina and spine for central lung cancer, the percentages were 57�55%, 53�77% and 16�04% in grade 0, 39�62%, 45�28%and 58�49% in grade 1, and 1�89%, 0�94% and 25�47% in grade 2, respectively. For peripheral lung cancer, the percentages were 47�89%, 14�08% and 2�82% in grade 0, 43�66%, 29�58% and 45�07% in grade 1, and 8�45%, 40�85% and 35�21% in grade 2, respectively. Conclusions For central lung cancer,the tumor was recommended as the best registration landmark, and the carina was recommended as well, while the spine was not recommended. For peripheral lung cancer, the tumor was recommended as the best registration landmark, while the spine and the carina were not recommended.%目的:研究肺癌患者图像引导IMRT中采用不同配准标志的靶区符合度差异,确定合理的图像配准方法。方法回顾性收集和分析25例肺癌患者CBCT影像,按原发肿瘤位置分为中央型和周围型两组,每组分别采用肿瘤、隆突、脊柱为标志的配准方法。根据肿瘤组织靶区符合度分为4

  4. Precision of identifying cephalometric landmarks with cone beam computed tomography in vivo

    Hassan, B.; Nijkamp, P.; Verheij, H.; Tairie, J.; Vink, C.; van der Stelt, P.; van Beek, H.

    2013-01-01

    The study aims were to assess the precision and time required to conduct cephalometric analysis with cone-beam computed tomography (CBCT) in vivo on both three-dimensional (3D) surface models and multi-planar reformations (MPR) images. Datasets from 10 patients scanned with CBCT were used to create

  5. Determination of foveal location using scanning laser polarimetry.

    VanNasdale, Dean A; Elsner, Ann E; Weber, Anke; Miura, Masahiro; Haggerty, Bryan P

    2009-03-25

    The fovea is the retinal location responsible for our most acute vision. There are several methods used to localize the fovea, but the fovea is not always easily identifiable. Landmarks used to determine the foveal location are variable in normal subjects and localization becomes even more difficult in instances of retinal disease. In normal subjects, the photoreceptor axons that make up the Henle fiber layer are cylindrical and the radial orientation of these fibers is centered on the fovea. The Henle fiber layer exhibits form birefringence, which predictably changes polarized light in scanning laser polarimetry imaging. In this study 3 graders were able to repeatably identify the fovea in 35 normal subjects using near infrared image types with differing polarization content. There was little intra-grader, inter-grader, and inter-image variability in the graded foveal position for 5 of the 6 image types examined, with accuracy sufficient for clinical purposes. This study demonstrates that scanning laser polarimetry imaging can localize the fovea by using structural properties inherent in the central macula.

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

    2012-06-01

    of Experimental Therapy and Molecular Pathology and Division of Epidemiology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam...Centre, University of Oxford, Oxford, UK. 81Family Cancer Clinic, Netherlands Cancer Institut–Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands

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

    2011-06-01

    Boggess, J.F., Basil , J., Blank, S.V., Friedman, E., Kaufman, B., Laitman, Y., Milgrom, R., Andrulis, I.L., Glendon, G., Ozcelik, H., Kirchhoff, T... Moore , L.E., Prokhortchouk, E., Wu, X., Kiemeney, L.A., Gaborieau, V., Jacobs, K.B., Chow, W.H., Zaridze, D., Matveev, V., Lubinski, J., Trubicka

  8. Genomic scans for selective sweeps using SNP data

    Nielsen, Rasmus; Williamson, Scott; Kim, Yuseob

    2005-01-01

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

  9. Estimating the age of Calliphora vicina eggs (Diptera: Calliphoridae): determination of embryonic morphological landmarks and preservation of egg samples.

    Martín-Vega, Daniel; Hall, Martin J R

    2016-05-01

    Blow fly eggs may sometimes be the only entomological evidence recovered in a forensic case, especially in cooler weather when hatching might take several days: hence, a method for estimating their age is greatly needed. However, developmental data on blow fly eggs are mainly limited to records of the time to larval hatching. The current paper describes the morphological changes occurring during embryogenesis of the blow fly Calliphora vicina Robineau-Desvoidy and their timing in relation to temperature, in order to determine those characters which can be used for simple egg age estimation using light microscopy. At 7.3 and 25 °C, 15 easily visualised morphological landmarks were determined in C. vicina living embryos, allowing for their age estimation with a resolution of 10-20% of total egg developmental time. The observed age intervals were compared to the embryonic stages described for the fruit fly Drosophila melanogaster Meigen, which are used as reference data in multiple developmental studies. Moreover, current guidelines for preservation of egg samples, which recommend the placement of living eggs directly into 80% ethanol, were tested against the hot water killing (HWK) method prior to preservation in 80% ethanol, recommended for larval and pupal specimens. Direct placement of eggs into 80% ethanol caused marked decomposition of samples, and no morphological landmarks were discernible. On the other hand, HWK fixation prior to preservation in 80% ethanol enabled visualisation of 11 of the 15 age-specific morphological landmarks that were discernible in living embryos. Therefore, HWK fixation prior to preservation in 80% ethanol is recommended for egg samples, thus unifying the protocols for collecting entomological evidence.

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

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

    2011-01-01

    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 tibial bone landmarks. (1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. (2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977-0.999 for computer analysis; 0.820-0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839-0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers.

  11. A comparative study of two techniques (electrocardiogram- and landmark-guided for correct depth of the central venous catheter placement in paediatric patients undergoing elective cardiovascular surgery

    Neeraj Kumar Barnwal

    2016-01-01

    Full Text Available Background and Aims: The complications of central venous catheterisation can be minimized by ensuring catheter tip placement just above the superior vena cava-right atrium junction. We aimed to compare two methods, using an electrocardiogram (ECG or landmark as guides, for assessing correct depth of central venous catheter (CVC placement. Methods: In a prospective randomised study of sixty patients of <12 years of age, thirty patients each were allotted randomly to two groups (ECG and landmark. After induction, central venous catheterisation was performed by either of the two techniques and position of CVC tip was compared in post-operative chest X-ray with respect to carina. Unpaired t-test was used for quantitative data and Chi-square test was used for qualitative data. Results: In ECG group, positions of CVC tip were above carina in 12, at carina in 9 and below carina in 9 patients. In landmark group, the positions of CVC tips were above carina in 10, at carina in 4 and below carina in 16 patients. Mean distance of CVC tip in ECG group was 0.34 ± 0.23 cm and 0.66 ± 0.35 cm in landmark group (P = 0.0001. Complications occurred in one patient in ECG group and in nine patients in landmark group (P = 0.0056. Conclusion: Overall, landmark-guided technique was comparable with ECG technique. ECG-guided technique was more precise for CVC tip placement closer to carina. The incidence of complications was more in the landmark group.

  12. Factors influencing superimposition error of 3D cephalometric landmarks by plane orientation method using 4 reference points: 4 point superimposition error regression model.

    Jae Joon Hwang

    Full Text Available Superimposition has been used as a method to evaluate the changes of orthodontic or orthopedic treatment in the dental field. With the introduction of cone beam CT (CBCT, evaluating 3 dimensional changes after treatment became possible by superimposition. 4 point plane orientation is one of the simplest ways to achieve superimposition of 3 dimensional images. To find factors influencing superimposition error of cephalometric landmarks by 4 point plane orientation method and to evaluate the reproducibility of cephalometric landmarks for analyzing superimposition error, 20 patients were analyzed who had normal skeletal and occlusal relationship and took CBCT for diagnosis of temporomandibular disorder. The nasion, sella turcica, basion and midpoint between the left and the right most posterior point of the lesser wing of sphenoidal bone were used to define a three-dimensional (3D anatomical reference co-ordinate system. Another 15 reference cephalometric points were also determined three times in the same image. Reorientation error of each landmark could be explained substantially (23% by linear regression model, which consists of 3 factors describing position of each landmark towards reference axes and locating error. 4 point plane orientation system may produce an amount of reorientation error that may vary according to the perpendicular distance between the landmark and the x-axis; the reorientation error also increases as the locating error and shift of reference axes viewed from each landmark increases. Therefore, in order to reduce the reorientation error, accuracy of all landmarks including the reference points is important. Construction of the regression model using reference points of greater precision is required for the clinical application of this model.

  13. Surface micromachined scanning mirrors

    Mattsson, Kent Erik

    1992-01-01

    Both aluminum cantilever and torsional scanning mirrors have been fabricated and their static and dynamic properties are studied experimentally and theoretically. The experiments showed resonance frequencies in the range of 163 k-Hz - 632 kHz for cantilever beams with Q values between 5 and 11....... Torsional mirrors showed resonance frequencies in the range of 410 kHz - 667 kHz with Q values of 10 - 17. All measurements performed at atmospheric pressure. Both types of mechanical structures were deflected electrostatically at large angles (± 5°) more than 1011 times without breaking and without any...

  14. Ultrafast scanning tunneling microscopy

    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.

  15. Bone Densitometry (Bone Density Scan)

    ... News Physician Resources Professions Site Index A-Z Bone Densitometry (DEXA) Bone densitometry, also called dual-energy ... limitations of DEXA Bone Densitometry? What is a Bone Density Scan (DEXA)? Bone density scanning, also called ...

  16. The location of midfacial landmarks according to the method of establishing the midsagittal reference plane in three-dimensional computed tomography analysis of facial asymmetry

    Kim, Min Sun; Lee, Eun Joo; Lee, Jae Seo; Kang, Byung Cheock; Yoon, Suk Ja [Dental Science Research Institute, Chonnam National University, Gwangju (Korea, Republic of); Song, In Ja [Dept. of Nursing, Kwangju Women' s University, Gwangju (Korea, Republic of)

    2015-12-15

    The purpose of this study was to evaluate the influence of methods of establishing the midsagittal reference plane (MRP) on the locations of midfacial landmarks in the three-dimensional computed tomography (CT) analysis of facial asymmetry. A total of 24 patients (12 male and 12 female; mean age, 22.5 years; age range, 18.2-29.7 years) with facial asymmetry were included in this study. The MRP was established using two different methods on each patient's CT image. The x-coordinates of four midfacial landmarks (the menton, nasion, upper incisor, and lower incisor) were obtained by measuring the distance and direction of the landmarks from the MRP, and the two methods were compared statistically. The direction of deviation and the severity of asymmetry found using each method were also compared. The x-coordinates of the four anatomic landmarks all showed a statistically significant difference between the two methods of establishing the MRP. For the nasion and lower incisor, six patients (25.0%) showed a change in the direction of deviation. The severity of asymmetry also changed in 16 patients (66.7%). The results of this study suggest that the locations of midfacial landmarks change significantly according to the method used to establish the MRP.

  17. Scanned-cantilever atomic force microscope with large scanning range

    Jintao Yang; Wendong Xu

    2006-01-01

    A scanned-cantilever atomic force microscope (AFM) with large scanning range is proposed, which adopts a new design named laser spot tracking. The scanned-cantilever AFM uses the separate flexure x-y scanner and z scanner instead of the conventional piezoelectric tube scanner. The closed-loop control and integrated capacitive sensors of these scanners can insure that the images of samples have excellent linearity and stability. According to the experimental results, the scanned-cantilever AFM can realize maximal 100 × 100 (μm) scanning range, and 1-nm resolution in z direction, which can meet the requirements of large scale sample testing.

  18. CADAVERIC STUDY ON THE LOCATION OF PHARYNGEAL ORIFICE OF AN EUSTACHIAN TUBE IN RELATION TO THE ANATOMICAL LANDMARKS

    Varalakshmi KL

    2015-09-01

    Full Text Available Introduction: Eustachian tube is a communication between the nasopharynx and middle ear extending between the lateral wall of the nasopharynx to anterior wall of tympanic cavity.It maintains the equilibrium of air pressure on either side of the tympanic membrane for proper vibration of sound. The pharyngeal orifice of Eustachian tube is an important landmark for endoscopic surgeries and also for transnasal approach to infratemporal fossa. Materials and Methods: A total of 50 (25 right &25 leftsagittal section of head and neck specimens from adult formalin fixed cadavers from the department of anatomy, MVJ Medical college and Research Hospital, Banglore, India, were used for the study.The distance of pharyngeal orifice to posterior border of hard palate,C1 vertebra,posterior choana,tip of uvula, spehenoid sinus were measured with the digital Vernier caliper.The mean and standard deviation of these parameters were calculated. Conclusion: The knowledge of the relationship of Eustachian tube with anatomical landmarks would be useful to surgeons,otolaryngologists and radiologists.

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

    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 μg/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.

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

    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.

  1. A Scanning Cavity Microscope

    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...

  2. Automatic Ultrasound Scanning

    Moshavegh, Ramin

    Medical ultrasound has been a widely used imaging modality in healthcare platforms for examination, diagnostic purposes, and for real-time guidance during surgery. However, despite the recent advances, medical ultrasound remains the most operator-dependent imaging modality, as it heavily relies...... on the user adjustments on the scanner interface to optimize the scan settings. This explains the huge interest in the subject of this PhD project entitled “AUTOMATIC ULTRASOUND SCANNING”. The key goals of the project have been to develop automated techniques to minimize the unnecessary settings...... on the scanners, and to improve the computer-aided diagnosis (CAD) in ultrasound by introducing new quantitative measures. Thus, four major issues concerning automation of the medical ultrasound are addressed in this PhD project. They touch upon gain adjustments in ultrasound, automatic synthetic aperture image...

  3. Micro scanning probes

    Niblock, T

    2001-01-01

    This thesis covers the design methodology, theory, modelling, fabrication and evaluation of a Micro-Scanning-Probe. The device is a thermally actuated bimorph quadrapod fabricated using Micro Electro Mechanical Systems technology. A quadrapod is a structure with four arms, in this case a planar structure with the four arms forming a cross which is dry etched out of a silicon diaphragm. Each arm has a layer of aluminium deposited on it forming a bimorph. Through heating each arm actuation is achieved in the plane of the quadrapod and the direction normal to it. Fabrication of the device has required the development of bulk micromachining techniques to handle post CMOS fabricated wafers and the patterning of thickly sputtered aluminium in bulk micro machined cavities. CMOS fabrication techniques were used to incorporate diodes onto the quadrapod arms for temperature measurement of the arms. Fine tungsten and silicon tips have also been fabricated to allow tunnelling between the tip and the platform at the centr...

  4. Listeria Genomics

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  5. Marine genomics

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  6. Ancient genomics

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    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...

  7. Genome Sequencing

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  8. Acetabular orientation variability and symmetry based on CT scans of adults

    Lubovsky, Omri; Liebergall, Meir; Khoury, Amal [Hadassah-Hebrew University Medical Center, Orthopedic Surgery Complex, Jerusalem (Israel); Peleg, Eran [Hadassah-Hebrew University Medical Center, Department of Medical Engineering, Jerusalem (Israel); Joskowicz, Leo [Hebrew University of Jerusalem, School of Engineering and Computer Science, Jerusalem (Israel)

    2010-09-15

    Understanding acetabular orientation is important in many orthopaedic procedures. Acetabular orientation, usually described by anteversion and abduction angles, has uncertain measurement variability in adult patients. The goals of this study are threefold: (1) to describe a new method for computing patient-specific abduction/anteversion angles from a single CT study based on the identification of anatomical landmarks and acetabular rim points; (2) to quantify the inaccuracies associated with landmark selection in computing the acetabular angles; and (3) to quantify the variability and symmetry of acetabular orientation. A total of 25 CT studies from adult patients scanned for non-orthopaedic indications were retrospectively reviewed. The patients were randomly selected from the hospital's database. Inclusion criteria were adults 20-65 years of age. Acetabular landmark coordinates were identified by expert observers and tabulated in a spreadsheet. Two sets of calculations were done using the data: (1) computation of the abduction and anteversion for each patient, and (2) evaluation of the variability of measurements in the same individual by the same surgeon. The results were tabulated and summary statistics computed. This retrospective study showed that acetabular abduction and anteversion angles averaged 54 and 17 , respectively, in adults. A clinically significant intra-patient variability of >20 was found. We also found that the right and left side rim plane orientation were significantly correlated, but were not always symmetric. A new method of computing patient-specific abduction and anteversion angles from a CT study of the anterior pelvic plane and the left and right acetabular rim planes was reliable and accurate. We found that the acetabular rim plane can be reliably and accurately computed from identified points on the rim. The novelty of this work is that angular measurements are performed between planes on a 3-D model rather than lines on 2-D

  9. Enhancer Identification through Comparative Genomics

    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.

  10. Can Achilles tendon be used as a new distal landmark for coronal tibial component alignment in total knee replacement surgery? An observational MRI study

    Tiftikçi, Uğur; Serbest, Sancar; Burulday, Veysel

    2017-01-01

    Background In total knee arthroplasty, it is better to use more than one reference point for correct alignment of the components. By measuring the distances of Achilles tendon (AT) and other conventional landmarks from the mechanical axis in magnetic resonance imaging (MRI) of the ankle, we aimed to demonstrate that, as a novel landmark which can help for correct alignment in the coronal plane, AT is a better option than other landmarks. Materials and methods This retrospective study was done on 53 ankle MRIs that met the criteria for inclusion to the study among 158 ankle MRIs. After identification of the mechanical axis, the distances of distal landmarks, which were extensor hallucis longus tendon (EHLT), tibialis anterior tendon (TAT), dorsalis pedis artery (DPA), AT, extensor digitorum longus tendon (EDLT), and malleoli, were measured from the mechanical axis and were statistically evaluated. Results In proximal measurements, the distances of the landmarks to the mechanical axis (on average) were AT, 2.64±1.62 mm lateral; EHLT, 3.89±2.45 mm medial; DPA, 4.69±2.39 mm medial; TAT, 8.24±3.60 mm medial; and EDLT, 14.2±4.14 mm lateral (P<0.001). In distal measurements, the distances of the landmarks to the mechanical axis (on average) were AT, 1.99±1.24 mm medial; EHLT, 4.27±2.49 mm medial; DPA, 4.79±2.10 mm medial; TAT, 12.9±4.07 mm medial; and EDLT, 12.18±4.17 mm lateral (P<0.001). Conclusion In this study, the mechanical axis line, which is the center of talus, passes through the AT. Our MRI investigations showed that the AT, EHLT, DPA, and malleolar center (3–5 mm medial) may help in correct alignment. PMID:28144149

  11. Design, recognition, localization and application of a new artificial landmark%新型人工地标的设计、识别、定位及应用

    姜海涛; 田国会; 薛英花; 李荣宽

    2011-01-01

    The artificial landmark is an important auxiliary method for robot localization and navigation.A kind of new artificial landmark based on QR Code (quick response code) technology was proposed.This new landmark not only stores rich environment information, but also provides effective pose information to the robot.An algorithm based on shape and color of the landmark was presented in order that the landmark could be recognized by the robot in the far distance.The localization algorithm using the vanishing line principle was designed to locate the artificial landmark quickly and accurately in the camera coordinates of the robot.A control scheme including searching in the far distance, recognition, localization and reading landmarks was proposed, which laid a solid foundation for robot autonomous localization and navigation.Experiments demonstrated that the new landmark had far recognition distance, high recognition speed,high positioning precision, high decoding efficiency and stability even in a complex indoor environment.%人工地标是机器人定位与导航的重要辅助手段.设计了一种基于QR Code(quick response code)技术的新型人工地标,该地标不仅能存储丰富的环境信息,还能为机器人提供有效的方位信息.为了让机器人能够在远距离找到人工地标,设计了基于颜色和形状的快速识别算法.利用消影线原理设计了定位算法,可在机器人摄像机坐标系中快速、准确地定位人工地标.给出了机器人远距离搜寻、识别、定位及读取人工地标的控制方案,为机器人自主定位及导航奠定了基础.实验表明,该人工地标识别距离远、识别速度快、定位精度高,在复杂室内环境下仍能有很高的识读效率和很好的稳定性.

  12. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

    Arumugam, Manimozhiyan; Wei, Chaochun; Brown, Randall H

    2006-01-01

    This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on trans alignments, in which expressed sequences are aligned to the genomic loci...... with de novo gene prediction by using N-SCAN_EST. N-SCAN_EST is based on a generalized HMM probability model augmented with a phylogenetic conservation model and EST alignments. It can predict complete transcripts by extending or merging EST alignments, but it can also predict genes in regions without EST...

  13. GPR scan assessment

    Abbas M. Abbas

    2015-06-01

    Full Text Available Mekaad Radwan monument is situated in the neighborhood of Bab Zuweila in the historical Cairo, Egypt. It was constructed at the middle XVII century (1635 AD. The building has a rectangle shape plan (13 × 6 m with the longitudinal sides approximately WNW-ESE. It comprises three storages namely; the ground floor; the opened floor (RADWAN Bench and the living floor with a total elevation of 15 m above the street level. The building suffers from severe deterioration phenomena with patterns of damage which have occurred over time. These deterioration and damages could be attributed to foundation problems, subsoil water and also to the earthquake that affected the entire Greater Cairo area in October 1992. Ground Penetrating Radar (GPR scan was accomplished against the walls of the opened floor (RADWAN Bench to evaluate the hazard impact on the walls textures and integrity. The results showed an anomalous feature through the southern wall of RADWAN Bench. A mathematical model has been simulated to confirm the obtained anomaly and the model response exhibited a good matching with the outlined anomaly.

  14. Differential scanning calorimetry.

    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.

  15. LANL Robotic Vessel Scanning

    Webber, Nels W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-25

    Los Alamos National Laboratory in J-1 DARHT Operations Group uses 6ft spherical vessels to contain hazardous materials produced in a hydrodynamic experiment. These contaminated vessels must be analyzed by means of a worker entering the vessel to locate, measure, and document every penetration mark on the vessel. If the worker can be replaced by a highly automated robotic system with a high precision scanner, it will eliminate the risks to the worker and provide management with an accurate 3D model of the vessel presenting the existing damage with the flexibility to manipulate the model for better and more in-depth assessment.The project was successful in meeting the primary goal of installing an automated system which scanned a 6ft vessel with an elapsed time of 45 minutes. This robotic system reduces the total time for the original scope of work by 75 minutes and results in excellent data accumulation and transmission to the 3D model imaging program.

  16. Cephalopod genomics

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  17. Ancient genomics

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , 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...

  18. Is the omega sign a reliable landmark for the neurosurgical team? An anatomical study about the central sulcus region.

    Rodrigues, Thiago; Rodrigues, Mariana; Paz, Daniel; Costa, Marcos Devanir; Santos, Bruno; Braga, Vinicius; Paiva Neto, Manoel de; Centeno, Ricardo; Cavalheiro, Sergio; Chaddad-Neto, Feres

    2015-11-01

    The central sulcus region is an eloquent area situated between the frontal and parietal lobes. During neurosurgical procedures, it is sometimes difficult to understand the cortical anatomy of this region.Objective Find alternative ways to anatomically navigate in this region during neurosurgical procedures.Method We analyzed eighty two human hemispheres using a surgical microscope and completed a review of the literature about central sulcus region.Results In 68/82 hemispheres, the central sulcus did not reach the posterior ramus of the lateral sulcus. A knob on the second curve of the precentral gyrus was reliably identified in only 64/82 hemispheres.Conclusion The morphometric data presented in this article can be useful as supplementary method to identify the central sulcus region landmarks.

  19. Is the omega sign a reliable landmark for the neurosurgical team? An anatomical study about the central sulcus region

    Thiago Rodrigues

    2015-11-01

    Full Text Available ABSTRACTThe central sulcus region is an eloquent area situated between the frontal and parietal lobes. During neurosurgical procedures, it is sometimes difficult to understand the cortical anatomy of this region.Objective Find alternative ways to anatomically navigate in this region during neurosurgical procedures.Method We analyzed eighty two human hemispheres using a surgical microscope and completed a review of the literature about central sulcus region.Results In 68/82 hemispheres, the central sulcus did not reach the posterior ramus of the lateral sulcus. A knob on the second curve of the precentral gyrus was reliably identified in only 64/82 hemispheres.Conclusion The morphometric data presented in this article can be useful as supplementary method to identify the central sulcus region landmarks.

  20. Verification of selected anatomic landmarks used as reference points for universal goniometer positioning during knee joint mobility range measurements.

    Szulc, P; Lewandowski, J; Marecki, B

    2001-01-01

    The study was concerned with verification of the selection of reference points used for knee joint mobility range goniometry. The verification was based on photometric and electrogoniometric methods of femorotibial angle measurements. The material for measurements were three knee joint preparations. The obtained data were subjected to descriptive analysis; photographic documentation of geometric relations between the reference points was also prepared. Considerable divergence of measurement results was observed with respect to the actual knee joint flexion angle, amounting even to 16 degrees. The differences are due to the selection of anatomic landmarks, and depend in particular on the distance of the point to which the goniometer axis is applied from the approximate location of the mechanical joint axis. The corrections of knee joint flexion angle measurements were also estimated on the basis of data obtained from the photographs and the derived mathematical formula.

  1. Gallium scans in myasthenia gravis

    Swick, H.M. (Univ. of Kentucky, Lexington); Preston, D.F.; McQuillen, M.P.

    1976-01-01

    A study was conducted to determine whether /sup 67/Ga scans could be used for the detection of thymomas and to investigate the activity of the thymus gland in patients with myasthenia gravis. Scans of the anterior mediastinum proved to be a reliable way to detect thymomas. The scans were positive in eight patients including three with myasthenia gravis and histologically proved thymomas, three others with severe myasthenia gravis and thymic tumors, and two with histologically proved thymomas not associated with myasthenia. Activity on /sup 67/Ga scans was not directly related to the increased activity of the thymus gland that is presumed to be associated with myasthenia gravis. (HLW)

  2. Navigating in small-scale space: the role of landmarks and resource monitoring in understanding saddleback tamarin travel.

    Garber, Paul A; Porter, Leila M

    2014-05-01

    Recent studies of spatial memory in wild nonhuman primates indicate that foragers may rely on a combination of navigational strategies to locate nearby and distant feeding sites. When traveling in large-scale space, tamarins are reported to encode spatial information in the form of a route-based map. However, little is known concerning how wild tamarins navigate in small-scale space (between feeding sites located at a distance of ≤60 m). Therefore, we collected data on range use, diet, and the angle and distance traveled to visit sequential feeding sites in the same group of habituated Bolivian saddleback tamarins (Saguinus fuscicollis weddelli) in 2009 and 2011. For 7-8 hr a day for 54 observation days, we recorded the location of the study group at 10 min intervals using a GPS unit. We then used GIS software to map and analyze the monkeys' movements and travel paths taken between feeding sites. Our results indicate that in small-scale space the tamarins relied on multiple spatial strategies. In 31% of cases travel was route-based. In the remaining 69% of cases, however, the tamarins appeared to attend to the spatial positions of one or more near-to-site landmarks to relocate feeding sites. In doing so they approached the same feeding site from a mean of 4.5 different directions, frequently utilized different arboreal pathways, and traveled approximately 30% longer than then the straight-line distance. In addition, the monkeys' use of non-direct travel paths allowed them to monitor insect and fruit availability in areas within close proximity of currently used food patches. We conclude that the use of an integrated spatial strategy (route-based travel and attention to near-to-goal landmarks) provides tamarins with the opportunity to relocate productive feeding sites as well as monitor the availability of nearby resources in small-scale space.

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

    Zhuang, Ziqing; Slice, DennisE; Benson, Stacey; Lynch, Stephanie; Viscusi, DennisJ

    2010-12-01

    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 conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA) to identify population variation. The first four principal components (PC) account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

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

    Slice DennisE

    2010-01-01

    Full Text Available 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 conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA to identify population variation. The first four principal components (PC account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

  5. Re-scan confocal microscopy: scanning twice for better resolution

    De Luca, G.M.R.; Breedijk, R.M.P.; Brandt, R.A.J.; Zeelenberg, C.H.C.; De Jong, B.E.; Timmermans, W.; Nahidi Azar, L.; Hoebe, R.A.; Stallinga, S.; Manders, E.M.M.

    2013-01-01

    We present a new super-resolution technique, Re-scan Confocal Microscopy (RCM), based on standard confocal microscopy extended with an optical (re-scanning) unit that projects the image directly on a CCD-camera. This new microscope has improved lateral resolution and strongly improved sensitivity wh

  6. Re-scan confocal microscopy : scanning twice for better resolution

    De Luca, G.M.R.; Breedijk, R.M.P.; Brandt, R.A.J.; Zeelenberg, C.H.C.; de Jong, B.E.; Timmermans, W.; Azar, L.N.; Hoebe, R.A.; Stallinga, S.; Manders, E.M.M.

    2013-01-01

    We present a new super-resolution technique, Re-scan Confocal Microscopy (RCM), based on standard confocal microscopy extended with an optical (re-scanning) unit that projects the image directly on a CCD-camera. This new microscope has improved lateral resolution and strongly improved sensitivity wh

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

    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.

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

    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.

  9. Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications.

    Chong, Shaorong

    2014-10-01

    During the early days of molecular biology, cell-free protein synthesis played an essential role in deciphering the genetic code and contributed to our understanding of translation of protein from messenger RNA. Owing to several decades of major and incremental improvements, modern cell-free systems have achieved higher protein synthesis yields at lower production costs. Commercial cell-free systems are now available from a variety of material sources, ranging from "traditional" E. coli, rabbit reticulocyte lysate, and wheat germ extracts, to recent insect and human cell extracts, to defined systems reconstituted from purified recombinant components. Although each cell-free system has certain advantages and disadvantages, the diversity of the cell-free systems allows in vitro synthesis of a wide range of proteins for a variety of downstream applications. In the post-genomic era, cell-free protein synthesis has rapidly become the preferred approach for high-throughput functional and structural studies of proteins and a versatile tool for in vitro protein evolution and synthetic biology. This unit provides a brief history of cell-free protein synthesis and describes key advances in modern cell-free systems, practical differences between widely used commercial cell-free systems, and applications of this important technology.

  10. Soft tissue landmark for ultrasound identification of the sciatic nerve in the infragluteal region: the tendon of the long head of the biceps femoris muscle.

    Bruhn, J.; Moayeri, N.; Groen, G.J.; Veenendaal, A. van; Gielen, M.J.M.; Scheffer, G.J.; Geffen, G.J. van

    2009-01-01

    BACKGROUND AND OBJECTIVES: The sciatic nerve block represents one of the more difficult ultrasound-guided nerve blocks. Easy and reliable internal ultrasound landmarks would be helpful for localization of the sciatic nerve. Earlier, during ultrasound-guided posterior approaches to the infragluteal s

  11. The function genomics study

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  12. Visualization for genomics: the Microbial Genome Viewer.

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  13. Can Achilles tendon be used as a new distal landmark for coronal tibial component alignment in total knee replacement surgery? An observational MRI study

    Tiftikçi U

    2017-01-01

    Full Text Available Uğur Tiftikçi,1 Sancar Serbest,1 Veysel Burulday2 1Department of Orthopaedics and Traumatology, 2Department of Radiology, Faculty of Medicine, Kırıkkale University, Kırıkkale, Turkey Background: In total knee arthroplasty, it is better to use more than one reference point for correct alignment of the components. By measuring the distances of Achilles tendon (AT and other conventional landmarks from the mechanical axis in magnetic resonance imaging (MRI of the ankle, we aimed to demonstrate that, as a novel landmark which can help for correct alignment in the coronal plane, AT is a better option than other landmarks. Materials and methods: This retrospective study was done on 53 ankle MRIs that met the criteria for inclusion to the study among 158 ankle MRIs. After identification of the mechanical axis, the distances of distal landmarks, which were extensor hallucis longus tendon (EHLT, tibialis anterior tendon (TAT, dorsalis pedis artery (DPA, AT, extensor digitorum longus tendon (EDLT, and malleoli, were measured from the mechanical axis and were statistically evaluated. Results: In proximal measurements, the distances of the landmarks to the mechanical axis (on average were AT, 2.64±1.62 mm lateral; EHLT, 3.89±2.45 mm medial; DPA, 4.69±2.39 mm medial; TAT, 8.24±3.60 mm medial; and EDLT, 14.2±4.14 mm lateral (P<0.001. In distal measurements, the distances of the landmarks to the mechanical axis (on average were AT, 1.99±1.24 mm medial; EHLT, 4.27±2.49 mm medial; DPA, 4.79±2.10 mm medial; TAT, 12.9±4.07 mm medial; and EDLT, 12.18±4.17 mm lateral (P<0.001. Conclusion: In this study, the mechanical axis line, which is the center of talus, passes through the AT. Our MRI investigations showed that the AT, EHLT, DPA, and malleolar center (3–5 mm medial may help in correct alignment. Keywords: total knee arthroplasty, tibial component, alignment, distal references, landmark, MRI, Achilles tendon

  14. Identifying biological landmarks using a novel cell measuring image analysis tool: Cell-o-Tape

    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. Bone Densitometry (Bone Density Scan)

    ... of DXA Bone Densitometry? What is a Bone Density Scan (DXA)? Bone density scanning, also called dual-energy x-ray absorptiometry ( ... is today's established standard for measuring bone mineral density (BMD). An x-ray (radiograph) is a noninvasive ...

  16. An interchangeable scanning Hall probe/scanning SQUID microscope.

    Tang, Chiu-Chun; Lin, Hui-Ting; Wu, Sing-Lin; Chen, Tse-Jun; Wang, M J; Ling, D C; Chi, C C; Chen, Jeng-Chung

    2014-08-01

    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 μm), 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 La(2/3)Ca(1/3)MnO3 thin film at 77 K, and superconducting vortices in a striped niobium film at 4.2 K.

  17. Combined bone scintigraphy and indium-111 leukocyte scans in neuropathic foot disease

    Schauwecker, D.S.; Park, H.M.; Burt, R.W.; Mock, B.H.; Wellman, H.N.

    1988-10-01

    It is difficult to diagnose osteomyelitis in the presence of neurotrophic osteoarthropathy. We performed combined (99mTc)MDP bone scans and indium-111 (111In) leukocyte studies on 35 patients who had radiographic evidence of neuropathic foot disease and clinically suspected osteomyelitis. The (111In)leukocyte study determined if there was an infection and the bone scan provided the anatomic landmarks so that the infection could be localized to the bone or the adjacent soft tissue. Seventeen patients had osteomyelitis and all showed increased (111In)leukocyte activity localized to the bone, giving a sensitivity of 100%. Among the 18 patients without osteomyelitis, eight had no accumulation of (111In)leukocytes, seven had the (111In)leukocyte activity correctly localized to the soft tissue, two had (111In)leukocyte activity mistakenly attributed to the bone, and one had (111In)leukocyte accumulation in a proven neuroma which was mistakenly attributed to bone. These three false-positive results for osteomyelitis reduced the specificity to 83%. Considering only the 27 patients with a positive (111In)leukocyte study, the combined bone scan and (111In)leukocyte study correctly localized the infection to the soft tissues or bone in 89%. Uninfected neurotrophic osteoarthropathy does not accumulate (111In)leukocytes. We found the combined bone scan and (111In) leukocyte study useful for the detection and localization of infection to soft tissue or bone in patients with neuropathic foot disease.

  18. 一种选择标注分层流形学习算法%A Selecting Landmark Hierarchical Manifold Learning Algorithm

    范自立; 李凡长

    2011-01-01

    The manifold data query needs the manifold embedded representation. Thus it often involves accessing considerable volume of data. An approach of hierarchical manifold learning algorithm based on selecting landmark points from the given samples is proposed for representing data on manifold. The landmarks set can help locate the novel points on the data manifold. Firstly, an adaptive nearest neighbor' s method is employed to extract the nearest neighborhood of each data. Then the geodesic matrix is constructed. Finally, a landmark point is randomly selected in landmark point set, and its maximum cell is found till the manifold set is empty and the rough landmark point set is formed. In addition, the landpoint set is optimized. The experimental results prove that the proposed method preserves the topological features of manifold, and it helps inquire the manifold data efficiently.%流形数据的查询需要使用流形的嵌入表示,因此查询流形数据需要访问大量的样本数据.提出一种选择标注分层流形学习算法,选择出的标注点集用来帮助查找流形数据.首先采用自适应近邻算法求出每个数据的最优近邻,然后构造测地线矩阵,最后逐步迭代随机选择标注点,求出每个标注点的极大单元子集,直到流形数据集变成空集,形成初始标注点集.此外,还要优化标注点集.实验结果证明所选择的标注点集保持流形的拓扑特性,可有效帮助查询流形数据.

  19. Dating the age of admixture via wavelet transform analysis of genome-wide data

    I. Pugach (Irina); R. Matveyev (Rostislav); A. Wollstein (Andreas); M.H. Kayser (Manfred); M. Stoneking (Mark)

    2011-01-01

    textabstractWe describe a PCA-based genome scan approach to analyze genome-wide admixture structure, and introduce wavelet transform analysis as a method for estimating the time of admixture. We test the wavelet transform method with simulations and apply it to genome-wide SNP data from eight admixe

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

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

    2015-01-01

    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.

  1. Re-scan confocal microscopy: scanning twice for better resolution.

    De Luca, Giulia M R; Breedijk, Ronald M P; Brandt, Rick A J; Zeelenberg, Christiaan H C; de Jong, Babette E; Timmermans, Wendy; Azar, Leila Nahidi; Hoebe, Ron A; Stallinga, Sjoerd; Manders, Erik M M

    2013-01-01

    We present a new super-resolution technique, Re-scan Confocal Microscopy (RCM), based on standard confocal microscopy extended with an optical (re-scanning) unit that projects the image directly on a CCD-camera. This new microscope has improved lateral resolution and strongly improved sensitivity while maintaining the sectioning capability of a standard confocal microscope. This simple technology is typically useful for biological applications where the combination high-resolution and high-sensitivity is required.

  2. Lidar arc scan uncertainty reduction through scanning geometry optimization

    H. Wang

    2015-10-01

    Full Text Available Doppler lidars are frequently operated in a mode referred to as arc scans, wherein the lidar beam scans across a sector with a fixed elevation angle and the resulting measurements are used to derive an estimate of the n minute horizontal mean wind velocity (speed and direction. Previous studies have shown that the uncertainty in the measured wind speed originates from turbulent wind fluctuations and depends on the scan geometry (the arc span and the arc orientation. This paper is designed to provide guidance on optimal scan geometries for two key applications in the wind energy industry: wind turbine power performance analysis and annual energy production. We present a quantitative analysis of the retrieved wind speed uncertainty derived using a theoretical model with the assumption of isotropic and frozen turbulence, and observations from three sites that are onshore with flat terrain, onshore with complex terrain and offshore, respectively. The results from both the theoretical model and observations show that the uncertainty is scaled with the turbulence intensity such that the relative standard error on the 10 min mean wind speed is about 30 % of the turbulence intensity. The uncertainty in both retrieved wind speeds and derived wind energy production estimates can be reduced by aligning lidar beams with the dominant wind direction, increasing the arc span and lowering the number of beams per arc scan. Large arc spans should be used at sites with high turbulence intensity and/or large wind direction variation when arc scans are used for wind resource assessment.

  3. Heart region segmentation from low-dose CT scans: an anatomy based approach

    Reeves, Anthony P.; Biancardi, Alberto M.; Yankelevitz, David F.; Cham, Matthew D.; Henschke, Claudia I.

    2012-02-01

    Cardiovascular disease is a leading cause of death in developed countries. The concurrent detection of heart diseases during low-dose whole-lung CT scans (LDCT), typically performed as part of a screening protocol, hinges on the accurate quantification of coronary calcification. The creation of fully automated methods is ideal as complete manual evaluation is imprecise, operator dependent, time consuming and thus costly. The technical challenges posed by LDCT scans in this context are mainly twofold. First, there is a high level image noise arising from the low radiation dose technique. Additionally, there is a variable amount of cardiac motion blurring due to the lack of electrocardiographic gating and the fact that heart rates differ between human subjects. As a consequence, the reliable segmentation of the heart, the first stage toward the implementation of morphologic heart abnormality detection, is also quite challenging. An automated computer method based on a sequential labeling of major organs and determination of anatomical landmarks has been evaluated on a public database of LDCT images. The novel algorithm builds from a robust segmentation of the bones and airways and embodies a stepwise refinement starting at the top of the lungs where image noise is at its lowest and where the carina provides a good calibration landmark. The segmentation is completed at the inferior wall of the heart where extensive image noise is accommodated. This method is based on the geometry of human anatomy and does not involve training through manual markings. Using visual inspection by an expert reader as a gold standard, the algorithm achieved successful heart and major vessel segmentation in 42 of 45 low-dose CT images. In the 3 remaining cases, the cardiac base was over segmented due to incorrect hemidiaphragm localization.

  4. Retinal locus for scanning text.

    Timberlake, George T; Sharma, Manoj K; Grose, Susan A; Maino, Joseph H

    2006-01-01

    A method of mapping the retinal location of text during reading is described in which text position is plotted cumulatively on scanning laser ophthalmoscope retinal images. Retinal locations that contain text most often are the brightest in the cumulative plot, and locations that contain text least often are the darkest. In this way, the retinal area that most often contains text is determined. Text maps were plotted for eight control subjects without vision loss and eight subjects with central scotomas from macular degeneration. Control subjects' text maps showed that the fovea contained text most often. Text maps of five of the subjects with scotomas showed that they used the same peripheral retinal area to scan text and fixate. Text maps of the other three subjects with scotomas showed that they used separate areas to scan text and fixate. Retinal text maps may help evaluate rehabilitative strategies for training individuals with central scotomas to use a particular retinal area to scan text.

  5. Scanning Gate Spectroscopy on Nanoclusters

    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-electron tunnelling sp...

  6. Electrostatic ion beam scanning system

    Harper, G.C.; Curtis, W.D.

    1978-04-01

    An electrostatic scanning system has been designed and built to uniformly implant a 1 cm/sup 2/ sample with a charged particle beam. The full angular scan capability for a 2 MeV beam is 0.5 degrees at 6 kV p-p. The design of the system is extremely simple so it is very compact, easy to operate, and has shown very good reliability.

  7. Unmasking true signal/tumor information from ProstaScint scans

    Lee, Benjamin Y.; DeWyngaert, J. Keith; Noz, Marilyn E.; Maguire, Gerald Q., Jr.; Murphy-Walcott, Antoinette; Kramer, Elissa L.

    2004-05-01

    Purpose: Improve tumor localization in In-111 ProstaScint SPECT scans through improved reconstruction and identification/removal of non-specific blood pool volumes using simultaneously acquired Tc-99m tagged red blood cell (RBC) SPECT scans. Methods: We chose 30 patients with a history of prostate cancer who had undergone CT/MR and simultaneous Tc-99m RBC/In-111 ProstaScint SPECT scans due to rising PSA. To estimate the impact of reconstruction methods on anatomic definition and artifacts, SPECT volume data sets were reconstructed using ordered set-expectation maximization (OS-EM) with varying numbers of iterations and subsets, and these were compared against each other and against standard filtered back projection (FBP) reconstruction. Non-blood pool bladder activity in the Tc-99m scans was suppressed prior to subtraction from the In-111 scans by using an averaging algorithm within an ellipsoid volume encompassing the bladder. Outside the ellipsoid volume, Tc-99m voxel values were subtracted from the corresponding In-111 voxels after normalization of the data sets based on peak activity within the descending aorta. Results: OS-EM reconstruction using 3 iterations and 45 subsets showed improved representation of anatomy compared with FBP. Bladder suppression reduced artifacts in the prostate bed. The subtraction method reduced the blood pool signal, confirmed visually by superimposition with matched CT/MR scans. Preliminary results using the Coefficient of Variation (CV) and a Student's t-test, show that the superimposition landmark distance differences are significantly different after subtraction. Conclusions: OS-EM reconstruction together with bladder suppression and subtraction of the blood pool may help improve the specificity of ProstaScint SPECT interpretation and increase its utility in radiation therapy treatment planning.

  8. THE POSSIBILITIES OF SPREADING OF THE DOWNSHIFTING IN MODERN SOCIETY: THE VALUE LANDMARKS ANALYSIS OF MOSCOW AND ST. PETERSBURG SPECIALISTS

    Yana Vadimovna Ovechkina

    2015-12-01

    Full Text Available This article provides an analysis of the «downshifting» phenomena, which is voluntary downward vertical mobility, as an alternative path to success. The author defines downshif-ters as a social group, analyzes the motives of this voluntary downward mobility. Basing on the own hypothesis, author takes an attempt to outline those social groups, which are subject to this so-called downward motion on the «social ladder». Author also tries to predict the possible spread of the «downshifting» phenomena in Russian Federation. The value landmarks of two groups of specialists were researched, one being the «young adults» group (ages 25-30, the other – «adults» (ages 31-36. Both their emotional tension and the quality of life satisfaction being closely examined. The attention to these problems and further examination of practices and standards of downshifters and followers of adjacent movements will help the researchers to determine zones of increased tension in society, professional staff and family. In addition, it will help to predict possible changes in the labour relations system.

  9. Interrater Reproducibility of Knee Movement Analyses during the Stance Phase: Use of Anatomical Landmark Calibration with a Rigid Marker Set

    Takashi Fukaya

    2013-01-01

    Full Text Available Objective. Measurements of knee joint movement in gait analysis may result in large errors caused by misplacement of reflective markers by the testers. To properly understand the measurement results, it is important to guarantee the reliability of the measurement method used for the purpose. The aim of this study was to confirm the interrater reproducibility of a measurement method with a rigid marker set (RMS. Methods. The study subjects were four healthy adults, and the testers were three physical therapists. The interrater reproducibility of the measurements was verified by using the coefficient of multiple correlations (CMCs and the standard error of measurement (SEM. Results. The average CMCs values of 4 subjects in knee joint movement at the stance phase were greater than 0.8, and the average SEM values of 4 subjects in knee joint movement at the stance phase were also relatively good (maximum error: 2.42°. Conclusion. Based on these results, the measurement method with estimation of anatomical landmarks using the RMS can prevent misplacement during attachment of the reflective markers, as long as the testers have sufficient experience in attaching reflective markers.

  10. When do objects become landmarks? A VR study of the effect of task relevance on spatial memory.

    Xue Han

    Full Text Available We investigated how objects come to serve as landmarks in spatial memory, and more specifically how they form part of an allocentric cognitive map. Participants performing a virtual driving task incidentally learned the layout of a virtual town and locations of objects in that town. They were subsequently tested on their spatial and recognition memory for the objects. To assess whether the objects were encoded allocentrically we examined pointing consistency across tested viewpoints. In three experiments, we found that spatial memory for objects at navigationally relevant locations was more consistent across tested viewpoints, particularly when participants had more limited experience of the environment. When participants' attention was focused on the appearance of objects, the navigational relevance effect was eliminated, whereas when their attention was focused on objects' locations, this effect was enhanced, supporting the hypothesis that when objects are processed in the service of navigation, rather than merely being viewed as objects, they engage qualitatively distinct attentional systems and are incorporated into an allocentric spatial representation. The results are consistent with evidence from the neuroimaging literature that when objects are relevant to navigation, they not only engage the ventral "object processing stream", but also the dorsal stream and medial temporal lobe memory system classically associated with allocentric spatial memory.

  11. The mid-fusiform sulcus: a landmark identifying both cytoarchitectonic and functional divisions of human ventral temporal cortex.

    Weiner, Kevin S; Golarai, Golijeh; Caspers, Julian; Chuapoco, Miguel R; Mohlberg, Hartmut; Zilles, Karl; Amunts, Katrin; Grill-Spector, Kalanit

    2014-01-01

    Human ventral temporal cortex (VTC) plays a pivotal role in high-level vision. An under-studied macroanatomical feature of VTC is the mid-fusiform sulcus (MFS), a shallow longitudinal sulcus separating the lateral and medial fusiform gyrus (FG). Here, we quantified the morphological features of the MFS in 69 subjects (ages 7-40), and investigated its relationship to both cytoarchitectonic and functional divisions of VTC with four main findings. First, despite being a minor sulcus, we found that the MFS is a stable macroanatomical structure present in all 138 hemispheres with morphological characteristics developed by age 7. Second, the MFS is the locus of a lateral-medial cytoarchitectonic transition within the posterior FG serving as the boundary between cytoarchitectonic regions FG1 and FG2. Third, the MFS predicts a lateral-medial functional transition in eccentricity bias representations in children, adolescents, and adults. Fourth, the anterior tip of the MFS predicts the location of a face-selective region, mFus-faces/FFA-2. These findings are the first to illustrate that a macroanatomical landmark identifies both cytoarchitectonic and functional divisions of high-level sensory cortex in humans and have important implications for understanding functional and structural organization in the human brain.

  12. Plant Genome Duplication Database.

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  13. Rodent malaria parasites : genome organization & comparative genomics

    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. falciparu

  14. Interesting bone scans - unusual findings

    Dobson, M.; Wadhwa, S.S.; Mansberg, R.; Fernandes, V.B. [Wollongong Hospital, Wollongong, NSW (Australia)

    1997-12-01

    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 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

  15. The boundary-scan handbook

    Parker, Kenneth P

    2016-01-01

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

  16. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

    Bartha, István; Carlson, Jonathan M; Brumme, Chanson J; McLaren, Paul J; Brumme, Zabrina L; John, Mina; Haas, David W; Martinez-Picado, Javier; Dalmau, Judith; López-Galíndez, Cecilio; Casado, Concepción; Rauch, Andri; Günthard, Huldrych F; Bernasconi, Enos; Vernazza, Pietro; Klimkait, Thomas; Yerly, Sabine; O'Brien, Stephen J; Listgarten, Jennifer; Pfeifer, Nico; Lippert, Christoph; Fusi, Nicolo; Kutalik, Zoltán; Allen, Todd M; Müller, Viktor; Harrigan, P Richard; Heckerman, David; Telenti, Amalio; Fellay, Jacques

    2013-10-29

    HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (pgenome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.

  17. Evaluating condylar head morphology as it relates to the skeletal vertical facial dimension: A three-dimensional semi-automated landmark study

    Curtis Contro

    2016-01-01

    Full Text Available Introduction: Condylar growth direction and rotation affect the occlusion, especially in the vertical dimension. The first objective of this study was to evaluate the reliability of a novel three-dimensional semi-automated landmark computer software on mapping the head of the mandibular condyle using cone-beam computed tomography (CBCT. The second objective was to evaluate qualitatively how condylar morphology differs three-dimensionally according to skeletal vertical pattern and mandibular morphology in healthy adults using CBCT. Materials and Methods: A total of 242 (169 females and 73 males participants were eligible for the study. Participants were selected at random from the 242 to create three groups of 10 participants based on their MP-SN° and assigned to a brachyfacial group, dolichofacial group, and mesofacial group. The thirty participants were also divided by mandibular symphyseal morphology according to the chin angle (Id-Pg-MP°. Each subject′s condyles were landmarked using Stratovan′s Checkpoint software. A Procrustes analysis was then used to generate an average condylar shape for each of the six groups from which to evaluate shape differences. Results: Checkpoint proved to be a reliable method of placing landmarks on the condyle with a low coefficient of variation of 1.81% (standard deviation/mean. Qualitative analysis of the Procrustes averages revealed brachyfacial average showed a moderate anterior lean from the sagittal, anterior convexity from the axial, and medial lean from the coronal views. The dolichofacial average showed a mild anterior lean from the sagittal, anterior concavity from the axial, and a symmetrical half-dome shape from the coronal. The obtuse chin angle group average displayed morphology similar to the brachyfacial average, whereas the acute chin angle group average displayed morphology similar to the dolichofacial average. Conclusions: Checkpoint is reliable software to landmark the

  18. 从城市兴趣点中提取多层次地标方法探究%Studyingon Extracting Hierarchical Landmarks from Urban POI Data

    陈香; 李晓明; 詹然; 徐卫民

    2015-01-01

    为了获取结构化空间知识,本文在前人研究基础上,提出一种依据显著度差异从城市POI数据中提取多层次地标的方法。分别从知名度、通达度以及个体特征三个方面量化分析了影响POI显著性的因素;然后利用这三个指标构建了POI显著性度量模型,并进行了武汉市武昌区地标提取实验。最后,以各层地标为种子生成Voronoi图,用来反映各层地标的空间影响范围及上下层地标之间蕴含的认知规律。%For acquiring the hierarchical spatial knowledge, a method of extracting hierarchical landmarks from urban POI data to their significances is proposed, based on previous work.After analyzing the factors influencing the significances of POI objects from promi-nence, accessibility, and individual characteristics, a significance measure model composed of the three vectors is built.An experi-ment is carried out to compute the significances of the POIs selected from the area of Wuchang region of Wuhan city.In this experi-ment, several levels of landmarks are extracted, and being used as seeds to compute Voronoi diagrams in every level, to reflect the in-fluence area of every landmark and associate the landmarks in the same level and between the sequential levels.

  19. Evaluating condylar head morphology as it relates to the skeletal vertical facial dimension: A three-dimensional semi-automated landmark study

    Curtis Contro; Miller, Arthur J.; David Hatcher; Snehlata Oberoi

    2016-01-01

    Introduction: Condylar growth direction and rotation affect the occlusion, especially in the vertical dimension. The first objective of this study was to evaluate the reliability of a novel three-dimensional semi-automated landmark computer software on mapping the head of the mandibular condyle using cone-beam computed tomography (CBCT). The second objective was to evaluate qualitatively how condylar morphology differs three-dimensionally according to skeletal vertical pattern and mandibular ...

  20. Comparative validity and reproducibility study of various landmark-oriented reference planes in 3-dimensional computed tomographic analysis for patients receiving orthognathic surgery.

    Hsiu-Hsia Lin

    Full Text Available Three-dimensional computed tomographic imaging has become popular in clinical evaluation, treatment planning, surgical simulation, and outcome assessment for maxillofacial intervention. The purposes of this study were to investigate whether there is any correlation among landmark-based horizontal reference planes and to validate the reproducibility and reliability of landmark identification.Preoperative and postoperative cone-beam computed tomographic images of patients who had undergone orthognathic surgery were collected. Landmark-oriented reference planes including the Frankfort horizontal plane (FHP and the lateral semicircular canal plane (LSP were established. Four FHPs were defined by selecting 3 points from the orbitale, porion, or midpoint of paired points. The LSP passed through both the lateral semicircular canal points and nasion. The distances between the maxillary or mandibular teeth and the reference planes were measured, and the differences between the 2 sides were calculated and compared. The precision in locating the landmarks was evaluated by performing repeated tests, and the intraobserver reproducibility and interobserver reliability were assessed.A total of 30 patients with facial deformity and malocclusion--10 patients with facial symmetry, 10 patients with facial asymmetry, and 10 patients with cleft lip and palate--were recruited. Comparing the differences among the 5 reference planes showed no statistically significant difference among all patient groups. Regarding intraobserver reproducibility, the mean differences in the 3 coordinates varied from 0 to 0.35 mm, with correlation coefficients between 0.96 and 1.0, showing high correlation between repeated tests. Regarding interobserver reliability, the mean differences among the 3 coordinates varied from 0 to 0.47 mm, with correlation coefficients between 0.88 and 1.0, exhibiting high correlation between the different examiners.The 5 horizontal reference planes were